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公开(公告)号：US20210217500A1
公开(公告)日：2021-07-15
申请号：US16757298
申请日：2018-10-18
申请人： Schrödinger, Inc.
发明人： Robert L. Abel , Lingle Wang , Sathesh Bhat , Sayan Mondal , Jeremy Robert Greenwood , Kyle Konze
摘要： A system, device, and method for predicting an active set of compounds that bind to a biomolecular target is disclosed. The system and device contain modules allowing for the prediction of an active set of compounds. A core identification module can identify the core of an initial lead compound. A core hopping module is used to identify potential lead compounds having different cores compared to the core of an initial lead compound. A scoring module can use computational techniques to calculate the relative binding free energy of each identified potential lead compound. An activity prediction module can use the relative binding free energy calculations to predict an active set of compounds that bind to the biomolecular target. Empirical analysis can be used to inform the accuracy and completeness of the predicted active set of compounds.
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公开(公告)号：US11043286B2
公开(公告)日：2021-06-22
申请号：US15889455
申请日：2018-02-06
摘要： A system and method for design of polymeric carrier for controlled release of molecules is provided. The method includes receiving a plurality of input parameters of a polymeric carrier, a solvent, and molecules to be released from the polymeric carrier from a database and performing Molecular Dynamics (MD) simulations to estimate thermodynamic and transport properties of the polymeric carrier, the solvent and the molecules to be released using on one or more input parameters from the plurality of input parameters. Based on the estimated thermodynamic and transport properties, swelling and degradation kinetics of the polymeric carrier and release kinetics of the molecules to be released from the polymeric carrier is estimated and generating a proposed formulation based on difference between estimated released kinetics and the targeted release kinetics of the molecules.
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公开(公告)号：US10978177B2
公开(公告)日：2021-04-13
申请号：US16482704
申请日：2018-05-11
发明人： Qun Zeng , Peiyu Zhang , Yingdi Jin , Jian Ma , Lipeng Lai , Shuhao Wen
摘要： A method for automatically and efficiently fitting repulsive potentials through DFTB includes: optimizing a molecule containing an atomic pair, and performing spacing scan on the atomic pair according to an acting interval of repulsive potentials; performing high-accuracy energy calculation on a scanning result; performing difference calculation on obtained energy to obtain second-order derivatives of force and energy; saving a structure, the energy, the second-order derivatives of force and energy into a database; acquiring energy without a repulsive potential as well as the second-order derivatives of force and energy to obtain target values of the repulsive potentials; transforming the separated target values of the repulsive potentials into splines; splicing multiple splines on a mean position between equilibrium position points to obtain new train data; constructing a train set by means of necessary samples and choosable samples; and fitting the repulsive potentials through singular value decomposition.
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24.发明申请公开(公告)号：US20210056159A1
公开(公告)日：2021-02-25
申请号：US16545099
申请日：2019-08-20
申请人： Anna Sorokina , Valeriy Anisimov
发明人： Anna Sorokina , Valeriy Anisimov
摘要： A system for calculating intermolecular forces over a communications network includes a computing device including a processor, a memory, an attached database, a user interface, a display and a programming module configured for reading initial data input by a user reading physical constants corresponding to a specific molecule, calculating a non-linear relationship between stresses and deformation of a comprehensive tension-compression of the specific molecule, an energy of sublimation of the specific molecule, parameters of the specific molecule, an interaction force between the specific molecule and an external surface of its body, a force acting on the specific molecule, wherein its displacement is relative to other molecules, and transmitting said resulting data. The system also includes a physical vapor deposition vacuum process system used to deposit a very thin film onto a substrate, which system adjusts a voltage according to data from the computing device.
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公开(公告)号：US20210035009A1
公开(公告)日：2021-02-04
申请号：US16976229
申请日：2018-08-10
申请人： Google LLC
发明人： Ryan Babbush , Jarrod Ryan McClean
摘要： Methods, systems and apparatus for simulating a physical system described by an electronic structure Hamiltonian expressed in an orthonormal basis. In one aspect, a method includes decomposing the electronic structure Hamiltonian into a sum of sub-Hamiltonians, wherein each sub-Hamiltonian in the sum of sub-Hamiltonians is expressed in one of multiple bases; simulating evolution of the physical system using the decomposed electronic structure Hamiltonian; and using the simulated evolution of the physical system using the decomposed electronic structure Hamiltonian to determine properties of the physical system.
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公开(公告)号：US20210035003A1
公开(公告)日：2021-02-04
申请号：US16526382
申请日：2019-07-30
摘要： Techniques regarding determining a three-dimensional structure of a heteropolymer are provided. For example, one or more embodiments described herein can comprise a system, which can comprise a memory that can store computer executable components. The system can also comprise a processor, operably coupled to the memory, and that can execute the computer executable components stored in the memory. The computer executable components can comprise a polymer folding component that can generate a course-grained model to determine a three-dimensional structure of a heteropolymer based on a first qubit registry that encodes a conformation of the heteropolymer on a lattice and a second qubit registry that encodes an interaction distance between monomers comprised within the heteropolymer.
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公开(公告)号：US20200342959A1
公开(公告)日：2020-10-29
申请号：US16397281
申请日：2019-04-29
发明人： Ivano Tavernelli , Panagiotis Barkoutsos , Stefan Woerner , Alessandro Curioni , Fotios Gkritsis
摘要： A method of designing a molecule for an environment of interest using a quantum computer includes providing a linear superposition of a plurality of molecular species, the plurality of molecular species being initially weighted by equal initial coefficients; determining a lowest-energy quantum state for the superposition of the plurality of molecular species in a vacuum environment and in the environment of interest using a quantum optimization process; calculating a difference in lowest energy states between the vacuum environment and the environment of interest for each molecular species to provide a cost of the superposition of the plurality of molecular species; performing a quantum optimization process to determine a minimum cost for the superposition of the plurality of molecular species and to determine updated coefficients weighting the plurality of molecular species; and identifying the molecule for the environment of interest based on a comparison of the updated coefficients.
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公开(公告)号：US20200342159A1
公开(公告)日：2020-10-29
申请号：US16465564
申请日：2018-05-04
发明人： Xuekun SHI , Fenglei CAO , Mingjun YANG , Guangxu SUN , Peiyu ZHANG , Jian MA , Lipeng LAI , Shuhao WEN
IPC分类号： G06F40/103 , G06F17/16 , G06F40/151 , G16C10/00
摘要： The invention belongs to the technical field force fields and particularly provides an atom type definition system and an atom type matching method. The atom type definition system includes an atom type visual UI interface, an atom type matching module, an atom type data management module and an atom type format transformation module. The atom type data management module includes an atom type definition data package. The system and method can describe various complicated atomic chemical environments, the description capability is improved, and the computation of a force field can be more accurate. According to the invention, convenient operation on an atom type can be realized, and addition, deletion, modification, inquiry as well as statistics of multiple dimensions are very visual and convenient.
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29.发明申请公开(公告)号：US20200294630A1
公开(公告)日：2020-09-17
申请号：US16817489
申请日：2020-03-12
发明人： Thomas F. Miller , Matthew G. Welborn , Lixue Cheng , Tamara Husch , Jialin Song , Nikola Kovachki , Dmitry Burov , Ying Shi Teh , Anima Anandkumar , Feizhi Ding , Sebastian Lee , Zhuoran Qiao , Ali Sahin Lale
摘要： Systems and methods for determining molecular structures based on molecular-orbital-based (MOB) features are described. MOB features can be utilized in combination with machine-learning methods to predict accurate properties, such as quantum mechanical energy, of molecular systems.
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公开(公告)号：US10691147B2
公开(公告)日：2020-06-23
申请号：US16040969
申请日：2018-07-20
摘要： In simulating a behavior of a particle system including a plurality of particles disposed in an analysis region, by using a molecular dynamics method, centroid velocities of the particles present in a local region including a particle of interest are converted on the basis of the number of particles present in the local region for each of the particles, and thus a conversion value of a centroid velocity of the local region is calculated. Temperature control of maintaining the temperature of the particle system to be a target temperature is performed by using a difference between a velocity of the particle and the conversion value of the centroid velocity of the local region including the particle as a velocity of the particle which is a basis for calculating the temperature of the particle system.
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