Accelerating continuum-based protein dynamics simulation using three-dimensional mixed overlapping element

Abstract

The conformational dynamics of proteins are crucial for their biological functions, requiring accurate modeling of both proteins and the surrounding solvent. This study focuses on the finite element framework of continuum-based protein dynamics simulation which integrates protein and solvent environments to simulate protein dynamics with explicit consideration of solvent effects. The conventional approach uses high-order mixed finite elements for incompressible analysis due to stability constraints, which results in a computationally burdensome process. To address this issue, we utilize three-dimensional mixed overlapping element to construct the solvent finite element models. This approach maintains stability while significantly reducing computational costs compared to conventional high-order methods, enabling the acceleration of continuum-based protein dynamics simulations.