Mean-field solution of the parity-conserving kinetic phase transition in one dimension

A two-offspring branching annihilating random walk model, with finite reaction rates, is studied in one-dimension. The model exhibits a transition from an active to an absorbing phase, expected to belong to the $DP2$ universality class embracing systems that possess two symmetric absorbing states, which in one-dimensional systems, is in many cases equivalent to parity conservation. The phase transition is studied analytically through a mean-field like modification of the so-called {\it parity interval method}. The original method of parity intervals allows for an exact analysis of the diffusion-controlled limit of infinite reaction rate, where there is no active phase and hence no phase transition. For finite rates, we obtain a surprisingly good description of the transition which compares favorably with the outcome of Monte Carlo simulations. This provides one of the first analytical attempts to deal with the broadly studied DP2 universality class.Comment: 4 Figures. 9 Pages. revtex4. Some comments have been improve

The binding dynamics of tropomyosin on actin

We discuss a theoretical model for the cooperative binding dynamics of tropomyosin to actin filaments. Tropomyosin binds to actin by occupying seven consecutive monomers. The model includes a strong attraction between attached tropomyosin molecules. We start with an empty lattice and show that the binding goes through several stages. The first stage represents fast initial binding and leaves many small vacancies between blocks of bound molecules. In the second stage the vacancies annihilate slowly as tropomyosin molecules detach and re-attach. Finally the system approaches equilibrium. Using a grain-growth model and a diffusion-coagulation model we give analytical approximations for the vacancy density in all regimes.Comment: REVTeX, 10 pages, 9 figures; to appear in Biophysical Journal; minor correction

Anomalous Dynamics of Translocation

We study the dynamics of the passage of a polymer through a membrane pore (translocation), focusing on the scaling properties with the number of monomers $N$. The natural coordinate for translocation is the number of monomers on one side of the hole at a given time. Commonly used models which assume Brownian dynamics for this variable predict a mean (unforced) passage time $\tau$ that scales as $N^2$, even in the presence of an entropic barrier. However, the time it takes for a free polymer to diffuse a distance of the order of its radius by Rouse dynamics scales with an exponent larger than 2, and this should provide a lower bound to the translocation time. To resolve this discrepancy, we perform numerical simulations with Rouse dynamics for both phantom (in space dimensions $d=1$ and 2), and self-avoiding (in $d=2$) chains. The results indicate that for large $N$, translocation times scale in the same manner as diffusion times, but with a larger prefactor that depends on the size of the hole. Such scaling implies anomalous dynamics for the translocation process. In particular, the fluctuations in the monomer number at the hole are predicted to be non-diffusive at short times, while the average pulling velocity of the polymer in the presence of a chemical potential difference is predicted to depend on $N$.Comment: 9 pages, 9 figures. Submitted to Physical Review

Moment and SDP relaxation techniques for smooth approximations of problems involving nonlinear differential equations

Combining recent moment and sparse semidefinite programming (SDP) relaxation techniques, we propose an approach to find smooth approximations for solutions of problems involving nonlinear differential equations. Given a system of nonlinear differential equations, we apply a technique based on finite differences and sparse SDP relaxations for polynomial optimization problems (POP) to obtain a discrete approximation of its solution. In a second step we apply maximum entropy estimation (using moments of a Borel measure associated with the discrete solution) to obtain a smooth closed-form approximation. The approach is illustrated on a variety of linear and nonlinear ordinary differential equations (ODE), partial differential equations (PDE) and optimal control problems (OCP), and preliminary numerical results are reported

Diffusion-limited loop formation of semiflexible polymers: Kramers theory and the intertwined time scales of chain relaxation and closing

We show that Kramers rate theory gives a straightforward, accurate estimate of the closing time $\tau_c$ of a semiflexible polymer that is valid in cases of physical interest. The calculation also reveals how the time scales of chain relaxation and closing are intertwined, illuminating an apparent conflict between two ways of calculating $\tau_c$ in the flexible limit.Comment: Europhys. Lett., 2003 (in press). 8 pages, 3 figures. See also, physics/0101087 for physicist's approach to and the importance of semiflexible polymer looping, in DNA replicatio