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The recently developed iterated stockholder atoms (ISA) approach of Lillestolen and Wheatley (Chem. Commun. {\bf 2008}, 5909 (2008)) offers a powerful method for defining atoms in a molecule. However, the real-space algorithm is known to…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
Global particle-in-cell (PIC) simulations of pulsar magnetospheres are performed with a volume, surface and pair production-based plasma injection schemes to systematically investigate the transition between electrosphere and force-free…
A novel second order family of explicit stabilized Runge-Kutta-Chebyshev methods for advection-diffusion-reaction equations is introduced. The new methods outperform existing schemes for relatively high Peclet number due to their favorable…
We describe an initial implementation of an electrostatic Particle-in-Cell (ES-PIC) module with adaptive Cartesian mesh in our Unified Flow Solver framework. Challenges of PIC method with cell-based adaptive mesh refinement (AMR) are…
Particle-In-Cell (PIC) codes are broadly applied to the kinetic simulation of plasmas, from laser-matter interaction to astrophysics. Their heavy simulation cost can be mitigated by using the Single Instruction Multiple Data (SIMD)…
We propose Poisson integrators for the numerical integration of separable Poisson systems. We analyze three situations in which the Poisson systems are separated in three ways and the Poisson integrators can be constructed by using the…
We discuss the fundamentals of the implicit moment method for Particle In Cell (PIC) simulation as presently implemented in the CELESTE3D code. We present the method in its fully electromagnetic and fully kinetic version. The application of…
We describe an implementation of a particle physics module available for the PLUTO code, appropriate for the dynamical evolution of a plasma consisting of a thermal fluid and a non-thermal component represented by relativistic charged…
With the great development of parallel computing techniques, the particle-particle (PP) model has been successfully applied in a number of plasma applications. Comparing to particle-mesh (PM) models, for example the widely used…
This paper presents a new Markov chain Monte Carlo method to sample from the posterior distribution of conjugate mixture models. This algorithm relies on a flexible split-merge procedure built using the particle Gibbs sampler. Contrary to…
An extended Hamiltonian approach to conduct isothermal-isobaric molecular dynamics simulations with full cell flexibility is presented. The components of the metric tensor are used as the fictitious degrees of freedom for the cell, thus…
With rheology applications in mind, we present a fast solver for the time-dependent effective viscosity of an infinite lattice containing one or more neutrally buoyant smooth rigid particles per unit cell, in a two-dimensional Stokes fluid…
Particle-in-cell (PIC) is the most used algorithm to perform self-consistent tracking of intense charged particle beams. It is based on depositing macro-particles on a grid, and subsequently solving on it the Poisson equation. It is well…
In the following, we discuss nonlinear simulations of nonlinear dynamical systems, which are applied in technical and biological models. We deal with different ideas to overcome the treatment of the nonlinearities and discuss a novel…
We describe a novel iterative strategy for Kohn-Sham density functional theory calculations aimed at large systems (> 1000 electrons), applicable to metals and insulators alike. In lieu of explicit diagonalization of the Kohn-Sham…
Polynomial dynamical systems describing interacting particles in the plane are studied. A method replacing integration of a polynomial multi--particle dynamical system by finding polynomial solutions of a partial differential equations is…
We present the standard electromagnetic Particle-in-Cell method, starting from the discrete approximation of derivatives on a uniform grid. The application to second-order, centered, finite-difference discretization of the equations of…
Complex valued systems with an indefinite matrix term arise in important applications such as for certain time-harmonic partial differential equations such as the Maxwell's equation and for the Helmholtz equation. Complex systems with…
I present a brief review of the existing models for particle multiplicity evaluation in heavy ion collisions which are at our disposal in the form of Monte Carlo simulators. Models are classified according to the physical mechanisms with…