A coarse-grained bead-spring-dashpot chain model with the dashpots representing the presence of internal friction, is solved exactly numerically, for the case of chains with more than two beads. Using a decoupling procedure to remove the explicit coupling of a bead's velocity with that of its nearest neighbors, the governing set of stochastic differential equations are solved with Brownian dynamics simulations to obtain material functions in oscillatory and steady simple shear flow. Simulation results for the real and imaginary components of the complex viscosity have been compared with the results of previously derived semi-analytical approximations, and the difference in the predictions are seen to diminish with an increase in the number of beads in the chain. The inclusion of internal friction results in a non-monotonous variation of the viscosity with shear rate, with the occurrence of continuous shear-thickening following an initial shear-thinning regime. The onset of shear-thickening in the first normal stress coefficient is pushed to lower shear rates with an increase in the internal friction parameter.
The motion of an adiabatic piston under dry friction is investigated to clarify the roles of dry friction in non-equilibrium steady states. We clarify that dry friction can reverse the direction of the piston motion and causes a discontinuity or a cusp-like singularity for velocity distribution functions of the piston. We also show that the heat fluctuation relation is modified under dry friction.
We report chain self-diffusion and viscosity data for sodium polystyrene sulfonate (NaPSS) in semidilute salt-free aqueous solutions measured by pulsed field gradient NMR and rotational rheometry respectively. The observed concentration dependence of $η$ and $D$ are consistent with the Rouse-Zimm scaling model with a concentration dependent monomeric friction coefficient. The concentration dependence of the monomeric friction coefficient exceeds that expected from free-volume models of diffusion, and its origin remains unclear. Correlation blobs and dilute chains with equivalent end-to-end dis…
In this paper, we propose a new derivation for the Green-Kubo relationship for the liquid-solid friction coefficient, characterizing hydrodynamic slippage at a wall. It is based on a general Langevin approach for the fluctuating wall velocity, involving a non-markovian memory kernel with vanishing time integral. The calculation highlights some subtleties of the wall-liquid dynamics, leading to superdiffusive motion of the fluctuating wall position.
We consider equilibrium relaxation properties of the end-to-end distance and of principal components in a one-dimensional polymer chain model with nonlinear interaction between the beads. While for the single-well potentials these properties are similar to the ones of a Rouse chain, for the double-well interaction potentials, modeling internal friction, they differ vastly from the ones of the harmonic chain at intermediate times and intermediate temperatures. This minimal description within a one-dimensional model mimics the relaxation properties found in much more complex polymer systems. Thu…
The Rouse model can be regarded as the standard model to describe the dynamics of a short polymer chain under melt conditions. In this contribution, we explicitly check one of the fundamental assumptions of this model, namely that of a uniform friction coefficient for all monomers, on the basis of MD simulation data of a poly(ethylene oxide) (PEO) melt. This question immediately arises from the fact that in a real polymer melt the terminal monomers have on average more intermolecular neighbors than the central monomers, and one would expect that exactly these details affect the precise value o…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This friction is termed as internal friction in the literature. Using a flexible Gaussian chain with internal friction we analyze the intra- chain reconfiguration and loop formation times for all three topology classes namely end-to- end, end-to-interior and interior-to-interior. In a nutshell, bypassing expensive simulations we show how simple models like that o…
We show that the correlated stochastic fluctuation of the friction coefficient can give rise to long-range directional motion of a particle undergoing Brownian random walk in a constant periodic energy potential landscape. The occurrence of this motion requires the presence of two additional independent bodies interacting with the particle via friction and via the energy potential, respectively, which can move relative to each other. Such three-body system generalizes the classical Brownian ratchet mechanism, which requires only two interacting bodies. In particular, we describe a simple two-l…
The Rouse model with internal friction (RIF), a widely used theoretical framework to interpret the effects of internal friction on conformational transitions in biomolecules, is shown to be an approximate treatment that is based on preaveraging internal friction. By comparison with Brownian dynamics simulations of an exact coarse-grained model that incorporates fluctuations in internal friction, the accuracy of the preaveraged model predictions is examined both at and away from equilibrium. While the two models predict intrachain autocorrelations that approach each other for long enough chain …
Recently single molecule experiments have shown the importance of internal friction in biopolymer dynamics. Such studies also suggested that the internal friction although independent of solvent viscosity has strong dependence on denaturant concentration. Recent simulations also support such propositions by pointing out weak interactions to be the origin of internal friction in proteins. Here we made an attempt to investigate how a single polymer chain with internal friction undergoes reconfiguration and looping dynamics in a confining potential which accounts for the presence of the denaturan…
We consider a phantom chain model of polymer with internal friction in a harmonic confinement and extend it to take care of effects of solvent quality following a mean field approach where an exponent $ν$ is introduced. The model termed as "Solvent Dependent Compacted Rouse with Internal Friction (SDCRIF)" is then used to calculate the reconfiguration time of a chain that relates to recent Förster resonance energy transfer (FRET) studies on folded and intrinsically disordered proteins (IDPs) and can account for the effects of solvent quality as well as the denaturant concentration on the recon…
We present a hybrid computational method for simulating the dynamics of macromolecules in solution which couples a mesoscale solver for the fluctuating hydrodynamics (FH) equations with molecular dynamics to describe the macromolecule. The two models interact through a dissipative Stokesian term first introduced by Ahlrichs and Dünweg [J. Chem. Phys. {\bf 111}, 8225 (1999)]. We show that our method correctly captures the static and dynamical properties of polymer chains as predicted by the Zimm model. In particular, we show that the static conformations are best described when the ratio $\frac…
We study the conformation and dynamics of a single polymer chain that is pulled by a constant force applied at its one end with the other end free. Such a situation is relevant to the growing technology of manipulating individual macromolecules, which offers a paradigm research for probing far-from-equilibrium responses of long flexible biological polymers. We first analyze the Rouse model for the Gaussian chains for which the exact analytical results can be obtained. More realistic features such as the finite extensibility, the excluded volume and the hydrodynamic interactions are taken into …
The existence of two types of internal friction wet and dry is revisited, and a simple protocol is proposed for distinguishing between the two types and extracting the appropriate internal friction coefficient. The scheme requires repeatedly stretching a polymer molecule, and measuring the average work dissipated in the process by applying the Jarzynski equality. The internal friction coefficient is then estimated from the average dissipated work in the extrapolated limit of zero solvent viscosity. The validity of the protocol is established through analytical calculations on a one-dimensional…
We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of external driving force, we consider a polymer which is initially placed in the middle of the pore and study the escape time $τ_e$ required for the polymer to completely exit the pore on either side. The distribution of the escape times is wide and has a long tail. We find that $τ_e$ scales with the chain length $N$ as $τ_e \sim N^{1+2ν}$, where $ν$ is the Flory exponent. For driven translocation, we concentrate on the influence of the friction coefficie…
Local chain structure and local environment play an important role in the dynamics of polymer chains in miscible blends. In general, the friction coefficients that describe the segmental dynamics of the two components in a blend differ from each other and from those of the pure melts. In this work, we investigate polymer blend dynamics with Monte Carlo simulations of a generalized bond-fluctuation model, where differences in the interaction energies between non-bonded nearest neighbors distinguish the two components of a blend. Simulations employing only local moves and respecting a non-bond c…
The effect of fluctuating internal viscosity and hydrodynamic interactions on a range of rheological properties of dilute polymer solutions is examined using a finitely extensible dumbbell model for a polymer. Brownian dynamics simulations are used to compute both transient and steady state viscometric functions in shear flow. The results enable a careful differentiation of the influence, on rheological properties, of solvent-mediated friction from that of a dissipative mechanism that is independent of solvent viscosity. In particular, hydrodynamic interactions have a significant influence on …
