Related papers: Computing the local pressure in molecular dynamics…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
In this paper, we are concerned with the simulation of blood flow in microvascular networks and the surrounding tissue. To reduce the computational complexity of this issue, the network structures are modeled by a one-dimensional graph,…
Constraining molecules in simulations (such as with constant bond lengths and/or angles) reduces their degrees of freedom (DoF), which in turn affects temperature calculations in those simulations. When local temperatures are measured, e.g.…
In this paper, we derive reduced models for the motion of gas bubbles in an ambient inviscid liquid, using Hamilton's least action principle. We first explain how to recover from this principle the classical sharp interface model, in which…
Molecular dynamics is a powerful method for studying the behaviour of materials at high temperature. In practice, however, its effectiveness in representing real systems is limited by the accuracy of the forces, finite size effects,…
The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…
Most of numerical methods for deterministic simulations of rarefied gas flows use the discrete velocity (or discrete ordinate) approximation. In this approach, the kinetic equation is approximated with a global velocity grid. The grid must…
We analyze the complexity of classically simulating continuous-time dynamics of locally interacting quantum spin systems with a constant rate of entanglement breaking noise. We prove that a polynomial time classical algorithm can be used to…
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…
In this paper, we explore various forms of osmotic transport in the regime of high solute concentration. We consider both the osmosis across membranes and diffusio-osmosis at solid interfaces, driven by solute concentration gradients. We…
In this work, we consider the pressure of Coulomb systems, in which particles interact via a volume-dependent potential (in particular, the Ewald potential). We confirm that the expression for virial pressure should be corrected in this…
The role of viscous forces coupled with Brownian forces in momentum conserving computer simulations is studied here in the context of their contribution to the total average pressure of a simple fluid as derived from the virial theorem, in…
We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non uniform density profile. Results match quite well as long as the lengthscale of density…
An improved approach to the simulation of strongly fluctuating Coulomb gases, based on a local lattice technique introduced by Maggs and Rossetto, is described and then tested in a problem of biophysical interest. The low acceptance rates…
Simulations of volumetrically forced granular media in two dimensions produce s tates with nearly homogeneous density. In these states, long-range velocity correlations with a characteristic vortex structure develop; given sufficient time,…
The dynamics of the spin-boson Hamiltonian is considered in the stochastic approximation. The Hamiltonian describes a two-level system coupled to an environment and is widely used in physics, chemistry and the theory of quantum measurement.…
We examine the phenomenon of dynamical heterogeneity in computer simulations of an equilibrium, glass-forming liquid. We describe several approaches to quantify the spatial correlation of single-particle motion, and show that spatial…
The efficiency of soft particles to stabilize emulsions is examined by measuring their desorption free energy, i.e., the mechanical work required to detach the particle from a fluid interface. Here, we consider rubber-like elastic as well…
Structural and thermodynamic properties of ionic fluids are related to those of a simpler ``mimic'' system with short ranged intermolecular interactions in a spatially varying effective field by use of Local Molecular Field (LMF) theory,…