Abstract: The invention provides novel polyketide compounds having desired bioactivity, including neuroregenerative activity without immunosuppressive activity, and methods of making and using these compounds.

Abstract: The disclosure relates to a method of estimating the polar component of the solvation energy for a molecule embedded in different media. In one embodiment, the molecule is partially embedded in a membrane. For an atom of the molecule, the polar component of the atom's solvation energy is represented as a combination of at least a self-energy term and a screening-effect term. The self-energy term represents the contribution to the atom's polar component made by the membrane and the molecule's other atoms located inside the membrane. The screening-effect term represents the typically negative contribution to the atom's polar component made by the molecule's other atoms located outside the membrane. An analytical function is used to calculate the self-energy term. In a preferred embodiment, the analytical function is a function of the distance from the atom to the membrane, the van der Waals radius of the atom, and the thickness of the membrane.

Abstract: The present invention provides an optical modeling method capable of inhibiting distortion in an object to be modeled and modeling with higher precision. A square exposure region is divided into a plurality of pixels which are further divided into first and second pixel sub-groups, the first pixel sub-group is exposed such that neighboring pixels or more are not exposed at one time, and then unexposed pixels incorporated in the second pixel sub-group are exposed two neighboring pixels or more are not exposed at one time. A photo-curable resin is exposed twice, and then cured in an amount of one photo-curable resin layer. Accordingly, the neighboring pixels are not exposed at one time, the producing of curing shrinkage is limited within one pixel, and distortion due to the curing shrinkage does not spread to the pixels neighboring the one pixel, whereby distortion in the object to be modeled can be inhibited significantly, and modeling with higher precision is made possible.

Abstract: The nuclear receptor for the steroid hormone 1&agr;,25-dihydroxyvitamin D3, its ligand binding domain, three-dimensional model thereof and a method for selection of suitable vitamin D3 binding to the 1&agr;,25-dihydroxyvitamin D3 receptor. A three-dimensional model for residues 142-427 of the ligand binding domain of the human nuclear receptor for 1&agr;,25-dihydroxyvitamin D3 used to identify the interaction of the conformationally flexible natural hormone 1&agr;,25(OH)2D3 and a number of related analogs with the receptor ligand binding domain. A method for identification and generation of new potential analog drug forms of dihydroxyvitamin D3.

Abstract: A computer assisted method for generating a representation of a three dimensional structure of a molecule is described. The invention recursively filters an a priori vector of structural parameters, representative of the three dimensional structure of the molecule, based upon experimental observations relating to the structural parameters. The invention produces a refined vector of structural parameters and an associated covariance matrix indicating the accuracy of the vector. The invention includes a set of non-linear functions which implement a model relating the observations to the vector of structural parameters. The recursive steps of the method include a prediction step and an update step. During the prediction step, the non-linear model is analyzed by statistical methods. Only the results of the prediction step are incorporated in the update step, thus isolating the non-linear aspects of the model within the prediction step.

Abstract: When chemical process conditions and chemical species are input on a spreadsheet software (1), a chemical model is selected according to the chemical species by a software (4, 5, 6) different from the spreadsheet software (1), thermodynamic property data for the chemical model is generated, and a chemical equilibrium is evaluated based on this data. The chemical equilibrium is simulated on the spreadsheet software (1) based on this evaluation result, and the simulation result is displayed on the spreadsheet software (1).

Abstract: A method and workstation for optimizing separation of a given racemate automation technology, and computer-controlled design is disclosed. The workstation includes a synthesizer, an analyzer, a robot and computer in communication with the synthesizer and analyzer. The computer includes one or more programs for regulating variables such as types of stationary phases; types of solvents; amounts of solvents; pressure; temperature; and employs methods for optimizing separation of a given racemate and for designing optimized experiments for further investigation.

Abstract: For the computer modeling of molecules, a model with reduced coordinates is used with sufficiently stable implicit integration methods integrating the model's equations of motion. The timesteps in the integration method can vary in a range over 100 to greatly increase the computer's efficiency and to hasten the computational results. Both static analysis and molecular dynamics simulations are some ready applications.

Abstract: A method and apparatus to predict the color of an overprint of a set of colorants at a set of respective coverage percentages on a substrate of a substrate type using a printing technique. The colorants include some for which a device profile is provided. The method includes determining the colorant parameters of the device profile colorants; determining the spectrum of the substrate, providing spectral colorant parameters for the non-device profile colorants, and determining the color of the overprint. One version including modifying the data of the device profile such that the colorant parameters determined in the step of determining colorant parameters determines the colorant parameters of modified colorants that match the color of the device profile colorants and that cover at least the gamut of the device profile colorants.

Abstract: In response to a user query that identifies a target chemical, a listing is displayed of reagent chemicals that are used to synthesize the target chemical. A listing also is displayed of equipment that is used to synthesize the target chemical. A listing also is displayed of a procedure that is used to synthesize the target chemical by reacting the reagent chemicals in the equipment according to the procedure. User input is accepted to electronically order the reagent chemicals that are used to synthesize the target chemical, the target chemical itself and/or the equipment that is used to synthesize the target chemical. In response, a transaction is performed to electronically order the reagent chemicals that are used to synthesize the target chemical, the equipment that is used to synthesize the target chemical and/or the target chemical itself.

Abstract: A method for measuring the quality properties of paper and/or board on moving webs is disclosed. The present invention utilizes a staged evaluation method in which the basic properties of the paper or board and further properties are determined via multi-stage modeling.

Abstract: A mathematical determination model is used to select cosmetic auxiliaries for cosmetic products and for the manufacture.

Abstract: A predictive modeling algorithm for deriving the outcome of UV photochemical reactions. The model is created in three sections: A parameter input section, a calculation section, and an output section. Input parameters are loaded into the model, calculations are made automatically by the algorithm, and output numbers given which constitute a theoretical test result. The model is adaptable in that it provides for various wavelengths and levels of input energy, a wide variety of reactive chemical components, and many different surface types. An extensive range of photochemical experiments can be modeled with a simple PC-type computer and commercially available software. This predictive model is designed to simulate real reactions as done in a lab, but many times faster and cheaper.

Abstract: Generally, the present invention provides and uses a set of descriptors of three-dimensional molecular property fields. A portion of the descriptors are calculated in such as way as to separate property fields from the underlying structure of the molecule. These descriptors are calculated through reference to a property field center. Thus, only if the property field changes, such as by moving an atom having a non-zero property value, will the descriptors need to be recalculated. Additionally, a portion of the descriptors do relate to the underlying molecular structure, only these descriptors contain information from more than one reference point. In particular, a displacement is determined between a property field center and the centroid of a molecule. This descriptor contains information from two reference points. Furthermore, components of a property field are mapped onto a principal geometric frame, which essentially references the property field to the molecular shape.

Abstract: A method for determining the most efficient way to synthesize compounds that form a combinatorial, chemical library is disclosed and described, with an example of the use of such method to develop a synthesis scheme.

Abstract: A method and workstation for optimizing optimization of biocatalyst performance based on combinatorial chemistry, automation technology, and computer-controlled design is disclosed. The workstation includes a synthesizer, an analyzer, a robot and computer in communication with the synthesizer and analyzer. The computer includes one or more programs for regulating reaction parameters such as types of enzymes; amounts of enzymes; types of solvents/buffers; amounts of solvents/buffers; temperature; pressure; pH; types of substrates; time; enzyme—substrate ratio; and agitation (whether to agitate and the speed of agitation) and employs statistical methods for optimizing multiple reaction parameters and for designing optimized experiments for further investigation.

Abstract: A component mapper is provided in connection with a process wherein a fluid stream having multiple physical components is modeled as a plurality of pseudo-components. Each physical component has a boiling point, and each pseudo-component has a pre-defined boiling point and includes all physical components from the fluid stream having approximately the pre-defined boiling point. Each pseudo-component in the model of the fluid stream has a varying pre-defined property and a varying amount. A plurality of sub-pseudo-components are defined for each pseudo-component such that the pseudo-component is replaceable therewith. Each sub-pseudo component has the pre-defined boiling point of the pseudo-component, a pre-defined value for the pre-defined property, and a varying amount. For each pseudo-component, a current value of the pre-defined property and a current amount of the pseudo-component are obtained, and a current amount for each sub-pseudo-component of the pseudo-component is then calculated.

Abstract: A process for simulating complex chemical reaction pathways, wherein the simulation is based on transformations with relative probabilities that helps predicting the outcome of processes that may involve multiple chain reactions and/or parallelism and/or feedback or feed forward loops.

Abstract: This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

Abstract: A Monte Carlo ion implantation simulation method speedily calculates an implanted ion distribution in a semiconductor substrate.

Abstract: A constrained non-linear approximator for empirical process control is disclosed. The approximator constrains the behavior of the derivative of a subject empirical model without adversely affecting the ability of the model to represent generic non-linear relationships. There are three stages to developing the constrained non-linear approximator. The first stage is the specification of the general shape of the gain trajectory or base non-linear function which is specified graphically, algebraically or generically and is used as the basis for transfer functions used in the second stage. The second stage of the invention is the interconnection of the transfer functions to allow non-linear approximation. The final stage of the invention is the constrained optimization of the model coefficients such that the general shape of the input/output mappings (and their corresponding derivatives) are conserved.

Abstract: A computer-implemented method and apparatus are provided for planning the generation of combinatorial chemical libraries produced by a series of chemical reaction stages, each stage involving a multiplicity of simultaneous chemical reactions utilizing a set of potential synthons. The disclosed method and apparatus involve enumerating the members of the proposed library and determining which of the members meet desired criteria.

Abstract: A computer-implemented molecular dynamics-based process simulates a distribution of ions implanted in a semiconductor substrate. The properties of the semiconductor substrate and ion dose to be simulated are first initialized, including an initial set of splitting depths that contain an equal number of virtual ions implanted in each substrate volume determined by the splitting depths. A first ion with selected velocity is input onto an impact position of the substrate that defines a first domain for the first ion during a first timestep, where the first domain includes only those atoms of the substrate that exert a force on the ion. A first position and velocity of the first ion is determined after the first timestep and a second domain of the first ion is formed at the first position. The first ion is split into first and second virtual ions if the first ion has passed through a splitting interval. The process then follows each virtual ion until all of the virtual ions have come to rest.

Abstract: The present invention relates to conducting a plurality of chemical reactions in a system including an apparatus which provides energy for the chemical reactions, such as chemical reactions in organic synthesis, where a particular advantage is the use of predetermined reaction parameters corresponding to similar chemical reactions. The present invention also relates to a system for performing said method and to corresponding kits and software. The system comprises an apparatus which can provide energy for the chemical reactions, said apparatus comprising a reaction cavity and a liquid handler, and a parameter selecting unit having a user interface means, a search unit means, apparatus control unit means, and storage means for carrying a database.

Abstract: A set of hybrid least squares multivariate spectral analysis methods in which spectral shapes of components or effects not present in the original calibration step are added in a following estimation or calibration step to improve the accuracy of the estimation of the amount of the original components in the sampled mixture. The “hybrid” method herein means a combination of an initial classical least squares analysis calibration step with subsequent analysis by an inverse multivariate analysis method. A “spectral shape” herein means normally the spectral shape of a non-calibrated chemical component in the sample mixture but can also mean the spectral shapes of other sources of spectral variation, including temperature drift, shifts between spectrometers, spectrometer drift, etc. The “shape” can be continuous, discontinuous, or even discrete points illustrative of the particular effect.

Abstract: Abnormal flows in an extractor are simulated, with a flow divider model and a flow merger model being introduced. Overflow state, entrainment occurrence state, and reflux state in the extractor are simulated. Moreover, abnormal flows under a variety of conditions are simulated efficiently by using object-oriented software as the simulation program.

Abstract: A simple mathematical model, given below, is constructed on the premise that reflected light other than light reflected at a metal surface is quantitatively taken into consideration the device to which the present invention is applied is a multilayer structure with a refractive index difference, so that only one reflection at an interface other than the metal surface can be taken into account that is, two or more reflections can be neglected. Further the concept of localized light emitting surfaces is extended to a non-localized model. The below simple mathematical model is used to treat reflected wave components so that an accurate simulation can be run.

Abstract: Impurity profiles Pi1 and Ps1 are determined for the same conditions by a reference acquiring means and a simulation capable of producing a result faster than the reference acquiring means, respectively. Errors between the impurity profile Pi1 determined by the reference acquiring means and the impurity profile Ps1 determined by the simulation are determined. An impurity profile Psx is calculated for another kind of conditions by the simulation, and a new impurity profile Psx′ is calculated by correcting the impurity profile Psx so as to reflect the errors.

Abstract: Methods for searching stable docking models of biopolymer-ligand molecule complex, which comprise the steps of: (1) searching possible hydrogen-bond schemes between a biopolymer and a ligand molecule by preparing possible combination sets of hydrogen-bonding heteroatoms in the ligand molecule with dummy atoms located at the positions of heteroatoms that can be hydrogen-bond partners to hydrogen-bonding functional groups in the biopolymer; (2) estimating the possible the hydrogen-bond schemes between the biopolymer and ligand molecule and the possible conformations of a hydrogen-bonding part of the ligand molecule at the same time by comparing the distances between the dummy atoms with the distances between the hydrogen-bonding heteroatoms; and (3) obtaining the possible docking models of the biopolymer-ligand molecule complex by changing the coordinates of all atoms of the ligand molecule into the coordinate system of the biopolymer, according to the correspondences between the hydrogen-bonding heteroatoms in

Abstract: A system method, and computer program product for visualizing and interactively analyzing data relating to chemical compounds. A user selects a plurality of compounds to map, and also selects a method for evaluating similarity/dissimilarity between the selected compounds. A non-linear map is generated in accordance with the selected compounds and the selected method. The non-linear map has a point for each of the selected compounds, wherein a distance between any two points is representative of similarity/dissimilarity between the corresponding compounds. A portion of the non-linear map is then displayed. Users are enabled to interactively analyze compounds represented in the non-linear map.

Abstract: A method and workstation for optimizing chemical processes based on combinatorial chemistry, automation technology, and computer-controlled design is disclosed. The workstation includes a synthesizer, an analyzer, a robot and computer in communication with the synthesizer and analyzer. The computer includes one or more programs for regulating reaction parameters such as temperature, pressure, concentration of reagents and employs statistical methods for optimizing multiple reaction parameters and for designing optimized experiments for further investigation.

Abstract: The single scatter Monte Carlo code CREEP models precise microscopic interactions of electrons with matter to enhance physical understanding of radiation sciences. It is designed to simulate electrons in any medium, including materials important for biological studies. It simulates each interaction individually by sampling from a library which contains accurate information over a broad range of energies.

Abstract: The present invention provides methods for the generation of virtual libraries of compounds. These compounds are generated in silico. The present invention encompasses methods for tracking the addition of fragments, use of reagents, and transformations performed. Further, methods for interfacing the information necessary to generate libraries of compounds with instrumentation that conducts the actual synthesis of the compounds are provided. Also provided are methods for the in silico docking of the library compounds to identified target molecules of interest.

Abstract: A method and apparatus are disclosed for predicting the presence of at least one congenital or acquired imbalance or therapeutic condition associated with thrombosis/hemostasis from at least one time-dependent measurement profile. At least one time-dependent measurement on an unknown sample is performed and a respective property of said sample is measured over time so as to derive a time-dependent measurement profile. A set of a plurality of predictor variables are defined which sufficiently define the data of the time-dependent measurement profile. A model is then derived that represents the relationship between the congenital or acquired imbalance or therapeutic condition, and the set of predictor variables. Subsequently, the model is utilized to predict the existence of the congenital or acquired imbalance or therapeutic condition in the unknown sample.

Abstract: The method and system for aiding in the design of an automotive vehicle enables dynamic placement of particle injection points into a flow domain to permit visual observation and alteration of resulting particle trajectories with respect to a computer aided design model representative of the vehicle. Various particle trajectories, representing windshield washer spray, water droplets along the vehicle surface, and the like can be simulated relative to the vehicle surface with or without the influence of a flow field around the vehicle surface to evaluate a vehicle design, compare alternate designs and compare results from physical aerodynamic tests to predicted results.

Abstract: The present invention provides methods for the generation of virtual libraries of compounds. These compounds are generated in silico. The present invention encompasses methods for tracking the addition of fragments, use of reagents, and transformations performed. Further, methods for interfacing the information necessary to generate libraries of compounds with instrumentation that conducts the actual synthesis of the compounds are provided. Also provided are methods for the in silico docking of the library compounds to identified target molecules of interest.

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.

Abstract: A computer-based method for the identification of binding targets in proteins and other macromolecules. More particularly, the invention includes an algorithm aimed at predicting binding targets in proteins. This algorithm, named Woolford, requires knowledge of the high resolution structure of the protein but no knowledge of the location or identity of natural binding sites or ligands. Binding targets in the protein are identified and classified according to their expected optimal affinities. Binding targets can be located at the protein surface or at internal surfaces that become exposed as a result of partial unfolding, conformational changes, subunit dissociation, or other events. The entire protein is mapped according to the binding potential of its constituent atoms. Once binding targets are identified, optimal ligands are designed and progressively built by the addition of individual atoms that complement structurally and energetically the selected target.

Abstract: A computer-based method for the identification of binding targets in proteins and other macromolecules. More particularly, the invention includes an algorithm aimed at predicting binding targets in proteins. This algorithm, named Woolford, requires knowledge of the high resolution structure of the protein but no knowledge of the location or identity of natural binding sites or ligands. Binding targets in the protein are identified and classified according to their expected optimal affinities. Binding targets can be located at the protein surface or at internal surfaces that become exposed as a result of partial unfolding, conformational changes, subunit dissociation, or other events. The entire protein is mapped according to the binding potential of its constituent atoms. Once binding targets are identified, optimal ligands are designed and progressively built by the addition of individual atoms that complement structurally and energetically the selected target.

Abstract: A predictive kinetic model is disclosed for simulating fluid catalytic cracking of large hydrocarbon molecules having a lumping scheme that includes hydrocarbon descriptions based on boiling point distribution and chemical properties. The simulation results in a nearly continuous prediction of products as function of boiling point temperature. The lumping scheme defines a relatively large number of small fixed boiling-point range pseudo-components for describing product material, and a smaller number of larger boiling-point range pseudo-components for describing feed conversion and selectivity. The chemical properties for describing hydrocarbons include total hydrogen, aromatic carbon and aromatic hydrogen.

Abstract: In a method of accurately determining an area that has been changed to an amorphous state which uses a computer simulation of a semiconductor manufacturing process, the impurity concentration at the crystalline-amorphous boundary is taken as the parameter C. The value obtained by dividing the implanted ion concentration obtained by means of an ion implantation simulator by the parameter Ca is defined as the amorphous conversion ratio parameter, and a region in which this amorphous conversion ratio parameter is 1 or greater is taken to be an area that is converted to an amorphous state.

Abstract: The present invention provides a method for producing a mass-coded combinatorial library comprising a set of compounds having the general formula X(Y)n, where X is a scaffold, each Y is, independently, a peripheral moiety, and n is an integer greater than 1. The method comprises selecting a peripheral moiety precursor subset from a peripheral moiety precursor set. The subset includes a sufficient number of peripheral moiety precursors that at least about 50 distinct combinations of n peripheral moieties derived from the peripheral moiety precursors in the subset exist. The subset of peripheral moiety precursors is selected so that at least about 90% of all possible combinations of n peripheral moieties derived from the subset have a molecular mass sum which is distinct from the molecular mass sums of all of the other combinations of n peripheral moieties. The method further comprises contacting the peripheral moiety precursor subset with a scaffold precursor which has n reactive groups.

Abstract: A topography simulation method using the Monte Carlo method is provided, which simulates the post-etching topography of a plasma-assisted etching process affected by different etching species such as the ion-assisted etching process. (a) A bulk- and/or sheath-plasma region is/are analyzed using a first random number, calculating a species energy of an incoming species. (b) A sort of the incoming species toward a minute surface region of a target material is selected using a second random number based on the species energy calculated in the step (a). (c) An absorption state of the incoming species with atoms of the target material on the minute surface region of the target material is selected using a third random number based on the species energy in the step (a) and the sort of the incoming species selected in the step (b).

Abstract: A method of using a computer processor to analyze electrical signals and data representative of a first molecule to determine conformational free energy of the first molecule so as to determine whether the first molecule is more stable than a second molecule, wherein both molecules have a predefined connectivity and exist in a predefined environment, includes generating a set of data representative of low-energy minimum conformations of the first molecule derived from connectivity of the first molecule, a potential energy function, and a conformational search method.

Abstract: A method and workstation for optimizing chemical processes based on combinatorial chemistry, automation technology, and computer-controlled design is disclosed. The workstation includes a synthesizer, an analyzer, a robot and computer in communication with the synthesizer and analyzer. The computer includes one or more programs for regulating reaction parameters such as temperature, pressure, concentration of reagents and employs statistical methods for optimizing multiple reaction parameters and for designing optimized experiments for further investigation.

Abstract: A distribution of the concentration of initial point-defects which generate in an ion implanting process is obtained with an ion implanting simulator. As a local function of the distribution, the distribution of the intensity of absorption of point-defects is obtained. A term of absorption of point-defects obtained from the distribution of the intensity is included in a diffusion equation. With the resultant diffusion equation, the diffusion simulation is performed. Thus the simulation using the diffusion equation may be extended to two or three dimension and cope with various ion implanting conditions.

Abstract: A diffusion simulating method which is capable of defining an impurity flux even if one impurity in one material region is changed into plural types of impurities in the other material region on a material interface. For simulating the diffusion of the impurities in a system which includes a first material region, a second material region and a interface disposed between the first material region and the second material region, impurity flux J(i.sub.A,j.sub.B) on the A/B interface is defined between optional impurity i.sub.A in material region A and optional impurity j.sub.B in material region B. Then, total fluxes J.sup.total (i.sub.A), J.sup.total (j.sub.B) of each type of impurity are determined and added to impurity diffusion equations, and simultaneous equations are set up by these diffusion equations and solved.

Abstract: A computer system whereby the user selects any combination of hazards and buildings which are of interest in modeling and simulating potential explosions. The software of the present invention automatically calculates distance and orientation of various building surfaces from the hazard, and accounts for side-on and reflected loads based on the orientation. The user is then provided with the pressure-impulse diagrams (P-i diagrams) where the software determines the damage expected for each building component. The results are displayed in a table which gives the applied blast load and damage level for each component on each building surface.

Abstract: Improved methods and apparatus for predicting physical properties of complex materials are provided. The physical properties are predicted from the electronic structure of the material. The electronic structure is determined using an iterative, computer-based technique. The iterative technique has been found to have a rate of convergence at least an order of magnitude faster than prior techniques for determining electronic structures. Among other applications, the invention is used to prepare materials having selected physical properties under selected conditions.

Abstract: A process control system determines optimal trajectories (input controls) using multiresolutional analysis of acquired data. In contrast to conventional control systems, the present control system does not use a predetermined mathematical model or algorithm to define the process in terms of a plurality of variables. Rather, the present system acquires system data and stores the data in a multiresolutional data structure. A knowledge base is created which can be searched at varying levels of resolution for determining optimal process trajectories. The continual addition of data to the data structure allows for continual top-down refinement of the determined trajectories and bottom-up improvement and updating of the system representation.