Related papers: Parametrisation in electrostatic DPD Dynamics and …
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
We propose two different macroscopic dynamics to describe the decay of metastable phases in many-particle systems with local interactions. These dynamics depend on the macroscopic order parameter $m$ through the restricted free energy…
Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic…
In biological and synthetic materials, many important processes involve charges that are present in a medium with spatially varying dielectric permittivity. To accurately understand the role of electrostatic interactions in such systems, it…
We review and compare numerical methods that simultaneously control temperature while preserving the momentum, a family of particle simulation methods commonly used for the modelling of complex fluids and polymers. The class of methods…
We derive a mesoscopic modeling and simulation technique that is very close to the technique known as dissipative particle dynamics. The model is derived from molecular dynamics by means of a systematic coarse-graining procedure. Thus the…
In this work we study the tertiary structure of ionic surfactants when the pH in the system is modified using electrostatic dissipative particle dynamics simulations (DPD). The dependence with pH and kind of surfactant is presented. Our…
We explore how the thermodynamic properties and dynamics of a self-interstitial prismatic dislocation loop are affected by microscopic-scale variations in its geometric configuration, an aspect that rarely received attention in literature.…
We consider two dimensional dispersions of droplets of isotropic phase in a liquid with an XY-like order parameter, tilt, nematic, and hexatic symmetries being included. Strong anchoring boundary conditions are assumed. Textures for a…
This article reports about a novel extension of dissipative particle dynamics (DPD) that allows the study of the collective dynamics of complex chemical and structural systems in a spatially resolved manner with a combinatorially complex…
The thermodynamics with medium effects expressed by the dispersion relation of the temperature and density dependent particle mass is studied. Many previous treatments have been reviewed. A new thermodynamical treatment based on the…
Basic principles of mathematical modeling are reviewed in this book, with the focus on physics and its practical applications, and examples of selected mathematical methods are presented. Most of the models have been imported from physics…
The work deals with the thermodynamical aspects of the cosmic substratum which is dissipative in nature. For homogeneous and isotropic model of the Universe this dissipative phenomenon is effective bulk viscous pressure in nature and is…
A mesoscopic multi-particle collision model for fluid dynamics is generalized to incorporate the chemical reactions among species that may diffuse at different rates. This generalization provides a means to simulate reaction-diffusion…
The behavior of the average velocity, its deviation and average squared velocity are characterized using three techniques for a 1-D dissipative impact system. The system -- a particle, or an ensemble of non interacting particles, moving in…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
The viscosity and self-diffusion constant of particle-based mesoscale hydrodynamic methods, multi-particle collision dynamics (MPC) and dissipative particle dynamics (DPD), are investigated, both with and without angular-momentum…
By detailed Molecular Dynamics and Monte Carlo simulations %of a realistic model we show that granular materials at rest can be described as thermodynamics systems. First we show that granular packs can be characterized by few parameters,…
The optical properties of molecules close to plasmonic nanostructures greatly differ from their isolated molecule counterparts. To theoretically investigate such systems in a Quantum Chemistry perspective, one has to take into account that…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…