Related papers: Atomistic simulations of electrolyte solutions and…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Several methods in nonadiabatic molecular dynamics are based on Madelung's hydrodynamic description of nuclear motion, while the electronic component is treated as a finite-dimensional quantum system. In this context, the quantum potential…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Ab initio modeling of electrochemical systems is becoming a key tool for understanding and predicting electrochemical behavior. Development and careful benchmarking of computational electrochemical methods are essential to ensure their…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
This study proposes and explores a linear hydrodynamic thermo-elasticity system within mixture models, comprising fluid and solid phases, with a focus on biological tissues, particularly tumor-related phenomena. Although tumor growth is not…
While fluids near a solid surface are at the core of applications in energy storage/conversion, electrochemistry/electrowetting and adsorption/catalysis, their nanoscale behavior remains only partially deciphered. Beyond conventional…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
Simulating quantum mechanics is known to be a difficult computational problem, especially when dealing with large systems. However, this difficulty may be overcome by using some controllable quantum system to study another less controllable…
The atomic-scale response of inhomogeneous fluids at interfaces and surrounding solute particles plays a critical role in governing chemical, electrochemical and biological processes at such interfaces. Classical molecular dynamics…
Dynamical heterogeneities in a colloidal fluid close to gelation are studied by means of computer simulations. A clear distinction between some fast particles and the rest, slow ones, is observed, yielding a picture of the gel composed by…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow…
An effective computer program for three dimensional relativistic hydrodynamical model has been developed. It implements a new approach to the early hot phase of relativistic heavy-ion collisions. The computer program simulates time-space…
We investigate active electrolytes within the mean-field level of description. The focus is on how the double-layer structure of passive, thermalized charges is affected by active dynamics of all constituting ions. One feature of active…
Using molecular dynamics simulations, we study supercritical fluids near the gas-liquid critical point under heat flow in two dimensions. We calculate the steady-state temperature and density profiles. The resultant thermal conductivity…
Modeling galaxy formation in a cosmological context presents one of the greatest challenges in astrophysics today, due to the vast range of scales and numerous physical processes involved. Here we review the current status of models that…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
A new computational method is presented to resolve hydrodynamic interactions acting on solid particles immersed in incompressible host fluids. In this method, boundaries between solid particles and host fluids are replaced with a continuous…
Electrolyte theories enable to describe the structural and dynamical properties of simple electrolytes in solution, such as sodium chloride in water. Using these theories for aqueous solutions of charged nanoparticles is a straightforward…