A computational model for structural dynamics and reconfiguration of DNA assemblies.

ABSTRACT: Recent advances in constructing a structured DNA assembly whose configuration can be dynamically changed in response to external stimuli have demanded the development of an efficient computational modeling approach to expedite its design process. Here, we present a computational framework capable of analyzing both equilibrium and non-equilibrium dynamics of structured DNA assemblies at the molecular level. The framework employs Langevin dynamics with structural and hydrodynamic finite element models that describe mechanical, electrostatic, base stacking, and hydrodynamic interactions. Equilibrium dynamic analysis for various problems confirms the solution accuracy at a near-atomic resolution, comparable to molecular dynamics simulations and experimental measurements. Furthermore, our model

SUBMITTER: Lee JY 

PROVIDER: S-EPMC10625641 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature