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Pulgon-tools is an open-source software package providing building blocks for the analysis and modeling of quasi-one-dimensional (quasi-1D) periodic systems based on line-group theory. While mature libraries exist for space-group detection…

The energy functional, the governing partial differential equation(s) (PDE), and the boundary conditions need to be consistent with each other in a modeling system. In electrolyte solution study, people usually use a free energy form of an…

Starting with a microscopic (individual-based) Brownian dynamics model of charged particles (ions), its macroscopic description is derived as a system of partial differential equations that govern the evolution of ion concentrations in…

A Multi-scale Boltzmann Equation (MBE) is found from the gas-kinetic theory and the direct modeling philosophy as a master equation for complex physical systems of neutral gases across all flow regimes, which locates between the continuum…

In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov…

The proximal bundle method (PBM) is a fundamental and computationally effective algorithm for solving nonsmooth optimization problems. In this paper, we present the first variant of the PBM for smooth objectives, achieving an accelerated…

Recently, a nonlinear Poisson equation has been introduced to model nonlinear and nonlocal hyperpolarization effects in electrostatic solute-solvent interaction for biomolecular solvation analysis. Due to a strong nonlinearity associated…

For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation…

The equations of classical spin-orbit motion can be extended to a Hamiltonian system in 9-dimensional phase space by introducing a coupled spin-orbit Poisson bracket and a Hamiltonian function. After this extension and by establishing…

We present an explicit solver of the three-dimensional screened and unscreened Poisson's equation which combines accuracy, computational efficiency and versatility. The solver, based on a mixed plane-wave / interpolating scaling function…

This work introduces ParAMS -- a versatile Python package that aims to make parameterization workflows in computational chemistry and physics more accessible, transparent and reproducible. We demonstrate how ParAMS facilitates the parameter…

Optical emission spectroscopy applied to non-equilibrium plasmas in molecular gases can give important information on basic plasma parameters, including the rotational, vibrational temperatures and densities of the investigated radiative…

We consider the Poisson-Boltzmann equation in a periodic cell, representative of a porous medium. It is a model for the electrostatic distribution of $N$ chemical species diluted in a liquid at rest, occupying the pore space with charged…

The Lattice Boltzmann method (LBM) is a well-established mesoscopic approach for simulating fluid dynamics by evolving particle distribution functions on discrete lattices. While the LBM is highly parallelizable on classical hardware, its…

We study the stationary states of an over-damped active Brownian particle (ABP) in a harmonic trap in two dimensions, via mathematical calculations and numerical simulations. In addition to translational diffusion, the ABP self-propels with…

Bayesian optimization (BO) is a model-based approach for gradient-free black-box function optimization. Typically, BO is powered by a Gaussian process (GP), whose algorithmic complexity is cubic in the number of evaluations. Hence, GP-based…

For multispecies ions, we study boundary layer solutions of charge conserving Poisson-Boltzmann (CCPB) equations [50] (with a small parameter \k{o}) over a finite one-dimensional (1D) spatial domain, subjected to Robin type boundary…

Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the…

Polymer-Attenuated Coulombic Self-Assembly (PACS) is a flexible experimental approach for generating crystals from simple colloidal building blocks. The central components are charged spherical particles coated with a polymer brush that…

We investigate the analytically solvable pion-laser model, and its generalization to arbitrary multiplicity distributions. Although this kind of extension of the model is possible, the pion laser model in its original form is unique: it is…