Related papers: NextGenPB: an analytically-enabled super resolutio…
This work proposes a fast iterative method for local steric Poisson--Boltzmann (PB) theories, in which the electrostatic potential is governed by the Poisson's equation and ionic concentrations satisfy equilibrium conditions. To present the…
The Poisson-Nernst-Planck (PNP) equations are one of the most effective model for describing electrostatic interactions and diffusion processes in ion solution systems, and have been widely used in the numerical simulations of biological…
This paper deals with the identification of linear stochastic dynamical systems, where the unknowns include system coefficients and noise variances. Conventional approaches that rely on the maximum likelihood estimation (MLE) require…
Non-linear convection-reaction-diffusion (CRD) partial differential equations (PDEs) are crucial for modeling complex phenomena in fields such as biology, ecology, population dynamics, physics, and engineering. Numerical approximation of…
The aim of this article is to analyze numerical schemes using two-layer neural networks with infinite width for the resolution of the high-dimensional Poisson-Neumann partial differential equations (PDEs) with Neumann boundary conditions.…
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
In this paper, we apply the range-separated (RS) tensor format [6] for the construction of new regularization scheme for the Poisson-Boltzmann equation (PBE) describing the electrostatic potential in biomolecules. In our approach, we use…
Parametric partial differential equations (PDEs) are fundamental for modeling a wide range of physical and engineering systems influenced by uncertain or varying parameters. Traditional neural network-based solvers, such as Physics-Informed…
This work uses the long-wavelength limit to compute LSPR response of biosensors, expanding the open-source PyGBe code to compute the extinction cross-section of metallic nanoparticles in the presence of any target for sensing. The target…
The Poisson equation has many applications across the broad areas of science and engineering. Most quantum algorithms for the Poisson solver presented so far either suffer from lack of accuracy and/or are limited to very small sizes of the…
We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation, for molecules represented as non-overlapping spherical cavities.…
Fully connected multilayer perceptrons are used for obtaining numerical solutions of partial differential equations in various dimensions. Independent variables are fed into the input layer, and the output is considered as solution's value.…
In this paper we have derived explicitly computable bounds on the error in energy norms for the fully nonlinear Poisson-Boltzmann equation. Together with the computable bounds, we have also obtained efficient error indicators which can…
Efficiently solving Poisson equations on complex, irregular domains remains a fundamental challenge in scientific computing, as classical iterative solvers often suffer from prohibitive runtime due to ill-conditioned systems. While neural…
We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the…
Semilinear parabolic partial differential equations (PDEs) are fundamental to modeling complex dynamical systems across scientific domains. The Deep Backward Stochastic Differential Equation (BSDE) method is a promising approach for…
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…
To accurately model the electron density and polarization, a polarizable multipole (PM) model using the AMOEBA force field has been introduced \cite{Ren:2003, Shi:2013} recently. In the AMOEBA force field, the traditional point atomic…
We construct deterministic particle solutions for linear and fast diffusion equations using a nonlocal approximation. We exploit the $2$-Wasserstein gradient flow structure of the equations in order to obtain the nonlocal approximating PDEs…
The rapid expansion of electric vehicles has intensified the need for accurate and efficient diagnosis of lithium-ion batteries. Parameter identification of electrochemical battery models is widely recognized as a powerful method for…