Related papers: Self Consistent Path Sampling: Making Accurate All…
We develop a formulation for molecular dynamics, Langevin, and hybrid Monte Carlo algorithms in the recently proposed generalized ensemble that is based on a physically motivated realisation of Tsallis weights. The effectiveness of the…
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…
We report a single-copy tempering method for simulating large complex systems. In a generalized ensemble, the method uses runtime estimate of the thermal average energy computed from a novel integral identity to guide a continuous…
We present three algorithms for calculating rate constants and sampling transition paths for rare events in simulations with stochastic dynamics. The methods do not require a priori knowledge of the phase space density and are suitable for…
When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Recently, fictitious identical particles have provided a promising way to overcome the fermion sign problem and have been used in path integral Monte Carlo (PIMC) to accurately simulate warm dense matter with up to 1000 electrons (T.…
We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics…
The precise description of quantum nuclear fluctuations in atomistic modelling is possible by employing path integral techniques, which involve a considerable computational overhead due to the need of simulating multiple replicas of the…
This work presents the implementation of a fragment-based, quantum-centric supercomputing workflow for computing molecular electronic structure using quantum hardware. The workflow is applied to predict the relative energies of two…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of…
Path reweighting is a principally exact method to estimate dynamic properties from biased simulations - provided that the path probability ratio matches the stochastic integrator used in the simulation. Previously reported path probability…
We address the problem of sampling double-ended diffusive paths. The ensemble of paths is expressed using a symmetric version of the Onsager-Machlup formula, which only requires evaluation of the force field and which, upon direct time…
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
The biological properties of proteins are uniquely determined by their structure and dynamics. A protein in solution populates a structural ensemble of metastable configurations around the global fold. From overall rotation to local…
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a…
A novel algorithm is presented for the estimation of collision probabilities between dynamic objects with uncertain trajectories, where the trajectories are given as a sequence of poses with Gaussian distributions. We propose an adaptive…