Improvements in continuum modeling for biomolecular systems

TL;DR

This paper reviews recent advancements in continuum modeling of biomolecular systems, focusing on improvements like size modifications, coupling theories, and numerical methods to better capture physical properties.

Contribution

It summarizes recent key developments in continuum models, including size-modified models and coupling approaches, enhancing simulation accuracy for biological processes.

Findings

Size-modified models improve physical accuracy.

Coupling of theories enhances simulation detail.

Numerical methods advance computational efficiency.

Abstract

Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulation. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and PNP equations, the coupling of polar and nonpolar interactions, and numerical progress.