相关论文: PICPANTHER: A simple, concise implementation of th…
Understanding sub-cellular protein localisation is an essential component to analyse context specific protein function. Recent advances in quantitative mass-spectrometry (MS) have led to high resolution mapping of thousands of proteins to…
Bottom-up coarse-grained (CG) modeling expands the spatial and temporal scales of molecular simulation by seeking a reduced, thermodynamically consistent representation of an atomistic model. Developments in CG theory have largely focused…
We have developed a parallel Particle-Particle, Particle-Mesh (P^3M) simulation code for the T3E well suited to studying the time evolution of systems of particles interacting via gravity and gas forces in cosmological contexts. The…
This perspective paper deals with an overview of particle-in-cell / Monte Carlo collision models applied to different plasma-propulsion configurations and scenarios, from electrostatic (E x B and pulsed arc) devices to electromagnetic (RF…
Development of particle in cell methods using finite element based methods (FEMs) have been a topic of renewed interest; this has largely been driven by (a) the ability of finite element methods to better model geometry, (b) better…
Learning of low dimensional structure in multidimensional data is a canonical problem in machine learning. One common approach is to suppose that the observed data are close to a lower-dimensional smooth manifold. There are a rich variety…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
Numerical algorithms to load relativistic Maxwell distributions in particle-in-cell (PIC) and Monte-Carlo simulations are presented. For stationary relativistic Maxwellian, the inverse transform method and the Sobol algorithm are reviewed.…
A moment body is a linear projection of the spectraplex, the convex set of trace-one positive semidefinite matrices. Determining whether a given point lies within a given moment body is a problem with numerous applications in quantum state…
Finite element methods for electromagnetic problems modeled by Maxwell-type equations are highly sensitive to the conformity of approximation spaces, and non-conforming methods may cause loss of convergence. This fact leads to an essential…
A multiscale QM/classical approach is presented, that is able to model the optical properties of complex nanostructures composed of a molecular system adsorbed on metal nanoparticles. The latter are described by a combined…
We describe a new parallel implementation, mplrs, of the vertex enumeration code lrs that uses the MPI parallel environment and can be run on a network of computers. The implementation makes use of a C wrapper that essentially uses the…
Within the MNPBEM toolbox, developed for the simulation of plasmonic nanoparticles using a boundary element method approach, we show how to include substrate and layer structure effects. We develop the methodology for solving Maxwell's…
We present a cut-cell method for the simulation of 2D incompressible flows past obstacles. It consists in using the MAC scheme on cartesian grids and imposing Dirchlet boundary conditions for the velocity field on the boundary of solid…
Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting…
We describe Pegasus, a new hybrid-kinetic particle-in-cell code tailored for the study of astrophysical plasma dynamics. The code incorporates an energy-conserving particle integrator into a stable, second-order--accurate, three-stage…
Strongly coupled quantum field theories in $(1+1)$ dimensions are notoriously hard to solve non-perturbatively. Variational methods, despite their success for quantum many-body physics on the lattice, have long lacked a natural ansatz…
This paper presents a Graphics Processing Units (GPUs) acceleration method of an iterative scheme for gas-kinetic model equations. Unlike the previous GPU parallelization of explicit kinetic schemes, this work features a fast converging…
We present a novel numerical scheme for simulating the motion of relativistic charged particles in magnetospheres of compact objects, typically filled with highly magnetized collisionless plasmas. The new algorithm is based on a dynamic…
Gaussian processes (GPs) defined through intrinsic random fields provide a flexible framework for modeling spatial phenomena, and have been advocated in a variety of applications over the past several decades. Nevertheless, their adoption…