Related papers: Replica-Permutation Method with the Suwa-Todo Algo…
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature/energy range around the critical point. By combining the replica-exchange algorithm with cluster updates…
We propose an improved prediction method of the tertiary structures of $\alpha$-helical membrane proteins based on the replica-exchange method by taking into account helix deformations. Our method allows wide applications because…
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
Methods to efficiently determine the relative stability of polymorphs of organic crystals are highly desired in crystal structure predictions (CSPs). Current methodologies include use of static lattice phonons, quasi-harmonic approximation…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
Pulay's Residual Metric Minimization (RMM) method is one of the standard techniques for achieving self consistency in ab initio electronic structure calculations. We describe a reformulation of Pulay's RMM which guarantees reduction of the…
We investigate the theoretical foundations of the simulated tempering method and use our findings to design efficient algorithms. Employing a large deviation argument first used for replica exchange molecular dynamics [Plattner et al., J.…
We present a new non-adiabatic ring polymer molecular dynamics (NRPMD) method based on the spin mapping formalism, which we refer to as the spin-mapping NRPMD (SM-NRPMD) approach. We derive the path-integral partition function expression…
We present a novel Exchange Monte Carlo (EMC) method designed for application in continuous-space Path Integral Monte Carlo (PIMC) simulations at finite temperature. Traditional PIMC methods for bosonic systems suffer from long…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative…
A novel overlap histogramming method based on Dual-Topology Hamiltonian-Replica-Exchange simulation technique is presented to efficiently calculate relative free energy difference in rough energy landscape, in which multiple conformers…
The random phase approximation (RPA) has emerged as a prominent first-principles method in material science, particularly to study the adsorption and chemisorption of small molecules on surfaces. However, its widespread application is…
We present a novel approach for accelerating convolutions during inference for CPU-based architectures. The most common method of computation involves packing the image into the columns of a matrix (im2col) and performing general matrix…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
We perform molecular dynamics simulations of a well-known water model (the TIP5P pair potential) and a simple liquid model (a two-scale repulsive ramp potential) to compare the regions of anomalous behavior in their phase diagrams. We…
Detecting multiple structural breaks in high-dimensional data remains a challenge, particularly when changes occur in higher-order moments or within complex manifold structures. In this paper, we propose REAMP (Resonance-Enhanced Analysis…
We introduce a new algorithm which we call the {Rational Hybrid Monte Carlo} Algorithm (RHMC). This method uses a rational approximation to the fermionic kernel together with a noisy Kennedy-Kuti acceptance step to give an efficient…