Related papers: Calculating free energy profiles in biomolecular s…
A promising method for calculating free energy differences Delta F is to generate non-equilibrium data via ``fast-growth'' simulations or experiments -- and then use Jarzynski's equality. However, a difficulty with using Jarzynski's…
Free energies are fundamental quantities governing phase behavior and thermodynamic stability in polymer systems, yet their accurate computation often requires extensive simulations and post-processing techniques such as the Bennett…
A self-consistent and universal description of friction and diffusion for Brownian particles (grains) in different systems, as a gas with Boltzmann collisions, dusty plasma with ion absorption by grains, and for active particles (e.g.,…
Reaction-diffusion PDEs and particle-based stochastic reaction-diffusion (PBSRD) models are commonly-used approaches for modeling the spatial dynamics of chemical and biological systems. Standard reaction-diffusion PDE models ignore the…
The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We…
An accurate modelling of bio-electrochemical processes that govern Microbial Fuel Cells (MFCs) and mapping their behaviour according to several parameters will enhance the development of MFC technology and enable their successful…
Comprehensive investigations of crystalline systems often require methods bridging atomistic and continuum scales. In this context, coarse-grained mesoscale approaches are of particular interest as they allow the examination of large…
The stochastic trajectories of molecules in living cells, as well as the dynamics in many other complex systems, often exhibit memory in their path over long periods of time. In addition, these systems can show dynamic heterogeneities due…
We investigate the impact of intermittent energy injections on a Brownian particle, modeled as stochastic renewals of its kinetic energy to a fixed value. Between renewals, the particle follows standard underdamped Langevin dynamics. For…
We introduce an efficient and robust method to compute alchemical free energy differences, resulting from the application of multiple walker Adaptive Biasing Force (ABF) in conjunction with strongly damped Langevin $\lambda$-dynamics.…
We present an efficient parametric model checking (PMC) technique for the analysis of software performability, i.e., of the performance and dependability properties of software systems. The new PMC technique works by automatically…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
The Fast Multipole Method (FMM) offers an acceleration for pairwise interaction calculation, known as $N$-body problems, from $\mathcal{O}(N^2)$ to $\mathcal{O}(N)$ with $N$ particles. This has brought dramatic increase in the capability of…
We propose a predictive Density Functional Theory (DFT) for the calculation of solvation free energies. Our approach is based on a Helmholtz free-energy functional that is consistent with the perturbed-chain SAFT (PC-SAFT) equation of…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
We introduce the Fast Free Memory method (FFM), a new fast method for the numerical evaluation of convolution products. Inheriting from the Fast Multipole Method, the FFM is a descent-only and kernel-independent algorithm. We give the…
Time-resolved photoemission with ultrafast pump and probe pulses is an emerging technique with wide application potential. Real-time recording of non-equilibrium electronic processes, transient states in chemical reactions or the interplay…
We present a new code, RCF("Radiative-Collisional code based on FAC"), which is used to simulate steady-state plasmas under non local thermodynamic equilibrium condition, especially photoinization dominated plasmas. RCF takes almost all of…