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

Doubly magic nuclei from Lattice QCD forces at MPS=M_{PS}=469 MeV/c2^2

We perform ab initio self-consistent Green's function calculations of the closed shell nuclei $^{\rm 4}$He, $^{\rm 16}$O and $^{\rm 40}$Ca, based on two-nucleon potentials derived from Lattice QCD simulations, in the flavor SU(3) limit and at the pseudo-scalar meson mass of 469~MeV/c$^{\rm 2}$. The nucleon-nucleon interaction is obtained using the HAL QCD method and its short-distance repulsion is treated by means of ladder resummations outside the model space. Our results show that this approach diagonalises ultraviolet degrees of freedom correctly. Therefore, ground state energies can be obtained from infrared extrapolations even for the relatively hard potentials of HAL QCD. Comparing to previous Brueckner Hartree-Fock calculations, the total binding energies are sensibly improved by the full account of many-body correlations. The results suggest an interesting possible behaviour in which nuclei are unbound at very large pion masses and islands of stability appear at first around the traditional doubly-magic numbers when the pion mass is lowered toward its physical value. The calculated one-nucleon spectral distributions are qualitatively close to those of real nuclei even for the pseudo-scalar meson mass considered here.Comment: 7 pages, 4 figures, RIKEN-QHP-286, RIKEN-iTHEMS-Report-1

Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore

The advent of solid state nanodevices allows for interrogating the physico-chemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been recently characterized by theoretical and computational studies of model polymer chains free from self-entanglement. However, sufficiently long equilibrated chains are necessarily knotted. The impact of such topological "defects" on the translocation process is largely unexplored, and is addressed in this study. By using Brownian dynamics simulations on a coarse-grained polyelectrolyte model we show that knots, despite being trapped at the pore entrance, do not "per se" cause the translocation process to jam. Rather, knots introduce an effective friction that increases with the applied force, and practically halts the translocation above a threshold force. The predicted dynamical crossover, which is experimentally verifiable, is of relevance in applicative contexts, such as DNA nanopore sequencing.Comment: 6 pages; 7 figure

Two Langevin equations in the Doi-Peliti formalism

A system-size expansion method is incorporated into the Doi-Peliti formalism for stochastic chemical kinetics. The basic idea of the incorporation is to introduce a new decomposition of unity associated with a so-called Cole-Hopf transformation. This approach elucidates a relationship between two different Langevin equations; one is associated with a coherent-state path-integral expression and the other describes density fluctuations. A simple reaction scheme $X \rightleftarrows X+X$ is investigated as an illustrative example.Comment: 14page

A Laplace Transform Method for Molecular Mass Distribution Calculation from Rheometric Data

Polydisperse linear polymer melts can be microscopically described by the tube model and fractal reptation dynamics, while on the macroscopic side the generalized Maxwell model is capable of correctly displaying most of the rheological behavior. In this paper, a Laplace transform method is derived and different macroscopic starting points for molecular mass distribution calculation are compared to a classical light scattering evaluation. The underlying assumptions comprise the modern understanding on polymer dynamics in entangled systems but can be stated in a mathematically generalized way. The resulting method is very easy to use due to its mathematical structure and it is capable of calculating multimodal molecular mass distributions of linear polymer melts

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

Enhanced diffusion by reciprocal swimming

Purcell's scallop theorem states that swimmers deforming their shapes in a time-reversible manner ("reciprocal" motion) cannot swim. Using numerical simulations and theoretical calculations we show here that in a fluctuating environment, reciprocal swimmers undergo, on time scales larger than that of their rotational diffusion, diffusive dynamics with enhanced diffusivities, possibly by orders of magnitude, above normal translational diffusion. Reciprocal actuation does therefore lead to a significant advantage over non-motile behavior for small organisms such as marine bacteria

Effective Medium Theory of Filamentous Triangular Lattice

We present an effective medium theory that includes bending as well as stretching forces, and we use it to calculate mechanical response of a diluted filamentous triangular lattice. In this lattice, bonds are central-force springs, and there are bending forces between neighboring bonds on the same filament. We investigate the diluted lattice in which each bond is present with a probability $p$. We find a rigidity threshold $p_b$ which has the same value for all positive bending rigidity and a crossover characterizing bending-, stretching-, and bend-stretch coupled elastic regimes controlled by the central-force rigidity percolation point at $p_{\textrm{CF}} \simeq 2/3$ of the lattice when fiber bending rigidity vanishes.Comment: 15 pages, 9 figure

Dynamics of end-linked star polymer structures

In this work we focus on the dynamics of macromolecular networks formed by end-linking identical polymer stars. The resulting macromolecular network can then be viewed as consisting of spacers which connect branching points (the cores of the stars). We succeed in analyzing exactly, in the framework of the generalized Gaussian model, the eigenvalue spectrum of such networks. As applications we focus on several topologies, such as regular networks and dendrimers; furthermore, we compare the results to those found for regular hyperbranched structures. In so doing, we also consider situations in which the beads of the cores differ from the beads of the spacers. The analytical procedure which we use involves an exact real-space renormalization, which allows to relate the star-network to a (much simpler) network, in which each star is reduced to its core. It turns out that the eigenvalue spectrum of the star-polymer structure consists of two parts: One follows in terms of polynomial equations from the relaxation spectrum of the corresponding renormalized structure, while the second part involves the motion of the spacer chains themselves. Finally, we show exemplarily the situation for copolymeric dendrimers, calculate their spectra, and from them their storage and the loss moduli.Comment: 15 pages, 11 eps-figures include

Kinetic Accessibility of Buried DNA Sites in Nucleosomes

Using a theoretical model for spontaneous partial DNA unwrapping from histones, we study the transient exposure of protein-binding DNA sites within nucleosomes. We focus on the functional dependence of the rates for site exposure and reburial on the site position, which is measurable experimentally and pertinent to gene regulation. We find the dependence to be roughly described by a random walker model. Close inspection reveals a surprising physical effect of flexibility-assisted barrier crossing, which we characterize within a toy model, the "semiflexible Brownian rotor."Comment: final version as published in Phys. Rev. Let