Related papers: Calculating free energy profiles in biomolecular s…
The hybrid particle-field molecular dynamics method is an efficient alternative to standard particle-based coarse grained approaches. In this work, we propose an automated protocol for optimisation of the effective parameters that define…
The Ribosome Flow Model (RFM) describes the unidirectional movement of interacting particles along a one-dimensional chain of sites. As a site becomes fuller, the effective entry rate into this site decreases. The RFM has been used to model…
We develop a framework for on-the-fly machine learned force field (MLFF) molecular dynamics (MD) simulations of warm dense matter (WDM). In particular, we employ an MLFF scheme based on the kernel method and Bayesian linear regression, with…
We present an implicit statistical model for the steric effect on the potential of mean force (PMF) of a molecule diffusing through a flexible nanochannel of varying size. The average cross sectional area profile of the channel and the…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
We show that the correlated stochastic fluctuation of the friction coefficient can give rise to long-range directional motion of a particle undergoing Brownian random walk in a constant periodic energy potential landscape. The occurrence of…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
The Targeted Free Energy Perturbation (TFEP) method aims to overcome the time-consuming and computer-intensive stratification process of standard methods for estimating the free energy difference between two states. To achieve this, TFEP…
Fastest arrival events, where the first among many diffusing particles reaches a target, are central in triggering signal initiation in molecular stochastic systems. Classical approaches to simulate such events rely on full trajectory…
Active Brownian particles (ABPs) function as self-driving agents that display non-equilibrium behavior through their pairwise interactions which lead to phase separation and vortex patterns in both soft matter and living systems. A…
In this paper we present a method for estimating unknown parameter that appear on a non-linear reaction-diffusion model of cancer invasion. This model considers that tumor-induced alteration of micro-enviromental pH provides a mechanism for…
According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the ligand apo ensemble and a rigid…
We extend the phase field crystal (PFC) framework to quantitative modeling of polycrystalline graphene. PFC modeling is a powerful multiscale method for finding the ground state configurations of large realistic samples that can be further…
Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or…
Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and the validation of reaction mechanism. For chemical reactions in condensed phase or enzymatic reactions, the computation of FE profile at ab…
We discuss an active phase field crystal (PFC) model that describes a mixture of active and passive particles. First, a microscopic derivation from dynamical density functional theory (DDFT) is presented that includes a systematic treatment…
The phase field crystal (PFC) method has emerged as a promising technique for modeling materials with atomistic resolution on mesoscopic time scales. The approach is numerically much more efficient than classical density functional theory…
We report a systematic and accurate approach for deriving the bulk free energy surface (FES), a function of temperature, polarization, and strain, from the first-principles density functional theory (DFT) of proper ferroelectrics. The core…
We present a real-space formulation and higher-order finite-difference implementation of periodic Orbital-free Density Functional Theory (OF-DFT). Specifically, utilizing a local reformulation of the electrostatic and kernel terms, we…
We investigate the equilibrium properties of bcc-liquid interfaces modeled with a continuum phase-field crystal (PFC) approach [K. R. Elder and M. Grant, Phys. Rev. E 70, 051605 (2004)]. A multiscale analysis of the PFC model is carried out…