Related papers: PB-AM: An Open-Source, Fully Analytical Linear Poi…
The Poisson-Boltzmann (PB) theory is one of the most important theoretical models describing charged systems continuously. However, it suffers from neglecting ion correlations, which hinders its applicability to more general charged systems…
We present an extension to the Poisson-Boltzmann model where the dipolar features of solvent molecules are taken explicitly into account. The formulation is derived at mean-field level and can be extended to any order in a systematic…
BHAM is a freely avaible R pakcage that implments Bayesian hierarchical additive models for high-dimensional clinical and genomic data. The package includes functions that generalized additive model, and Cox additive model with the…
We present the Physics-Informed Optimal Homotopy Analysis Method (PI-OHAM) for solving nonlinear differential equations. PI-OHAM, based on classical HAM, employs a physics-informed residual loss to optimize convergence-control parameters…
Adaptive Partition-based Methods (APM) are numerical methods to solve two-stage stochastic linear problems (2SLP). The core idea is to iteratively construct an adapted partition of the space of alea in order to aggregate scenarios while…
Classical polarizable approaches have become the gold standard for simulating complex systems and processes in the condensed phase. These methods describe intrinsically dissipative polarizable media, requiring a formal definition within the…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
The package performs molecular-dynamics-like agent-based simulations for models of aligning self-propelled particles in two dimensions such as e.g. the seminal Vicsek model or variants of it. In one class of the covered models, the…
We present the design of a flexible quantum-chemical method development framework, which supports employing any type of basis function. This design has been implemented in the light-weight program package molsturm, yielding a…
The Boltzmann equation describes the evolution of the phase-space probability distribution of classical particles under binary collisions. Approximations to it underlie the basis for several scholarly fields, including aerodynamics and…
We describe a three-stage procedure to analyze the dependence of Poisson Boltzmann calculations on the shape, size and geometry of the boundary between solute and solvent. Our study is carried out within the boundary element formalism, but…
A variational solution procedure is reported for the many-particle no-pair Dirac-Coulomb-Breit Hamiltonian aiming at a parts-per-billion (ppb) convergence of the atomic and molecular energies, described within the fixed nuclei…
Analytical solutions of the Bohr Hamiltonian are obtained in the $\gamma$-unstable case, as well as in an exactly separable rotational case with $\gamma\approx 0$, called the exactly separable Morse (ES-M) solution. Closed expressions for…
This paper presents a 2D/3D Free Surface Lattice Boltzmann Method simulation package called LBfoam for the simulation of foaming processes. The model incorporates the essential physics of foaming phenomena: gas diffusion into nucleated…
This paper analyzes various schemes for the Euler-Poisson-Boltzmann (EPB) model of plasma physics. This model consists of the pressureless gas dynamics equations coupled with the Poisson equation and where the Boltzmann relation relates the…
A new protocol for linearization of the Poisson-Boltzmann equation is proposed and the resultant electrostatic equation coincides formally with the Debye-Huckel equation, the solution of which is well known for many electrostatic problems.…
We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule…
We present qlbm, a Python software package designed to facilitate the development, simulation, and analysis of Quantum Lattice Boltzmann Methods (QBMs). qlbm is a modular framework that introduces a quantum component abstraction hierarchy…
Immersed boundary-lattice Boltzmann method (IB-LBM) has been widely used for simulation of particle-laden flows recently. However, it was limited to small-scale simulations with no more than O(103) particles. Here, we expand IB-LBM for…
Active Brownian particles (ABPs) function as self-driving agents that display non-equilibrium behavior through their pairwise interactions which lead to phase separation and vortex patterns in both soft matter and living systems. A…