Related papers: Discontinuous Molecular Dynamics for Rigid Bodies:…
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…
We propose an approach that links density functional theory (DFT) and molecular dynamics (MD) simulation to study fluid behavior in nanopores in contact with bulk (macropores). It consists of two principal steps. First, the theoretical…
We investigate by Molecular-Dynamics simulations the fast mobility - the rattling amplitude of the particles temporarily trapped by the cage of the neighbors - in mildly supercooled states of dense molecular (linear trimers) and atomic…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Vulcanian explosive eruption, which is a nonlinear and nonequilibrium abrupt dynamics of magma-gas mixture, is modeled by a two-component Lennard-Jones particle system. Molecular-dynamics simulation of a shock-tube experiment gives…
Several physical systems in condensed matter have been modeled approximating their constituent particles as hard objects. The hard spheres model has been indeed one of the cornerstones of the computational and theoretical description in…
We study compressible fluid flow in narrow two-dimensional channels using a novel molecular dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream…
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…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
A framework for performing event-driven, adaptive time step simulations of systems of rigid bodies interacting under stepped or terraced potentials in which the potential energy is only allowed to have discrete values is outlined. The…
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…
We use molecular dynamics simulations to study the behavior of a compressible Lennard-Jones fluid in simple shear flow in a two-dimensional nanochannel. The system is equilibrated in the fluid phase close to the triple point at which gas,…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
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…
Ring polymer molecular dynamics (RPMD) is used to directly simulate the dynamics of an excess electron in a supercritical fluid over a broad range of densities. The accuracy of the RPMD model is tested against numerically exact path…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
The systematic errors due to the practical implementation of the Contact Dynamics method for simulation of dense granular media are examined. It is shown that, using the usual iterative solver to simulate a chain of rigid particles,…