Brownian dynamics simulation of a polymer molecule in solution under elongational flow

Abstract

We use Brownian dynamics simulation to study coil-stretch transition of macromolecules in solution. Into a simple elongational flow field, we introduce freely jointed bead-rod chain model molecules in their coiled and stretched states, and follow the conformational changes. We find good agreement of our simulation results with the available theoretical predictions for low and high strain rates (⑀ ). At the intermediate elongation rates ͑near the onset of coil-stretch transition͒ of the flow field, we find that the residence time required for stretching of an initially coiled chain can be extremely large as compared to predicted (1ϩln(ͱN))⑀ Ϫ1, especially for the non-free-draining case. Hence, the chain conformation is dependent on the initial state of the chain molecule for residence time as long as 100⑀Ϫ1 . Thus, hysteresis is predicted when chain residence time in such an elongational flow field is limited, as in practical situations. Further, at such intermediate ⑀ , the chain molecule is seen to undergo Brownian fluctuation induced jumps between a randomly coiled state and another partially stretched state. This suggests the existence of more than one equilibrium conformation that is unstable to Brownian fluctuations.

The effects of shear flow on protein structure and function

“…84,93 In addition, the authors observed that whereas the grafted protein chains unfold through a series of intermediate states in uniform flow, consistent with that reported earlier, 90 synthetic helices unraveled smoothly with no detectable intermediate states. 91 This highlights the fact that proteins and homopolymers do indeed differ in their hydrodynamic properties in shear flow.…”

Effect of initial conformation, flow strength, and hydrodynamic interaction on polymer molecules in extensional flows

“…The values of ⑀ 1 for these representative simulations are different for the free-draining case (⑀ 1 ϭ0.02) and the non-free-draining case (⑀ 1 ϭ0.06), because coil-stretch transition behavior is dependent on HI, as seen in the previous paper. 8 The chosen ⑀ 1 here are much higher than ⑀ cs ͑0.003 and 0.022 for the free-draining and the non-free-draining cases, respectively 8 ͒ because the objective here is to examine the effect of chain folding that hinders the stretching process. The simulations were begun by starting with initially randomly coiled chains that were generated by successively joining 100 links.…”

“…͑8͔͒ with increase in strain rate, due to the smaller relative contribution of Brownian fluctuations. 8,28,29 Comparing Figs. 6͑a͒ and 8͑a͒, we find that most fold forming chains ͑i.e., other than chains 9 and 5͒, with the exception of chain 3, require higher strains for stretching at the higher strain rate ͓Figs.…”

“…If this strain is not sufficient for complete stretching of the polymer molecules, then the solution rheology is dependent on the extent and rate of stretching, and hence on the strain history of the solution. [8][9][10][11] Various models ͑dumbbells, bead-spring or bead-rod chains, etc.͒ are used to represent polymers, and in each case, predictions about stretching and rheology are made based on calculations of averages. 2 Simulations are often used in the case of more complicated models or flow situations.…”

Kinetics of hexagonal cylinders to face-centered cubic spheres transition of triblock copolymer in selective solvent: Brownian dynamics simulation

“…Thus compared to all atom molecular dynamics, BD is more efficient and saves computational time in simulating the polymer solution system. For example, BD methods have been used for simulating polymer flow, 16 phase diagram in surfactants modeled as sphere tethered to a chain 15,17 and in block copolymer melts, 14 solution, 18 and polymer brushes systems. 11,19 To the best of our knowledge, BD simulation has not been reported to study the kinetics of the HEX cylinders to FCC or BCC spheres transition for block copolymer in a selective solvent system.…”