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Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins' properties via mutations causes stability effects as well. Accurate computational method to predict how mutations affect protein stability…
Investigation of protein self-assembly processes is important for the understanding of the growth processes of functional proteins as well as disease-causing amyloids. Inside cells, intrinsic molecular fluctuations are so high that they…
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…
Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…
Coarse-grained (CG) molecular dynamics enables simulations of atomic systems such as biomolecules at timescales inaccessible to all-atom (AA) methods, but existing CG neural potentials trained via force matching capture only the gradient of…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
While existing mathematical descriptions can accurately account for phenomena at microscopic scales (e.g. molecular dynamics), these are often high-dimensional, stochastic and their applicability over macroscopic time scales of physical…
Many physical and biological processes are stochastic in nature. Computational models and simulations of such processes are a mathematical and computational challenge. The basic stochastic simulation algorithm was published by D. Gillespie…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Recent developments in specialized computer hardware have greatly accelerated atomic level Molecular Dynamics (MD) simulations. A single GPU-attached cluster is capable of producing microsecond-length trajectories in reasonable amounts of…