Related papers: Calculating particle pair potentials from fluid-st…
Accurate path integral Monte Carlo or molecular dynamics calculations of isotope effects have until recently been expensive because of the necessity to reduce three types of errors present in such calculations: statistical errors due to…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
We establish quantitative convergence rates for stochastic particle approximation based on Nanbu-type Monte Carlo schemes applied to a broad class of collisional kinetic models. Using coupling techniques and stability estimates in the…
The electrostatic potential in the neighborhood of a biomolecule can be computed thanks to the non-linear divergence-form elliptic Poisson-Boltzmann PDE. Dedicated Monte-Carlo methods have been developed to solve its linearized version (see…
We consider in this paper random batch interacting particle methods for solving the Poisson-Nernst-Planck (PNP) equations, and thus the Poisson-Boltzmann (PB) equation as the equilibrium, in the external unbounded domain. To justify the…
In this paper we use Lagrange-Poincare reduction to understand the coupling between a fluid and a set of Lagrangian particles that are supposed to simulate it. In particular, we reinterpret the work of Cendra et al. by substituting velocity…
We develop a generalized Newton scheme IHNC for the construction of effective pair potentials for systems of interacting point-like particles.The construction is made in such a way that the distribution of the particles matches a given…
Quantum lattice models describe a wide array of physical systems, and are a canonical way to numerically solve the Schrodinger equation. Here we prove the potential inversion theorem, which says that wavefunction probability in these models…
The implicit particle filter is a sequential Monte Carlo method for data assimilation that guides the particles to the high-probability regions via a sequence of steps that includes minimizations. We present a new and more general…
A jump-diffusion process along with a particle scheme is devised as an accurate and efficient particle solution to the Boltzmann equation. The proposed process (hereafter Gamma-Boltzmann model) is devised to match the evolution of all…
Integral equations frequently arise in surface science, and in some cases, they must be treated as inverse problems. In our previous work on optical tweezers, atomic force microscopy, and surface force measurement apparatus, we performed…
Discrete particle simulations are widely used to study large-scale particulate flows in complex geometries where particle-particle and particle-fluid interactions require an adequate representation but the computational cost has to be kept…
An efficient real space method is derived for the evaluation of the Madelung's potential of ionic crystals. The proposed method is an extension of the Evjen's method. It takes advantage of a general analysis for the potential convergence in…
Reverse Monte Carlo modeling of liquid water, based on one neutron and one X-ray diffraction data set, applying also the most popular interatomic potential for water, SPC/E, has been performed. The strictly rigid geometry of SPC/E water…
We compare three model-free numerical methods for inverting structural data to obtain interaction potentials, namely iterative Boltzmann inversion (IBI), test-particle insertion (TPI), and a machine-learning (ML) approach called ActiveNet.…
Chemical potential is an effective way to drive phase transition or express wettability. In this letter, we present a chemical-potential-based lattice Boltzmann model to simulate multiphase flows. The nonideal force is directly evaluated by…
Ions are critical to the structure and stability of polyelectrolytes such as nucleic acids. In this work, we systematically calculated the potentials of mean force between two like-charged nanoparticles in salt solutions by Monte Carlo…
Particle filters are broadly used to approximate posterior distributions of hidden states in state-space models by means of sets of weighted particles. While the convergence of the filter is guaranteed when the number of particles tends to…
Using molecular dynamics simulations, we perform the first direct tests of three proposed models for the pair correlation functions of strongly coupled plasmas with species of unequal temperature. The models are all extensions of the…
An idea for evaluating transition probabilities in chemical reaction systems is proposed, which is efficient for repeated calculations with various rate constants. The idea is based on duality relations; instead of direct time-evolutions of…