Abstract: Methods, systems and computer readable media for quantifying and removing offset bias signals in a chemical array data set having one or more channels. In one embodiment, for each channel of data in the data set, a first set of features is selected from the data set. Surface intensities are calculated for features in the first selected set of features and surface intensifies of features not in the first selected set are calculated from the calculated surface intensities. A second set of features is selected, the intensity values of which are within a range of correspondingly located surface intensity values defined by upper and lower threshold intensities. Secondary surface intensifies are calculated for features in the second selected set of features and secondary surface intensities for all other locations on the array that were not locations corresponding to the features having secondary surface intensities calculated therefore, are calculated.

Abstract: Techniques for determining effects on a biological system include determining rate constants for a particular time interval starting at an initial time. Each rate constant indicates a rate of transition from one of four states to a different one of the four states for a component of a biological system in presence of an external factor. A temporal change in a probability that the component is in a particular state after the initial time is determined without numerical iteration over multiple time steps. This includes determining three relaxation time constants that describe exponential changes based on the rate constants. The effect of the external factor on the biological system is determined based on the temporal change in the probability that the component is in the particular state. The probability at an arbitrary time is determined based on the rate constants and initial probabilities.

Abstract: An apparatus for simulating special nuclear material is provided. The apparatus typically contains a small quantity of special nuclear material (SNM) in a configuration that simulates a much larger quantity of SNM. Generally the apparatus includes a spherical shell that is formed from an alloy containing a small quantity of highly enriched uranium. Also typically provided is a core of depleted uranium. A spacer, typically aluminum, may be used to separate the depleted uranium from the shell of uranium alloy. A cladding, typically made of titanium, is provided to seal the source. Methods are provided to simulate SNM for testing radiation monitoring portals. Typically the methods use at least one primary SNM spectral line and exclude at least one secondary SNM spectral line.

Abstract: Systems and Methods for determining flame blow-off conditions are disclosed. These methods provide efficient and reliable tools for determining the lean blow-off conditions for a variety of combustion system. By utilizing localized characteristics within a flame-holding region a user is enabled to assess the likelihood of flame blow-off with fine granularity within a combustor. The flame blow-out determination may be carried out with the aid of an output representation that provides a contour of likely blow-off cells within a combustor region.

Abstract: The present invention provides an apparatus including a compound database which has been produced by extracting fingerprints of compound related to plural atoms in a compound for each candidate compound, characterized by extracting the fingerprints of compound of binding compounds that are already known to bind to family proteins having 3-dimensional structure that is identical or similar to that of target protein, together with the 3-dimensional coordinates that have been converted into the coordinate system of the target protein, to produce a fingerprint set of binding compound, and for a candidate compound stored in the compound database, computing the 3-dimensional structure of the candidate compound with respect to the target protein, so that the interaction score based on the root-mean-square deviation of a unit of fingerprint of compound calculated on the basis of the 3-dimensional coordinates of the fingerprint set of binding compound is optimized.

Abstract: Methods and related systems are described for the detection of nuclear radiation. The system can include a scintillator material that intrinsically generates radiation and a photodetection system coupled to the scintillator material and adapted to generate electrical signals based on light emitted from the scintillator material. A processing system adapted and programmed to receive the electrical signals, to generate a count rate reference value based at least in part on electrical signals generated in response to the light emitted from the scintillator material due to the intrinsically generated radiation.

Abstract: A process for selecting shaped particles for use in a tube which is capable of being packed with shaped particles to form a packed bed in the tube. A desired value of one or more properties of the packed bed is defined. The dimensions of the shaped particles are calculated such that a packed bed in the tube of the shaped particles having the calculated dimensions meets or substantially meets the desired value(s), and shaped particles are selected in accordance with the calculated dimensions. The properties of the packed bed may be the volume fraction which is occupied by shaped particles, the packing density, and the resistivity for a gas flowing through the packed bed.

Abstract: This invention constructs a highly safe system for processing information for providing semantic information and/or information associated with the semantic information useful for each individual organism through effective utilization of differences in nucleotide sequence-related information among individual organisms. This system comprises steps of: (a) obtaining positional information representing a position in a nucleotide sequence in accordance with a request for an object and/or service; and (b) evaluating adequacy of transmission of nucleotide sequence-related information corresponding to the positional information obtained in step (a), based on the flag information associated with the positional information for evaluating adequacy of transmission of nucleotide sequence-related information associated with the positional information representing a position in a nucleotide sequence.

Abstract: An apparatus and a method of chemical analysis entail acquiring a chromatogram, median filtering the chromatogram to produce a model baseline, smoothing the model baseline to reduce noise, and subtracting the smoothed model baseline from the acquired chromatogram to produce a modified chromatogram having a substantially flat baseline.

Abstract: A method includes assessing corrosion in a refinery operation having a piping network. Assessing can include identifying in a petroleum sample a presence and an amount of a species determined to be potentially corrosive to corrodible equipment in a refinery. A corrosion risk presented by the presence, the amount, and the boiling point of the species is determined. And, the corrosion risk is evaluated in view of piping network information. A system for implementing the method is provided, also.

Abstract: A simulation system includes at least one processor configured to execute a computer program product, stored upon a storage medium. The computer program product includes a spreadsheet application, a process simulation application, and an integration tool (e.g., eSim), where the spreadsheet application and the process simulation application are discrete, stand alone products. The process simulation application can simulate chemical processes using at least one flowsheet, which models a general flow of chemical plant processes and equipment. The integration tool can map process simulation application objects and properties to spreadsheet application objects, can convey information between mapped objects, can perform case management functions, and can perform orchestrated calculation functions.

Abstract: In the present invention the NonRandom Two-Liquid segment activity coefficient model system of the parent application is extended for computation of ionic activity coefficients and solubilities of electrolytes, organic and inorganic, in common solvents and solvent mixtures. The invention method and system may be applied to the chemical and/or pharmaceutical design process. In addition to the three types of molecular parameters defined for organic nonelectrolytes, i.e., hydrophobicity X, polarity Y, and hydrophilicity Z, an electrolyte parameter, E, is introduced to characterize both local and long-range ion-ion and ion-molecule interactions attributed to ionized segments of electrolytes. Successful representations of mean ionic activity coefficients and solubilities of electrolytes, inorganic and organic, in aqueous and nonaqueous solvents are presented.

Abstract: The Lennard-Jones parameters for metals, such as fcc metals, have been developed which are suitable for the simulation of the metals, alloys, and interfaces with water, organic, inorganic, and biological molecules. The models are compatible with common materials-oriented and biomolecular force fields, and can thus be integrated in commercial simulation packages to extend their applicability to any metal-related systems.

Abstract: A particle size distribution creating method includes a particle size range determining step, an integrating step of integrating the frequency of appearance of particles within the particle size range determined in the particle size range determining step, a division point determining step of determining particle sizes that provide division points, using the integral of the frequency of appearance obtained in the integrating step, and a typical point determining step of determining the minimum particle size, maximum particle size and the particle sizes of the division points as typical points.

Abstract: A method of comparing two conformers in which an overlay score is obtained, comprises providing a set of field points representing field extrema of a first molecule, wherein each field point has a position and a field size value; determining at the position of each of the field points of the first molecule the field of a second molecule to obtain a set of field sample values; and combining the field sample values with the field size values to obtain a score indicative of the field similarity of the first molecule to the second molecule. The method overcomes a limitation of conventional pseudo-Coulombic scoring in which a low score is achieved when extrema of large extent overlap but have their minimum points widely separated. The method can be applied to molecular mechanics modeling using atom centered charges (ACCs) and extended electron distributions (XEDs) as well as to quantum mechanics models.

Abstract: Source data is analyzed and visualized for a user. As the user adjusts graphical query devices, the displayed data is filtered and the visualization is updated accordingly. The invention is particularly useful where the data relates to chemical compounds in that a SAR table is preferably generated, presented in the visualization, and updated according to the query device settings. The displayed SAR table entries may also be clustered as a function of similarity with respect to a chosen property, such as molecular weight or some topological characteristic. A hierarchy of similarity may then be indicated in the SAR table using, for example, a dendrogram.

Abstract: A method of simulating interactive communication between a user and a human subject. The method comprises: assigning at least one phrase to a stored content sequence, wherein the content sequence comprises a content clip of the subject; parsing the at least one phrase to produce at least one phonetic clone; associating the at least one phonetic clone with the stored content sequence; receiving an utterance from the user; matching the utterance to the at least one phonetic clone; and displaying the stored content sequence associated with the at least one phonetic clone.

Abstract: Subterranean formation treatment methods incorporating a rheology model which enables prediction of fluid rheology properties during a treatment operation, where the foundation of the model is a description of the reaction chemistry which describes how the number of crosslinks and broken polymer linkages develops in time under the influence of crosslinkers, breakers, and/or thermally induced effects and pressure effects. In one aspect, when used as a tool for simulating the fluid viscosity, the model can help optimizing the fluid design and optional breaker schedule for a hydraulic fracturing treatment.

Abstract: A method and a system for evaluating results of differentiating genotype signals and noise signals when a DNA fragment containing a gene to be analyzed is amplified by PCR and detected by electrophoresis are provided. An outlier of genotyping results is detected based on the fact that, when using the same marker, the height ratio of a stutter peak to a true peak and the height ratio of a +A peak to a true peak are reproducible, and that a constant size value is obtained with the use of the same allele of the same marker. In addition, a waveform obtained in past processes with the use of the same marker or the same allele is obtained utilizing a database by focusing on reproducibility. Also, a database is extended so as to obtain improved evaluation ability in a manner such that appropriate waveform data from which an outlier is not obtained is additionally registered in a database.

Abstract: A system for modeling chemical reactions using analog or hybrid-analog-digital electronic circuits. The system exploits similarities between the kinetic rates of chemical reaction and the rates governing current flow in electronic devices such as bipolar junction transistors (BJTs) and metal oxide semiconductor field effect transistors (MOSFETs) operating at subthreshold conditions. These devices, which accurately model the stochastics of chemical processes, can networked into large array to model chemical reaction networks, including biochemical reactions and genetic processes such as activation, induction, transcription, and translation.

Abstract: The instant invention is a method for improving the prediction of polymer properties and a system having improved polymer property prediction capabilities.

Abstract: A system for modeling, simulating and analyzing chemical and biochemical reactions includes a modeling environment for constructing a model of a chemical or biochemical system comprising a plurality of chemical reactions. Each chemical reaction has a probability distribution associated therewith based on the kinetics of the particular chemical reaction. The probability distribution may be set by a user, determined automatically, or experimentally determined. The system also includes a simulation engine accepting as input said constructed model of the chemical or biochemical system and generating as output an expected result. The simulation engine calculates a reaction time for each chemical reaction based on the probability distribution associated with the particular chemical reaction. An analysis environment communicates with the simulation engine and displays the expected result.

Abstract: A computer system and a method for calculating an ADME properties of a substance on the basis of molecular properties of the substance by using a biophysical model, into which the molecular properties are entered as input quantities. The biophysical model establishes a relationship between the molecular properties and the ADME properties.

Abstract: A method for predicting petroleum production is provided. An exemplary embodiment of the method comprises computing a first approximation of an amount of generated petroleum that is retained with a complex organic product using a Threshold and a Maximum Retention value. The exemplary method also comprises revising the first approximation by approximating a process of chemical fractionation using at least one partition factor to create a revised approximation and predicting petroleum production based on the revised approximation.

Abstract: The present invention relates in general to anti-cancer drug design. More specifically, the invention provides methods of mapping and screening for anti-cancer agents using pharmacophore models. The invention demonstrates that, conformational sampling of a small lead molecule, followed by representative pharmacophore model development, is an efficient approach for rational design of novel anticancer agents with similar or better potency than the original lead but with different physicochemical properties.

Abstract: Methods, apparatus and computer program products are provided for identifying a component of culture medium based on the parameters (e.g., physical, chemical, biological and/or topological characteristics) of compounds from within a compound library. In preferred embodiments, the compound library is a peptide library. Also provided are methods of selecting a compound library from a larger compound space based on whole molecule (i.e., global) parameters of the compounds. Preferably, this method is practiced in conjunction with a method of identifying a component of a culture medium. Further provided are methods of predicting a biological activity of a peptide based on at least one whole molecule parameter of the peptide. This method finds use in methods of drug discovery, identifying components of culture medium, and identifying and/or designing peptides with particular pharmacological or therapeutic activities.

Abstract: Methods, systems, and computer program products for generating theoretical mass spectral fragmentation patterns of a chemical structure is provided. The method includes obtaining a description of a chemical structure and generating, from the description, a list of chemical structure information. A binary tree data structure is used to organize the list of chemical structure information. The binary tree data structure may be fragmented by determining, based on a set of predetermined rules, a fragmentation point between two nodes in the binary tree data structure thereby dividing the binary tree data structure into a fragment and a complement. The molecular formula and molecular weight of each fragment is determined. The binary tree data structure is traversed and appropriate fragmentation rules are applied to produce a plurality of theoretical molecular fragments.

Abstract: The invention provides methods of dynamically simulating molecular interactions between a target molecule and a plurality of ligand molecules. The ligand molecules may be presented in the model as a homogeneous set of identical ligands or as a heterogeneous set of different ligands, such as, for example, a set of structural variants of a ligand molecule. Typically, the ligand molecule will be a small organic compound, such as a drug or other small molecule, and the ligand will be a protein or a protein domain, a nucleic acid (i.e., DNA, RNA), or a biomolecular complex of proteins and/or nucleic acid molecules. Unlike all known molecular dynamics simulation methods, the invention provides ligand molecules to the simulation's interaction environment(s) in excess relative to the target molecule.

Abstract: A design support apparatus supports wiring design for bond wires that connect a semiconductor chip and an interposer. The design support apparatus includes a creating unit that creates simulated design data simulating occurrence of fluctuation in an arrangement position of a semiconductor chip on an interposer and occurrence of fluctuation in bond wire connection terminal positions of the interposer, and an analyzing unit that analyzes, based on the simulated design data, deficiencies in manufacturing of semiconductor devices due to the fluctuation in the arrangement position of the semiconductor chip on the interposer and the fluctuation in the bond wire connection terminal positions of the interposer.

Abstract: A method and system of physically solving the charge, mass, and current density functions of organic molecules using Maxwell's equations and computing and rendering the physical nature of the chemical bond using the solutions. The solutions can be used to solve the dipole moments in molecules or induced dipole moments between species that in turn can be used to solve condensed matter parameters and reaction kinetics. The results can be displayed on visual or graphical media. The display can be static or dynamic such that electron motion and specie's vibrational, rotational, and translational motion can be displayed in an embodiment. The displayed information is useful to anticipate reactivity and physical properties. The insight into the nature of the chemical bond of at least one species can permit the solution and display of those of other species to provide utility to anticipate their reactivity and physical properties.

Abstract: Methods of identifying potential ligands for macromolecular targets are disclosed herein. The methods comprise providing models of three dimensional structural information for ligands or a ligand:macromolecule complex, mapping spatial relationships between the models, and identifying one or more pairs of matching bonds. Databases and apparatuses are also provided.

Abstract: Included are methods for modeling at least one physical property of a mixture of at least two chemical species. One or more chemical species of the mixture are approximated or represented by at least one conceptual segment. The conceptual segments are then used to compute at least one physical property of the mixture. An analysis of the computed physical properties forms a model of at least one physical property of the mixture. Also included are computer program products and computer systems for implementing the modeling methods.

Abstract: A method for characterizing the three-dimensional surface structure of molecules, particularly proteins and protein complexes, employing mass spectrometric analysis, an electrospray ionization (ES) source, a novel data interpretation process that utilizes comparisons of particular binding constants (KB) and heats of formation (?Hf), and computational feedback modeling.

Abstract: The present invention takes place of solid oxide fuel cell (SOFC) in tests. Some tests among them are done to find ways to recycle exhausts of the SOFC. And, some other tests among them are done to evaluate benefits of re-burning the exhausts. All tests save cost and time.

Abstract: A method of associating a phenotype with one or more candidate chromosomal regions in a genome of an organism includes the step of deriving a phenotypic data structure that represents differences in phenotypes between different strains of the organism. Further, a genotypic data structure is established. The genotypic data structure corresponds to a locus selected from a plurality of loci in the genome of the organism. The genotypic data structure represents variations of at least one component of the locus between different strains of the organism. The phenotypic data structure is compared to the genotypic data structure to form a correlation value. The process of establishing a genotypic data structure and comparing it to the phenotypic data structure is repeated for each locus in the plurality of loci, thereby identifying one or more genotypic data structures that form a high correlation value relative to all other compared genotypic data structures.

Abstract: A method of optimising apparatus utilised within a processing system includes defining a system model indicative of a predetermined range of apparatus options within a processing system, constraints indicative of feasible interconnections between each apparatus, and parameters indicative of performance criteria associated with each apparatus. The system model is analysed with respect to predetermined criteria to determine a preferred arrangement of apparatus within the processing system. A parameter relating to at least one apparatus is indicative of the availability and/or the reliability of the apparatus expressed as a function of time.

Abstract: A method, system and apparatus for the monitoring, diagnosis and evaluation of the state of a dynamic drug display system is disclosed. This invention provides for the rapid cognitive grasp of the overall state of drug combination effects with respect to a dynamic system. The system provides for displayed objects, which change in real-time to show the changes of the functions of the system. In particular, this invention is directed to the processing and display of drug data for the use of doctors in the process of monitoring or administering drugs to patients.

Abstract: Various implementations of the invention provide methods and apparatus for calibrating models of an optical lithographic process. In various implementations, a complete model of an optical lithographic process may be formed by combining different physical ranges and components describing the optical lithographic process. With various implementations of the invention, an optical lithographic process model may be calibrated by generating and applying a set of test patterns to the optical lithographic process, identifying test patterns and associated measured results that correspond to the discrete components of the optical lithographic model, calibrating the discrete components of the optical lithographic model based on the identified test patterns and measured results, and combining the calibrated components into a complete model. In some implementations of the invention, the discrete components of the optical lithographic model represent different physical effects of the optical lithographic process.

Abstract: A system and method for providing hazardous incident decision support and training includes a user interface component that receives situation definition data, a hazard assessment component and a decision aid. Decision support advice and decision prompts are presented by the system in response to the situation definition interface and hazard assessment. The hazard assessment and expert advice of the system are updated with elapsed time. In another embodiment of the present invention, graphical user interfaces are provided to display a set of menu entries wherein individual menu entries represent a hazardous incident characteristic. The user may select one or more of the menu entries to create a situation definition. Such definitions may be used, for example, to identify a hazardous agent based upon user-inputted signs and symptoms data.

Abstract: The present disclosure provides, among other things, a method for generating a simulated aggregate based on one or more input parameters. A test aggregate is constructed and rotated. Stable orientations of the aggregate on a surface are determined. In specific examples, two-dimensional properties are calculated for stable orientations of the test aggregate and stored or displayed. In particular implementations of the method, the test aggregate is constructed through successive monomer addition.

Abstract: The virtual screening of a database of molecules is based on explicit three-dimensional molecular superpositions. The torsional flexibility of the database molecules is taken fully into account, and an arbitrary number of conformation-dependent molecular features may be considered. A fragmentation-reassembly approach is utilized, which allows for an efficient sampling of the conformational space. A fast clique-based pattern-matching algorithm generates alignments of pairs of adjacent molecular fragments on the (rigid) query molecule that are subsequently reassembled to complete database molecules. Using conventional molecular features (hydrogen bond donors and acceptors, charges, and hydrophobic groups), it is possible to rapidly produce accurate alignments of medium-sized drug-like molecules. Examples with a test database containing a diverse set of 1780 drug-like molecules (including all conformers) show that average query processing times of the order of 0.

Abstract: Included are methods for modeling at least one physical property of a mixture of at least two chemical species. One or more chemical species of the mixture are approximated or represented by at least one conceptual segment. The conceptual segments are then used to compute at least one physical property of the mixture. An analysis of the computed physical properties forms a model of at least one physical property of the mixture. Also included are computer program products and computer systems for implementing the modeling methods.

Abstract: Embodiments of the present invention provide a method, system and computer program product for computer visualization of drugs for drug interaction information retrieval. In an embodiment of the invention, a method for computer visualization of drugs for drug interaction information retrieval can be provided. The method can include acquiring imagery of multiple different substances and detecting identifying content in each acquired image to determine an identity of each substance corresponding to each acquired image. The method also can include retrieving drug interaction data for each substance using the determined identity and correlating the drug interaction data for at least one of the substances with at least one other of the substances. Finally, the method can include displaying the correlated drug interaction data.

Abstract: A method for designing a metal ion for use in a molecular dynamics simulation can include the steps of building a metal ion molecule having a center atom and a dummy atom, assigning a van der Waals radius to the center atom, and assigning a charge to the dummy atom. A metal ion molecule may have the center atom covalently linked to one or more dummy atoms resulting in the metal ion molecule having a polyhedron geometry. New force field parameters may be used in methods for designing metal ions for use in molecular dynamics simulations.

Abstract: Disclosed is a method of searching for a ligand capable of binding to a target biomacromolecule, comprising the step of: (1) subjecting a number of low-molecular compounds to docking simulation, based on three-dimensional structural data concerning the low-molecular compounds and three-dimensional structural data concerning a ligand-binding region of the target biomacromolecule, to calculate a docking score for each of the low-molecular compounds, and simultaneously acquire three-dimensional positional data which enable each of the low-molecular compounds to stably bind within the ligand-binding region, (2) acquiring, from among the three-dimensional positional data obtained, all three-dimensional positional data concerning one or more molecular fragments, with respect to each of low-molecular compounds belonging to a higher group based on docking scores, (3) counting the three-dimensional positional data concerning each molecular fragment obtained, for each of the molecular fragments, (4) selecting the type

Abstract: Computer-implemented method of determining a composition of hydrocarbons present in a sedimentary basin as a result of biodegradation. The displacement rates of the hydrocarbons and the displacement rates of the water present in the porous medium are estimated, from a genesis time in a mother rock to a possible accumulation in a reservoir rock. The biodegradation in the entire porous medium is then modelled as a function of time, from the genesis in the mother rock, considering that the hydrocarbon composition varies proportionally to the displacement rates.

Abstract: A combination of a styrene reduction agent and a catalyst that effectively and economically reduces styrene emissions in Cured-In-Place Pipe, closed molding processes. The reduction agent generally comprises a calibrated mixture of salts including sodium chloride plus three persulfate salts: ammonium (APS), potassium (KPS), and sodium (NPS). These ingredients are combined in powder form and are compressed into soluble capsules containing calibrated amounts of the mixture. The capsule(s) may be prescribed through the use of software. The catalyst is hydrogen peroxide (H2O2). A calibrated amount of the styrene reduction agent capsule(s) are added to the cure water prior to starting the boiler equipment for the Cured-In-Place Pipe process, and this is followed by a calibrated amount of the H2O2 catalyst in order to reduce the residual monomer content in either process or waste streams.

Abstract: Subterranean treatment formation using a model which takes into account the pore level physics by coupling the local pore scale phenomena to the macroscopic variables (Darcy velocity, pressure and reactant cup-mixing concentration) through the structure-property relationships (permeability-porosity, average pore size-porosity and interfacial area-porosity) and the dependence of the fluid-solid mass transfer coefficient and fluid phase dispersion coefficient on the evolving pore scale variables (average pore size, local Reynolds and Schmidt numbers).

Abstract: A devolatilization performance prediction apparatus for a solution devolatilization process using a twin-screw extruder including a flow state computation means 101 for computationally determining information relating to the flow state of solution existing in a devolatilization region 600, or a target region, of a devolatilization process on a screw 200 conveying the solution of nonvolatile mass containing volatile mass according to the flow state of the solution 700 existing on the channel surface at the upstream side in the conveying direction of the screw channel, the solution 800 existing in the gap between the screw 200 and a barrel 100 and the solution 900 existing on the channel surface at the downstream side in the conveying direction of the screw channel, and a devolatilization performance prediction means 102 for predicting the devolatilization performance in the devolatilization process according to the information relating to the flow state computationally determined according to the flow state of

Abstract: An automated tuning method of a large-scale multivariable model predictive controller for multiple array papermaking machine cross-directional (CD) processes can significantly improve the performance of the controller over traditional controllers. Paper machine CD processes are large-scale spatially-distributed dynamical systems. Due to these systems' (almost) spatially invariant nature, the closed-loop transfer functions are approximated by transfer matrices with rectangular circulant matrix blocks, whose input and output singular vectors are the Fourier components of dimension equivalent to either number of actuators or number of measurements. This approximation enables the model predictive controller for these systems to be tuned by a numerical search over optimization weights in order to shape the closed-loop transfer functions in the two-dimensional frequency domain for performance and robustness.