Unraveling of a Tethered Polymer Chain in Uniform Solvent Flow

Abstract

The separation of electrophoresing DNA molecules of varying lengths, actuated by their sizedependent collision with a stationary obstacle or array of obstacles, has recently gained prominence. To gain insight into how a chain initially unravels subsequent to a polymer-obstacle collision, we investigate the stretching dynamics of a tethered polymer chain initially at equilibrium, following the imposition of a uniform flow of solvent. The solution for the Rouse model of the polymer chain is obtained via an analysis into normal modes. We examine the consequences of finite chain extensibility by performing Brownian dynamics simulations of the wormlike chain model, which describes DNA elasticity. Detailed results are presented for the propagation of tension with time in Rouse and wormlike chains. Our results suggest the diffusive propagation of tension in Rouse chains, whereas a convective mechanism of tension propagation in wormlike chains under conditions of strong flow is demonstrated.

Continuous‐time random walk models of DNA electrophoresis in a post array: Part II. Mobility and sources of band broadening

“…The extension of the chain can be estimated from the Marko-Siggia worm-like chain interpolation formula [8, 22, 35],…”

A Progressive Rupture Model of Soft Tissue Stress Relaxation

“…18 If fluid movement takes place on a local scale over timescales that are short compared to the duration of stress relaxation, this could result in the transmission of local stress from one region of the tissue to another. Even the classic Rouse viscoelastic theory 21 based on the relative movement of worm-like chains, known as reptation, would seem to fit within the current framework if one considers that reptation on a local scale could correspond to a local yield event. It should also be pointed out that if a collection of parallel fibers either increases its relaxation length or decreases its stiffness, the result under constant stress would be an increase in the length of the entire collection.…”

Nanocarrier Hydrodynamics and Binding in Targeted Drug Delivery: Challenges in Numerical Modeling and Experimental Validation

“…where Dh i is the relative angle formed between the i and i þ 1 links and the terms comprising of f i (hydrodynamic force on link i) and T i (hydrodynamic torque on link i) are the work done in translating (by displacement Dr i ) and rotating (by angular displacement DW i ) the center of mass of the ith link against the fluid; these terms may be determined from the stress and velocity distributions in the fluid obtained from solving the fluid equations discussed in the earlier section and also provided; for example, in Ref. [113]. The explicit coupling of hydrodynamic stress of the flow descriptions of the earlier section (through the computation of the force and torque terms) to the tether (link) dynamics through the definition of the energy function (Hamiltonian) E[h(s)] represents an explicit bridging of length-scales.…”