curvedSpaceSim: A framework for simulating particles interacting along geodesics

TL;DR

curvedSpaceSim is a flexible simulation framework that models particles interacting along geodesics on arbitrarily curved surfaces, enabling advanced studies of complex biological and physical systems.

Contribution

it introduces a novel framework combining particle simulations with discrete differential geometry to efficiently simulate particles on curved surfaces.

Findings

computational cost varies with surface complexity

framework supports both equilibrium and non-equilibrium dynamics

parallelization improves simulation efficiency

Abstract

A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains. These packages typically simulate particles in free (Euclidean) space, with options to specify a variety of boundary conditions. While more exotic, many physical systems are constrained to and interact across curved surfaces, such as organisms moving across the landscape, colloids pinned at curved fluid-fluid interfaces, and layers of epithelial cells forming highly curved tissues. The calculation of distances and the updating of equations of motion in idealized geometries (namely, on surfaces of constant curvature) can be done analytically, but it is much more challenging to efficiently perform molecular-dynamics-like simulations on arbitrarily curved surfaces. This article discusses a simulation framework which combines tools from particle-based simulations with recent work in discrete differential geometry to model particles that interact via geodesic distances and move on an arbitrarily curved surface. We present computational cost estimates for a variety of surface complexities with and without various algorithmic specializations (e.g., restrictions to short-range interaction potentials, or multi-threaded parallelization). Our flexible and extensible framework is set up to easily handle both equilibrium and non-equilibrium dynamics, and will enable researchers to access time- and particle-number-scales previously inaccessible.