Related papers: Computing the local pressure in molecular dynamics…
We propose a local, O(N) molecular dynamics algorithm for the simulation of charged systems. The long ranged Coulomb potential is generated by a propagating electric field that obeys modified Maxwell equations. On coupling the…
Osmosis plays a central role in the function of living and soft matter systems. While the thermodynamics of osmosis is well understood, the underlying microscopic dynamical mechanisms remain the subject of discussion. Unraveling these…
Cosmological field-level inference requires differentiable forward models that solve the challenging dynamics of gas and dark matter under hydrodynamics and gravity. We propose a hybrid approach where gravitational forces are computed using…
Line-by-line calculations are becoming the standard procedure for carrying spectral simulations. However, it is important to insure the accuracy of such spectral simulations through the choice of adapted models for the simulation of key…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…
Soft particles at fluid interfaces play an important role in many aspects of our daily life, such as the food industry, paints and coatings, and medical applications. Analytical methods are not capable of describing the emergent effects of…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…
We use computer simulations to test a simple idea for mapping between long-time self diffusivities obtained from molecular and Brownian dynamics. The strategy we explore is motivated by the behavior of fluids comprising particles that…
In this work, we introduce an algorithm to compute the derivatives of physical observables along the constrained subspace when flexible constraints are imposed on the system (i.e., constraints in which the hard coordinates are fixed to…
We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…
The concept of local pressure is pivotal to describe many important physical phenomena, such as buoyancy or atmospheric phenomena, which always require the consideration of space-varying pressure fields. These fields have precise…
We discuss the application of the local lattice technique of Maggs and Rossetto to problems that involve the motion of objects with different dielectric constants than the background. In these systems the simulation method produces a…
Building upon recent developments of force-based estimators with a reduced variance for the computation of densities, radial distribution functions or local transport properties from molecular simulations, we show that the variance can be…
We perform molecular dynamics simulations to characterize the occurrence of inhomogeneous shear flows in soft jammed materials. We use rough walls to impose a simple shear flow and study the athermal motion of jammed assemblies of soft…
Local Hamiltonians, $H_k$, describe non-trivial $k$-body interactions in quantum many-body systems. Here, we address the dynamical simulatability of a $k$-local Hamiltonian by a simpler one, $H_{k'}$, with $k'<k$, under the realistic…
Human blood flow is a multi-scale problem: in first approximation, blood is a dense suspension of plasma and deformable red cells. Physiological vessel diameters range from about one to thousands of cell radii. Current computational models…
We present a derivation of the stress field for an interacting quantum system within the framework of local density functional theory. The formulation is geometric in nature and exploits the relationship between the strain tensor field and…
We present a method for computing parameter sensitivities and response coefficients in Brownian dynamics simulations. The method involves tracking auxiliary variables (Malliavin weights) in addition to the usual particle positions, in an…
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…
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…