Related papers: Statistical mechanical approximations to more effi…
The probability distribution describing the state of a Stochastic Reaction Network evolves according to the Chemical Master Equation (CME). It is common to estimated its solution using Monte Carlo methods such as the Stochastic Simulation…
The self-consisted harmonic approximation (SCHA) allows the computation of free energy of anharmonic crystals considering both quantum and thermal fluctuations. Recently, a stochastic implementation of the SCHA has been developed, tailored…
Most methods for estimating configurational entropy from molecular simulation data yield upper limits except for harmonic systems where they are exact. Problems arise at diffusive systems and the presence of conformational transitions.…
Molecular Density Functional Theory (MDFT) offers an efficient implicit- solvent method to estimate molecule solvation free-energies whereas conserving a fully molecular representation of the solvent. Even within a second order ap-…
Harmonic calculations based on density-functional theory are generally the method of choice for the description of phonon spectra of metals and insulators. The inclusion of anharmonic effects is, however, delicate as it relies on…
We propose a discrete transition-based reweighting analysis method (dTRAM) for analyzing configuration-space-discretized simulation trajectories produced at different thermodynamic states (temperatures, Hamiltonians, etc.) dTRAM provides…
In order to calculate thermal properties in automatic fashion, the Quasi-Harmonic Approximation (QHA) has been combined with the Automatic Phonon Library (APL) and implemented within the AFLOW framework for high-throughput computational…
Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…
Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as Common…
This paper considers master equations for Markovian kinetic schemes that possess the detailed balance property. Chemical kinetics, as a prime example, often yields large-scale, highly stiff equations. Based on chemical intuitions, Sumiya et…
Constant potential method molecular dynamics simulation (CPM MD) enables the accurate modelling of atomistic electrode charges when studying the electrode-electrolyte interface at the nanoscale. Here we extend the theoretical framework of…
The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande, J.…
It is well known that closed-form analytical solutions for AC power flow equations do not exist in general. This paper proposes a multi-dimensional holomorphic embedding method (MDHEM) to obtain an explicit approximate analytical AC…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
Calculating sublimation enthalpies of molecular crystal polymorphs is relevant to a wide range of technological applications. However, predicting these quantities at first-principles accuracy -- even with the aid of machine learning…
While the treatment of chemically relevant systems containing hundreds or even thousands of electrons remains beyond the reach of quantum devices, the development of quantum-classical hybrid algorithms to resolve electronic correlation…
We propose a single-step simplified lattice Boltzmann algorithm capable of performing magnetohydrodynamic (MHD) flow simulations in pipes for very small values of magnetic Reynolds numbers $R_m$. In some previous works, most lattice…
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…
Ring polymer molecular dynamics (RPMD) is used to directly simulate the dynamics of an excess electron in a supercritical fluid over a broad range of densities. The accuracy of the RPMD model is tested against numerically exact path…
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics…