Rouse Modes of Self-avoiding Flexible Polymers

Using a lattice-based Monte Carlo code for simulating self-avoiding flexible polymers in three dimensions in the absence of explicit hydrodynamics, we study their Rouse modes. For self-avoiding polymers, the Rouse modes are not expected to be statistically independent; nevertheless, we demonstrate that numerically these modes maintain a high degree of statistical independence. Based on high-precision simulation data we put forward an approximate analytical expression for the mode amplitude correlation functions for long polymers. From this, we derive analytically and confirm numerically several scaling properties for self-avoiding flexible polymers, such as (i) the real-space end-to-end distance, (ii) the end-to-end vector correlation function, (iii) the correlation function of the small spatial vector connecting two nearby monomers at the middle of a polymer, and (iv) the anomalous dynamics of the middle monomer. Importantly, expanding on our recent work on the theory of polymer translocation, we also demonstrate that the anomalous dynamics of the middle monomer can be obtained from the forces it experiences, by the use of the fluctuation-dissipation theorem.Comment: 16 pages (double spaced), 5 figures, small changes and corrections, to appear in J. Chem. Phy

Chain motion and viscoelasticity in highly entangled solutions of semiflexible rods

Brownian dynamics simulations are used to study highly entangled solutions of semiflexible polymers. Bending fluctuations of semiflexible rods are signficantly affected by entanglement only above a concentration $c^{**}$, where $c^{**}\sim 10^{3}L^{-3}$ for chains of similar length $L$ and persistence length. For $c > c^{**}$, the tube radius $R_{e}$ approaches a dependence $R_{e} \propto c^{-3/5}$, and the linear viscoelastic response develops an elastic contribution that is absent for $c < c^{**}$. Experiments on isotropic solutions of $F$-actin span concentrations near $c^{**}$ for which the predicted asymptotic scaling of the plateau modulus $G \propto c^{7/5}$ is not yet valid.Comment: 4 pages, 5 figures, submitted to PR

Response of Single Polymers to Localized Step Strains

In this paper, the response of single three-dimensional phantom and self-avoiding polymers to localized step strains are studied for two cases in the absence of hydrodynamic interactions: (i) polymers tethered at one end with the strain created at the point of tether, and (ii) free polymers with the strain created in the middle of the polymer. The polymers are assumed to be in their equilibrium state before the step strain is created. It is shown that the strain relaxes as a power-law in time $t$ as $t^{-\eta}$. While the strain relaxes as $1/t$ for the phantom polymer in both cases; the self-avoiding polymer relaxes its strain differently in case (i) than in case (ii): as $t^{-(1+\nu)/(1+2\nu)}$ and as $t^{-2/(1+2\nu)}$ respectively. Here $\nu$ is the Flory exponent for the polymer, with value $\approx0.588$ in three dimensions. Using the mode expansion method, exact derivations are provided for the $1/t$ strain relaxation behavior for the phantom polymer. However, since the mode expansion method for self-avoiding polymers is nonlinear, similar theoretical derivations for the self-avoiding polymer proves difficult to provide. Only simulation data are therefore presented in support of the $t^{-(1+\nu)/(1+2\nu)}$ and the $t^{-2/(1+2\nu)}$ behavior. The relevance of these exponents for the anomalous dynamics of polymers are also discussed.Comment: 10 pages, 1 figure; minor errors corrected, introduction slightly modified and references expanded; to appear in Phys. Rev.

The lattice QCD simulation of the quark-gluon mixed condensate g<\bar{q} \sigma G q> at finite temperature and the phase transition of QCD

The thermal effects on the quark-gluon mixed condensate g<\bar{q} \sigma G q>, which is another chiral order parameter, are studied using the SU(3)c lattice QCD with the Kogut-Susskind fermion at the quenched level. We perform the accurate measurement of the mixed condensate as well as the quark condensate for 0MeV<=T<=500MeV. We observe the sharp decrease of both the condensates around T_c \simeq 280MeV, while the thermal effects below T_c are found to be weak. We also find that the ratio m_0^2 = g<\bar{q} \sigma G q>/ is almost independent of the temperature even in the very vicinity of T_c, which indicates that the two condensates have nontrivial similarity in the chiral behaviors. We also present the correlation between the condensates and the Polyakov loop to understand the vacuum structure of QCD.Comment: Talk given at the XXII International Symposium on Lattice Field Theory (LATTICE 2004), Fermilab, Batavia, Illinois, USA, 21-26 June 2004, Lattice2004(non-zero), 3 pages, 3 figure

Field-theoretical approach to a dense polymer with an ideal binary mixture of clustering centers

We propose a field-theoretical approach to a polymer system immersed in an ideal mixture of clustering centers. The system contains several species of these clustering centers with different functionality, each of which connects a fixed number segments of the chain to each other. The field-theory is solved using the saddle point approximation and evaluated for dense polymer melts using the Random Phase Approximation. We find a short-ranged effective inter-segment interaction with strength dependent on the average segment density and discuss the structure factor within this approximation. We also determine the fractions of linkers of the different functionalities.Comment: 27 pages, 9 figures, accepted on Phys. Rev.

On a modification method of Lefschetz thimbles

The QCD at finite density is not well understood yet, where standard Monte Carlo simulation suffers from the sign problem. In order to overcome the sign problem, the method of Lefschetz thimble has been explored. Basically, the original sign problem can be less severe in a complexified theory due to the constancy of the imaginary part of an action on each thimble. However, global phase factors assigned on each thimble still remain. Their interference is not negligible in a situation where a large number of thimbles contribute to the partition function, and this could also lead to a sign problem.In this study, we propose a method to resolve this problem by modifying the structure of Lefschetz thimbles such that only a single thimble is relevant to the partition function. It can be shown that observables measured in the original and modified theories are connected by a simple identity. We exemplify that our method works well in a toy model.Comment: 7 pages, 4 figures, talk presented at the 35th International Symposium on Lattice Field Theory, 18-24 June 2017, Granada, Spai

Non-equilibrium tube length fluctuations of entangled polymers

We investigate the nonequilibrium tube length fluctuations during the relaxation of an initially stretched, entangled polymer chain. The time-dependent variance $\sigma^2$ of the tube length follows in the early-time regime a simple universal power law $\sigma^2 = A \sqrt{t}$ originating in the diffusive motion of the polymer segments. The amplitude $A$ is calculated analytically both from standard reptation theory and from an exactly solvable lattice gas model for reptation and its dependence on the initial and equilibrium tube length respectively is discussed. The non-universality suggests the measurement of the fluctuations (e.g. using flourescence microscopy) as a test for reptation models.Comment: 12 pages, 2 figures. Minor typos correcte

Kinetic Regimes and Cross-Over Times in Many-Particle Reacting Systems

We study kinetics of single species reactions ("A+A -> 0") for general local reactivity Q and dynamical exponent z (rms displacement x_t ~ t^{1/z}.) For small molecules z=2, whilst z=4,8 for certain polymer systems. For dimensions d above the critical value d_c=z, kinetics are always mean field (MF). Below d_c, the density n_t initially follows MF decay, n_0 - n_t ~ n_0^2 Q t. A 2-body diffusion-controlled regime follows for strongly reactive systems (Q>Qstar ~ n_0^{(z-d)/d}) with n_0 - n_t ~ n_0^2 x_t^d. For Q<Qstar, MF kinetics persist, with n_t ~ 1/Qt. In all cases n_t ~ 1/x_t^d at the longest times. Our analysis avoids decoupling approximations by instead postulating weak physically motivated bounds on correlation functions.Comment: 10 pages, 1 figure, uses bulk2.sty, minor changes, submitted to Europhysics Letter