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If the following links do not work (due to them being part of a boolean search) - just go to the above search page and type in the patent number.

Also, there might be some duplication due to using different Patent databases as well as different search techniques.

US Patent system last checked 27th September 2002

US Patent Number: 5,249,137 US Patent Title: Computer-aided chemical illustration system Date of Patent: September 28, 1993 Abstract: A computer-aided chemical illustration system is disclosed. Techniques provided include: 1) efficient drawing of bonds; 2) drawing different bond types during a single mode; 3) determining bisect angles for bonds; 4) labeling atoms on the fly; 5) automatic alignment of atom labels; 6) custom alignment of atom labels; 7) changing the type, style, or orientation of an object while it is being drawn; 8) detection of ring structures; and 9) shifting bonds around on a ring.

US Patent Number: 6,582,233 Patent Title: Apparatus and method for monitoring the validity of a molecular model Date of Patent: June 24, 2003 Abstract: A computer implemented molecular modeler displays information concerning structural validity to the user. The display of information may be updated substantially continuously while the user modifies the molecular model. The display of information may comprise a color coded indicator and/or text associated with the atoms of the molecular model.

US / European / World Patent Number/ Request: WO9906824 Patent Title: Method and apparatus for determining molecular crystal structures Publication Date: 1999-02-11 Abstract: An improved method and apparatus for determining molecular crystal structures is provided which enables molecular crystal structures to be identified using only powder diffraction data, that is considerably faster than conventional crystal modelling techniques. With the improved crystal modelling method and apparatus trial molecular crystal structures are reduced to a unique set of variables based on co-ordinates representative of the location and orintation of the molecule and where appropriate at least one co-ordinate representative of a torsion angle, bond length or bond angle. In addition, the total quantity of experimental powder diffraction data is reduced to provide a reduced representation of the diffraction data in the form of a structure factor intensity listing and covariance matrix. Trial crystal structures are postulated and each is defined using the set of variables which are used in determining a fitness of each trial structure with respect to the reduced representation of the experimental data. A trial crystal structure is output as an accurate representation of the actual crystal structure, when the fitness value for the trial structure is less than or equal to a predetermined threshold value. With the improved crystal modelling method and apparatus, identification of complex molecular crystal structures can be performed in seconds or minutes using the current generation of conventional personal computers or workstations as opposed to the hours and often days required with conventional techniques.

European Patent Number: EP0526516 World Patent Number: WO 91/16682 Patent Title: Handling Data Date of Patent: 1991-10-30 Abstract: A method of structuring or storing data within a file has the following steps: (i) arranging the file into a plurality of data blocks each preceded by a respective data block code; and (ii) arranging the data within each block into a plurality of data items each preceded by a respective data name; wherein the data block codes are taken from a first predetermined set, may occur in any order, and have a first common feature, and wherein the data names are taken from a second predetermined set, may occur in any order, and have a second common feature, the first and second common features being readily distinguishable. The file is visually readable as text in addition to being machine readable

United States Patent Application: 20020107643 Patent Title: Process for pan-genomic determination of macromolecular atomic structures August 8, 2002 Abstract: A process for pan-genomic determination of three-dimensional macromolecular atomic structures uses a unique combination of components. All known structural information, sequence information and functional information are systematically organized into a genomics database. Advanced tools of bioinformatics are used to cluster all known gene products into families of homologous sequences. Simultaneously, in parallel for each such family, a few cDNAs from appropriately representatives species are cloned into expression vectors for a few expressions systems. Constructs are then screened for expression, and those that are effective advance to the preparative step. Expressed proteins are prepared, purified and characterized. Purified proteins are set to crystallize in parallel against crystallization screens. Crystals that grow are tested for suitable diffraction characteristics. A suitable crystal is frozen, and diffraction data are measured using the multiwavelength anomalous diffraction (MAD) method at a synchrotron which uses undulator beamlines for high-throughput crystallography. Diffraction data are analyzed by the MAD phasing method, an atomic model is built, and the model is refined against the diffraction data. The refined model is analyzed in the context of (1) sequence information from other family members, (2) all other known 3D structures, and (3) functional motifs. It is also analyzed for surface characteristics with the aim to define active sites and macromolecular contact sites. For relevant structures, the active site properties are used to define classes of compounds predicted to have binding potency. Computational tools for homology model building are used to develop models for homologs. The homology models may be used in target selection, drug design, or design of more appropriate constructs for experimental analysis. The ensemble of all known structures is used to further advance the effectiveness of the bioinformatics tools.

US Patent Number: 6,411,676 Patent Number: US6411676 Patent Application Number: EP1075653 (WO9956115) Patent Title: Method for determining parameters of a unit cell of a crystal structure using diffraction Publication Date: 2002-06-25 Abstract: A method for determining the parameters of a unit cell of a crystal structure using diffraction is presented. The method includes the steps of repeatedly rotating the crystal at a predetermined angle, while the crystal moves in relation to a detection surface and measuring the position of radiation reflected from the crystal. The resulting combined measurements are utilized to accurately determine the unit cell dimension and orientation of the crystal

EPO Patent Application: EP1260812 Patent Title: Process and apparatus for the x-ray diffraction characterization of a material with amorphous phase Date of Patent: March 6, 2001 Abstract: The invention relates to a process for the qualitative and quantitative characterisation of a material (2) containing at least one amorphous portions by analysis of X-ray diffraction pattern in which a combined diffraction pattern of the material and of a crystalline Standard is analyzed with Rietveld method in a computerized device. According to the invention, the combined diffraction pattern (11) is obtained by the linear mathematical combination of a measured diffraction pattern of the material to be analyzed. An apparatus for working the process is also claimed.

US Patent Number: 6,198,796 Patent Title: Method and apparatus of automatically selecting bragg reflections, method and system of automatically determining crystallographic orientation Date of Patent: March 6, 2001 Abstract: A novel method and novel apparatus that are capable of selecting, with a computer, reference Bragg reflections pc1 and pc2, which form a basis for determination of the crystallographic orientation of a crystal sample by the two-reflection method, automatically and easily and accurately, wherein; firstly, x-ray intensities and diffraction conditions of all Bragg reflections which are measurable are calculated using the crystallographic information, secondly, a weight-point according to both the x-ray intensity and the angle between the sample normal and the scattering vector is obtained for each of the Bragg reflections, thirdly, two Bragg reflections having the two largest weight-points are selected as the reference Bragg reflections pc1 and pc2, respectively.

United States Patent Application: 20020116133 United States Patent Application Title: Method for removing atomic-model bias in macromolecular crystallography Date of Patent: August 22, 2002 Abstract: Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

World Patent Number: WO0190715 Patent Title: Maximum likelihood density modification by pattern recognition of structural motifs Date of Publication: 2001-11-29 Abstract: An electron density for a crystallographic structure having protein regions and solvent regions is improved by maximizing the log likelihood of a set of structures factors {F(sub)h(end sub)} using a local log-likelihood function: LL((rho)(x,{F(sub)h(end sub)})) = 1n p((rho)(x. PROT)p(sub)PROT(end sub)(x) + p((rho)(x) . SOLV)p(sub)SOLV(end sub)(x) + p((rho)(x). H)p(sub)H(end sub)(x) , where .(sub)PROT(end sub)(x) is the probability that x is in the protein regions, p((rho)(x).PROT) is the conditional probability for (rho)(x) given that x is in the protein region, and p(sub)SOLV(end sub)(x) and p((rho)(x).SOLV) are the corresponding quantities for the solvent region, p(sub)H(end sub)(x) refers to the probability that there is a structural motif at a known location, with a known orientation, in the vicinity of the point x; andp ((rho)(x).H) is the probability distribution for electron density at this point given that the structural motif actually is present. One appropriate structural motif is a helical structure within the crystallographic structure.

US Patent Number: 6,438,205 Patent Title: System and method for reducing phase ambiguity of crystal structure factors Date of Patent: August 20, 2002 Abstract: A method reduces the structure factor phase ambiguity corresponding to a selected reciprocal lattice vector. The method includes generating an original phase probability distribution corresponding to a selected structure factor phase of the selected reciprocal lattice vector. The original phase probability distribution includes a first structure factor phase ambiguity. The method further includes combining the original phase probability distribution with a plurality of phase probability distributions of a plurality of structure factor phases of other reciprocal lattice vectors using a phase equation or inequality. The phase equation or inequality defines a mathematical relationship between the selected structure factor phase of the selected reciprocal lattice vector and the plurality of structure factor phases of other reciprocal lattice vectors. The method further includes producing a resultant phase probability distribution for the selected structure factor phase of the selected reciprocal lattice vector. The resultant phase probability distribution includes a second structure factor phase ambiguity which is smaller than the first structure factor phase ambiguity. Lachlan's Note: Looks defined for powder diffraction??

US Patent Number: 6,438,204 Patent Title: Linear prediction of structure factors in x-ray crystallography Date of Patent: August 20, 2002 Abstract: A method uses linear prediction analysis to define a first structure factor component for a first reflection from x-ray crystallography data. The x-ray crystallography data includes a set of cognizable reflections. The method includes expressing the first structure factor component as a first linear equation in which the first structure factor component is equal to a sum of a first plurality of terms. Each term includes a product of (1) a structure factor component for a cognizable reflection from the x-ray crystallography data, wherein the cognizable reflection has a separation in reciprocal space from the first reflection, and (2) a linear prediction coefficient corresponding to the separation between the cognizable reflection and the first reflection. The method further includes calculating values for the linear prediction coefficients. The method further includes substituting the values for the linear prediction coefficients into the first linear equation, thereby defining the first structure factor component for the first reflection.

US Patent Number: 6,345,235 Patent Title: Method and apparatus for determining multi-dimensional structure Date of Patent: February 5, 2002 Abstract: This invention relates to methods and apparatus for determining the multi-dimensional topology of a substance (system) within a volume (space). A method according to a preferred embodiment of the invention comprises the steps of: acquiring a set of relative values for the density (scalar properties) of the volume, each value for a given location (point) within the volume; interpolating a set of functions to generate a continuous relative density for the volume; identifying critical points of the continuous relative density by using an eigenvector following method; and associating critical points with one another by following a gradient path of the continuous relative density between the critical points, The method is applicable to a wide range of data relating to fields such as crystallography, fluid dynamics, edge detection, and financial markets, to determine the topology of structures contained therein.

US Patent Number: 4,991,191 Patent Title: Quantitative analysis of the active table ingredient by powder x-ray diffractometry Date of Patent: February 5, 1991 Abstract: A method for quantitatively analyzing solid mixtures of a crystalline ingredient and an excipient component in commercial pharmaceutical tablets by x-ray powder diffractometry using the intact tablet as is, without special sample preparation. The method comprises the steps of: irradiating the table with x-rays in a powder x-ray diffraction device and determining the integrated intensity of diffracted x-rays, I, at an angular range producing at least one x-ray diffraction line characteristic of said crystalline ingredient; determining the ratio of said value I to a diffracted x-ray intensity value, I.sub.o, obtained on a second compressed tablet consisting of said crystalline ingredient at said angular range; and comparing the determined ratio I/I.sub.o to a set of predetermined standard values of said ratio for known mixtures of said crystalline ingredient and said excipient component to quantitate said crystalline ingredient in said first compressed tablet.

US Patent Number: 4,592,082 Patent Title: Quantitative determination of mineral composition by powder X-ray diffraction Date of Patent: May 27, 1986 Abstract: An external standard intensity ratio method is used for quantitatively determining mineralogic compositions of samples by x-ray diffraction. The method uses ratios of x-ray intensity peaks from a single run. Constants are previously determined for each mineral which is to be quantitatively measured. Ratios of the highest intensity peak of each mineral to be quantified in the sample and the highest intensity peak of a reference mineral contained in the sample are used to calculate sample composition.

US Patent Number: 5,353,236 Patent Title: High-resolution crystallographic modelling of a macromolecule Date of Patent: October 4, 1994 Abstract: A method for constructing an image of a macromolecular crystal includes steps of providing an envelope which defines the region of a unit cell occupied by the macromolecule; distributing a collection of scattering bodies within the envelope; condensing the collection of scattering bodies to an arrangement that maximizes the correlation between the diffraction pattern of the crystal and a pattern of Fourier amplitudes for the collection of scattering bodies; determining the phase associated with at least one of the Fourier amplitudes of the condensed collection of scattering bodies; calculating an electron density distribution of the crystal from the phase information; and defining an image of the macromolecule in the electron density distribution.

US Patent Number: 6,192,103 Patent Title: Fitting of X-ray scattering data using evolutionary algorithms Date of Patent: February 20, 2001 Abstract: Evolutionary algorithms are used to find a global solution to the fitting of experimental X-ray scattering data to simulated models. A recombination operator combines two or more parameter vectors from one iteration of simulated scattering data to form a new parameter vector for the next iteration, in a manner such that there is a high probability that the new parameter will better fit the experimental data than any of the parent parameters. A mutation operator perturbs the value of a parent vector, to permit new regions of the error function to be examined, and thereby avoid settling on local minima. The natural selection guarantees that the parameter vectors with the best fitness will be propagated into future iterations.

US Patent Number: 6,345,235 Patent Title: Method and apparatus for determining multi-dimensional structure Date of Patent: February 5, 2002 Abstract: This invention relates to methods and apparatus for determining the multi-dimensional topology of a substance (system) within a volume (space). A method according to a preferred embodiment of the invention comprises the steps of: acquiring a set of relative values for the density (scalar properties) of the volume, each value for a given location (point) within the volume; interpolating a set of functions to generate a continuous relative density for the volume; identifying critical points of the continuous relative density by using an eigenvector following method; and associating critical points with one another by following a gradient path of the continuous relative density between the critical points, The method is applicable to a wide range of data relating to fields such as crystallography, fluid dynamics, edge detection, and financial markets, to determine the topology of structures contained therein.

US Patent Number: 6,356,845 Patent Title: Crystallization and structure determination of Staphylococcus aureus UDP-N-acetylenolpyruvylglucosamine reductase (S. aureus MurB) Date of Patent: March 12, 2002 Abstract: The substrate free form of Staphylococcus aureus UDP-N-acetylenolpyruvylglucosamine reductase (S. aureus MurB) has been crystallized, and the three dimensional x-ray crystal structure has been solved to 2.3 .ANG. resolution. The x-ray crystal structure is useful for solving the structure of other molecules or molecular complexes, and designing inhibitors of S. aureus MurB

US Patent Number: 6,131,072 Patent Title: Lane tracking system and method Date of Patent: October 10, 2000 Abstract: A system and method for identifying lanes in images generated from DNA sequencing and fragment analysis is described. One example method includes a computer implemented method of determining the locations of lanes of separated samples. Each lane corresponds to a sample being separated by flowing the sample through a media. The method includes the following elements. Place some samples on the media. Cause the samples to separate into the lanes. Create a digital image of the lanes. Fit some curves to the lane images. Each curve corresponds to a lane formed from a separated sample.

US Patent Number: 6,128,582 Patent Title: Molecules comprising an IMPDH-like binding pocket and encoded data storage medium capable of graphically displaying them Date of Patent: October 3, 2000 Abstract: The present invention relates to a data storage medium encoded with the corresponding structure coordinates of molecules and molecular complexes which comprise the active site binding pockets of IMPDH. Such data storage material is capable of displaying such molecules and molecular complexes, or their structural homologues, as a graphical three-dimensional representation on a computer screen. This invention also relates to methods of using the structure coordinates to solve the structure of homologous proteins or protein complexes. In addition, this invention relates to methods of using the structure coordinates to screen and design compounds, including inhibitory compounds, that bind to IMPDH or homologues thereof. This invention also relates to molecules and molecular complexes which comprise the active site binding pockets of IMPDH or close structural homologues of the active site binding pockets. This invention also relates to compounds and pharmaceutical compositions which are inhibitors of IMPDH.

US Patent Number: 6,037,949 Patent Title: Texture mapping and other uses of scalar fields on subdivision surfaces in computer graphics and animation Date of Patent: March 14, 2000 Abstract: Methods for defining smooth scalar fields on arbitrary polygonal meshes which can be consistently carried through the subdivision process involve computing mesh vertices after subdivision to a suitable resolution and computing scalar field values at the vertices corresponding to an arbitrary smooth surface, including the limit surface. The methods allow one to define and compute the value of scalar fields over an arbitrarily dense set of points on the limit surface. Applications of these techniques in computer graphics and computer animation include: (1) the definition of pseudo-coordinates for use in parametric shading including texture mapping; (2) the assignment of smoothly varying articulation weights over the control points of a model to more efficiently define the transformation of a highly detailed object or character under specific animation controls; and (3) the assignment of smoothly varying local parameters for specifying the local behavior of dynamic or quasi-static objects or surfaces.

US Patent Number: 6,014,449 Patent Title: Computer-implemented system for analyzing rigidity of substructures within a macromolecule Date of Patent: January 11, 2000 Abstract: A computer-implemented system and method is provided for analyzing the rigidity of substructures within a molecule represented as atomic coordinate and bond data. The system includes a preprocessor for selectively eliminating from the data those bonds below a predetermined strength to thereby generate filtered data. The system also has a data structure for representing the filtered data as a network of vertices and constraints from which rigidity information is inferred. A topography processor is provided for extracting the rigidity information from the network and constructing an index data structure to represent the extracted rigidity information. The system also includes an analyzer coupled to the index data structure for identifying rigid and floppy substructures within the molecule based on the indices.

US Patent Number: 5,752,019 Patent Title: System and method for confirmationally-flexible molecular identification Date of Patent: May 12, 1998 Abstract: A reference storage process populates a data structure so that the data structure contains all of the molecular structures and/or rigid substructures in the database classified according to attributes of tuples. In a preferred embodiment, the tuples are derived from sites (e.g. atomic sites) of the molecular structures and the attributes can be derived from geometric (and other) information related to the tuples. The attributes are used to define indices in the data structure that are associated with invariant vector information (e.g. information about rotatable bond(s) in skewed local coordinate frames created from tuples). These representations are invariant with respect to the rotation and translation of molecular structures and/or the rotation of substructures about attached rotatable bond(s). Accordingly, the invariant vector information is classified in the data structure with the respective tuple attributes in locations determined by the index derived from the respective tuple. A matching process creates one or more tuples, skewed local reference frames, and indices (called test frame tuple indices) for the structure (substructures) of a test molecule using the same technique that was used to populate the data structure. The test frame tuple index accesses the invariant vector information and tallies the frequency of matching in order to determine the identity of molecules/substructures in the database that are structurally similar to the test molecule. This identification can be achieved even in the presence of conformationally flexible molecules in the database.

US Patent Number: 5,577,239 Patent Title: Chemical structure storage, searching and retrieval system Date of Patent: November 19, 1996 Abstract: The present invention is a chemical structure search system and method which expands the capabilities of existing systems by capitalizing on the strengths of relational database technology. The system allows the user to optimally store and search chemical structure information including information relating to multi-valued atoms, multi-typed bonds, Markush searching and various other options in a relational database management system. The system provides a complete chemical information system which includes capabilities for: (1) exact structure searching; (2) substructure searching; (3) key searching; (4) chemical name searching; (5) molecular formula searching; (6) registration of new molecules; (7) structure import/export; and (8) data editing. Additionally, the present invention allows the routine integration of chemical structure data with other related information such as inventory, spectroscopic data and clinical data via standard relational database methods. The system also has dynamic querying capabilities which allow the user to be notified of any new chemicals that are entered into the database that are responsive to previously run queries. Furthermore, structure classes can also be implemented which allow the user to store certain types of information about particular types of chemical structures such as steroids. Accordingly, users can later call up this information in a quick and efficient manner without re-entering or performing previously run queries.

US Patent Number: 5,463,564 Patent Title: System and method of automatically generating chemical compounds with desired properties Date of Patent: October 31, 1995 Abstract: A computer based, iterative process for generating chemical entities with defined physical, chemical and/or bioactive properties. During each iteration of the process, (1) a directed diversity chemical library is robotically generated in accordance with robotic synthesis instructions; (2) the compounds in the directed diversity chemical library are analyzed to identify compounds with the desired properties; (3) structure-property data are used to select compounds to be synthesized in the next iteration; and (4) new robotic synthesis instructions are automatically generated to control the synthesis of the directed diversity chemical library for the next iteration.

US Patent Number: 5,331,573 Patent Title: Method of design of compounds that mimic conformational features of selected peptides Date of Patent: July 19, 1994 Abstract: A method of rational drug design includes simulating polypeptides in a way that predicts the most probable secondary and/or tertiary structures of a polypeptide, e.g., an oligopeptide, without any presumptions as to the conformation of the underlying primary or secondary structure. The method involves computer simulation of the polypeptide, and more particularly simulating a real-size primary structure in an aqueous environment, shrinking the size of the polypeptide isobarically and isothermally, and expanding the simulated polypeptide to its real size in selected time periods. A useful set of tools, termed Balaji plots, energy conformational maps, and probability maps, assist in identifying those portions of the predicted peptide structure that are most flexible or most rigid. The rational design of novel compounds, useful as drugs, e.g., bioactive peptidomimetic compounds, and constrained analogs thereof, is thus made possible using the simulation methods and tools of the described invention.

US Patent Number: 5,081,584 Patent Title: Computer-assisted design of anti-peptides based on the amino acid sequence of a target peptide Date of Patent: January 14, 1992 Abstract: A computer-implemented method for designing at least one anti-peptide sequence having affinity for target peptide or a fragment thereof suitable for synthesizing peptides and micromolecules, assaying for a target peptides, purifying target peptides, and/or preventing proteolyis of a polypeptide includes identification of the members of the amino acid sequence of the target peptide and their anti-sense or hydropathically complementary amino acids and determining the moving average hydropathy for the target and anti-sense members. The resulting lowest hydropathy identifies the anti-sense amino acid sequence for the target peptide. The members of the target peptide amino acid sequence are obtained along with their member-specific hydropathic values with the hydropathic values summed as a moving average. Anti-sense or complementary amino acid members are identified from the moving average information to generate an array of anti-sense amino acid sequences. The hydropathic values of the array of anti-sense amino acids are obtained along with their moving average hydropathic values from which a hydropathic complementary score is obtained with the lowest score identifying the anti-sense amino acid sequence having affinity for the target peptide.

US Patent Number: 4,939,666 Patent Title: Incremental macromolecule construction methods Date of Patent: July 3, 1990 Abstract: A preferred embodiment of the invention is a method for constructing a polypeptide chain having a substantially predetermined conformation. Preferably a known stable well-mapped polypeptide structure is used as a starting point, and additional peptide units are incrementally added on while maintaining favorable enthalpic and entropic contributions to stability. Preferably a library of oligopeptide blocks is used to provide candidates for the additional peptide units. Preferably the library includes numerous precomputed parameters for each of the blocks, e.g. parameters for estimating energetic effects of varying the conformation parameters.

US Patent Number: 4,908,773 Patent Title: Computer designed stabilized proteins and method for producing same Date of Patent: March 13, 19 Abstract: Proteins, such as enzymes having enhanced stability are designed through the use of a computer method. The method identifies amino acid residues of a protein which may be replaced with a cysteine residue in order to promote the formation of a protein-stabilizing disulfide bond. The computer-designed, stabilized proteins can be produced using recombinant DNA technology.

US Patent Number: 5,418,944 Patent Title: Knowledge-based molecular retrieval system and method using a hierarchy of molecular structures in the knowledge base Date of Patent: May 23, 1995 Abstract: A molecular retrieval system and method answering to similarity queries for retrieving molecular structures, stored into a source database (22) and having a required similarity with an input structure, which can contain a set of property regions. A target database (23) stores the molecular structures described in hierarchical way and a knowledge base (24) stores well-known molecular fragments at different levels of description together with a set of physical and chemical properties associated to each fragment. A fragment recognizer (21) analyzes the fragments of the input structure to represent them in a hierarchical way. A query analyzer (25) analyzes the similarity queries and selects the appropriate level of molecular representation on the basis of the required similarity. Matching means (26, 27, 29), when called by the query analyzer (25), perform a matching of the representation of the input structure against the representations of the molecular structures stored into the target database (23) at the selected level of molecular representation.

US Patent Number: 5,386,507 Patent Title: Computer graphics system for selectively modelling molecules and investigating the chemical and physical properties thereof Date of Patent: January 31, 1995 Abstract: A computer graphics system for modeling chemical molecules includes simultaneous two-dimensional and three-dimensional display of models of molecules from a single data set, and allows a user to edit in either two dimensions or three dimensions. A two-dimensional model may be stylized while a three-dimensional model of the same molecule remains chemically (geometrically) correct. The system has editing tools for use in both two dimensions and three dimensions, and changes made in one mode are immediately reflected in the other, and the editing tools include manipulation components for the user to display on elements of a model, and to use to move parts of a model of a molecule relative to other parts. The system includes techniques for structure determination and display that significantly reduce the computer power required to perform system functions, rendering techniques formally reserved to supercomputers usable on smaller computer platforms. Physically based modeling is included, allowing the user to perturb the geometry of a model and to investigate interactively the effects of perturbation according to a dynamic force equation. The system also includes a procedure for displaying multiple models of molecules and performing docking studies between the models.

US Patent Number: 4,980,840 Patent Title: Computerized editing and composing system Date of Patent: December 25, 1990 Abstract: A computerized editing and composing system and method which conveniently and directly edits and composes complex scientific formulas, chemical structural formulas and music staves. The system comprises a computer, an I/O interface, an input device, a character library and character generating system, a display, an editing and composing process device and peripheral devices, and automatically processes the corresponding text while providing the user with a simple and convenient operational interface with inputting, editing, composing and outputting techniques to generate the different resolutions of the output.

US Patent Number: 4,855,931 Patent Title: Stochastic method for finding molecular conformations Date of Patent: August 8, 1989 Abstract: This is a stochastic method for determining the likely conformations of a molecule by starting with an initial molecular structure along with given atomic coordinate positions and defined bonds between atoms. Each of the atom's initial X, Y and Z coordinates are modified by the combination therewith of random numbers to create a new random coordinate position for each atom. A predetermined constraint is placed on the distance of each new coordinate from each initial coordinate. The steric energy of the reconfigured molecule is then calculated, stored and a new set of randon numbers combined with the atomic coordinates and the steric energy of the new structure calculated. The process is repeated until most, if not all, steric minima are detected and the structures associated therewith are determined.

US Patent Number: 4,835,528 Patent Title: Cursor control system Date of Patent: May 30, 1989 Abstract: A cursor control system for computer displays moves a cursor unambiguously in three dimensions using a two dimensional input device. The plane of movement of the two dimensional device is divided into logical regions which correspond to movement along a three dimensional axis. Movement of the two dimensional device into one of these regions causes the cursor to move along the corresponding axis of the display.

US Patent Number: 4,473,890 Patent Title: Method and device for storing stereochemical information about chemical compounds Date of Patent: September 25, 1984 Abstract: The structure of a compound is expressed as an atom connection table using an electronic computer. The structure is registered in a three-dimensional manner, making it possible to effect the interconversion between the atom connection table and symbols R, S that represent absolute configuration of asymmetric carbon atoms, or .alpha., .beta. that represent directions of substitution relative to the plane the ring. Namely, in the case of a ring compound, bonded atoms in the clockwise and counterclockwise directions, and bonded atoms in the upward and downward directions of the ring are stored in the separate predetermined registers. In the case of a chain compound, bonded atoms in the right and left directions, and bonded atoms in the upward and downward directions are stored in the separate predetermined registers. On the atom connection table, therefore, the rotational directing of bonded atoms can be defined as viewed from a given direction. It is therefore possible to prepare the atom connection table reflecting the symbols in the compound name, to store three-dimensional structures of compounds, and to process and produce the data.

US Patent Number: 5,379,234 Patent Title: Computer-aided chemical illustration system Date of Patent: January 3, 1995 Abstract: A computer-aided chemical illustration system is disclosed. Techniques provided include: 1) efficient drawing of bonds; 2) drawing different bond types during a single mode; 3) determining bisect angles for bonds; 4) labeling atoms on the fly; 5) automatic alignment of atom labels; 6) custom alignment of atom labels; 7) changing the type, style, or orientation of an object while it is being drawn; 8) detection of ring structures; and 9) shifting bonds around on a ring.

US Patent Number: 5,056,035 Patent Title: Method for processing information on chemical reactions Date of Patent: October 8, 1991 Abstract: A method for processing information of chemical reactions of producing at least one product from at least one starting material, said information being given in the form of imaginary transition structures (ITS) in which the starting material is topologically superposed upon the product and bonds are distinguished and classified into three categories of (1) bonds linking two nodes appearing both in the starting and product stages, (2) bonds linking two nodes appearing only in the starting stage and (3) bonds linking two nodes appearing only in the product stage and/or in the form of connection tables of ITS, which comprises extracting from the imaginary transition structure and/or the connection table a reaction string composed of said bonds (2) and said bonds (3) which are alternately arranged to each other.

US Patent Number: 5,025,388 Patent Title: Comparative molecular field analysis (CoMFA) Date of Patent: June 18, 1991 Abstract: Comparative Molecular Field Analysis (CoMFA) is an effective computer implemented methodology of 3D-QSAR employing both interactive graphics and statistical techniques for correlating shapes of molecules with their observed biological properties. For each molecule of a series of known substrates the steric and electrostatic interaction energies with a test probe atom are calculated at spatial coordinates around the molecule. Subsequent analysis of the data table by a partial least squares (PLS) cross-validation technique yields a set of coefficients which reflect the relative contribution of the shape elements of the molecular series to differences in biological activities. Display in three dimensions in an interactive graphics environment of the spatial volumes highly associated with biological activity, and comparison with molecular structures yields an understanding of intermolecular associations. CoMFA will also predict the biological activity of new molecular species.

US Patent Number: 5,555,366 Patent Title: Computer graphics system for selectively modelling molecules and investigating the chemical and physical properties thereof Date of Patent: September 10, 1996 Abstract: A computer graphics system for modeling chemical molecules includes simultaneous two-dimensional and three-dimensional display of models of molecules from a single data set, and allows a user to edit in either two dimensions or three dimensions. A two-dimensional model may be stylized while a three-dimensional model of the same molecule remains chemically (geometrically) correct. The system has editing tools for use in both two dimensions and three dimensions, and changes made in one mode are immediately reflected in the other, and the editing tools include manipulation components for the user to display on elements of a model, and to use to move parts of a model of a molecule relative to other parts. The system includes techniques for structure determination and display that significantly reduce the computer power required to perform system functions, rendering techniques formally reserved to supercomputers usable on smaller computer platforms. Physically based modeling is included, allowing the user to perturb the geometry of a model and to investigate interactively the effects of perturbation according to a dynamic force equation. The system also includes a procedure for displaying multiple models of molecules and performing docking studies between the models.

US Patent Number: 5,424,963 Patent Title: Molecular dynamics simulation method and apparatus Date of Patent: June 13, 1995 Abstract: A computer-assisted method for generating a dynamic model of a molecule is described based on information of the atomic structure. The model data is defined by rigid bodies corresponding to groups of atoms of the molecule with substantially no relative movement between the atoms, flexible bodies corresponding to groups of atoms which are characterized by relative movement between the atoms, and flexure elements which define an interconnection of two of the rigid bodies and the flexible bodies and predetermined degrees of freedom.

US Patent Number: 4,811,217 Patent Title: Method of storing and searching chemical structure data Date of Patent: March 7, 1989 Abstract: Chemical structure data containing generic representation of component atoms in a storage device is searched by finding a match between a query structure and a stored candidate structure by mathematically comparing attribute data of chemical units of a query structure and attribute data of chemical unit of a stored candidate structure, where attribute data represent chemical characteristics of chemical units of those structures.

US Patent Number: 5,619,421 Patent Title: Computer-implemented process and computer system for estimating the three-dimensional shape of a ring-shaped molecule and of a portion of a molecule containing a ring-shaped structure Date of Patent: April 8, 1997 Abstract: A computer-implemented process determines candidate three-dimensional shapes of ring-shaped molecules through an exhaustive search of combinations of torsion angles of the bonds of the ring, given known bond lengths and bond angles for the bonds between atoms of the rings, a range of torsion angles and a resolution. Candidate combinations of the torsion angles are selected according to the range and resolution and coordinates of the atoms of the ring are determined for each candidate combination. It is then determined whether each candidate combination defines a physically possible ring. Indications of such candidate combinations are recorded. Candidate combination may then be selected from those recorded so that coordinates of atoms in candidate repetitive structures may be determined.

US Patent Number: 5,930,784 Patent Title: Method of locating related items in a geometric space for data mining Date of Patent: July 27, 1999 Abstract: A method for locating related items in a geometric space transforms relationships among items to geometric locations. The method locates items in the geometric space so that the distance between items corresponds to the degree of relatedness. The method facilitates communication of the structure of the relationships among the items. The method is especially beneficial for communicating databases with many items, and with non-regular relationship patterns. Examples of such databases include databases containing items such as scientific papers or patents, related by citations or keywords. A computer system adapted for practice of the present invention can include a processor, a storage subsystem, a display device, and computer software to direct the location and display of the entities. The method comprises assigning numeric values as a measure of similarity between each pairing of items. A matrix is constructed, based on the numeric values. The eigenvectors and eigenvalues of the matrix are determined. Each item is located in the geometric space at coordinates determined from the eigenvectors and eigenvalues. Proper construction of the matrix and proper determination of coordinates from eigenvectors can ensure that distance between items in the geometric space is representative of the numeric value measure of the items' similarity.

US Patent Number: 5,884,230 Patent Title: Method and system for protein modeling Date of Patent: March 16, 1999 Abstract: A method in a computer system for modeling a three-dimensional structure of a model protein is provided. In one embodiment, the modeling is based upon a three-dimensional structure of a template protein and an amino acid sequence alignment of the model protein and the template protein. For each amino acid in the model protein, when the template protein has an amino acid aligned with the amino acid of the model protein, the position of the backbone atom of the amino acid of the model protein is established based on the position of a topologically equivalent backbone atom in the aligned amino acid of the template protein. In another embodiment, the modeling of a variable region of the model protein is based on a collection of .psi. and .phi. angle values for amino acid pairs in a family of proteins. In a further embodiment, these .psi. and .phi. angle values are classified according to a tetramer of adjacent amino acids and filtered based on a most probable conformation of portions of the variable region of the model protein.

US Patent Number: 5,557,535 Patent Title: Method and system for protein modeling Date of Patent: September 17, 1996 Abstract: A method in a computer system for modeling a three-dimensional structure of a model protein is provided. In a preferred embodiment, the modeling is based upon a three-dimensional structure of a template protein and an amino acid sequence alignment of the model protein and the template protein. The proteins comprise a plurality of amino acids having backbone atoms and side chain atoms. For each amino acid in the model protein, when the template protein has an amino acid aligned with the amino acid of the model protein, the position of each backbone atom of the amino acid of the model protein is established based on the position of a topologically equivalent backbone atom in the aligned amino acid of the template protein. The inter-atomic distance constraints for each pair of atoms with an established position is generated. Finally, the position of each atom in the model protein is set so that the inter-atomic distances are in accordance with the constraints.

US Patent Number: 5,764,872 Patent Title: Method and system for displaying vector data as stream lines in a space represented by tetrahedral cells Date of Patent: June 9, 1998 Abstract: A method and apparatus for displaying stream lines in a space are disclosed. First, the space is divided into a plurality of tetrahedral cells. Position data of each vertex of the tetrahedral cells and vector data at each position are collected. A critical point for each tetrahedral cell is then computed. The critical point is within the tetrahedral cell and for which the vector data becomes zero. Using the collected position and vector data, a Jacobian matrix J is calculated when such a critical point is found, and eigenvalues of the Jacobian matrix J are also calculated. Next, the starting point of a stream line within a tetrahedral cell is calculated for each of the eigenvalues by moving a microscopic distance from the critical point. Finally, a stream line is calculated from the starting point, and the stream line is displayed.

US Patent Number: 6,438,204 Patent Title: Linear prediction of structure factors in x-ray crystallography Date of Patent: August 20, 2002 Abstract: A method uses linear prediction analysis to define a first structure factor component for a first reflection from x-ray crystallography data. The x-ray crystallography data includes a set of cognizable reflections. The method includes expressing the first structure factor component as a first linear equation in which the first structure factor component is equal to a sum of a first plurality of terms. Each term includes a product of (1) a structure factor component for a cognizable reflection from the x-ray crystallography data, wherein the cognizable reflection has a separation in reciprocal space from the first reflection, and (2) a linear prediction coefficient corresponding to the separation between the cognizable reflection and the first reflection. The method further includes calculating values for the linear prediction coefficients. The method further includes substituting the values for the linear prediction coefficients into the first linear equation, thereby defining the first structure factor component for the first reflection.

US Patent Number: 5,200,910 Patent Title: Method for modelling the electron density of a crystal Date of Patent: April 6, 1993 Abstract: A method for modelling the electron density distribution of a macromolecule in a defined asymmetric unit of a crystal lattice having locations of uniformly diffracting electron density includes the steps of: producing an initial distribution of scattering bodies within a asymmetric unit having the same dimensions as the defined asymmetric unit; calculating scattering amplitudes of the initial distribution and determining the correlation between the calculated scattering amplitudes and the normalized amplitudes; moving at least one of the scattering bodies within the asymmetric unit to create a modified distribution; calculating scattering amplitudes and phases of the modified distribution and determining the correlation between the calculated amplitudes and the normalized values; and producing a final distribution of scattering bodies by repeating moving and calculating steps until the correlation between the calculated scattering amplitudes and the normalized amplitudes is effectively maximized, the final distribution of scattering bodies defining the electron density of the crystal.

US Patent Number: 5,241,470 Patent Title: Prediction of protein side-chain conformation by packing optimization Date of Patent: August 31, 1993 Abstract: A method is provided for determining the packing conformation of amino acid side chains on a fixed peptide backbone. Using a steric interaction potential, the side chain atoms are rotated about carbon-carbon bonds such that the side chains preferably settle in a low energy packing conformation. Rotational moves are continued according to a simulated annealing procedure until a set of low energy conformations are identified. These conformations represent the structure of the actual peptide. The method may be employed to identify the packing configuration of mutant peptides.

US Patent Number: 5,365,456 Patent Title: Method for modelling the electron density of a crystal Date of Patent: November 15, 1994 Abstract: A method for modelling the electron density distribution of a macromolecule in a defined asymmetric unit of a crystal lattice having locations of uniformly diffracting electron density includes the steps of: producing an initial distribution of scattering bodies with a asymmetric unit having the same dimensions as the defined asymmetric unit; calculating scattering amplitudes of the initial distribution and determining the correlation between the calculated scattering amplitudes and the normalized amplitudes; moving at least one of the scattering bodies within the asymmetric unit to create a modified distribution; calculating scattering amplitudes and phases of the modified distribution and determining the correlation between the calculated amplitudes and producing a final distribution of scattering bodies by repeating moving and calculating steps until the correlation between the calculated scattering amplitudes and the normalized amplitudes is effectively maximized, the final distribution of scattering bodies defining the electron density of the crystal.

US Patent Number: 6,408,047 Patent Title: Method of providing high throughput protein crystallography Date of Patent: June 18, 2002 Abstract: The invention provides a method of performing x-ray crystallography on samples by using a robot to select the target sample, to position the sample for x-ray crystallography, and to deposit the sample, all without transferring the sample to another device, such as a goniometer. This method allows high throughput, automated crystallography, thereby providing a high volume of samples to be tested while lessening the need for human intervention.

US Patent Number: 6,404,849 Patent Title: Automated sample handling for X-ray crystallography Date of Patent: June 11, 2002 Abstract: Method and apparatus for mounting a sample comprising a crystal for X-ray crystallographic analysis, a method for aligning a sample comprising a crystal for X-ray crystallographic analysis, which sample is mounted on a positioning device, and a method for determining the structure of a sample containing a crystal by means of X-ray crystallography.

US Patent Number: 6,400,797 Patent Title: Sample changer for capillary geometry X-ray diffractometers Date of Patent: June 4, 2002 Abstract: This present invention provides a sample changer for automatically changing from one sample to the next in support of high throughput X-ray powder diffraction data acquisition in a capillary geometry. The samples are mounted on the outer rim of a disk or turntable, with each sample having its capillary axis parallel to a radius emanating from the center of the disk on which the samples are mounted. Each sample is mounted on a separate motor shaft which permits the sample to be rotated about the longitudinal axis of the capillary during data acquisition. To change from one sample to the next, the disk or turntable is rotated about its axis thereby presenting in turn each new sample to a X-ray beam. When the data acquisition is completed for that sample, a new sample is rotated into the beam and its data collection is carried out.

US Patent Number: 6,111,930 Patent Title: Automatic sample changer for an X-ray diffractometer Date of Patent: August 29, 2000 Abstract: A sample changer (2) for the automatic intake of a multitude of samples into the measurement position on the goniometer axis (a) of an X-ray diffractometer (20) in which the individual samples--each showing a surface, which meets the goniometer axis at a tangent in the measurement position--are linearly arranged on an insertable magazine (3). The samples on the magazine (3) can be moved in the direction of the goniometer axis (a) in order to transport each sample translationally into the measurement position. Furthermore the sample changer (2), the magazine (3) and the mountings (10) show recesses, which allow the refracted X-ray beams from the sample in transmission mode to pass through to the detector (14) unimpeded. The sample changer is suitable for reflection mode as well as transmission mode measurements without having to redesign the system.

US Patent Number: 5,127,039 Patent Title: Sample holder for X-ray diffractometry Date of Patent: June 30, 1992 Abstract: A sample holder for use with X-ray diffractometers with the capability to rotate the sample, as well as to adjust the position of the sample in the x, y, and z directions. Adjustment in the x direction is accomplished through loosening set screws, moving a platform, and retightening the set screws. Motion translators are used for adjustment in the y and z directions. An electric motor rotates the sample, and receives power from the diffractometer.

US Patent Number: 4,770,593 Patent Title: Sample changer for X-ray diffractometer Date of Patent: September 13, 1988 Abstract: A sample changer for powder X-ray diffractometry includes a cylindrical dispensing container for holding a stack of pre-test sample holders, a cylindrical receiving container for holding a stack of post-test sample holders and a changer arm which automatically picks up the topmost sample disk in the dispensing container and rotatably positions the sample disk on the sample holder stage of an X-ray diffractometer for analysis. After analysis, the changer arm removes the sample holder and releases it into the receving container. The sample holders have a circumferential groove which coacts with semi-circular rotatable cams positioned on the distal end of the changer arm to enable the changer arm to lift and place the sample holders.

US Patent Number: 4,641,329 Patent Title: Fixture for supporting and aligning a sample to be analyzed in an X-ray diffraction apparatus Date of Patent: February 3, 1987 Abstract: A fixture is provided for supporting and aligning small samples of material on a goniometer for X-ray diffraction analysis. A sample-containing capillary is accurately positioned for rotation in the X-ray beam by selectively adjusting the fixture to position the capillary relative to the x and y axes thereof to prevent wobble and position the sample along the z axis or the axis of rotation. By employing the subject fixture relatively small samples of materials can be analyzed in an X-ray diffraction apparatus previously limited to the analysis of much larger samples.

US Patent Number: 6,371,640 Patent Title: Apparatus and method for characterizing libraries of different materials using X-ray scattering Date of Patent: April 16, 2002 Abstract: An apparatus for characterizing a library is provided in which the library contains an array of elements and each element contains a different combination of materials. The apparatus includes an x-ray beam directed at the library, a chamber which houses the library and a beamline for directing the x-ray beam onto the library in the chamber. The chamber may include a translation stage that holds the library and that is programmable to change the position of the library relative to the x-ray beam and a controller that controls the movement of the translation stage to expose an element to the x-ray beam in order to rapidly characterize the element in the library. During the characterization, the x-ray beam scatters off of the element and a detector detects the scattered x-ray beam in order to generate characterization data for the element.

US Patent Number: 5,600,571 Patent Title: Method for determining protein tertiary structure Date of Patent: February 4, 1997 Abstract: The subject invention provides a method for determining the most stable tertiary structure of a protein having a known primary structure which comprises the steps of (a) producing a reduced representation of the protein by assigning to the protein (i) all secondary structural motifs present therein and (ii) all .phi. and .PHI. dihedral angles for the amino acid residues present therein; (b) determining which conformations of the reduced representation are physically permissible, so as to determine which conformations of the protein are physically permissible; and (c) determining which of the physically permissible conformations of the protein possesses the lowest free energy, so as to thereby determine the most stable tertiary structure of the protein.

US Patent Number: 5,265,030 Patent Title: System and method for determining three-dimensional structures of proteins Date of Patent: November 23, 1993 Abstract: A computer system and method are disclosed for determining a protein's tertiary structure from a primary sequence of amino acid residues. The system uses a dynamic Monte Carlo method with Metropolis sampling criterion, and a selected (2,1,0) lattice model, to simulate protein folding during the transition of the protein from an unfolded (denatured) state to its native, folded state. The system generates, for display, a folding trajectory representing successive three-dimensional images of the protein at a level of two Angstrom resolution as it folds to its native conformation. The system permits interaction between all proximate pairs of sidechains of the protein and provides faster processing through the use of the lattice. The system comprises an input means such as a keyboard for specifying (entering) selected amino acid sequences and other data such as temperature and fold preferences, a RAM (random access memory) for storing such data, a ROM (read-only memory) with a stored program, a CRT (cathode ray tube) display unit and/or printer, an optional auxiliary disc storage device for storage of relevant data bases, and a microprocessor for processing the entered data, for simulating, under control of the stored program, the folding of the protein from its unfolded state to its folded (tertiary) state, and for displaying via the display unit (or printer) tertiary conformations of the protein in three dimensions.

US Patent Number: 5,008,831 Patent Title: Method for producing high quality chemical structure diagrams Date of Patent: April 16, 1991 Abstract: A computer operated method for transforming the appearance of a chemical structure entered into a computer wherein at least one alternate equivalent structure is generated within the computer (or by keyboard entry). A series of parameters applicable to chemical structures are established along with values for such parameters. Following that it is established which of such parameters are present in the first structure and the values thereof are summed to obtain a score. The parameters present in the alternate structures are then established and summed to establish a score for each. The scores are then compared and the highest score is selected and the structure corresponding to the highest score is outputted or printed.

US Patent Number: 4,747,059 Patent Title: Process and apparatus for naming chemical structures and the application thereof Date of Patent: May 24, 1988 Abstract: A novel method for naming chemical compounds comprises the steps of identifying a first component constituting the core of the compound according to predetermined first rules, naming the first component according to predetermined second rules, naming a secondary component of the first component according to predetermined third rules, modifying the name given for the first component by adding the name given for the second component to the name of the first component, and repeating the secondary-component naming and name-modifying steps for all of the secondary components in the compound. Such a method will give uniform rules for naming chemical compound, especially for organic compounds and for simply and easily naming new compounds.

US Patent Number: 4,205,391 Patent Title: Device for encoding and inputting to computer alphabetic and topologically represented graphic data that describes, in particular, structural formulae of chemical compounds Date of Patent: May 27, 1980 Abstract: A device for encoding and inputting to a computer alphabetic and topologically represented graphic data that describes, in particular, structural formulae of chemical compounds, comprising an encoding tablet, a changeable encoding form placed on the encoding tablet, a coordinate counter coupled to a computer communication line and to coordinate decoders which, in turn, are coupled to the encoding tablet, a pulse generator, a pulse distributor coupled to the pulse generator, to the coordinate decoders and to the coordinate counter, a code-pulse decoder coupled to the pulse generator and to the computer communication line, an electronic writing means which is a unique and sufficient facility exercising control over the operation of the device and including an amplifier coupled to a code-pulse decoder, a coordinate pickup coupled to the amplifier, a pressure sensor coupled to the pulse generator, a beginning-of-line symbol generator coupled to the computer communication line, and a changeable writing member which is designed as part of the pressure sensor and of the beginning-of-line symbol generator.

US Patent Number: 4,085,443 Patent Title: Keyboard operated apparatus for simultaneous coding and display of chemical structure and similar graphical information Date of Patent: April 18, 1978 Abstract: Graphical information, such as a structural chemical formulae, composed of nodes and links between the nodes, or in a chemical formula ring positions and bonds, are coded by means of logic circuits responsive to actuation of a keyboard. The graphical data coded in binary digit form are stored, while contents of the store are scanned, decoded and applied in analog form to a display device. When recorded on a suitable medium they are made machine readable, for searching or similar processing. A luminous cursor indicates on the display the part of a structural formula that is subject to the next keyboard action. The store is organized about fixed display locations available as nodes. Alphanumeric characters identify atoms at nodes. Single, double or triple bonds in any of eight directions from a node towards another node may be registered and displayed. A cursor address register, a store address register and a comparator are used. Registering at one node a bond designated by character and direction transfers the cursor to the node at the other end of the designated bond. Other transfers of the cursor may be effected by the space bar with the use of the appropriate directional keyed instruction.

US Patent Number: 4,704,692 Patent Title: Computer based system and method for determining and displaying possible chemical structures for converting double- or multiple-chain polypeptides to single-chain polypeptides Date of Patent: November 3, 1987 Abstract: A computer based system and method determines, and displays possible chemical structures for converting two naturally aggregated but chemically separated polypeptide chains into a single polypeptide chain which will fold into a three dimensional structure very similar to the original structure made of the two polypeptide chains. A data base contains a large number of amino acid sequences for which the three dimensional structure is known. After plausible sites have been selected, this data base is examined to find which amino acid sequences (linkers) can bridge the gap between the plausible sites to create a plausible one-polypeptide structure. The testing of each possible linker proceeds in three steps. First, the span (a scaler quantity) of the candidate is compared to the span of the gap. If the span is close enough, step two is done which involves aligning the first peptides of the candidate with the initial peptide of the gap. The three dimensional vector from tail to head of the candidate is compared to the three dimensional vector from tail to head of the gap. If there is a sufficient match between the two vectors, step three is done, which involves fitting the termini of the candidate (using, for example, at least squares procedure) to the termini of the gap. If these two termini fit well enough, the candidate is enrolled for a ranking process.

US Patent Number: 4,476,462 Patent Title: Use of context to simplify two-dimensional computer input Date of Patent: October 9, 1984 Abstract: The number of key strokes required to enter two-dimensional figures, such as chemical structures, into a computer from a keyboard display is reduced by utilizing contextual relationships between the character being typed at a specific location and the characters surrounding that location to predict the next character and/or location of that character to be typed. For example, when a horizontal bond between chemical elements is to be typed, the keyboard carriage moves horizontally to the next position, as with a conventional keyboard; but when a vertical or diagonal bond is typed, the carriage moves in the direction of the bond. In addition, symbols representing various atoms are predicted and automatically displayed at a next position location following typing of a bond when the contextual relationship at that location so requires.

US Patent Number: 4,982,338 Patent Title: Method for processing information on chemical reactions Date of Patent: January 1, 1991 Abstract: There is disclosed a method for recording and storing information on chemical reactions of producing at least one product from at least one starting material, which comprises representing the chemical reaction in such a manner that the starting material is topologically superposed upon the product, and bonds are distinguished and classified into three categories of (1) bonds linking two nodes appearing both in the starting and product stages, (2) bonds linking two nodes appearing only in the starting stage and (3) bonds linking two nodes appearing only in the product stage. Methods for processing information on chemical reactions to record and store, which include preparing an imaginary transition structure (ITS) of a chemical reaction and a connection table of ITS according to the representation are also disclosed.

US Patent Number: 4,881,175 Patent Title: Computer based system and method for determining and displaying possible chemical structures for converting double- or multiple-chain polypeptides to single-chain polypeptides Notice: The portion of the term of this patent subsequent to November 3, 2004 has been disclaimed Date of Patent: November 14, 1989 Abstract: A computer based system and method determines and displays possible chemical structures for converting two naturally aggregated but chemically separated polypeptide chains into a single polypeptide chain which will fold into a three dimensional structure very similar to the original structure made of the two polypeptide chains. A data base contains a large number of amino acid sequences for which the three dimensional structure is known. After plausible sites have been selected, this data base is examined to find which amino acid sequences (linkers) can bridge the gap between the plausible sites to create a plausible one-polypeptide structure. The testing of each possible linker proceeds in three steps. First, the span (a scalar quantity) of the candidate is compared to the span of the gap. If the span is close enough, step two is done which involves aligning the first peptides of the candidate with the initial peptide of the gap. The three dimensional vector from tail to head of the candidate is compared to the three dimensional vector from tail to head of the gap. If there is a sufficient match between the two vectors, step three is done, which involves fitting the termini of the candidate (using, for example, a least squares procedure) to the termini of the gap. If these two termini fit well enough, the candidate is enrolled for a ranking process.

US Patent Number: 4,853,871 Patent Title: Computer-based method for designing stablized proteins Date of Patent: August 1, 1989 Abstract: A computer-based method evaluates the structure of a protein to thereby identify sites in the protein molecule at which the natural amino acid residues can be replaced with cysteine residues in order to permit the formation of a potentially stabilizing disulfide bond.

US Patent Number: 4,719,582 Patent Title: Method and apparatus for determining the chemical structure of an unknown substance Date of Patent: January 12, 1988 Abstract: A method and apparatus for determining the chemical structure of an unknown substance wherein spectral data of the unknown substance is detected, a point-assessment is calculated which expresses the degree of possibility of partial structures being contained in the unknown substance based on the spectral data and prememorized chemical shift values corresponding to the partial structures of known substances, it is judged whether the point-assessment is a predetermined threshold value or more and the partial structures with a large possibility of being contained in the unknown substance based on the output of the judgement results are found and displayed. The partial structures thus found are used to determine a molecular structure of the unknown substance.

US Patent Number: 4,378,218 Patent Title: Protein molecule model Date of Patent: March 29, 1983 Abstract: A ball-and-stick model system representing alpha carbon positions and the peptide link between adjacent alpha carbons as modeling elements of two-piece sets. Each two-piece set comprises complementary ring rods and ball rods, the latter having a generally cylindrical body enlarged at one end to a sphere form with a slot through a portion of the enlargement. The ring rod also includes a generally cylindrical body with an enlarged end portion to fit snugly within the slot of the ball rod so that when they are fitted together they appear as a sphere with the cylindrical body portions extending outwardly therefrom. The cylindrical portions of adjacent model sets are united by a pintle and hole structure configured so that when fitted together a continuous cylindrical body extends between adjacent spheres. Scales and indices are arranged on the adjacent surfaces of the rod and ball elements to mark the angles or bend and torsion of consecutive amino acids in the molecule and the sets are color coded to identify particular amino acids in the molecule.

US Patent Number: 5,260,882 Patent Title: Process for the estimation of physical and chemical properties of a proposed polymeric or copolymeric substance or material Date of Patent: November 9, 1993 Abstract: A process for estimation of properties utilizing experimental information using constraint determined by chemical kinetics, statistical thermodynamics and molecular mechanics including experimental information on proposed polymeric or copolymeric substances of large molecules for the estimation of the physical properties of the substances by first defining the substances molecular chemical composition, second, estimating properties of the molecular chemical composition when 3-dimensionally folded, third, forming the composition into a polymeric cluster, fourth, estimating the physical properties of the polymeric cluster, and finally preparation of the polymeric substances having the properties as estimated. The present invention overcomes the "multiple stable minimum " which is associated with prior polymer modeling approaches of large molecules.

US Patent Number: 6,334,314 Patent Title: Cryostat nozzle a method of using a cryostat Date of Patent: January 1, 2002 Abstract: A method of using a cryostat comprises supplying a stream of cold cryogas over a specimen, and surrounding said stream in the vicinity of the specimen by a dry annular flow of the same cryogas at ambient temperature. A nozzle for the cryostat comprises a central feed tube (36) for supplying the stream of cold cryogas over a specimen (35), and an annular feed opening (34) for supplying the dry annular flow of the same cryogas at ambient temperature.

United States Patent Application: 20020117553 Patent Title: Cryostat nozzle a method of using a cryostat Date of Patent: August 29, 2002 Abstract: The invention provides an improved nozzle and method for delivering a coolant stream to a location in an ambient atmosphere.

US Patent Number: 6,326,619 Patent Title: Crystal phase identification Date of Patent: December 4, 2001 Abstract: A method and apparatus for determining the crystalline phase and crystalline characteristics of a sample. This invention provides a method and apparatus for unambiguously identifying and determining the crystalline phase and crystalline characteristics of a sample by using an electron beam generator, such as a scanning electron microscope, to obtain a backscattered electron Kikuchi pattern of a sample, and extracting crystallographic and composition data that is matched to database information to provide a quick and automatic method to identify crystalline phases.

US Patent Number: 6,282,263 Patent Title: X-ray generator Date of Patent: August 28, 2001 Abstract: An X-ray generator comprises an evacuated and sealed X-ray tube, an electron gun, an X-ray target, an internal electron mask, and an X-ray window consisting of a thin tube of material with low X-ray absorption and high mechanical strength, for example beryllium. The window connects the tube to the target assembly containing the X-ray target. The generator preferably also includes a system for focusing and steering the electron beam onto the target, a cooling system to cool the target material, kinematic mounts to allow precise and repeatable mounting of X-ray devices for focusing the X-ray beam, and X-ray focusing devices of varying configurations and methods. The X-ray generator of the invention produces an X-ray source having a focal spot or line of very small dimensions and is capable of producing a high intensity X-ray beam at a relatively small point of application using a low operating power.

US Patent Number: 6,282,259 Patent Title: X-ray mirror system providing enhanced signal concentration Date of Patent: August 28, 2001 Abstract: A focusing device for x-radiation is disclosed. The device is fabricated from a block of optical material. The block can be monolithic or formed of multiple pieces joined together. A groove is cut into the monolithic block preferably in the form of a "V" groove. The active surfaces of the groove are finished and coated so that they are optically reflective, or can be coated with material forming a multilayer surface so that they are optically diffractive. The active surfaces thereby form two side-by-side mirrors which are preferably at right angles to one another. Means for deforming the groove are provided. The focal length of x-radiation impinging upon the groove is defines as a function of controlled deformation of the groove.

US Patent Number: 6,278,764 Patent Title: High efficiency replicated x-ray optics and fabrication method Date of Patent: August 21, 2001 Abstract: Replicated x-ray optics are fabricated by sputter deposition of reflecting layers on a super-polished reusable mandrel. The reflecting layers are strengthened by a supporting multilayer that results in stronger stress-relieved reflecting surfaces that do not deform during separation from the mandrel. The supporting multilayer enhances the ability to part the replica from the mandrel without degradation in surface roughness. The reflecting surfaces are comparable in smoothness to the mandrel surface. An outer layer is electrodeposited on the supporting multilayer. A parting layer may be deposited directly on the mandrel before the reflecting surface to facilitate removal of the layered, tubular optic device from the mandrel without deformation. The inner reflecting surface of the shell can be a single layer grazing reflection mirror or a resonant multilayer mirror. The resulting optics can be used in a wide variety of applications, including lithography, microscopy, radiography, tomography, and crystallography.

US Patent Number: 6,228,286 Patent Title: Class of high energy detecting phosphors Date of Patent: May 8, 2001 Abstract: An elpasolite phosphor is provided corresponding to the general formula: A.sub.2-y B.sub.1+y Me.sup.3+ X.sub.6 :xD wherein: A=a monovalent ion B=a monovalent ion A is different from B Me.sup.3+ =a trivalent ion D is a dopant X is at least one of F, Cl, Br and I 0.ltoreq.y.ltoreq.1 0.ltoreq.x.ltoreq.0.2 and wherein said phosphor has a specific gravity (sg).gtoreq.4. An elpasolite phosphor corresponding to the general formula above is especially useful in the production of prompt emitting X-ray screens and in the production of X-ray energy storage screens.

US Patent Number: 6,221,153 Patent Title: Method for producing large crystals of complex molecules Date of Patent: April 24, 2001 Abstract: Compressed gases, liquefied gases, or supercritical fluids are utilized as anti-solvents in a crystal growing process for complex molecules. Crystals of the present invention exhibit greater crystal size and improved morphology over crystals obtained by conventional methods.

US Patent Number: 6,188,965 Patent Title: Apparatus and method for automated protein design Date of Patent: February 13, 2001 Abstract: The present invention relates to apparatus and methods for quantitative protein design and optimization. Claims: We claim: 1. A method executed by a computer under the control of a program, said computer including a memory for storing said program, said method comprising the steps of:

United States Patent Application: 20020106660 United States Patent Application Title: Crystal structure of the 30s ribosome and its use Date of Patent: August 8, 2002 Abstract: The invention provides an X-ray crystal structure of the 30S ribosome, obtained from Thermus thermophilus 30S subunit, having a tetragonal space group P4.sub.12.sub.12 with unit cell dimensions of a=401.4.+-.4.0 .ANG., b=401.4.+-.4.0 .ANG., c=175.9.+-.5.0 .ANG.. An advantageous feature of the structure is that it diffracts beyond 3 .ANG. resolution. The invention also provides a crystal of 30S having the three dimensional atomic coordinates of the 30S ribosome, the coordinates being provided in Tables 1A and 1B. The data may be used for the rational design and modelling of inhibitors for the 30S ribosome, which have potential use as antibiotics.

United States Patent Application: 20020072864 United States Patent Application: COMPUTER-BASED METHOD FOR MACROMOLECULAR ENGINEERING AND DESIGN Date of Patent: June 13, 2002 Abstract: The present invention relates to a system and method for engineering and designing a macromolecule. An experimentally determined or de novo atomic structure that corresponds to the macromolecule is identified. The atomic structure is composed of building blocks. When the macromolecule is a peptide or a protein, the building blocks are amino acid residues. A target subset of the building blocks in the atomic structure to be optimized is identified. The coordinates of those building blocks that are not in the target subset are fixed. For each building block in the target subset, a large number of potential conformers is sample d. Each conformer to be sampled is substituted into the atomic structure and tested against an energy function that includes the equivalent energy of the conformer in a reference state. Combinations of conformers that best satisfy an interaction energy function are identified.

United States Patent Application: 20020064253 United States Patent Application Title: Apparatus and method for generating a high intensity X-ray beam with a selectable shape and wavelength Date of Patent: May 30, 2002 Abstract: An X-ray source is provided for delivering a high intensity X-ray beam with a predefined energy level of monochromatization, intensity and spatial distribution to a desired region of a sample. The source includes a linear accelerator with a thin anode 4, an electron trap 5 for separating an electron beam from an X-ray beam and conditioning optics which direct, shape and monochromatize the X-ray beam. The conditioning optics include a housing 8 within which are contained entrance slits, multi layer Kirkpatrick-Baez mirrors, exit slits, and a stop diaphragm. The invention also include a method of generating X-rays and a method of using them.

United States Patent Application: 20020027972 United States Patent Application Title: Microfocus-polycapillary optic x-ray system for x-ray analysis Date of Patent: March 7, 2002 Abstract: A microfocus x-ray system for producing a quasi-parallel x-ray beam is disclosed which includes an x-ray source, a polycapillary optic and a monochromator. The x-ray system achieves a high rate of x-ray flux, and the angular divergence of the x-ray beam has been reduced. The x-ray system is particularly well suited for use on small macromolecular crystals.

United States Patent Application: 20010032052 United States Patent Application Title: Apparatus and method for automated protein design Date of Patent: October 18, 2001 Abstract: The present invention relates to apparatus and methods for quantitative protein design and optimization. Claims: We claim: 1. A method executed by a computer under the control of a program, said computer including a memory for storing said program, said method comprising the steps of:

United States Patent Application: 20020094060 United States Patent Application Title: Method and apparatus for X-ray diffraction analyses Date of Patent: July 18, 2002 Abstract: A method and apparatus for continuously presenting a sample from a stream of particulate material which contains crystalline substances and for effectively continuously analysing the sample by X-ray diffraction are provided. An extracted sample flow is fed onto a continuously moving carrier and its surface smoothed and flattened for X-ray diffraction patterns to be detected and analysed to provide a compositional analysis for the crystalline substances. The sample is continuously removed from the carrier prior to further sample being fed onto the carrier. The invention is particularly applicable for phase composition analysis of cement and cement clinker and provides an effectively continuous analysis substantially in real time in contrast to prior art laboratory analyses of discrete samples.

US Patent Number: 6,108,401 Patent Title: Method of standard-less phase analysis by means of a diffractogram Date of Patent: August 22, 2000 Abstract: A method of determining the concentrations of the constituents in a mixture of substances by way of an X-ray diffractogram of the mixture. The fundamental difficulty that it is not possible to determine the entire power spectrum (PS) of the diffraction is avoided by making a suitable estimate of the PS on the basis of the diffractions that can be observed. Using an estimate of the dispersive power of the individual atoms in the unity cells of the constituents and the PS, the absolute intensities are determined from the relative intensities and on the basis thereof the concentrations of the constituents in the mixture are determined.

US Patent Number: 3,961,186 Patent Title: Method and apparatus for the determination of electron density in a part volume of a body Date of Patent: June 1, 1976 Abstract: A method of and an apparatus for the determination of the electron density of small volumes of a body. Two narrow beams of ionizing radiation of substantially equal intensity are subsequently directed through the small volume in two different directions. The intensity of the transmitted radiation as well as the scattered radiation along said two directions is measured extra-corporally, which measurements are employed in computing the electron density of the small volume. The employed radiation is of such high energy that the Compton effect will be the wholly dominant absorption phenomenon in the volume as well as in the radiation paths in the two mentioned directions, and that the change in the absorption cross-section from primary to secondary radiation caused by the Compton shift will be substantial.

US Patent Number: 6,327,334 Patent Title: Method of rapidly screening X-ray powder diffraction patterns Date of Patent: December 4, 2001 Abstract: A method for rapidly screening multiple X-ray powder diffraction patterns, such as those generated through combinatorial chemistry, has been developed. The method is directed toward measuring X-ray powder diffraction patterns of a set of samples, factoring the patterns using a suitable statistical technique into a small number of discrete components or factors, determining the scores corresponding to the factors for each X-ray powder diffraction pattern, and plotting the scores. The graphs of the scores are then inspected for clusters, trends, or outliers, which may represent new material or, perhaps, faulty data.

US Patent Number: 5,862,060 Patent Title: Maintenance of process control by statistical analysis of product optical spectrum Date of Patent: January 19, 1999 Abstract: Control of many chemical processes is optimized using compositional data, rather than physical properties, as the means of control. Using near infrared spectroscopy as the analytical tool affords the opportunity for on-line measurements in real time. A calibration set of NIR spectra bounding the acceptable process space within which a particular property is to be controlled is obtained by conventional means. Applying a multivariant statistical method to the calibration set affords a method of identifying the most important characteristics of the set which governs the controlled property, and is inherently related to the composition of the process product. Control then is effected by using only a small number (2-4) of such characteristics, which can be determined quickly and simply from the measured spectra, as the control criteria to be applied to the process as a whole. The result is a very effective way of controlling a complex process using only 2-4 non-obvious criteria objectively determined from a calibration set and which can be applied in real time and virtually continuously resulting in a well-controlled process whose product composition is (ideally) invariant.

US / European / World Patent Number/ Request: US2002054663 EP1210589 (WO0111345) Patent Title: AUTOMATED SAMPLE HANDLING FOR X-RAY CRYSTALLOGRAPHY Publication Date: 2002-05-09 Abstract: Method and apparatus for mounting a sample comprising a crystal for X-ray crystallographic analysis, a method for aligning a sample comprising a crystal for X-ray crystallographic analysis, which sample is mounted on a positioning device, and a method for determining the structure of a sample containing a crystal by means of X-ray crystallography

US / European / World Patent Number/ Request: US2002107643 Patent Title: PROCESS FOR PAN-GENOMIC DETERMINATION OF MACROMOLECULAR ATOMIC STRUCTURES Publication Date: 2002-08-08 Abstract: A process for pan-genomic determination of three-dimensional macromolecular atomic structures uses a unique combination of components. All known structural information, sequence information and functional information are systematically organized into a genomics database. Advanced tools of bioinformatics are used to cluster all known gene products into families of homologous sequences. Simultaneously, in parallel for each such family, a few cDNAs from appropriately representatives species are cloned into expression vectors for a few expressions systems. Constructs are then screened for expression, and those that are effective advance to the preparative step. Expressed proteins are prepared, purified and characterized. Purified proteins are set to crystallize in parallel against crystallization screens. Crystals that grow are tested for suitable diffraction characteristics. A suitable crystal is frozen, and diffraction data are measured using the multiwavelength anomalous diffraction (MAD) method at a synchrotron which uses undulator beamlines for high-throughput crystallography. Diffraction data are analyzed by the MAD phasing method, an atomic model is built, and the model is refined against the diffraction data. The refined model is analyzed in the context of (1) sequence information from other family members, (2) all other known 3D structures, and (3) functional motifs. It is also analyzed for surface characteristics with the aim to define active sites and macromolecular contact sites. For relevant structures, the active site properties are used to define classes of compounds predicted to have binding potency. Computational tools for homology model building are used to develop models for homologs. The homology models may be used in target selection, drug design, or design of more appropriate constructs for experimental analysis. The ensemble of all known structures is used to further advance the effectiveness of the bioinformatics tools

US / European / World Patent Number/ Request: WO0188515 Patent Title: METHOD FOR DETERMINING STRUCTURE OF SOFT MATERIAL Publication Date: 2001-11-22 Abstract: A method for determining the three-dimensional structure of a low-density material called a soft material not ordered on an atomic scale but ordered on a mesoscale (20 to 500 angstroms), especially by means of a high-resolution transmission microscope. A soft material is imaged by means of a transmission microscope in three or more directions meaningful in crystallography. The image is Fourier-transformed to calculate the amplitude and phase of the crystal structure factor. Fourier inverse transform using the values is carried out and hence a space group of the soft material is determined.

US / European / World Patent Number/ Request: WO0186271 Patent Title: STRUCTURE FACTOR DETERMINATIONS Publication Date: 2001-11-15 Abstract: A method reduces the structure factor phase ambiguity corresponding to a selected reciprocal lattice vector. The method includes generating an original phase probability distribution corresponding to a selected structure factor phase of the selected reciprocal lattice vector. The original phase probability distribution includes a first structure factor phase ambiguity. The method further includes combining the original phase probability distribution with a plurality of phase probability distributions of a plurality of structure factor phases of other reciprocal lattice vectors using a phase equation or inequality. The method further includes producing a resultant phase probability distribution for the selected structure factor phase of the selected reciprocal lattice vector. The resultant phase probability distribution includes a second structure factor phase ambiguity which is smaller than the first structure factor phase ambiguity. In addition, a method uses linear prediction analysis to define a first structure factor component for a first reflection from x-ray crystallography data. The method includes expressing the first structure factor component as a first linear equation in which the first structure factor component is equal to a sum of a first plurality of terms.

US / European / World Patent Number/ Request: WO9949109 Patent Title: METHOD FOR GROWING CRYSTALS IN DOMESTIC CONDITIONS Publication Date: 1999-09-30 Abstract: The present invention pertains to the field of crystallography and may be used for growing monocrystals as well as crystal junctions in domestic conditions and for decorative purposes. The purpose of this invention is to provide a technique for creating monocrystals or crystals junctions having decorative shapes. To this end, this invention comprises preparing an aqueous solution of a base substance, such as vitriol blue CuSO4*5H2O or a blood-red salt K<3>[Fe(CN6)], until a saturated solution is obtained, said solution being then heated at a temperature of up to 45 DEG . An unsaturated solution is then obtained and a crystal seed previously grown on a frame with a weight and a loop is added thereto at a temperature of (Troom + 8 DEG ). It is thus possible to grow large-size crystals having predetermined dimensions and decorative shapes. Apart from those mentioned above, the base solutions may consist in aqueous solutions of mineral salts such as nickel vitriol NiSO4*7H2O, magnesium sulphate MgSO4*7H2O, potassium dichromate K2Cr2O7, a yellow blood-red salt K4[Fe(CN)6]*3H2O, manganese dichloride MnCl2*4H2O, copper dichloride CuCl2*2H2O, etc.

US / European / World Patent Number/ Request: DE19727437 WO9900328 Patent Title: IMPROVED STRUCTURAL DETERMINATION OF BIOLOGICAL AGGREGATES IN X-RAY CRYSTALLOGRAPHY Publication Date: 1999-01-14 Abstract: The invention relates to novel crystalline heavy metal cluster compounds and the crystallographic data thereof, in addition to the use of said crystallographic data in x-ray structural analysis. The invention specially relates to improvements in determining the structure of biological molecules. By using said method, the identification of effectors for such biological molecules can also be improved.

US Patent Number: 5,878,106 Patent Title: X-ray diffractometer Date of Patent: March 2, 1999 Abstract: In an x-ray diffractometer having (i) first and second motors 10, 17 for respectively rotating a sample 4 and an x-ray detector 13 around a rotational axis 7 and (ii) .theta.-2.theta. interlock control means 22 for supplying drive signals to the motors 10, 17, such that a .theta.-2.theta. relationship is always maintained between the angles of the sample 4 and the x-ray detector 13 with respect to irradiated x-rays 2, there is disposed a rotational vibration control unit 23 for supplying, to the first motor for rotating the sample holding member 6, a drive signal for rotationally vibrating the sample, in addition to the drive signal for .theta.-2.theta. interlock. Eliminating an individual drive mechanism for rotationally vibrating the sample 4, this arrangement makes it possible that, with a simple and economical structure, diffracted x-rays are efficiently detected even for a sample having an uneven surface, thereby to obtain an accurate measurement result.

US Patent Number: 4,885,688 Patent Title: Minimization of directed points generated in three-dimensional dividing cubes method Date of Patent: December 5, 1989 Abstract: A system for displaying three-dimensional surface structures according to computer graphics methods extracts a surface definition from a tomographic array of data using interpolation of the data for smooth, high resolution images. Interpolation can be performed to a degree where artifact-free images are produced for all viewing orientations. Data-processing capacity and time requirements can be reduced with less interpolation while image quality is maintained for all viewing orientations by inspecting the viewing orientation and appropriately scaling the image. Note: A Marching Cubes Algorithm

US Patent Number: 4,710,876 Patent Title: System and method for the display of surface structures contained within the interior region of a solid body Date of Patent: December 1, 1987 Abstract: A method and apparatus for displaying three dimensional surface images includes the utilization of a case table for rapid retrieval of surface approximation information. Eight cubically adjacent data points associated with a given voxel element are compared with a predetermined threshold value or range to generate an eight bit vector. This eight bit vector is employed to rapidly produce vector lists of approximating surfaces. An interpolation operation is performed so as to more closely approximate the desired surface and to provide more accurate representations of vectors normal to the desired surface. The accurate representation of these normal directions provides means for accurately representing shading information on a display screen. The method and apparatus of the present invention are particularly useful for the display of medical images both, from x-ray generated data and from data generated from various other sources including magnetic resonance imaging and positron emission tomography. The present invention provides a means for rapid generation of three dimensional images so as to enable interactive use by medical practitioners. Note: A Marching Cubes Algorithm

US Patent Number: 4,873,662 Patent Title: Information handling system and terminal apparatus therefor Date of Patent: October 10, 1989 Abstract: Informaton for display at a terminal apparatus of a computer is stored in blocks the first part of which contains the information which is actually displayed at the terminal and the second part of which contains information relating to the display and which may be used to influence the display at the time or in response to a keyboard entry signal. For example, the second part of the block could include information for providing the complete address of an another block which would be selected by the operation of a selected key of the keyboard. The second part of the block could alternatively influence the format and/or color of the display at the terminal. When a block is read from the store of the computer the second part is retained in another store which may be located in the terminal or in the computer itself or perhaps both. The invention is particularly useful in reducing the complexity of the operating protocol of the computer.

US Patent Number: 4,885,697 Patent Title: Method of identifying spectra Date of Patent: December 5, 1989 Abstract: A hierarchial library of spectra representing the point-by-point characteristics of known samples is created. Vectors representing each spectrum are classified according to their similarlity and dissimilarity. Vectors representing unknown samples are compared to known groups of vectors according to similarity until a near match is found.

US Patent Number: 4,766,551 Patent Title: Method of comparing spectra to identify similar materials Date of Patent: August 23, 1988 Abstract: In a method of identifying or comparing compositions of material, the reflectivity of a material to be identified or compared is measured at index points distributed through the near infrared spectrum. A similar measurement is made for at least one standard or known material. From the reflectivity measurements, sets of values representing the first or higher order derivative curves are determined. These values mathematically define vectors by representing the coordinates of the end points of the vectors and multiple dimensional space. An index of a similarity between the composition of a test sample and a standard material is calculated by determining the cosine of the angle between the corresponding vectors.

US Patent Number: 4,660,151 Patent Title: Multicomponent quantitative analytical method and apparatus Date of Patent: April 21, 1987 Abstract: A multicomponent quantitative analytical method and apparatus wherein the method includes the steps of and the apparatus is capable of performing steps of obtaining a plurality of calibration spectra, transforming the calibration spectra using a transform with orthogonal basis vectors, obtaining a calibration matrix relating the transform spectra to concentrations of analytes in the calibration samples, obtaining a spectrum for an unknown sample, transforming the unknown sample spectrum, and relating the transformed unknown sample spectrum to the calibration matrix to thereby determine the concentration of analytes in the unknown sample.

US Patent Number: 4,590,574 Patent Title: Method for determining oxygen and carbon in silicon semiconductor wafer having rough surface Date of Patent: May 20, 1986 Abstract: An infrared Fourier transform spectrometer is used to measure the absorbance spectrum of a sample of unknown oxygen or carbon content. From the spectrum, the roughness of the wafer is defined, and such roughness definition is then used to calculate the oxygen or carbon content. The roughness can be defined by using the slope of the absorbance spectrum or by the degree of shift of the baseline of the oxygen or carbon peak.

US Patent Number: 4,449,819 Patent Title: Arrangement for determining the concentration of a substance in a mixture of substances Date of Patent: May 22, 1984 Abstract: A mixture of substances is analyzed by spectral analysis to establish the concentration of one component of the mixture. For this purpose signals U.sub.1 (.lambda.) representative of the spectrum of the substance under investigation and U.sub.2 (.lambda.) representative of the spectrum of the mixture of substances are manipulated electronically so as to remove the effects of cross-sensitivity and to yield an accurate value for the concentration of the substance in the mixture of substances. This concentration is normally difficult to determine because of the effects of cross-sensitivity, i.e. because other components in the mixture of substances have similar spectral lines to those of the substance under investigation. In one arrangement the two signals U.sub.1 (.lambda.) and U.sub.2 (.lambda.) are first differentiated in respective differentiating stages 13 and 14 and the differentiated signals are multiplied in a multiplier 17. The output signal from the multiplier is subsequently integrated in an integrator 20 and the output of the integration is a measure of the concentration of the substance under investigation. The signal F derived from the multiplier 17 has two components F.sub.N +F.sub.S. The component F.sub.N is a product of the wanted signal in respect of the substance under investigation from the reference source 11 and of the wanted component from the measured signal U.sub.2 (.lambda.). This product is always positive and thus leads to a maximum value at the output of the integrator. The component F.sub.S is equivalent to a product of the wanted signal from the reference source with unwanted signals from the measurement and is in fact a value which statistically flucutates about zero. The result of integrating this component is thus a value which approximates to zero. In other words the result of the integration provides exclusively information about the substance under investigation.

US Patent Number: 4,365,303 Patent Title: Method and apparatus for determining the nature of an unknown chemical substance Date of Patent: December 21, 1982 Abstract: Disclosed herein is method and apparatus for determining the nature of an unknown substance, which includes apparatus for entering a peak table of the spectrum of an unknown substance into computing apparatus, apparatus for adjusting the peak table to a first preselected standardized format, computing apparatus for comparing the so standardized peak table of the unknown with a first library of chemical structural units contained in memory in the computing apparatus, apparatus for making a list of the possible chemical structural units most closely corresponding to the unknown substance, apparatus for readjusting the peak table to a second preselected standardized format, apparatus for forming a file for the unknown substance including data corresponding to the readjusted peak table and to the list of possible chemical structural units, computing apparatus for comparing the file of the unknown substance with a second library containing files of known substances contained in memory in the computing apparatus, each known substance having a file containing data corresponding to its respective peak table in the second standardized format and to its respective chemical structural unit, and apparatus for outputting a list of known substances which most closely correspond to the unknown substance. In a form of the invention, apparatus is provided for adding data corresponding to a known substance to the second library contained in memory in the computing apparatus.

US Patent Number: 4,719,582 Patent Title: Method and apparatus for determining the chemical structure of an unknown substance Date of Patent: January 12, 1988 Abstract: A method and apparatus for determining the chemical structure of an unknown substance wherein spectral data of the unknown substance is detected, a point-assessment is calculated which expresses the degree of possibility of partial structures being contained in the unknown substance based on the spectral data and prememorized chemical shift values corresponding to the partial structures of known substances, it is judged whether the point-assessment is a predetermined threshold value or more and the partial structures with a large possibility of being contained in the unknown substance based on the output of the judgement results are found and displayed. The partial structures thus found are used to determine a molecular structure of the unknown substance.

US Patent Number: 4,651,289 Patent Title: Pattern recognition apparatus and method for making same Date of Patent: March 17, 1987 Abstract: In a pattern recognition system for speech or print, a first memory stores predetermined reference vectors. A second memory stores subsequently-determined reference vectors subsequent to misrecognition when a new speaker or font is inputted, whereby only the deformations (differences) from a predetermined category of vectors are stored.

US Patent Number: 4,642,778 Patent Title: Method and device for spectral reconstruction Date of Patent: February 10, 1987 Abstract: A method is presented for spectral reconstruction which comprises first obtaining component concentrations of a series of mixtures, which component concentrations constitute a set of reference values. The spectral value of each member of that series of mixtures is measured at a first wavelength, which spectral value possesses contribution from individual components in the mixture, whose individual contribution is unknown. The spectral values for the series of mixtures are then mathematically cross-correlated with the component concentrations in said series of mixtures, at the first wavelength, thereby obtaining the spectral contribution for said components at that first wavelength. The spectral value of each member of that series of mixtures is measured at the second wavelength, which spectral values are then cross-correlated with component concentrations in the series of mixtures thereby obtaining the spectral contribution for said components at the second wavelength. This operation is repeated for a series of wavelengths until the spectrum of the desired component in the mixture is reconstructed. Devices are presented which implement the methods for spectral reconstruction of the present invention.

US Patent Number: 4,837,687 Patent Title: Method for analyzing an autoradiograph Date of Patent: June 6, 1989 Abstract: A method for analyzing autoradiography by subjecting digital signals corresponding to an autoradiograph having information on two-dimensional location of radioactively labeled substances resolved on a support medium to signal processing, to obtain the locational information on the radioactively labeled substances in the form of visual indicia, which includes the steps of: (1) electrically displaying the autoradiograph in the form of an image on the basis of the digital signals; (2) extracting signals in a given area along resolved rows of the radioactively labeled substances on the basis of input information on the rows determined from the display image; and (3) subjecting the extracted signals to one-dimensional signal processing to detect resolved portions.

US Patent Number: 6,037,949 Patent Title: Texture mapping and other uses of scalar fields on subdivision surfaces in computer graphics and animation Date of Patent: March 14, 2000 Abstract: Methods for defining smooth scalar fields on arbitrary polygonal meshes which can be consistently carried through the subdivision process involve computing mesh vertices after subdivision to a suitable resolution and computing scalar field values at the vertices corresponding to an arbitrary smooth surface, including the limit surface. The methods allow one to define and compute the value of scalar fields over an arbitrarily dense set of points on the limit surface. Applications of these techniques in computer graphics and computer animation include: (1) the definition of pseudo-coordinates for use in parametric shading including texture mapping; (2) the assignment of smoothly varying articulation weights over the control points of a model to more efficiently define the transformation of a highly detailed object or character under specific animation controls; and (3) the assignment of smoothly varying local parameters for specifying the local behavior of dynamic or quasi-static objects or surfaces.

US Patent Number: 6,430,587 Patent Title: Method and apparatus for FFT computation Date of Patent: August 6, 2002 Abstract: A method and an apparatus for computing Fast Fourier Transforms (FFT) on a serial input of data blocks are described. Two input buffers share one data processing device in such a way that, at any given time, one buffer is receiving input data while the data in the other buffer is being processed. The need for bit reversal of the data block in the input buffer is eliminated, thus removing one time consuming step in the FFT. This is achieved by writing blocks of input data to the buffer alternately in natural order and in bit reversed order. When the output data in the buffer is in the reverse order, the buffer is addressed in the same reverse order so that the data points are sent in the correct order to the output. At the same time, the new input data is written to the buffer in the reverse order.

US Patent Number: 6,434,583 Patent Title: Fast fourier transform apparatus and method Date of Patent: August 13, 2002 Abstract: A apparatus for providing a Fast Fourier Transform (FFT) and an inverse FFT is provided. The apparatus comprises a radix-N core. The radix-N core includes at least N multipliers. The radix-N core also includes a twiddle-factor lookup table that stores complex twiddle-factors. The twiddle-factor lookup table is coupled to one input of each of the multipliers. The radix-N core also includes a conversion random access memory (RAM) that stores transform points. The conversion RAM is coupled to another input of each of the multipliers. The radix-N core also includes an array of at least N-times-N adder-subtracter-accumulators.

US Patent Number: 6,021,423 Patent Title: Method for parallel-efficient configuring an FPGA for large FFTS and other vector rotation computations Date of Patent: February 1, 2000 Abstract: A method using replication of distributed arithmetic logic circuits and recursive interpolation of reduced angular increments of sine and cosine sum constants in logic look-up tables permits the computation of vector rotation and large FFTs in an efficient-parallel fashion within a unitary field programmable gate array chip, without off-chip memory for storing constants.

US Patent Number: 5,371,696 Patent Title: Computational structures for the fast Fourier transform analyzers Date of Patent: December 6, 1994 Abstract: Since the invention of the radix-2 structure for the computation of the discrete Fourier transform (DFT) by Cooley and Tukey in 1965, the DFT has been widely used for the frequency-domain analysis and design of signals and systems in communications, digital signal processing, and in other areas of science and engineering. While the Cooley-Tukey structure is simpler, regular, and efficient, it has some drawbacks such as more complex multiplications than required by higher-radix structures, and the overhead operations of bit-reversal and data-swapping. The present invention provides a large family of radix-2 structures for the computation of the DFT of a discrete signal of N samples. A member of this set of structures is characterized by two parameters, u and v, where u (u=2.sup.r, r=1,2, . . . , (log.sub.2 N)-1) specifies the size of each data vector applied at the two input nodes of a butterfly and v represents the number of consecutive stages of the structure whose multiplication operations are merged partially or fully. It is shown that the nature of the problem of computing the DFT is such that the sub-family of the structures with u=2 suits best for achieving its solution. These structures have the features that eliminate or reduce the drawbacks of the Cooley-Tukey structure while retaining its simplicity and regularity. A comprehensive description of the two most useful structures from this sub-family along with their hardware implementations is presented.

US Patent Number: 5,042,000 Patent Title: Integral transform method Date of Patent: August 20, 1991 Abstract: A method of performing an integral transform operation (such as a Fast Fourier Transform), wherein the underlying algorithm is partitioned to provide an efficient sequence of data operations. Preferably the address calculations are performed separately from the data calculations, and the algorithm is partitioned so that the microcode sequence for all but the last few data calculations is constant. Thus, the bandwidth at the interface to the numeric processor is conserved, and control storage in the numeric processor is also efficiently conserved. Moreover, the preferred partition for performing Fast Fourier Transform manipulates data in reasonably large subsets (e.g. 8 floating-point words at a time). This turns out to use less data bandwidth than would be required using smaller data subsets.

US Patent Number: 6,035,313 Patent Title: Memory address generator for an FFT Date of Patent: March 7, 2000 Abstract: A fast Fourier transformer (160) includes an FFT engine (162) having a twiddle index input and a memory bus coupled to a data input (167), a memory (164) coupled to the memory bus, an address generator (163) coupled to the memory (164), a twiddle index generator (150) including an output coupled to the twiddle index input, a counter (161) having an output coupled to inputs of the twiddle index generator (150) and the address generator (163) and a data output (168) coupled to the FFT engine (162) and to the memory (164).

US Patent Number: 6,058,409 Patent Title: Computation apparatus and method Date of Patent: May 2, 2000 Abstract: A computation apparatus such as a Fast Fourier Transform (FFT) apparatus which processes ordered sets of data in a computation unit (4, 24) operating according to a high-speed clock includes an input buffer (1, 21) arranged to accept data in synchronism with a relatively low-speed clock, and an output buffer (6, 26) arranged to discharge the data in synchronism with the low-speed clock. The apparatus includes an internal memory (3, 23) as well as means such as selectors (2, 22) and (5, 25) for transferring data in synchronism with the high-speed clock from the input buffer to the computation unit or the memory; between the computation unit and the memory; and from the computation unit or the memory to the output buffer. The transferring means is arranged to reorder the data, preferably in reverse-digit sequence, during transfer from the input buffer or during transfer to the output buffer. This avoids the need for a separate reordering memory at the input end or output end of the device.

US Patent Number: 5,854,758 Patent Title: Fast fourier transformation computing unit and a fast fourier transformation computation device Date of Patent: December 29, 1998 Abstract: To provide FFT computing units, FFT computation devices, and pulse counters that can achieve computational precision using the smallest possible circuit size. FFT computing unit 602 comprises a data shift circuit for standardizing FFT computation target data to a specified bit width, adders/subtracters, multipliers, and data converters for standardizing the bit width to a certain bit width by truncating part of the output data of each computing unit, etc. FFT computation device comprises FFT computing unit 602, sensor 620, amplification circuit 621, gain control circuit 623, AD converter 622, first RAM 625 for sequentially storing the A/D conversion data, second RAM 626 for storing the FFT computation target data and the data being computed, coefficient ROM 101, and level determination circuit 624; and the level determination circuit determines the size of the data being transferred when the data is being transferred from RAM 1 to RAM 2, and the result is used for the data shift adjustment and gain control during FFT computation.

US Patent Number: 5,832,531 Patent Title: Method and apparatus for identifying words described in a page description language file Date of Patent: November 3, 1998 Abstract: A method and apparatus for identifying words described in a page description file. A computer device stores a page description language file which includes characters that have not been identified as words by the page description language. A word identifying mechanism reads the page description language file and groups characters to form at least one word from the characters. The system preferably transfers words to a client process capable of processing words at a request of the client process. In a method for identifying words from a page description file, characters are read from the file and are stored in a word buffer until a word break is detected based upon character position data stored in the file. The contents of the word buffer are then provided to a client process as an identified word. The method can also sort the characters from the file into a display order prior to storing the characters in the word buffer. The method and apparatus can be used for searching for words in a page description file. Adobe Acrobat.

US Patent Number: 4,662,635 Patent Title: Video game with playback of live events Date of Patent: May 5, 1987 Abstract: A video game in which a television screen or cathode ray tube is used to display a variety of plays previously preformed by living beings and recorded at the time on a video recording medium, such as video tape or video disks, the particular previously performed play which is displayed during each turn, or each play of the video game in accordance with this invention depending on the number, or combination or numbers, selected by one or more players, such number corresponding to one of the previously performed and recorded plays. The number selected is fed into an electronic control console, which includes circuitry to signal an electronic playback unit in which the previously performed and recorded plays have been stored to re-run the particular play corresponding to the number selected through a pick-up circuit connected to the cathode ray tube or television screen. Plays of a variety of games, including football, baseball, soccer, hockey, basketball, tennis and the like may be recorded to play any of such games in accordance with this invention. The invention includes a record keeping system to record the progress, if any, of each player towards a score or goal indicated by the particular play selected and displayed during each player's turn

US Patent Number: 5,963,916 Patent Title: Network apparatus and method for preview of music products and compilation of market data Date of Patent: October 5, 1999 Abstract: A system for on-line user-interactive multimedia based point-of-preview. The system provides for a network web site and accompanying software and hardware for allowing users to access the web site over a network such as the internet via a computer. The user is uniquely identified to the web site server through an identification name or number. The hardware associated with the web site includes storage of discrete increments of pre-selected portions of music products for user selection and preview. After user selection, a programmable data processor selects the particular pre-recorded music product from data storage and then transmits that chosen music product over the network to the user for preview. Subscriber selection and profile data (i.e. demographic information) can optionally be collected and stored to develop market research data. Since the system provides for multiple embodiments, the system contemplates previewing of audio programs such as music on compact discs, video programs such as movies and text from books and other written documents. Furthermore, it is contemplated that the network web site can be accessed from a publicly accessible kiosk, available, e.g. at a retail store location, or from a desk top computer.

US Patent Number: 5,533,051 Patent Title: Method for data compression Date of Patent: July 2, 1996 Abstract: Methods for compressing data including methods for compressing highly randomized data are disclosed. Nibble encode, distribution encode, and direct bit encode methods are disclosed for compressing data which is not highly randomized. A randomized data compression routine is also disclosed and is very effective for compressing data which is highly randomized. All of the compression methods disclosed operate on a bit level and accordingly are insensitive to the nature or origination of the data sought to be compressed. Accordingly, the methods of the present invention are universally applicable to any form of data regardless of its source of origination.

US Patent Number: 6,453,002 Patent Title: Differential measurement of X-ray microfluorescence Date of Patent: September 17, 2002 Abstract: A method of X-ray analysis includes irradiating a spot on a sample with X-rays along an X-ray beam axis. X-rays emitted from the sample, responsive to irradiating the spot, are simultaneously detected at a plurality of different azimuthal angles relative to the beam axis. X-ray intensities detected at the different angles in a common energy range are compared in order to determine a property of the sample.

United States Patent Application: 20020126802 Patent Title: Automated sample handling for X-ray crystallography September 12, 2002 Abstract: Method and apparatus for mounting a sample comprising a crystal for X-ray crystallographic analysis, a method for aligning a sample comprising a crystal for X-ray crystallographic analysis, which sample is mounted on a positioning device, and a method for determining the structure of a sample containing a crystal by means of X-ray crystallography.

United States Patent Application: 20020126129 Patent Title: Sampling-efficient mapping of images September 12, 2002 Abstract: Spherical-like textures are useful to simulate reflections and to generate arbitrary views from a point. For addressing simplicity, graphics systems typically require rectangular arrays of texture samples but an infinite variety of functions can be used to map these samples to a sphere-like object. A new metric is presented for measuring how well various maps use a given number of samples to provide the greatest worst-case frequency content of the image everywhere over the sphere. Using this metric and other important local properties, a comparison is presented of maps used previously in computer graphics as well as other mapping techniques borrowed from cartography. Based on these analysis several novel mapping techniques are presented that are fairly simple to implement and significantly more efficient in terms of the amount of processing and data required, and the quality of the resulting images. The novel metric and mapping techniques can be employed to analyze or otherwise improve the sampling efficiency of mapping textures onto any three-dimensional surface.

United States Patent Application: 20020120405 Patent Title: Protein data analysis August 29, 2002 Abstract: The disclosure includes a description of a method of data mining protein data. The method includes accessing data identifying respective outcomes associated with a set of proteins subjected to a set of conditions and analyzing the data based on the outcomes

United States Patent Application: 20020120429 Patent Title: Methods for modeling multi-dimensional domains using information theory to resolve gaps in data and in theories August 29, 2002 Abstract: Disclosed are methods for modeling multi-dimensional domains by merging multiple input data sets into a model, applying multiple dynamic theories to evolve the model, and using information theory to resolve gaps in, and discrepancies among, the data sets and the theories. One example is a three-dimensional geologic basin simulator that integrates seismic inversion techniques with other data to predict fracture location and characteristics. The geologic simulator delineates the effects of regional tectonics, petroleum-derived overpressure, and salt tectonics and constructs maps of high-grading zones of fracture producibility. A second example is a living cell simulator that uses chemical kinetic rate laws of transcription and translation polymerization to compute mRNA and protein populations as they occur autonomously, in response to changes in the surroundings, or from injected viruses or chemical factors. Features such as the eukaryotic nucleus are treated with a novel mesoscopic reaction-transport theory. Metabolic reactions take place in appropriate compartments.

United States Patent Application: 20020111761 Patent Title: Method for determining multi-dimensional topology August 15, 2002 Abstract: This invention relates to methods and apparatus for determining the multi-dimensional topology of a substance (system) within a volume (space). A method according to a preferred embodiment of the invention comprises the steps of: acquiring a set of relative values for the density (scalar properties) of the volume, each value for a given location (point) within the volume; interpolating a set of functions to generate a continuous relative density for the volume; identifying critical points of the continuous relative density by using an eigenvector following method; and associating critical points with one another by following a gradient path of the continuous relative density between the critical points. The method is applicable to a wide range of data relating to fields such as crystallography, fluid dynamics, edge detection, and financial markets, to determine the topology of structures contained therein.

United States Patent Application: 20020107359 Patent Title: Three dimensional structures and models of fc receptors and uses thereof August 8, 2002 Abstract: Disclosed are crystals, crystal structure Fc.gamma.RIIa protein, three dimensional coordinates of Fc.gamma.RIIa protein, and structures and models derived from the Fc.gamma.RIIa structure. Also disclosed are crystals of Fc.epsilon.RI protein and three dimensional coordinates of Fc.epsilon.RI protein monomers and dimers derived from the Fc.gamma.RIIa structure. Also disclosed are three dimensional coordinates of Fc.gamma.RIIIb proteins and models of Fc.gamma.RIIIb derived from the Fc.gamma.RIIa structure. The present invention also includes methods to produce such crystals, crystal structures and models. Uses of such crystals, crystal structures and models are also disclosed, including structure based drug design and therapeutic compositions.

United States Patent Application: 20020106694 Patent Title: Apparatus and method for automated protein design August 8, 2002 Abstract: The present invention relates to apparatus and methods for quantitative protein design and optimization.

United States Patent Application: 20020091490 Patent Title: System and method for representing and manipulating biological data using a biological object model July 11, 2002 Abstract: A system for representing and manipulating biological data using a biological object model. The system comprises a biological database, a database engine, a biological object model, and a data-mapping engine. The database engine searches and retrieves biological data from the database. The data-mapping engine substantiates biological objects from retrieved data using definitions from the biological object model.

United States Patent Application: 20020067800 Patent Title: Apparatus and method for identification of crystals by in-situ X-ray diffraction June 6, 2002 Abstract: The apparatus comprises a crystal growing incubator having opposing first and second sides. The apparatus also includes an X-ray system which comprises an X-ray source disposed adjacent to the first side of the crystal growing incubator and an X-ray detector disposed adjacent to the second side of the crystal growing incubator. The X-ray source is configured to irradiate crystalline material grown in the crystal growing incubator and the X-ray detector is configured to detect the presence of diffracted X-rays from crystals grown in the crystal growing incubator. The apparatus preferably further comprises a positioner that positions the incubator and the X-ray system relative to each other. Also provided is a method of screening for crystalline material in its in-situ growth environment using the above described apparatus.

US Patent Number: 6,370,479 Patent Title: Method and apparatus for extracting and evaluating mutually similar portions in one-dimensional sequences in molecules and/or three-dimensional structures of molecules Date of Patent: April 9, 2002 Abstract: In the analysis of one-dimensional sequences of molecules, the longest common subsequence, the number of elements constituting the subsequence, and appearance positions of the subsequence are determined by a novel and simple method, and processes, such as homology decision, homology search, motif search and alignment are performed based on the results. In the analysis of these-dimensional structures of molecules, limiting conditions, such as geometrical arrangements of elements, are introduced to realize the determination of correspondence of three-dimensional structures at high speeds, and whereby it is made possible to achieve such processing as superposed display of three-dimensional structure of molecules, retrieval of three-dimensional structure, and evaluation of functions. Moreover, the molecules are divided into secondary structure that are then related to each other based on spatial similarity among the secondary structures. Furthermore, similarity among the molecules is decided based on a relationship of spatial positions of the corresponding secondary structures.

US Patent Number: 5,446,798 Patent Title: Method and apparatus for measuring position and orientation of an object based on a sequence of projected points Date of Patent: August 29, 1995 Abstract: A method for measuring a position and an orientation of an object. A sequence of movement points which line up on an intersection line of a predetermined projection surface and a plane which contains a predetermined projection center corresponding to a position of a camera, is obtained by obtaining projected points respectively generated for a plurality of positions of the camera, onto a point on the predetermined projection surface where the camera position is deemed as the projection center. Then, a sequence of reference points which line up on an intersection line of a plane containing the center of projection and the predetermined projection surface, shares a point with the sequence of movement points, and has the same cross ratio (inharmonic ratio) as a cross ratio of the sequence of movement points, is generated. An intersection point of intersection lines which are respectively intersection lines of the predetermined projection surface and planes each containing the center of projection and a pair of corresponding points one of which belongs to the sequence of movement points, and the other of which belongs to the sequence of reference points, is obtained. Then, geometrical information on the image element of the object when using the projection center in the three-dimensional space as a reference position is obtained based on the position of the above intersection point.

US Patent Number: 6,341,256 Patent Title: Consensus configurational bias Monte Carlo method and system for pharmacophore structure determination Date of Patent: January 22, 2002 Abstract: In a specific embodiment, this invention includes a method for determining an accurate, consensus pharmacophore structure shared by compounds that bind selectively to a target molecule. Optionally, the method begins with screening a diversity library against the target molecule of interest to pick the selectively binding members. Next the structure of the selected members is examined and a candidate pharmacophore responsible for the binding to the target molecule is determined. Next, preferably by REDOR nuclear magnetic resonance, several highly accurate interatomic distances are determined in certain of the selected members which are related to the candidate pharmacophore. A highly accurate consensus, configurational bias, Monte Carlo method determination of the structure of the candidate pharmacophore is made using the structure of the selected members and incorporating as constraints the shared candidate pharmacophore and the several measured distances. This determination is adapted to efficiently examine only relatively low energy configurations while respecting any structural constraints present in the organic diversity library. If the diversity library contains short peptides, the determination respects the known degrees of freedom of peptides as well as any internal constraints, such as those imposed by disulfide bridges. Finally, the highly accurate pharmacophore so determined is used to select lead organics for drug development targeted at the initial target molecule.

US Patent Number: 6,038,514 Patent Title: Materials design system and storage medium storing computer program for causing computer system to analyze stable structure or dynamic behavior of system at atomic or molecular level to assist materials design based on this analysis Date of Patent: March 14, 2000 Abstract: Disclosed is a materials design system for obtaining the structural stability or dynamic behavior of an aperiodic system (S.sup.2), which includes a reference system S.sup.0 processing unit (1-1), an aperiodic system S.sup.2 processing unit (1-2), an interatomic potential processing unit (1-3), a reference system S.sup.0 calculation unit (1-4), an aperiodic system S.sup.2 calculation unit (1-5), an MM calculation unit (1-6) for analyzing the stable structure, and an MD calculation unit (1-7) for analyzing the dynamic behavior. The structure of the aperiodic system (S.sup.2) is described on the basis of a deviation from a reference system (S.sup.0). When the potential energy of the aperiodic system (S.sup.2) and the force acting on each atom or each molecule of the aperiodic system (S.sup.2) are to be calculated, calculation is performed within a unit cell of the reference system (S.sup.0) and a predetermined range (region where lattice relaxation is taken into consideration) containing the disorder in the aperiodic system (S.sup.2). According to this arrangement, in materials design, the stable structure or dynamic behavior of a system containing a disorder (aperiodic system (S.sup.2)) can be efficiently calculated without approximation.

US Patent Number: 5,740,072 Patent Title: Rapidly convergent method for boltzmann-weighted ensemble generation in free energy simulations Date of Patent: April 14, 1998 Abstract: The invention is directed to a method for generating possible conformations of a molecule comprising the steps of: a) selecting a first conformation of the molecule characterized by a first set of coordinates associated with each atom in the molecule by the presence of a pattern of forces among such atoms and by a series of intrinsic forces associated with each atom; b) varying the pattern of forces among such atoms in a non-random manner and randomly varying the series of intrinsic forces associated with each atom so as to generate a second conformation of the molecule characterized by a second set of coordinates associated with each atom in the molecule, by a second pattern of forces among each atom and by a second series of intrinsic forces associated with each atom; and c) randomly varying the second set of coordinates so as to obtain a third set of coordinates and thereby generating such possible conformations of the molecule.

US Patent Number: 5,448,498 Patent Title: Apparatus for generating a constraint condition in a molecular dynamics simulation Date of Patent: September 5, 1995 Abstract: A constraint condition generating apparatus generates a constraint condition which should be output to a molecular dynamics simulator for simulating a behavior of a molecule based on a molecular dynamics method under the constraint condition for freezing a part of the degree of freedom within the molecule. This apparatus comprises bond constraint condition setting and releasing unit for setting a bond constraint list comprising the number of two atoms whose bond are to be constrained and a bonding distance between two atoms, and for releasing the constraint of the bond of two atoms, angle constraint condition setting and releasing means for setting an angle constraint condition including a bonding distance between two atoms which are not common and for releasing a part of angle constraint condition in accordance with a designation by a user; and a torsion constraint condition setting and releasing unit for setting a torsion constraint condition including a bonding distance between two atoms which are not common, and for releasing a part of a constraint condition in accordance with a designation by a user.

US Patent Number: 6,349,265 Patent Title: Method and apparatus for mapping components of descriptor vectors for molecular complexes to a space that discriminates between groups Date of Patent: February 19, 2002 Abstract: The method of the present invention transforms descriptor vectors that characterize molecular complexes partitioned into groups into a space that discriminates between those groups in a well defined optimal sense. First data is generated that represents a differences between the groups of descriptor vectors. Second data is generated representing variation within the groups of descriptor vectors. A set of component vectors is then identified that maximizes an F distributed criterion function that measures differences of desciptor vectors between groups relative to varations of descriptor vectors within groups. A statistic is generated for subsets of the component vectors. For each particular subset of component vectors, a probability value for the statistic associated with the particular subset is calculated. The subset with the minimum probability value is selected. Finally, one or more of the descriptor vectors for the molecular vs complexes are mapped to a space corresponding to the selected subset of component vectors.

US Patent Number: 5,612,894 Patent Title: System and method for molecular modeling utilizing a sensitivity factor Date of Patent: March 18, 1997 Abstract: A computerized molecular modeling system is provided which graphically displays at least an initial and most likely structure of a molecule utilizing energy minimization and/or molecule dynamics techniques. The system utilizes a sensitivity factor to determine how often the less sensitive interactions, especially non-bonded interaction in a molecule should be recalculated during an energy minimization or molecular dynamics procedure. The sensitivity factor is based on each interaction's sensitivity to changes in the positions of the atoms that comprise it.

US Patent Number: 5,740,072 Patent Title: Rapidly convergent method for boltzmann-weighted ensemble generation in free energy simulations Date of Patent: April 14, 1998 Abstract: The invention is directed to a method for generating possible conformations of a molecule comprising the steps of: a) selecting a first conformation of the molecule characterized by a first set of coordinates associated with each atom in the molecule by the presence of a pattern of forces among such atoms and by a series of intrinsic forces associated with each atom; b) varying the pattern of forces among such atoms in a non-random manner and randomly varying the series of intrinsic forces associated with each atom so as to generate a second conformation of the molecule characterized by a second set of coordinates associated with each atom in the molecule, by a second pattern of forces among each atom and by a second series of intrinsic forces associated with each atom; and c) randomly varying the second set of coordinates so as to obtain a third set of coordinates and thereby generating such possible conformations of the molecule.

US Patent Number: 5,796,632 Patent Title: Method for converting information of peripheral space of a three-dimensional compound structure into numerical data and method for converting interactions between a three-dimensional compound structure and peripheral space into numerical data Date of Patent: August 18, 1998 Abstract: A method for converting information of a peripheral space of a three-dimensional compound structure into numerical data is disclosed. This method comprises the steps of designating a peripheral region that includes the entire three-dimensional structure of a compound on the periphery thereof, designating a plurality of small regions in the peripheral region, generating a plurality of points in the peripheral region, calculating the interaction between the three-dimensional structure of a compound and each of points at least included in the points as numerical data so as to allocate the numerical data to corresponding individual points, and determining at least one of numerical data that represents each of the small regions corresponding to the numerical data allocated to each of the individual points. After a representative value of each small region is obtained, the representative value is supplied to a portion that performs various analyzing techniques such as the linear multiple regression method without any statistical defects.

US Patent Number: 6,240,374 Patent Title: Further method of creating and rapidly searching a virtual library of potential molecules using validated molecular structural descriptors Date of Patent: May 29, 2001 Abstract: The problem of how to select out of a large chemically accessible universe molecules representative of the diversity of that universe is resolved by the discovery of a method to validate molecular structural descriptors. Using the validated descriptors, optimally diverse subsets can be selected. In addition, from the universe, molecules with characteristics similar to a selected molecule can be identified. The validated descriptors also enable the generation of a huge virtual library of potential product molecules which could be formed by combinatorial arrangement of structural variations and cores. In this virtual library it is possible to search billions of possible product compounds in relatively short time frames.

US Patent Number: 5,453,937 Patent Title: Method and system for protein modeling Date of Patent: September 26, 1995 Abstract: A method in a computer system for modeling a three-dimensional structure of a model protein is provided. In a preferred embodiment, the modeling is based upon a three-dimensional structure of a template protein and an amino acid sequence alignment of the model protein and the template protein. The proteins comprise a plurality of amino acids having backbone atoms and side chain atoms. For each amino acid in the model protein, when the template protein has an amino acid aligned with the amino acid of the model protein, the position of each backbone atom of the amino acid of the model protein is established based on the position of a topologically equivalent backbone atom in the aligned amino acid of the template protein. The inter-atomic distance constraints for each pair of atoms with an established position is generated. Finally, the position of each atom in the model protein is set so that the inter-atomic distances are in accordance with the constraints.

US Patent Number: 5,448,498 Patent Title: Apparatus for generating a constraint condition in a molecular dynamics simulation Date of Patent: September 5, 1995 Abstract: A constraint condition generating apparatus generates a constraint condition which should be output to a molecular dynamics simulator for simulating a behavior of a molecule based on a molecular dynamics method under the constraint condition for freezing a part of the degree of freedom within the molecule. This apparatus comprises bond constraint condition setting and releasing unit for setting a bond constraint list comprising the number of two atoms whose bond are to be constrained and a bonding distance between two atoms, and for releasing the constraint of the bond of two atoms, angle constraint condition setting and releasing means for setting an angle constraint condition including a bonding distance between two atoms which are not common and for releasing a part of angle constraint condition in accordance with a designation by a user; and a torsion constraint condition setting and releasing unit for setting a torsion constraint condition including a bonding distance between two atoms which are not common, and for releasing a part of a constraint condition in accordance with a designation by a user.

US Patent Number: 5,625,579 Patent Title: Stochastic simulation method for processes containing equilibrium steps Date of Patent: April 29, 1997 Abstract: A system and method for simulating a mechanistic kinetic process, such as a chemical process including one or more chemical reactions, over a predetermined time period is provided. The simulation proceeds stochastically, by taking discrete time steps through the time period, and performing events (i.e., chemical reactions), based on the relationship between their probabilities of occurrence and the time steps taken. The system and method of the invention include means or method steps for detecting equilibrium conditions, in which a reaction moves forward and backward with a reaction probability which is high, relative to the probabilities of other reactions being simulated. When a reaction in equilibrium is detected, a probability calculation is made, based on the non-equilibrium reactions being simulated. Time steps are made, and events are simulated, based only on the non-equilibrium reactions. Thus, processing time, which would otherwise be consumed simulating back-and-forth events in the equilibrium reaction, is saved.

US Patent Number: 5,790,421 Patent Title: Computer apparatus for expressing a three dimensional structure of a G-CSF molecule or analogs thereof Date of Patent: August 4, 1998 Abstract: The present invention is directed towards a computer apparatus for expressing a three dimensional structure of a G-CSF molecule or analogs thereof.

US Patent Number: 5,307,287 Patent Title: Comparative molecular field analysis (COMFA) Date of Patent: April 26, 1994 Abstract: Comparative Molecular Field Analysis (CoMFA) is an effective computer implemented methodology of 3D-QSAR employing both interactive graphics and statistical techniques for correlating shapes of molecules with their observed biological properties. For each molecule of a series of known substrates the steric and electrostatic interaction energies with a test probe atom are calculated at spatial coordinates around the molecule. Subsequent analysis of the data table by a partial least squares (PLS) cross-validation technique yields a set of coefficients which reflect the relative contribution of the shape elements of the molecular series to differences in biological activities. Display in three dimensions in an interactive graphics environment of the spatial volumes highly associated with biological activity, and comparison with molecular structures yields an understanding of intermolecular associations. CoMFA will also predict the biological activity of new molecular species.

US Patent Number: 6,453,246 Patent Title: System, method, and computer program product for representing proximity data in a multi-dimensional space Date of Patent: September 17, 2002 Abstract: A system, method and computer program product for representing precise or imprecise measurements of similarity/dissimilarity (relationships) between objects as distances between points in a multi-dimensional space that represents the objects. Self-organizing principles are used to iteratively refine an initial (random or partially ordered) configuration of points using stochastic relationship/distance errors. The data can be complete or incomplete (i.e. some relationships between objects may not be known), exact or inexact (i.e. some or all of the relationships may be given in terms of allowed ranges or limits), symmetric or asymmetric (i.e. the relationship of object A to object B may not be the same as the relationship of B to A) and may contain systematic or stochastic errors. The relationships between objects may be derived directly from observation, measurement, a priori knowledge, or intuition, or may be determined indirectly using any suitable technique for deriving proximity (relationship) data.

US Patent Number: 5,225,788 Patent Title: Single-bunch synchrotron shutter Date of Patent: July 6, 1993 Abstract: An apparatus for selecting a single synchrotron pulse from the millions of pulses provided per second from a synchrotron source includes a rotating spindle located in the path of the synchrotron pulses. The spindle has multiple faces of a highly reflective surface, and having a frequency of rotation f. A shutter is spaced from the spindle by a radius r, and has an open position and a closed position. The pulses from the synchrotron are reflected off the spindle to the shutter such that the speed s of the pulses at the shutter is governed by: s=4.times..pi..times.r.times.f. such that a single pulse is selected for transmission through an open position of the shutter.

US Patent Number: 5,104,478 Patent Title: Method for making single crystals Date of Patent: April 14, 1992 Abstract: A method for making single crystals, comprising osmotically removing the solvent from a solution containing the material to be grown into a crystal.

US Patent Number: 5,096,676 Patent Title: Crystal growing apparatus Date of Patent: March 17, 1992 Abstract: An apparatus for growing diffraction quality, protein crystals by vapor diffusion techniques. The apparatus includes a plurality of equilibrating solution reservoirs each having a side wall terminating in a top wall disposed in a first plane; a column disposed within each of the equilibrating solution reservoirs, each column having a protein solution receptacle including a side wall terminating in a top wall disposed in a second plane spaced from the first plane; and a cover having a non-greasy adhesive on one surface therof for sealable engagement with the top walls of the equilibrating solution reservoirs for sealing the reservoirs relative to atmosphere.

US Patent Number: 5,093,095 Patent Title: Crystallization in a force field Date of Patent: March 3, 1992 Abstract:

US Patent Number: 6,371,640 Patent Title: Apparatus and method for characterizing libraries of different materials using X-ray scattering Date of Patent: April 16, 2002 Abstract: An apparatus for characterizing a library is provided in which the library contains an array of elements and each element contains a different combination of materials. The apparatus includes an x-ray beam directed at the library, a chamber which houses the library and a beamline for directing the x-ray beam onto the library in the chamber. The chamber may include a translation stage that holds the library and that is programmable to change the position of the library relative to the x-ray beam and a controller that controls the movement of the translation stage to expose an element to the x-ray beam in order to rapidly characterize the element in the library. During the characterization, the x-ray beam scatters off of the element and a detector detects the scattered x-ray beam in order to generate characterization data for the element.

US Patent Number: 6,453,006 Patent Title: Calibration and alignment of X-ray reflectometric systems Date of Patent: September 17, 2002 Abstract: The present invention relates to the calibration and alignment of an X-ray reflectometry ("XRR") system for measuring thin films. An aspect of the present invention describes a method for accurately determining C.sub.0 for each sample placement and for finding the incident X-ray intensity corresponding to each pixel of a detector array and thus permitting an amplitude calibration of the reflectometer system. Another aspect of the present invention relates to a method for aligning an angle-resolved X-ray reflectometer that uses a focusing optic, which may preferably be a Johansson crystal. Another aspect of the present invention is to validate the focusing optic. Another aspect of the present invention relates to the alignment of the focusing optic with the X-ray source. Another aspect of the present invention concerns the correction of measurements errors caused by the tilt or slope of the sample. Yet another aspect of the present invention concerns the calibration of the vertical position of the sample.

US Patent Number: 5,923,720 Patent Title: Angle dispersive x-ray spectrometer Date of Patent: July 13, 1999 Abstract: An x-ray spectrometer is provided comprising an X-ray source, a curved crystal monochromator which focuses a monochromatic x-ray beam onto a sample surface, the curved crystal monochromator comprising a shape which is substantially identical to a logarithmic spiral, and a position-sensitive x-ray detector. A method of measuring diffraction intensities from oriented samples in real time including providing an x-ray spectrometer comprising an X-ray source, a curved crystal monochromator which focuses a monochromatic x-ray beam onto a sample surface, the curved monochromator comprising the shape of a logarithmic spiral, and a position-sensitive x-ray detector; and providing a crystallographically oriented sample, exposing the sample to the focused x-ray beam of the x-ray spectrometer; and measuring the diffraction intensity at the position-sensitive detector.

US Patent Number: 5,406,609 Patent Title: X-ray analysis apparatus Date of Patent: April 11, 1995 Abstract: An X-ray analysis apparatus including an artificial multi-layered grating for rendering X-ray beams to be monochromatic before they are incident on a specimen to be analyzed. This artificial multi-layered grating operates to diffract the X-ray beam, generated from an X-ray radiation source and subsequently impinging on a reflective surface of the artificial multi-layered grating, at a predetermined angle of diffraction to provide the monochromatic X-ray beams. The periodicity of the spacing of lattice planes of the artificial multi-layered grating is so chosen as to be of a value progressively varying along the reflective surface thereof with an increase in distance from the X-ray radiation source. The X-ray analysis apparatus herein disclosed is designed to avoid any possible reduction of the intensity of the X-ray beams which would occur when they are rendered to be monochromatic, and to increase the intensity of the X-ray beams to ensure an improved accuracy in spectroscopic analysis.

US Patent Number: 5,724,401 Patent Title: Large angle solid state position sensitive x-ray detector system Date of Patent: March 3, 1998 Abstract: A method and apparatus for x-ray measurement of certain properties of a solid material. In distinction to known methods and apparatus, this invention employs a specific fiber-optic bundle configuration, termed a reorganizer, itself known for other uses, for coherently transmitting visible light originating from the scintillation of diffracted x-radiation from the solid material gathered along a substantially one dimensional linear arc, to a two-dimensional photo-sensor array. The two-dimensional photodetector array, with its many closely packed light sensitive pixels, is employed to process the information contained in the diffracted radiation and present the information in the form of a conventional x-ray diffraction spectrum. By this arrangement, the angular range of the combined detector faces may be increased without loss of angular resolution. Further, the prohibitively expensive coupling together of a large number of individual linear diode photodetectors, which would be required to process signals generated by the diffracted radiation, is avoided.

US Patent Number: 5,418,828 Patent Title: Nondestructive method and apparatus for imaging grains in curved surfaces of polycrystalline articles Date of Patent: May 23, 1995 Abstract: A nondestructive method, and associated apparatus, are provided for determining the grain flow of the grains in a convex curved, textured polycrystalline surface. The convex, curved surface of a polycrystalline article is aligned in a horizontal x-ray diffractometer and a monochromatic, converging x-ray beam is directed onto the curved surface of the polycrystalline article so that the converging x-ray beam is diffracted by crystallographic planes of the grains in the polycrystalline article. The diffracted x-ray beam is caused to pass through a set of horizontal, parallel slits to limit the height of the beam and thereafter. The linear intensity of the diffracted x-ray is measured, using a linear position sensitive proportional counter, as a function of position in a direction orthogonal to the counter so as to generate two dimensional data. An image of the grains in the curved surface of the polycrystalline article is provided based on the two-dimensional data.

US Patent Number: 5,373,544 Patent Title: X-ray diffractometer Date of Patent: December 13, 1994 Abstract: An x-ray diffractometer is equipped with a position sensitive detector and a collimator preceding the detector. The lamellae of the collimator are radially aligned to the specimen, which is arranged in the center of a measurement circle along which the detector and collimator move during a measurement. Therefore, only the x-radiation scattered at the specimen contributes to the measured signal. An elliptically deformed multi-layer mirror is provided at the primary beam side, which deflects the source radiation in the direction of the specimen without great intensity loss and focuses it at a point lying on the measurement circle. Analysis of powdered specimens that are enclosed in glass capillaries can be undertaken. A low-background measurement of diffraction diagrams in an x-ray diffractometer given efficient use of the primary beam is achieved.

US Patent Number: 5,247,562 Patent Title: Tunable source of monochromatic, highly-directional x-rays and a method for producing such radiation Date of Patent: September 21, 1993 Abstract: In a first preferred embodiment, the invention is an apparatus for generating radiation comprising: means for generating a beam of electrons; means for constraining the beam of electrons to travel in a substantially straight path over a predetermined distance; means for generating a standing wave of light; and means for causing the beam of electrons to pass through the standing wave of light during a portion of the straight path, thereby causing certain of said electrons to emit radiation. The standing wave of light is preferably generated by a continuous wave beam of light that is circulating in a power build up cavity. In another preferred embodiment, the invention is a method of generating radiation, the method comprising the steps of U.S. GOVERNMENT INTEREST The U.S. Government has certain rights in this invention pursuant to Contract No. F19628-90-C-0002, awarded by the United States Air Force (Electronic Systems Division), which supported some of the work that contributed to this invention.

US Patent Number: 5,016,267 Patent Title: Instrumentation for conditioning X-ray or neutron beams Date of Patent: May 14, 1991 Abstract: In one embodiment, an x-ray neutron instrument includes an x-ray or neutron lens (10) disposed in a path for x-rays or neutrons in the instrument. The lens (10) comprises multiple elongate open-ended channels (12) arranged across the path to receive and pass segments of an x-ray or neutron beam (14). The channels (12) have side walls reflective to x-rays or neutrons of the beam incident at a grazing angle less than the critical grazing angle for total external reflection of the x-rays or neutrons, whereby to cause substantial focusing or collimation and/or concentration of the thus reflected x-rays or neutrons. In a different embodiment, a condensing-collimating channel-cut monochromator comprises a channel (22) in a perfect-crystal or near perfect-crystal body (20). This channel (22) is formed with lateral surfaces (24, 26) which multiply reflect, by Bragg diffraction from selected Bragg planes, an incident beam (28) which has been collimated at least to some extent. The lateral surfaces (24, 26) are at a finite angle to each other whereby to monochromatize and spatially condense the beam (28) as it is multiply reflected, without substantial loss of reflectivity or transmitted power.

US Patent Number: H313 Patent Title: Monochromator for continuous spectrum x-ray radiation Date of Patent: July 7, 1987 Abstract: A monochromator for use with synchrotron x-ray radiation comprises two diffraction means which can be rotated independently and independent means for translationally moving one diffraction means with respect to the other. The independence of the rotational and translational motions allows Bragg angles from 3.5.degree. to 86.5.degree., and facilitates precise and high-resolution monochromatization over a wide energy range. The diffraction means are removably mounted so as to be readily interchangeable, which allows the monochromator to be used for both non-dispersive and low dispersive work.

US Patent Number: 4,752,945 Patent Title: Double crystal X-ray spectrometer Date of Patent: June 21, 1988 Abstract: A Dual Channel Spectrometer system is provided for measurement of X-ray spectra in which at least two pairs of crystals are arranged in a crystal changer so that different pairs of such crystals can be selected in the X-ray spectrometer. This selection is achieved by rotating a drum on which pairs of crystals are mounted about an axis to bring one pair of crystals into alignment with a collimated X-ray beam. This enables the selection of the wavelength range used in the spectrometer to be made without deactivating the spectrometer or without loosing the vacuum in the spectrometer.

US Patent Number: 4,535,469 Patent Title: X-Ray analysis apparatus having an adjustable stray radiation slit Date of Patent: August 13, 1985 Abstract: In an X-ray analysis apparatus, there is provided between a test specimen (5) or an analyzing crystal and a detector (9) a stray radiation slit (15) that can be adjusted in dependence on the goniometer angle. By an optimum adjustment of this slit in correspondence with the variation in the goniometer angle it can be achieved that the detector will always see the same portion of the surface of the test sample or analyzing crystal. Especially, the adjustment of the slit is coupled to the adjustment of an automatic divergence slit (11) so that the portion of the surface which is irradiated, remains unaltered. Especially for small goniometer angles, that is to say for the analysis of a substance in which there is a large distance between crystal planes, a considerably improved signal-to-noise ratio in the measurement signal is thus obtained.

US Patent Number: 6,005,914 Patent Title: Arc diffractometer Date of Patent: December 21, 1999 Abstract: An x-ray diffractometer has an x-ray detector and an x-ray source mounted on vehicles traveling along an arc-shaped track around a sample. The vehicles move independently. Alternatively, the vehicles can move independently on separate parallel tracks.

US Patent Number: 6,418,190 Patent Title: Imaging plate X-ray diffraction apparatus Date of Patent: July 9, 2002 Abstract: A space-efficient imaging-plate-type X-ray diffraction apparatus featuring an expanded 2.theta. goniometry range, high speed, high resolution, and design for convenient use is provided. The imaging-plate-type X-ray diffraction apparatus includes an X-ray measurement device composed of an X-ray optical system (5) and a goniometer (1) and is adapted to cause a single-crystal sample (3) to diffract X-rays. A cylindrical imaging plate (21) is disposed vertically so as to record X-rays diffracted by the sample (3), and covering a 2.theta. goniometry range of -60.degree. to +144.degree.. A drive motor (11) and a transmission mechanism (12) transfer the cylindrical imaging plate vertically; and a rotary reader (20) is disposed so as to be coaxial with the transferred cylindrical imaging plate (21) and is adapted to read data of diffracted X-rays from an inner cylindrical surface of the cylindrical imaging plate (21).

US Patent Number: 4,412,345 Patent Title: Apparatus and method for precise determinations of crystallographic orientation in crystalline substances Date of Patent: October 25, 1983 Abstract: An apparatus and method for precisely measuring the angles of cut of single and doubly rotated cuts of quartz crystal blanks on a high volume production basis.

US Patent Number: 4,710,259 Patent Title: Setting the orientation of crystals Date of Patent: December 1, 1987 Abstract: A method of and apparatus for setting the orientation of a single crystal which may be a seed crystal, boule, wafer or a growing boule. The crystal is irradiated with a beam of X-rays having a peak of energy at a given wavelength and the orientation of the crystal is adjusted while moving the crystal and the beam about an axis perpendicular to the equatorial plane containing the X-ray beam until a pair of reflexions that are symmetrical with respect to the equatorial plane occur simultaneously at the said wavelength of radiation. When the X-ray beam has a peak of energy at the said wavelength against a back ground of white radiation, symmetrical reflexions can be detected and will flash simultaneously only when one of the crystallographic planes of symmetry is set in a predetermined or determinable orientation relative to a given datum. In contrast to conventional techniques which involve quantitative analysis or measurements of one diffracted beam at a time, the present invention depends only upon detecting simultaneous flashing of symmetrical reflexions above and below the equatorial plane, in order to set the orientation of a crystal with a high degree of accuracy.

US Patent Number: 5,359,640 Patent Title: X-ray micro diffractometer sample positioner Date of Patent: October 25, 1994 Abstract: An X-ray diffractometer having a simple yet accurate means for locating the surface of the sample to be examined with respect to the zero point of the X-ray (RS) is disclosed. Briefly stated, a laser (LA) and camera (KA) are positioned at preferably 90.degree. with respect to each other such that the intersection of the optical axis of the camera and the laser passes through the zero point of the diffractometer. In this fashion, the camera will see at its center, the zero point of the X-ray despite the fact that the X-ray is of course invisible to the naked eye. Accordingly, by movement of the sample (P) with respect to this camera image, the true and correct zero point of the X-ray with respect to the surface of the sample to be examined may be determined without the need for experimental and unnecessary X-ray or examination runs being taken.

Patent Number: AU1138202 Patent Title: Method of providing high throughput protein crystallography Publication Date: 2002-06-18 Abstract: The invention provides a method of performing x-ray crystallography on samples by using a robot to select the target sample, to position the sample for x-ray crystallography, and to deposit the sample, all without transferring the sample to another device, such as a goniometer. This method allows high throughput, automated crystallography, thereby providing a high volume of samples to be tested while lessening the need for human intervention

Patent Number: EP1210589 (WO0111345) Patent Title: AUTOMATED SAMPLE HANDLING FOR X-RAY CRYSTALLOGRAPHY Publication Date: 2002-05-09 Abstract: Method and apparatus for mounting a sample comprising a crystal for X-ray crystallographic analysis, a method for aligning a sample comprising a crystal for X-ray crystallographic analysis, which sample is mounted on a positioning device, and a method for determining the structure of a sample containing a crystal by means of X-ray crystallography

Patent Number: US5978444 Patent Title: Direct detection of x-rays for protein crystallography employing a thick, large area CCD Publication Date: 1999-11-02 Abstract: An apparatus and method for directly determining the crystalline structure of a protein crystal. The crystal is irradiated by a finely collimated x-ray beam. The interaction of the x-ray beam with the crystal produces scattered x-rays. These scattered x-rays are detected by means of a large area, thick CCD which is capable of measuring a significant number of scattered x-rays which impact its surface. The CCD is capable of detecting the position of impact of the scattered x-ray on the surface of the CCD and the quantity of scattered x-rays which impact the same cell or pixel. This data is then processed in real-time and the processed data is outputted to produce a image of the structure of the crystal. If this crystal is a protein the molecular structure of the protein can be determined from the data received.

Patent Number: ES2134680 Patent Title: Prediction of the strengths of CLINKER or CEMENT, using crystallographic factors of their constituent minerals, determined by means of X-RAY DIFFRACTION Publication Date: 1999-10-01 Abstract: Prediction of the strengths of CLINKER or CEMENT, using crystallographic factors of their constituent minerals, determined by means of X-RAY DIFFRACTION. With the procedure presented in this PATENT, the MECHANICAL STRENGTHS which clinker or Portland cement will have at 28 days are calculated, this procedure being suitable for control of the manufacturing process. By means of X-RAY DIFFRACTION, the structural characteristics of the minerals of the clinker are determined: crystalline size "D", content of micro- tensions in the matrix "T", and coefficient of structural variation "DIF D", to which end the scanning of two peaks of the region of its spectrum is carried out on a sample of powder. On the basis of the values of the DIFFRACTION intensities, the crystallographic factors are calculated by the variance method and with the data obtained, together with the mineralogical composition and the fineness of crushing, the strengths are calculated automatically following a computer calculation programme.

Patent Number: US5003570 Patent Title: Powder diffraction method and apparatus Publication Date: 1991-03-26 Abstract: PCT No. PCT/US87/02669 Sec. 371 Date Oct. 16, 1987 Sec. 102(e) Date Oct. 16, 1987 PCT Filed Oct. 16, 1987 PCT Pub. No. WO89/03526 PCT Pub. Date Apr. 20, 1989.In a stimulable phosphor powder diffraction apparatus, a circularly symmetric diffraction pattern is recorded in the stimulable phosphor. The 2-D diffraction pattern is read out, and the resulting signal is processed to produce a 1-D signal representing the average of the 2-D diffraction pattern at points equidistant from the center of the diffraction pattern.

Patent Number: 1983-05-24 Patent Title: Wide angular range X-ray diffraction reference standard composite Publication Date: 1983-05-24 Abstract: A unique composite structure is provided for calibration of diffractometer at low values of 2 theta . This composite structure involves a layer of silicon powder and a plurality of monolayers of a heavy metal stearate on the silicon powder. A lead stearate layered material has been found to provide significant results for enabling calibration below 20 DEG

Patent Number: US4144450 Patent Title: X-ray powder diffractometer Publication Date: 1979-03-13 Abstract: An X-ray powder diffractometer and associated computing system is disclosed for diffraction analysis of samples by the generation of an intensity diagram. A detector having a position sensitive element is advanced along an arc over a desired angle by a step motor. A control circuit connected to the step motor produces impulses corresponding to advancement of the step motor. These impulses are continually summed as an indication of the current position of the detector along the arc. The position sensitive element in the detector produces position signals corresponding to the position at which the detected X-rays strike the element. These position signals are digitallized. The position address is added to the sum of the impulses from the step motor control means to produce a composite sum which is indicative of the precise angle at a given moment at which an X-ray photon is detected by the sensitive element in the detector. As the detector moves along the arc, the composite sum is continually updated. By these means all X-rays falling successively into a certain diffraction angle are accumulated in the same channel of a multichannel analyzer independent of the movement of the position sensitive detector along the arc.

Patent Number: US3903415 Patent Title: X-ray diffraction measurement device using white X-rays Publication Date: 1975-09-02 Abstract: A diaphragm with an annular slot is placed between a powder sample and a detector, which may be a disc or annulus, while the sample is irradiated with white X-rays directed towards the center of the diaphragm. The distance of the diaphragm behind the sample and the radius of the annular slot determine the diffraction angle of the rays that will be detected. A semiconductor detector with high energy resolution produces an output signal that depends upon the wavelength of the detector radiation. A thick block with a conical slot may be used instead of a thin diaphragm.

Patent Number: DE19536707 Patent Title: X-ray diffractometry system Publication Date: 1996-03-21 Abstract: The invention concerns a method of obtaining an X-ray diffractogram with an X-ray diffractometer using an energy-resolving detector, influences from the operation of the diffractometer, detector properties and the background (radiation of energy other than that the useful radiation) being eliminated and full use being made of the available useful radiation (inter alia the characteristic radiation of an X-ray tube). In this way, the measuring time can be reduced to a quarter in comparison with an X-ray diffractometer using a crystal monochromator, whilst the measuring results have the same degree of statistical reliability. The method offers particular advantages for the measuring of weak reflexes in the presence of a high-energy background.

Patent Number: WO9508763 Patent Title: OPTIMIZED DEVICE FOR OBTAINING GANDOLFI DIFFRACTOGRAMS Publication Date: 1995-03-30 Abstract: A new device for obtaining dust diffractograms from a single crystal through spreading of its orientation with simultaneous rotation about two axes (technique of Gandolfi), with an angle X between the axes which is optimized in order to achieve a maximum of orientations and a maximum diffraction angle up to when is recorded a total quantity of possible reflections. Mounted in a diffractometer or chamber with Debye-Scherrer geometry, the device causes the crystal, at the crossing of the two axes, to simulate a polycrystalline sample in order to produce a diffractogram similar to that of a powder, as used for the identification of crystalline materials. The device comprises the axis GC, its coupling to the axis FC of the diffractometer through a part which defines X, a mechanism to produce its rotation through friction at the bottom of the diffractometer and a mechanism which supports the crystal and provides for its centering in the diffractometer.

Patent Number: US6005913 Patent Title: System and method for using X-ray diffraction to detect subsurface crystallographic structure Publication Date: 1999-12-21 Abstract: A system with three parts: a testing apparatus, a computer system, and a communications line between the two. The testing apparatus has a device that emits x-rays into the sample, a device to position the sample relative to the x-rays and an electro-optical x-ray detector for detecting diffracted x-rays. The computer system has a computer, a computer program, a storage device, a database, and monitor or other means of announcing the results of a test. The computer program directs the computer to accept data from the sample testing system concerning the relationships of the devices, the x-rays, and diffracted x-rays. The computer program also directs the computer to compare this data with a database of previously determined relationships and possible diffraction patterns stored in the storage device. Based on the comparison, the computer program directs the computer to announce the results of the comparison via the monitor or other means, thereby revealing the crystallographic grain structures of the sample. The method encompasses positioning the sample in a path of x-rays projecting from an x-ray means, detecting x-rays that are diffracted by the sample with an electro-optical detector, analyzing the data and announcing the crystallographic grain structures of the sample based on the analyzing step.

Patent Number: WO0216615 Patent Title: CRYSTAL STRUCTURE Publication Date: 2002-02-28 Abstract: Structural coordinates obtainable by subjecting a crystal comprising a dimethylarginine dimethylaminohydrolase (DDAH) or a fragment thereof or an arginine deliminase (DI) or a fragment thereof to X-ray diffraction measurements and deducing the structural coordinates from the diffraction measurements are used to identify, screen, characterise, design or modify a chemical entity. The chemical entities so generated may be used in methods of therapy or to identify the presence or absence of a DDAH or DI substrate.

Patent Number: US2002014589 Patent Title: Three-dimensional atom microscope, three-dimensional observation method of atomic arrangemment, and stereoscopic measuring method of atomic arrangement Publication Date: 2002-02-07 Abstract: Forward scattering peaks of photoelectrons having different angular momenta is generated by radiating to a sample two rays of circularly polarized light that differ in a rotary direction. Two images of photoelectron diffraction patterns are formed by two-dimensionally detecting the photoelectron diffraction patterns formed with the photoelectron forward scattering peaks. The observer can three-dimensionally observe the structure in an atomic arrangement by observing these photoelectron diffraction pattern images with his or hers right and left eyes, respectively

Patent Number: US6285736 Patent Title: Method for X-ray micro-diffraction measurement and X-ray micro-diffraction apparatus Publication Date: 2001-09-04 Abstract: An X-ray micro-diffraction measuring method for detecting X-rays diffracted at a minute portion of a specimen upon irradiating the minute portion with X-rays is disclosed. A cylindrical stimulation type fluorescent member is arranged around the specimen. A sample facet of the specimen is tilted by, for example, 45 with respect to the stimulation type fluorescent member such that the stimulation type fluorescent member can receive both diffracted X-rays passing along a direction tangential to the sample facet and diffracted X-rays passing along a direction perpendicular to the sample facet. Diffracted X-ray images can be obtained on the stimulation type fluorescent by merely rotating the specimen about only the phi axis thereof so as to perform the in-plane rotation without a rotation about the &khgr; axis. By eliminating a rotation about one axis from rotations about two axes for the specimen, it may be possible to avoid a degradation of measurement preciseness due to a crossing error of the two axes. Also, the elimination of the axis mentioned above may cause the structure of the apparatus to be simplified and the time required for the measurement to be shortened

Patent Number: DE19729150 Patent Title: X-ray diffraction spectra production method and determination and refinement of crystallographic structure models Publication Date: 1999-01-14 Abstract: The method measures the record associated with a probe of the X-ray spectra patterns (intensities of radiation of energies E) IM(E, PHI ), using an energy resolving detector in the area of the scattering angle. In measuring the spectra through the probe, the coherently and incoherently scattered intensity components of the primary radiation IO(E), as well as perhaps the fluorescence radiation of the test and influences of the function of the apparatus, are contained. The X-ray spectra are obtained and crystallographic structure models defined and refined. By exploiting the entire spectral information within the measured spectrum for each individual scattering angle phi and by correlating all measured spectra a structural parameter set is determined, for which the best simultaneous agreement is reached through connection of an operator PMC(E, PHI ) obtained from these parameters with correction from indices derivable from the X-ray diffraction spectrometry KME(E, PHI ) and a operator O(E PHI ) obtained from theoretical X-ray spectra of all or a certain number of measured spectra.

US Patent Number: 4,821,303 Patent Title: Combined thermal analyzer and x-ray diffractometer Date of Patent: April 11, 1989 Abstract: Scientific apparatus and a method are described for observing simultaneously both structural and thermodynamic properties of materials. An X-ray diffractometer and a thermal analyzer and mounted to cooperate and coact on the same sample and to complete a meaningful analysis in a very few minutes. The diffractometer is equipped with a rapid position-sensitive detector connected to a multichannel analyzer to record and display X-ray diffraction data from the sample over an angle of 20.degree. (two theta) or more. The thermal analyzer is preferably a differential scanning calorimeter. By correlating X-ray diffraction and thermal data taken simultaneously while the sample is passing through a range of temperatures and/or environments, structural changes corresponding to thermal events can be identified and elucidated.

US Patent Number: 6,459,763 Patent Title: Combinatorial X-ray diffractor Date of Patent: October 1, 2002 Abstract: A combinatorial X-ray diffractor, particularly a combinatorial X-ray diffractor which can measure one row of samples among a plurality of samples arranged into a matrix simultaneously by X-ray diffraction. For the purpose of high throughput screening, a plurality of samples (10) are arranged into a row X1, a row X2, a row X3, and a row X4 on a sample stage and samples in each row are measured simultaneously by X-ray diffraction, measured data are processed by an information processor (20), information data useful for the evaluation of thin film material are automatically extracted and arranged and the extracted and arranged information data are displayed on a display apparatus (27).

US Patent Number: 6,460,175 Patent Title: Program product for modular, parallel, remote software installation with repeatable, externally-invocable steps Date of Patent: October 1, 2002 Abstract: A program product recorded on a computer readable medium in which the program product includes a method of performing a software operation on a target of one or more processors in a distributed processing system wherein another processor is designated as a server. The method includes running a configuration program on the server to condition the server to serve on the target, the software operation which includes resource creation and object definitions; testing entry conditions in the configuration program for determining if entry conditions are met to serve the software operation on the target; if the entry conditions are met, serving the software operation on the target; at the completion of the software operation, testing exit conditions in the configuration program for determining if the software operation on the target completed successfully; if the exit conditions are met, exiting the software operation; returning to the configuration program to serve a second software operation on the target; and repeating until all software operations are served on the target.

US Patent Number: 6,460,026 Patent Title: Multidimensional data ordering Date of Patent: October 1, 2002 Abstract: A method, apparatus, software and data structure is disclosed for more efficient mapping of three dimensional data to linear storage mediums. These embodiments provide that multidimensional space is divided into volumes based on the priority of levels of one or more dimensions. Spatial to linear mapping is then applied to the multidimensional data such that records in the same volume will be close to each other. According to another aspect, a data structure is provided wherein data from a multidimensional space is stored in a one-dimensional space in a storage medium in accordance with the above-described method.

US Patent Number: 6,457,107 Patent Title: Method and apparatus for reducing false sharing in a distributed computing environment Date of Patent: September 24, 2002 Abstract: A method, system, and computer program product for reducing false sharing in a distributed computing environment, and in particular to a multi-processor data processing system. A method is proposed to define a virtual address range, within the system memory available to the processors, which will have a finer granularity than the default page size. These smaller sections, called "sub-pages," allow more efficient memory management. For example, a 64 Kilobyte range may be defined to have a 512 byte granularity rather than 4 Kilobytes, with each 512-byte sub-page capable of being separately managed.

US Patent Number: 6,330,649 Patent Title: Multiprocessor digital data processing system Date of Patent: December 11, 2001 Abstract: A multiprocessor digital data processing system comprises a plurality of processing cells arranged in a hierarchy of rings. The system selectively allocates storage and moves exclusive data copies from cell to cell in response to access requests generated by the cells. Routing elements are employed to selectively broadcast data access requests, updates and transfers on the rings.

US Patent Number: 6,088,758 Patent Title: Method and apparatus for distributing data in a digital data processor with distributed memory Date of Patent: July 11, 2000 Abstract: A digital data processing system and method with shared, distributed memory transfers data between corresponding data sets within memory. The digital data processing system includes a plurality of processing cells interconnected by a hierarchical network, at least some of the processing cells including a processor and a memory. Each memory provides storage space which is arranged in sets, with each set being capable of holding a plurality of data pages. At least one of the processing cells, as a first processing cell, includes a page distributor for determining when at least a first set in the associated memory has reached a predetermined storage commitment condition (for example, a filled condition). Under such a condition, the page distributor invokes a page-transfer element that selects a candidate processing cell from among the other processing cells and transfers one or more pages from the first set to a corresponding set in the candidate processing cell.

US Patent Number: 5,950,228 Patent Title: Variable-grained memory sharing for clusters of symmetric multi-processors using private and shared state tables Date of Patent: September 7, 1999 Abstract: In a distributed shared memory system, clusters of symmetric multi-processors are connected to each other by a network. Each symmetric multi-processor includes a plurality of processors, a memory having addresses, and an input/output interface to interconnect the processors. A software implemented method enables data sharing between the clusters of symmetric multi-processors using variable sized quantities of data called blocks. A set of the addresses of the memories are designated as virtual shared addresses to store shared data, and a portion of the virtual shared addresses are allocated to store a shared data structure as one or more blocks. The size of a particular allocated block can vary for different shared data structures. Each block includes an integer number of lines, and each line includes a predetermined number of bytes of shared data. Directory information of a particular block is stored in the memory of a processor designed as the home of the block. The directory information includes the size of the particular block, the identity of the processor that last modified the data in the particular block and the identity of all processors having a copy of the block.

US Patent Number: 5,761,729 Patent Title: Validation checking of shared memory accesses Date of Patent: June 2, 1998 Abstract: In a computer system a plurality of workstations are connected to each other by a network. Each workstation including a processor, a memory having addresses, and an input/output interface connected to each other by a bus. The input/output interfaces connect the workstations to each other via the network. Valid data accesses are checked by a software implemented method. A set of the addresses of the memories are designated as virtual shared addresses to store shared data. A particular one of the programs allocates a portion of the virtual shared addresses to store a shared data structure as one or more blocks accessible by the programs executing in any of the processors. The size of a particular block depends on the size of the shared data structure. Each block including an integer number of lines, each line including a predetermined number of bytes. The program is instrumented to initialize the bytes allocated for the shared data structure to a predetermined flag value. The flag value indicates that the data are in an invalid state. Load instructions of the programs are instrumented to check if data loaded from the shared data structure are different than the predetermined flag value. The load instructions are executed if the data are different than the predetermined flag value. Otherwise, miss handling code is executed before the load instructions are executed.

US Patent Number: 6,457,103 Patent Title: Method and apparatus for caching content in a data processing system with fragment granularity Date of Patent: September 24, 2002 Abstract: A method and apparatus in a data processing system for caching a page containing dynamic content. Dynamic content in a page is divided into a plurality of objects. Each object is stored within the plurality of objects in a cache, wherein an object within the plurality of objects is selectively stored in the cache based on a rate change in data of the object.

US Patent Number: 6,256,632 Patent Title: Method and system for enabling dynamic cache structures in a networked environment Date of Patent: July 3, 2001 Abstract: Methods, systems and computer program products are provided for managing shared data elements among a plurality of different client processes in a network environment. Shared data elements are associated with a Flow. A Flow is a logical stream of data that is only transmitted to a client process that explicitly subscribes for updates from the Flow. Update requests for the shared data elements are transmitted from client processes along the Flow so as to request the receipt of update notifications along the Flow. Update notifications are also transmitted about the shared data elements to the client processes along the Flow which have requested update notifications. Content of the shared data elements is, thereby, delivered to applications executing within said at least one client process which have requested updates of the shared data elements.

US Patent Number: 6,253,234 Patent Title: Shared web page caching at browsers for an intranet Date of Patent: June 26, 2001 Abstract: Each client in an intranet includes at least the minimum functionality required to serve a remote request such as an HTTP request. Existing browsers within the intranet may share their collective local caches to form a scalable cache. The intranet proxy routes page requests from one client within the intranet to another when a local cache within the intranet contains a current copy of the requested page. A trust protocol insures that clients serving as caches may be trusted by the proxy, while a refresh mechanism such as a time-out policy ensures that the page is reloaded after a predetermined period of time. The collective cache thus scales with the number of browsers in the intranet, and existing browsers may be employed without direct modification. The same mechanism may be utilized, either within a network or through an Internet service provider, to permit individuals and companies to maintain Web sites on their own personal systems without paying fees for uninterrupted connection to the Internet.

US Patent Number: 6,094,662 Patent Title: Apparatus and method for loading and reloading HTML pages having cacheable and non-cacheable portions Date of Patent: July 25, 2000 Abstract: On an embedded device with a web server, pages are marked as having non-cacheable HTML portions and cacheable graphics portions. Marking the HTML portion as non-cacheable allows for the retrieval of a web page containing the latest status information without retrieving the graphics images. A refresh function is provided that allows for the comparing of non-cached portion time stamps with the stamps of the page on the web server. When the time stamp of the page on the web server is more current than the time stamp of the non-cached portion, the non-cacheable portion of the web page is retrieved from the web server. Retrieving the non-cacheable HTML portion from the web site without retrieving the cached portion reduces the amount of time needed to refresh the display image. A timer may be employed to refresh the web page at predetermined intervals, while using the current URL or the history list of the browser to reach the desired web site and retrieve the current status of the embedded device. The refresh function may be activated by a button available on the browser or by a refresh button on the web page.

US Patent Number: 6,457,130 Patent Title: File access control in a multi-protocol file server Date of Patent: September 24, 2002 Abstract: The invention provides a method and system for enforcing file access control among client devices using multiple diverse access control models and multiple diverse file server protocols. A multi-protocol file server identifies each file with one particular access control model out of a plurality of possible models, and enforces that one particular model for all accesses to that file. When the file server receives a file server request for that file using a different access control model, the file server translates the access control limits for that file into no-less-restrictive limits in the different model. The file server restricts access by the client device using the translated access control limits. Each file is assigned the access control model of the user who created the file or who last set access control limits for the file. When a user having a different access control model sets access control limits, the access control model for the file is changed to the new model. Files are organized in a tree hierarchy, in which each tree is limited to one or more access control models (which can limit the ability of users to set access control limits for files in that tree). Each tree can be limited to NT-model-only format, Unix-model-only format, or mixed NT-or-Unix-models format.

US Patent Number: 6,457,040 Patent Title: Method and system for a distributed network computing system for providing application services Date of Patent: September 24, 2002 Abstract: The server computer 155 is provided with an access section 151, a security section 152, a application function conversion section 153, application service supply section 154 and a remote agent 155 therein. The data terminals 13 is provided with a local agent 131, client software 132, key management client 133, enciphering section 134 therein. In this way, the server computer 15 and the data terminals 13 connected through a network 14 can realize a countermeasure for the circuit breakdown and an improvement of the security function regarding the data cache function and vicarious login.

US Patent Application: 20020147547 Patent Application Title: Apparatus and method for designing proteins and protein libraries Date: October 10, 2002 Abstract: Methodology for the automated design of proteins is disclosed. Various methods executed by a computer for generating probability matrices, protein sequences, combinatorial libraries of proteins, and optimization of various parameters related to protein design are disclosed. Methodology is applicable to the design and analysis of protein structures and protein sequences.

US Patent Application Number: 20020133297 Patent Application Title: Ligand docking method using evolutionary algorithm Date: September 19, 2002 Abstract: A flexible ligand docking method based on evolutionary algorithms is provided. The proposed method incorporates family competition and adaptive rules to integrate decreasing-based mutations and self-adaptive mutations to act as global and local search strategies, respectively. The invention is to provide a method for screening and evaluating conformationally flexible ligands as potential lead compounds, because the method can be applied to search space for possible configurations of ligands in order to correctly dock into the active site of an enzyme. Therefore, the proposed method can be used to guide drug-design strategies and explore evolutionary relationships. Furthermore, the method of this invention has implications for protein engineering and protein folding.

US Patent Number: 5,555,366 Patent Title: Computer graphics system for selectively modelling molecules and investigating the chemical and physical properties thereof Date of Patent: September 10, 1996 Abstract: A computer graphics system for modeling chemical molecules includes simultaneous two-dimensional and three-dimensional display of models of molecules from a single data set, and allows a user to edit in either two dimensions or three dimensions. A two-dimensional model may be stylized while a three-dimensional model of the same molecule remains chemically (geometrically) correct. The system has editing tools for use in both two dimensions and three dimensions, and changes made in one mode are immediately reflected in the other, and the editing tools include manipulation components for the user to display on elements of a model, and to use to move parts of a model of a molecule relative to other parts. The system includes techniques for structure determination and display that significantly reduce the computer power required to perform system functions, rendering techniques formally reserved to supercomputers usable on smaller computer platforms. Physically based modeling is included, allowing the user to perturb the geometry of a model and to investigate interactively the effects of perturbation according to a dynamic force equation. The system also includes a procedure for displaying multiple models of molecules and performing docking studies between the models.

US Patent Number: 6,327,334 Patent Title: Method of rapidly screening X-ray powder diffraction patterns Date of Patent: December 4, 2001 Abstract: A method for rapidly screening multiple X-ray powder diffraction patterns, such as those generated through combinatorial chemistry, has been developed. The method is directed toward measuring X-ray powder diffraction patterns of a set of samples, factoring the patterns using a suitable statistical technique into a small number of discrete components or factors, determining the scores corresponding to the factors for each X-ray powder diffraction pattern, and plotting the scores. The graphs of the scores are then inspected for clusters, trends, or outliers, which may represent new material or, perhaps, faulty data.

US Patent Number: 6,577,970 Patent Title: Method of determining a crystallographic quality of a material located on a substrate Date of Patent: June 10, 2003 Abstract: The present invention provides a method of determining a crystallographic quality of a material located on a substrate. The method includes determining a set of crystallographic solutions for an unknown crystallographic orientation, and subsequently comparing the set of crystallographic solutions to adjacent known crystallographic orientations to determine the unknown crystallographic orientation. In a preferred embodiment, the set of crystallographic solutions may be a rank of crystallographic solutions which may represent the most probable crystallographic orientations. The rank of crystallographic solutions, in an alternative embodiment, may be represented by a vote, a fit and a confidence index.

US Patent Number: 5,557,104 Patent Title: Method and apparatus for determining crystallographic characteristics in response to confidence factors Date of Patent: September 17, 1996 Abstract: An apparatus for determining the reliability of crystallographic solutions of a specimen includes an electron beam generator, a stage for holding the specimen, an image collection system for obtaining diffraction images of crystals within the specimen, and processor for processing the diffraction images to obtain most probable indexing solutions for the crystals and to generate confidence factors associated with the most probable indexing solutions. The apparatus may utilize the confidence factors to determine the phase of the crystals within the specimen. The confidence factors may also be incorporated into reports representing the statistical confidence of various crystallographic characteristics of the specimen.

US Patent Number: 6,577,705 Patent Title: Combinatorial material analysis using X-ray capillary optics Date of Patent: June 10, 2003 Abstract: Method and system for analyzing local composition and structure of a compound having one or more non-zero gradients in concentration for one or more selected constituents in a selected direction. A beam of X rays having representative energy E is received by a mono-capillary or poly-capillary device and is directed at a selected small region of the compound. A portion of the X rays is diffracted at the selected region by one or more constituents of the compound, at each of two or more diffraction angles relative to a selected surface or lattice plane(s) of the compound; and the diffracted portion of X rays for each of these diffraction angles is received and analyzed at an X-ray detector. A portion of the X rays excites fluorescence radiation that is received by a fluorescence detector to estimate the relative concentrations in a compound having two or more constituents. Fluorescence X rays and diffraction X rays can be detected at each desired translational position and rotation for a target site. As a result, a concentration map for various constituents in the compound can be prepared, together with a phase map illustrating the structure of a combinatorial compound. An X-ray detector monochromator can be removed and a capillary diameter can be reduced in some situations.

US Patent Number: 6,118,850 Patent Title: Analysis methods for energy dispersive X-ray diffraction patterns Date of Patent: September 12, 2000 Abstract: Energy dispersive x-ray diffraction spectra are obtained from numerous volume elements within an object. A feature set such as a set of cepstrum coefficients is extracted from each spectrum and classified by a trained classifier such as a neural network to provide an indication of whether or not contraband such as explosives is present in the volume element. Indications for adjacent volume elements are evaluated in conjunction with one another, as by an erosion process, to suppress isolated indications and thereby suppress false alarms.

US Patent Number: 5,936,255 Patent Title: X-ray, neutron or electron diffraction method using an imaging plate and apparatus therefor Date of Patent: August 10, 1999 Abstract: An X-ray, neutron or electron diffraction method, which is devoid of the defects of conventional diffraction apparatus using an imaging plate, which can analyzing a sample, in a non-destructive mode without contact and with a good S/N ratio, even when the sample significantly generates fluorescence or scattered X-rays. The method includes the steps of irradiating a predetermined area of the sample with an X-ray, neutron or electron beam whose axis is oriented at a fixed direction to obtain a diffraction ray, rotating the sample while maintaining the irradiated predetermined area substantially unchanged and while maintaining the angle between the axis of the X-ray, neutron or electron beam relative to the tangential plane of the predetermined area substantially unchanged, forming an image of the diffraction ray from the sample during the rotation of the sample through every predetermined angle using an imaging plate, reading a data of the image formed on the imaging plate to obtain an output data for each rotation of the sample through the predetermined angle, and processing the output data to obtain desired analysis information.

US Patent Number: 5,418,829 Patent Title: Method for determining unknown structure of crystal Date of Patent: May 23, 1995 Abstract: The method for determining unknown structure of a solid by means of corpuscular beams or electromagnetic waves, includes the steps of radiating first incident waves to the solid to thereby obtain first scattering waves. radiating second incident waves to the solid in the direction opposite to the direction in which the first scattering waves had travelled, to thereby obtain second scattering waves, and measuring the intensity of the second scattering waves and the direction in which the second scattering waves had travelled.

US Patent Number: 5,235,523 Patent Title: Apparatus and methods for identifying and comparing lattice structures and determining lattice structure symmetries Date of Patent: August 10, 1993 Abstract: A converse transformation matrix generation approach is used either i) to late a lattice structure of one crystalline material to the lattice structure(s) of one or more other crystalline materials for determining interlattice relationships which allow materials to be identified and classified relative to other materials; or ii) to relate a lattice structure of a material to itself for determining lattice symmetry. In particular, matrices which transform any primitive cell defining a lattice structure either into itself or into another cell defining a second lattice structure to within predetermined maximum tolerances of the cell parameters are generated.

US Patent Number: 4,788,702 Patent Title: Orientation of crystals Date of Patent: November 29, 1988 Abstract: The invention comprises apparatus for determining the orientation of the crystallographic axes of a single crystal. The crystal is rotated on a turntable while an X-ray beam containing characteristic radiation is directed onto it. A stationary position-sensitive detector, preferably positioned at right angles to the beam detects Bragg reflections from the crystal, and computing means responsive to the signals from the detector, and signals representing the angular position of the turntable determines the crystal orientation.

US Patent Number: 4,553,030 Patent Title: Method for automatic analysis of electron beam diffraction pattern Date of Patent: November 12, 1985 Abstract: A video image of an electron diffraction pattern is digitized and captured as a two dimensional array of intensity values. From the array of intensity values, the frequency distribution of said intensity values is obtained. It is determined that the diffraction pattern is composed of only diffraction spots, only diffraction rings, or both diffraction spots and rings by analyzing said frequency distribution. The diffraction pattern is thus analyzed easily and automatically.

US Patent Number: 5,136,624 Patent Title: A video image of an electron diffraction pattern is digitized and captured as a two dimensional array of intensity values. From the array of intensity values, the frequency distribution of said intensity values is obtained. It is determined that the diffraction pattern is composed of only diffraction spots, only diffraction rings, or both diffraction spots and rings by analyzing said frequency distribution. The diffraction pattern is thus analyzed easily and automatically. Date of Patent: August 4, 1992 Abstract: In the manufacture and processing of monocrystalline material, it is important to be able to detect and measure deviations from the ideal crystal structure. Data are required on the density and average extent of impurity precipitations. The irradiation of discrete crystal areas with wave or particle beams, the determination of the intensity distribution of the beams scattered under Bragg conditions, and the determination of static Debye-Waller factors are to be performed automatically and universally, on different specimen thicknesses, with high resolution and flexibility regarding changes in wavelength. For this purpose, a variation of the angle of incidence of the beams on the diffracting lattice planes is performed, and the reflection factor is measured by means of a photon or particle detector, and the integral reflection factor Rint is determined. Pivoting the specimen around an axis which is perpendicular to the diffracting lattice planes leads to a variation of the specimen thickness. Rint is measured as a function of the specimen thickness. From the measured dependence, fitted to a theoretical function, the static Debye-Waller factor is determined, and when several diffraction orders are measured, the density or number and the average extent of the precipitations can also be determined. Important applications include the in situ determination of impurity precipitations in inspections of Si wafers, which can be mapped with high-sensitivity resolutions as a function of density and size of SiO2 precipitations, etc.

US Patent Number: 6,072,853 Patent Title: Material analysis Date of Patent: June 6, 2000 Abstract: A method and apparatus for analyzing drill core rock samples is described, utilizing a collimated beam of polychromatic X-ray photons of a brightness of at least 10.sup.15 photons/sec/mrad.sup.2 /0.1% bandwidth and energies of at least 20 keV. A suitable source of such X-rays is a synchrotron.