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The convergence and optimality of adaptive mixed finite element methods for the Poisson equation are established in this paper. The main difficulty for mixed finite element methods is the lack of minimization principle and thus the failure…
This work blends the inexact Newton method with iterative combined approximations (ICA) for solving topology optimization problems under the assumption of geometric nonlinearity. The density-based problem formulation is solved using a…
The shell-model coupling scheme of the proton-neutron symplectic model (PNSM), defined by the following dynamical symmetry chain $Sp(12,R) \supset SU(1,1) \otimes SO(6) \supset U(1) \otimes SU_{pn}(3) \otimes SO(2) \supset SO(3)$, is…
In this work a dynamical system approach is taken to systematically investigate the one-dimensional classical Poisson-Boltzmann (PB) equation with various boundary conditions. This framework, particularly, the phase space portrait, has a…
Numerical resolution of high-dimensional nonlinear PDEs remains a huge challenge due to the curse of dimensionality. Starting from the weak formulation of the Lawson-Euler scheme, this paper proposes a stochastic particle method (SPM) by…
The excess entropy of restricted primitive model electrolytes is calculated using a potential based approach through the symmetric Poisson-Boltzmann and the modified Poisson-Boltzmann theories. The theories are utilized in conjunction with…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
While the lattice Boltzmann method (LBM) has proven robust in areas like general fluid dynamics, heat transfer, and multiphase modeling, its application to mass transfer has been limited. Current modeling strategies often oversimplify the…
We derive the partial differential equation (PDE) to which the pseudo-potential lattice Boltzmann method (P-LBM) converges under diffusive scaling, providing a rigorous basis for its consistency analysis. By establishing a direct link…
Electrokinetic phenomena in nanopore sensors and microfluidic devices require accurate simulation of coupled fluid-electrostatic interactions in geometrically complex domains with irregular boundaries and adaptive mesh refinement. We…
We present a linear scaling formulation for the solution of the all-electron Coulomb problem in crystalline solids. The resulting method is systematically improvable and well suited to large-scale quantum mechanical calculations in which…
We present an efficient numerical method, inspired by transformation optics, for solving the Poisson equation in complex and arbitrarily shaped geometries. The approach operates by mapping the physical domain to a uniform computational…
Porous electrodes are widely used in electrochemical systems, where accurately determining electric potentials, particularly overpotentials, is essential for understanding electrode behavior. At the macroscopic scale, porous electrodes are…
Non-homogeneous Poisson processes are used in a wide range of scientific disciplines, ranging from the environmental sciences to the health sciences. Often, the central object of interest in a point process is the underlying intensity…
We describe a path-integral approach for including nuclear quantum effects in non-adiabatic chemical dynamics simulations. For a general physical system with multiple electronic energy levels, a corresponding isomorphic Hamiltonian is…
Markov state models (MSMs) are valuable for studying dynamics of protein conformational changes via statistical analysis of molecular dynamics (MD) simulations. In MSMs, the complex configuration space is coarse-grained into conformational…
Model counting is a fundamental task that involves determining the number of satisfying assignments to a logical formula, typically in conjunctive normal form (CNF). While CNF model counting has received extensive attention over recent…
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 Linearized Poisson--Boltzmann (LPB) equation is a popular and widely accepted model for accounting solvent effects in computational (bio-) chemistry. In the present article we derive the analytical forces of the…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…