11,520 research outputs found

### 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

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