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The evaluation of Coulomb forces is a difficult task. The summations that are involved converge only conditionally and care has to be taken in selecting the appropriate procedure to define the limits. The Ewald method is a standard method…
Lattice-Boltzmann (LB) simulations are a common tool to numerically estimate the permeability of porous media. For valuable results, the porous structure has to be well resolved resulting in a large computational effort as well as high…
This paper is committed to investigate an extension of the classical adaptive biasing force method, which is used to compute the free energy related to the Boltzmann-Gibbs measure and a reaction coordinate function. The issue of this…
We present a comparative study of two computer simulation methods to obtain static and dynamic properties of dilute polymer solutions. The first approach is a recently established hybrid algorithm based upon dissipative coupling between…
Starting from the recently proposed energy-based deviational formulation for solving the Boltzmann equation [J.-P. Peraud and N. G. Hadjiconstantinou, Phys. Rev. B 84, 2011], which provides significant computational speedup compared to…
The Poisson--Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to…
The direct method is one of the most important algorithms for solving linear systems of equations, with LU decomposition comprising a significant portion of its computation time. This study explores strategies to accelerate complex LU…
Combining analytical and numerical methods, we study within the framework of the homogeneous non-linear Boltzmann equation, a broad class of models relevant for the dynamics of dissipative fluids, including granular gases. We use the new…
Over the past few decades, tremendous progress has been made in the development of particle-based discrete simulation methods versus the conventional continuum-based methods. In particular, the lattice Boltzmann (LB) method has evolved from…
Modeling and simulation of multiphase flows in complex geomerties are challenging due to the complexity in describing the interface topology changes among different phases and the difficulty in implementing the boundary conditions on the…
Numerical discretization of the large-scale Maxwell's equations leads to an ill-conditioned linear system that is challenging to solve. The key requirement for successive solutions of this linear system is to choose an efficient solver. In…
In this paper, a new progressive mesh algorithm is introduced in order to perform fast physical simulations by the use of a lattice Boltzmann method (LBM) on a single-node multi-GPU architecture. This algorithm is able to mesh automatically…
We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with…
In this paper, for the first time we propose two linear, decoupled, energy-stable numerical schemes for multi-component two-phase compressible flow with a realistic equation of state (e.g. Peng-Robinson equation of state). The methods are…
Our method proposes the efficient generation of samples from an unnormalized Boltzmann density by solving the underlying continuity equation in the low-rank tensor train (TT) format. It is based on the annealing path commonly used in MCMC…
We propose a parallel algorithm for the numerical solution of a class of second order semi-linear equations coming from stochastic optimal control problems, by means of a dynamic domain decomposition technique. The new method is an…
We present a computational study of static and dynamic linear polarizabilities in solution. We use different theoretical approaches to describe solvent effects, ranging from quantum mechanics/molecular mechanics (QM/MM) to quantum embedding…
We propose a hybrid model, coupling Lattice Boltzmann and Molecular Dynamics models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB…
The linearized collision operator of the Boltzmann equation for single species can be written as a sum of a positive multiplication operator, the collision frequency, and a compact integral operator. This classical result has more recently,…
The nonlinear Poisson-Boltzmann equation (NPBE) is an elliptic partial differential equation used in applications such as protein interactions and biophysical chemistry (among many others). It describes the nonlinear electrostatic potential…