Convolutional neural networks are constructed and validated for the crystal structure classification of simple binary salts such as the alkali halides. The inputs of the neural network classifiers are the local bond orientational order parameters of ...
An unsolved challenge in developing molecular representation is determining an optimal method to characterize the molecular structure. Comprehension of intramolecular interactions is paramount toward achieving this goal. In this study, ComABAN, a new...
Equilibrium structures determine material properties and biochemical functions. We here propose to machine learn phase space averages, conventionally obtained by ab initio or force-field-based molecular dynamics (MD) or Monte Carlo (MC) simulations. ...
Fast evolution of modern society stimulates intense development of new materials with novel functionalities in energy and environmental applications. Due to rapid progress of computer science, computational design of materials with target properties ...
A neural network-assisted molecular dynamics method is developed to reduce the computational cost of open boundary simulations. Particle influxes and neural network-derived forces are applied at the boundaries of an open domain consisting of explicit...
Finding a low dimensional representation of data from long-timescale trajectories of biomolecular processes, such as protein folding or ligand-receptor binding, is of fundamental importance, and kinetic models, such as Markov modeling, have proven us...
Drug resistance is a major threat to the global health and a significant concern throughout the clinical treatment of diseases and drug development. The mutation in proteins that is related to drug binding is a common cause for adaptive drug resistan...
Accurate simulation of protein folding is a unique challenge in understanding the physical process of protein folding, with important implications for protein design and drug discovery. Molecular dynamics simulation strongly requires advanced force f...
Hydrophobic interactions drive numerous biological and synthetic processes. The materials used in these processes often possess chemically heterogeneous surfaces that are characterized by diverse chemical groups positioned in close proximity at the n...
Proceedings of the National Academy of Sciences of the United States of America
Jan 4, 2022
RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-at...
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