Multiscale Modeling of Protein Stretching in Nanofluidic Flows

Abstract

The deformation of biological macroparticles such as DNA and proteins in a flow has been a subject of great important in the last decade due to the interest in single molecule analysis. In this paper, a multiscale numerical method was used to analyze deformation of biological macroparticles in uniform flows. To bridge the gap between huge scale differences between the protein dynamics (in Pico scales) and the underlying hydrodynamics (from nano to micro scales), a hybrid coarse-grained model is coupled with the continuum Navier-Stokes solver. Based on the Go¯-type modeling, biological dynamics is governed by the Langevin equation for which the biological macroparticles are represented by a collection of micro-sized spherical beads that are tethered by harmonic potentials. The velocity vector is coupled through the friction factors, which are amino acid dependent, in the stochastic Langevin equation. With this model, simulation results show that flow may stretch biological macroparticles to partially unravel stationary conformations that depend on the flow rate and on the terminus which is anchored. These features potentially offer richer diagnostic results to investigate biological macroparticles configuration process, as compared to force clamp results using AFM.