Related papers: Calculating free energy profiles in biomolecular s…

We present a new method that combines alchemical transformation with physical pathway to accurately and efficiently compute the absolute binding free energy of receptor-ligand complex. Currently, the double decoupling method (DDM) and the…

This paper deals with state estimation of stochastic models with linear state dynamics, continuous or discrete in time. The emphasis is laid on a numerical solution to the state prediction by the time-update step of the grid-point-based…

We have studied the dynamics of chloride and potassium ions in the interior of the OmpF porin under the influence of an external electric field. From the results of extensive all-atom molecular dynamics simulations of the system we computed…

In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…

Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small…

We present and discuss the development of an unconditionally stable algorithm used to solve the evolution equations of the Phase Field Crystal (PFC) model. This algorithm allows for an arbitrarily large algorithmic time step. As the basis…

Hybrid particle-field molecular dynamics combines standard molecular potentials with density-field models into a computationally efficient methodology that is well-adapted for the study of mesoscale soft matter systems. Here, we introduce a…

Using molecular simulation, we determine Ginzburg-Landau free energy functions for molecular fluids. To this aim, we extend the Expanded Wang-Landau method to calculate the partition functions, number distributions and Landau free energies…

There are several approaches to describe flows with particles e.g. Lattice-Gas Automata (LGA), Lattice-Boltzmann method (LBM) or smoothed particle hydrodynamics (SPH). These approaches do not use fixed grids on which the Navier-Stokes…

Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Generalized Gradient Approximation (GGA). AIMD simulations…

We present an ``equation-free'' multiscale approach to the simulation of unsteady diffusion in a random medium. The diffusivity of the medium is modeled as a random field with short correlation length, and the governing equations are cast…

We consider a molecular machine described as a Brownian particle diffusing in a tilted periodic potential. We evaluate the absorbed and released power of the machine as a function of the applied molecular and chemical forces, by using the…

To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…

This paper introduces the Asymptotic-Preserving Random Feature Method (APRFM) for the efficient resolution of multiscale radiative transfer equations. The APRFM effectively addresses the challenges posed by stiffness and multiscale…

Predicting the adsorption affinity of a small molecule to a target surface is of importance to a range of fields, from catalysis to drug delivery and human safety, but a complex task to perform computationally when taking into account the…

A method combining denoising diffusion probabilistic models (DDPMs) with the string method is presented to generate minimum free energy paths between metastable states in molecular systems. It has been demonstrated in recent work that DDPMs…

Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…

A variety of simulation methodologies have been used for modeling reaction-diffusion dynamics -- including approaches based on Differential Equations (DE), the Stochastic Simulation Algorithm (SSA), Brownian Dynamics (BD), Green's Function…

The dynamics of phase field crystal (PFC) modeling is derived from dynamical density functional theory (DDFT), for both single-component and binary systems. The derivation is based on a truncation up to the three-point direct correlation…

Parametric model checking (PMC) computes algebraic formulae that express key non-functional properties of a system (reliability, performance, etc.) as rational functions of the system and environment parameters. In software engineering, PMC…