Hydrodynamics of DNA confined in nanoslits and nanochannels

Modeling the dynamics of a confined, semi exible polymer is a challenging problem, owing to the complicated interplay between the configurations of the chain, which are strongly affected by the length scale for the confinement relative to the persistence length of the chain, and the polymer-wall hydrodynamic interactions. At the same time, understanding these dynamics are crucial to the advancement of emerging genomic technologies that use confinement to stretch out DNA and “read” a genomic signature. In this mini-review, we begin by considering what is known experimentally and theoretically about the friction of a wormlike chain such as DNA confined in a slit or a channel. We then discuss how to estimate the friction coefficient of such a chain, either with dynamic simulations or via Monte Carlo sampling and the Kirk-wood pre-averaging approximation. We then review our recent work on computing the diffusivity of DNA in nanoslits and nanochannels, and conclude with some promising avenues for future work and caveats about our approach

A Framework for Modeling DNA Based Molecular Systems

Abstract. In this paper, we propose a framework for a discrete event simulator for simulating the DNA based nano-robotical systems. We describe a physical model that captures the conformational changes of the solute molecules. We also present methods to simulate various chemical reactions due to the molecular collisions, including hybridization, dehybridization and strand displacement. The feasibility of such a framework is demonstrated by some preliminary results. 1 Introduction and Related Work Recent research has explored DNA as a material for self-assembly of nanoscale object

Multi-scale simulation method for electroosmotic flows

Electroosmotic transport in micro-and nano- channels has important applications in biological and engineering systems but is difficult to model because nanoscale structure near surfaces impacts flow throughout the channel. We develop an efficient multi-scale simulation method that treats near-wall and bulk subdomains with different physical descriptions and couples them through a finite overlap region. Molecular dynamics is used in the near-wall subdomain where the ion density is inconsistent with continuum models and the discrete structure of solvent molecules is important. In the bulk region the solvent is treated as a continuum fluid described by the incompressible Navier-Stokes equations with thermal fluctuations. A discrete description of ions is retained because of the low density of ions and the long range of electrostatic interactions. A stochastic Euler-Lagrangian method is used to simulate the dynamics of these ions in the implicit continuum solvent. The overlap region allows free exchange of solvent and ions between the two subdomains. The hybrid approach is validated against full molecular dynamics simulations for different geometries and types of flows