Related papers: Modeling excitable cells with the EMI equations: s…
In the present study, we consider the Extra-Membrane-Intra model (EMI) for the simulation of excitable tissues at the cellular level. We provide the (possibly large) system of partial differential equations (PDEs), equipped with ad hoc…
The Extracellular-Membrane-Intracellular (EMI) model is a novel mathematical framework for cardiac electrophysiology simulations. The EMI model provides a more detailed description of the heart's electrical activity compared to traditional…
The activity and dynamics of excitable cells are fundamentally regulated and moderated by extracellular and intracellular ion concentrations and their electric potentials. The increasing availability of dense reconstructions of excitable…
The EMI (Extracellular-Membrane-Intracellular) model describes electrical activity in excitable tissue, where the extracellular and intracellular spaces and cellular membrane are explicitly represented. The model couples a system of partial…
Mathematical models for excitable tissue with explicit representation of individual cells are highly detailed and can, unlike classical homogenized models, represent complex cellular geometries and local membrane variations. However, these…
We propose a boundary element method for the accurate solution of the cell-by-cell bidomain model of electrophysiology. The cell-by-cell model, also called Extracellular-Membrane-Intracellular (EMI) model, is a system of reaction-diffusion…
Mathematical models for excitable cells are commonly based on cable theory, which considers a homogenized domain and spatially constant ionic concentrations. Although such models provide valuable insight, the effect of altered ion…
Quantum embedding schemes have the potential to significantly reduce the computational cost of first principles calculations, whilst maintaining accuracy, particularly for calculations of electronic excitations in complex systems. In this…
We formulate and analyze interior penalty discontinuous Galerkin methods for coupled elliptic PDEs modeling excitable tissue, represented by intracellular and extracellular domains sharing a common interface. The PDEs are coupled through a…
We propose a novel algorithm based on inexact GMRES methods for linear response calculations in density functional theory. Such calculations require iteratively solving a nested linear problem $\mathcal{E} \delta\rho = b$ to obtain the…
A spectral method is described for solving coupled elliptic problems on an interior and an exterior domain. The method is formulated and tested on the two-dimensional interior Poisson and exterior Laplace problems, whose solutions and their…
We simulate the electrical response of multiple disjoint biological 3D cells undergoing an electropermeabilization process. Instead of solving the boundary value problem in the unbounded volume, we reduce it to a system of boundary…
We consider the solution of large stiff systems of ordinary differential equations with explicit exponential Runge--Kutta integrators. These problems arise from semi-discretized semi-linear parabolic partial differential equations on…
We propose a framework for training neural networks that are coupled with partial differential equations (PDEs) in a parallel computing environment. Unlike most distributed computing frameworks for deep neural networks, our focus is to…
Elliptic partial differential equations (PDEs) arise in many areas of computational sciences such as computational fluid dynamics, biophysics, engineering, geophysics and more. They are difficult to solve due to their global nature and…
In this paper, we propose an efficient parallelization strategy for boundary element method (BEM) solvers that perform the electromagnetic analysis of structures with lossy conductors. The proposed solver is accelerated with the adaptive…
Fast and accurate solutions of time-dependent partial differential equations (PDEs) are of pivotal interest to many research fields, including physics, engineering, and biology. Generally, implicit/semi-implicit schemes are preferred over…
The efficient solution of discretisations of coupled systems of partial differential equations (PDEs) is at the core of much of numerical simulation. Significant effort has been expended on scalable algorithms to precondition Krylov…
We study the existence of weak solutions for a model of cell invasion into the extracellular matrix (ECM), which consists of a non-linear partial differential equation for the density of cells, coupled with an ordinary differential equation…
Endmember (EM) spectral variability can greatly impact the performance of standard hyperspectral image analysis algorithms. Extended parametric models have been successfully applied to account for the EM spectral variability. However, these…