The unreasonable effectiveness of equilibrium-like theory for interpreting non-equilibrium experiments

There has been great interest in applying the results of statistical mechanics to single molecule experiements. Recent work has highlighted so-called non-equilibrium work-energy relations and Fluctuation Theorems which take on an equilibrium-like (time independent) form. Here I give a very simple heuristic example where an equilibrium result (the barometric law for colloidal particles) arises from theory describing the {\em thermodynamically} non-equilibrium phenomenon of a single colloidal particle falling through solution due to gravity. This simple result arises from the fact that the particle, even while falling, is in {\em mechanical} equilibrium (gravitational force equal the viscous drag force) at every instant. The results are generalized by appeal to the central limit theorem. The resulting time independent equations that hold for thermodynamically non-equilibrium (and even non-stationary) processes offer great possibilities for rapid determination of thermodynamic parameters from single molecule experiments.Comment: 6 page

A field theoretic approach to master equations and a variational method beyond the Poisson ansatz

We develop a variational scheme in a field theoretic approach to a stochastic process. While various stochastic processes can be expressed using master equations, in general it is difficult to solve the master equations exactly, and it is also hard to solve the master equations numerically because of the curse of dimensionality. The field theoretic approach has been used in order to study such complicated master equations, and the variational scheme achieves tremendous reduction in the dimensionality of master equations. For the variational method, only the Poisson ansatz has been used, in which one restricts the variational function to a Poisson distribution. Hence, one has dealt with only restricted fluctuation effects. We develop the variational method further, which enables us to treat an arbitrary variational function. It is shown that the variational scheme developed gives a quantitatively good approximation for master equations which describe a stochastic gene regulatory network.Comment: 13 pages, 2 figure

Thermally activated breakdown in a simple polymer model

We consider the thermally activated fragmentation of a homopolymer chain. In our simple model the dynamics of the intact chain is a Rouse one until a bond breaks and bond breakdown is considered as a first passage problem over a barrier to an absorbing boundary. Using the framework of the Wilemski-Fixman approximation we calculate activation times of individual bonds for free and grafted chains. We show that these times crucially depend on the length of the chain and the location of the bond yielding a minimum at the free chain ends. Theoretical findings are qualitatively confirmed by Brownian dynamics simulations

Viscoplasticity and large-scale chain relaxation in glassy-polymeric strain hardening

A simple theory for glassy polymeric mechanical response which accounts for large scale chain relaxation is presented. It captures the crossover from perfect-plastic response to strong strain hardening as the degree of polymerization $N$ increases, without invoking entanglements. By relating hardening to interactions on the scale of monomers and chain segments, we correctly predict its magnitude. Strain activated relaxation arising from the need to maintain constant chain contour length reduces the $N$ dependence of the characteristic relaxation time by a factor $\sim \dot\epsilon N$ during active deformation at strain rate $\dot\epsilon$. This prediction is consistent with results from recent experiments and simulations, and we suggest how it may be further tested experimentally.Comment: The theoretical treatment of the mechanical response has been significantly revised, and the arguments for coherent relaxation during active deformation made more transparen

Gaussian approximation for finitely extensible bead-spring chains with hydrodynamic interaction

The Gaussian Approximation, proposed originally by Ottinger [J. Chem. Phys., 90 (1) : 463-473, 1989] to account for the influence of fluctuations in hydrodynamic interactions in Rouse chains, is adapted here to derive a new mean-field approximation for the FENE spring force. This "FENE-PG" force law approximately accounts for spring-force fluctuations, which are neglected in the widely used FENE-P approximation. The Gaussian Approximation for hydrodynamic interactions is combined with the FENE-P and FENE-PG spring force approximations to obtain approximate models for finitely-extensible bead-spring chains with hydrodynamic interactions. The closed set of ODE's governing the evolution of the second-moments of the configurational probability distribution in the approximate models are used to generate predictions of rheological properties in steady and unsteady shear and uniaxial extensional flows, which are found to be in good agreement with the exact results obtained with Brownian dynamics simulations. In particular, predictions of coil-stretch hysteresis are in quantitative agreement with simulations' results. Additional simplifying diagonalization-of-normal-modes assumptions are found to lead to considerable savings in computation time, without significant loss in accuracy.Comment: 26 pages, 17 figures, 2 tables, 75 numbered equations, 1 appendix with 10 numbered equations Submitted to J. Chem. Phys. on 6 February 200

Shear-stress controlled dynamics of nematic complex fluids

Based on a mesoscopic theory we investigate the non-equilibrium dynamics of a sheared nematic liquid, with the control parameter being the shear stress $\sigma_{\mathrm{xy}}$ (rather than the usual shear rate, $\dot\gamma$). To this end we supplement the equations of motion for the orientational order parameters by an equation for $\dot\gamma$, which then becomes time-dependent. Shearing the system from an isotropic state, the stress- controlled flow properties turn out to be essentially identical to those at fixed $\dot\gamma$. Pronounced differences when the equilibrium state is nematic. Here, shearing at controlled $\dot\gamma$ yields several non-equilibrium transitions between different dynamic states, including chaotic regimes. The corresponding stress-controlled system has only one transition from a regular periodic into a stationary (shear-aligned) state. The position of this transition in the $\sigma_{\mathrm{xy}}$-$\dot\gamma$ plane turns out to be tunable by the delay time entering our control scheme for $\sigma_{\mathrm{xy}}$. Moreover, a sudden change of the control method can {\it stabilize} the chaotic states appearing at fixed $\dot\gamma$.Comment: 10 pages, 11 figure

Strain-dependent localization, microscopic deformations, and macroscopic normal tensions in model polymer networks

We use molecular dynamics simulations to investigate the microscopic and macroscopic response of model polymer networks to uniaxial elongations. By studying networks with strands lengths ranging from $N_s=20$ to 200 we cover the full crossover from cross-link to entanglement dominated behavior. Our results support a recent version of the tube model which accounts for the different strain dependence of chain localization due to chemical cross-links and entanglements

Force-Extension Relation and Plateau Modulus for Wormlike Chains

We derive the linear force-extension relation for a wormlike chain of arbitrary stiffness including entropy elasticity, bending and thermodynamic buckling. From this we infer the plateau modulus $G^0$ of an isotropic entangled solution of wormlike chains. The entanglement length $L_e$ is expressed in terms of the characteristic network parameters for three different scaling regimes in the entangled phase. The entanglement transition and the concentration dependence of $G^0$ are analyzed. Finally we compare our findings with experimental data.Comment: 5 pages, 1 eps-figure, to appear in PR

DNA-Protein Binding Rates: Bending Fluctuation and Hydrodynamic Coupling Effects

We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory focuses on two competing effects: polymer shape fluctuations, which speed up association, and the hydrodynamic coupling between the diffusing particle and the chain, which slows down association. Polymer bending fluctuations are described using a mean field dynamical theory, while the hydrodynamic coupling between polymer and particle is incorporated through a simple heuristic approximation. Both of these we validate through comparison with Brownian dynamics simulations. Neither of the effects has been fully considered before in the biophysical context, and we show they are necessary to form accurate estimates of reaction processes. The association rate depends on the stiffness of the polymer and the particle size, exhibiting a maximum for intermediate persistence length and a minimum for intermediate particle radius. In the parameter range relevant to DNA-protein binding, the rate increase is up to 100% compared to the Smoluchowski result for simple center-of-mass motion. The quantitative predictions made by the theory can be tested experimentally.Comment: 21 pages, 11 figures, 1 tabl