Related papers: Multicanonical molecular dynamics by variable-temp…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
We conduct molecular dynamics computer simulations of a system of Lennard-Jones particles, polydisperse in both size and mass, at a fixed density and temperature. We test for and quantify systematic changes in dynamical properties that…
This paper presents the first thermodynamic assessment of binary and pseudo-binary phase diagrams in the Ba--La--S and Ga--La--S systems by means of the CALPHAD method. Experimental phase diagram equilibrium data and thermodynamic…
Multiparticle collision dynamics (MPC), a particle-based mesoscale simulation technique for com- plex fluid, is widely employed in non-equilibrium simulations of soft matter systems. To maintain a defined thermodynamic state, thermalization…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Recently we proposed a new constant-pressure molecular dynamics method for finite systems. In this paper, we discuss the current understanding of this method and its technique details. We also review the recent theoretical advances of…
A thermodynamics for systems at a stationary states is formulated. It is based upon the assumption of the existence of local equilibrium in phase space which enables one to interpret the probability density ans its conjugated nonequilibrium…
Multi-particle collision dynamics is an appealing numerical technique aiming at simulating fluids at the mesoscopic scale. It considers molecular details in a coarse-grained fashion and reproduces hydrodynamic phenomena. Here, the…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Thermodynamics with internal variables is a common approach in continuum mechanics to model inelastic (i.e., non-equilibrium) material behavior. While this approach is computationally and theoretically attractive, it currently lacks a…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
We derive a new formulation to calculate the excess chemical potential of a fraction of $N_1$ particles interacting with $N_2$ particles of a different species. The excess chemical potential is calculated numerically from first principles…
Reliable dynamical properties from molecular dynamics simulations require careful control of thermostatting artifacts. We systematically assess how NVE, deterministic thermostats, velocity-rescale dynamics, and stochastic Langevin-type…
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…
Equilibrium statistical mechanics is intended to link the microscopic dynamics of particles to the thermodynamic laws for macroscopic quantities. However, the modern statistical theory is faced with significant difficulties, as applied to…
Sampling the phase space of molecular systems -- and, more generally, of complex systems effectively modeled by stochastic differential equations -- is a crucial modeling step in many fields, from protein folding to materials discovery.…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
Microcanonical statistics can be well applied to non-extensive systems like nuclei, atomic clusters and systems at phase transitions of first order with inhomogeneous configurations like phase separation. No thermodynamic limit has to be…
Many scientific and engineering systems exhibit intrinsically multimodal behavior arising from latent regime switching and non-unique physical mechanisms. In such settings, learning the full conditional distribution of admissible outcomes…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…