Related papers: Particle-Particle, Particle-Scaling function (P3S)…
We are interested in the online prediction of the electricity load, within the Bayesian framework of dynamic models. We offer a review of sequential Monte Carlo methods, and provide the calculations needed for the derivation of so-called…
High-resolution simulations of particle-based kinetic plasma models typically require a high number of particles and thus often become computationally intractable. This is exacerbated in multi-query simulations, where the problem depends on…
Quasi-2D Coulomb systems are of fundamental importance and have attracted much attention in many areas nowadays. Their reduced symmetry gives rise to interesting collective behaviors, but also brings great challenges for particle-based…
This paper develops a consistent particle method for capturing the highly non-linear behavior of violent free-surface flows, based on an Enhanced Weakly Compressible Moving Particle Semi-implicit (EWC-MPS) method. It pays special attention…
A finite-element algorithm for computing free-surface flows driven by arbitrary body forces is presented. The algorithm is primarily designed for the microfluidic parameter range where (i) the Reynolds number is small and (ii) force-driven…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…
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…
Many problems arise in computational biology can be reduced to the minimization of energy function, that determines on the geometry of considered molecule. The solution of this problem allows in particular to solve folding and docking…
A recently proposed method for computer simulations in the isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion for the particle coordinates and the ``piston'' degree of freedom, is re-derived by straightforward…
We develop a linearly-scaling variant of the Force Coupling Method [K. Yeo and M. R. Maxey, J. Fluid Mech. 649, 205-231 (2010)] for computing hydrodynamic interactions among particles confined to a doubly-periodic geometry with either a…
We present efficient algorithms to calculate trajectories for periodic Lorentz gases consisting of square lattices of circular obstacles in two dimensions, and simple cubic lattices of spheres in three dimensions; these become increasingly…
In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a…
The Particle-Particle-Particle-Mesh algorithm elegantly extends the standard Particle-In-Cell scheme by direct summation of interaction that happens over distances below or around mesh size. Generally, this allows for a more accurate…
In this work the free energy of solid phases is computed for the Lennard-Jones potential and for a model of NaCl. The free energy is evaluated through the Einstein crystal/molecule methodologies using the Molecular Dynamics programs:…
This study presents two different machine learning approaches for the modeling of hydrodynamic force on particles in a particle-laden multiphase flow. Results from particle-resolved direct numerical simulations (PR-DNS) of flow over a…
The key problem of statistical physics standing over one hundred years is how to exactly calculate the partition function (or free energy) of many-body interaction systems, which severely hinders application of the theory for realistic…
In the design of probabilistic timed systems, bounded requirements concerning behaviour that occurs within a given time, energy, or more generally cost budget are of central importance. Traditionally, such requirements have been…
We present the Multi-Particle-Collision (MPC) dynamics approach to simulate properties of low-dimensional systems. In particular, we illustrate the method for a simple model: a one-dimensional gas of point particles interacting through…
We describe a computational framework for simulating suspensions of rigid particles in Newtonian Stokes flow. One central building block is a collision-resolution algorithm that overcomes the numerical constraints arising from particle…
This work discusses the main analogies and differences between the deterministic approach underlying most cosmological N-body simulations and the probabilistic interpretation of the problem that is often considered in mathematics and…