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This paper presents a theoretical analysis of the closure kinetics of a polymer with hydrodynamic interactions. This analysis, which takes into account the non-Markovian dynamics of the end-to-end vector and relies on the preaveraging of the mobility tensor (Zimm dynamics), is shown to reproduce very accurately the results of numerical simulations of the complete nonlinear dynamics. It is found that Markovian treatments based on a Wilemski-Fixman approximation significantly overestimate cyclization times (up to a factor 2), showing the importance of memory effects in the dynamics. In addition, this analysis provides scaling laws of the mean first cyclization time (MFCT) with the polymer size N and capture radius b, which are identical in both Markovian and non-Markovian approaches. In particular, it is found that the scaling of the MFCT for large N is given by T - N3/2ln(N/b²), which differs from the case of the Rouse dynamics where T - N². The extension to the case of the reaction kinetics of a monomer of a Zimm polymer with an external target in a confined volume is also presented. [ABSTRACT FROM AUTHOR]

In this communication, we show that the residence time of a Brownian particle, defined as the cumulative time spent in a given region of space, can be optimized as a function of the diffusion coefficient. We discuss the relevance of this effect to several schematic experimental situations classified in nature—random or deterministic—both of the observation time and of the starting position of the Brownian particle. [ABSTRACT FROM AUTHOR]

The authors study an intermittent search process combining diffusion and “teleportation” phases in a d-dimensional spherical continuous system and in a regular lattice. The searcher alternates diffusive phases, during which targets can be discovered, and fast phases (teleportation) which randomly relocate the searcher, but do not allow for target detection. The authors show that this alternation can be favorable for minimizing the time of first discovery, and that this time can be optimized by a convenient choice of the mean waiting times of each motion phase. The optimal search strategy is explicitly derived in the continuous case and in the lattice case. Arguments are given to show that much more general intermittent motions do provide optimal search strategies in d dimensions. These results can be useful in the context of heterogeneous catalysis or in various biological examples of transport through membrane pores. [ABSTRACT FROM AUTHOR]

For diffusion-limited reversible A+A⇋B reactions we reexamine two fundamental concepts of classical chemical kinetics—the notion of “chemical equilibrium” and the “law of mass action.” We consider a general model with distance-dependent reaction rates, such that any pair of A particles, performing standard random walks on sites of a d-dimensional lattice and being at a distance μ apart of each other at time moment t, may associate forming a B particle at the rate k+(μ). In turn, any randomly moving B particle may spontaneously dissociate at the rate k-(λ) into a geminate pair of As “born” at a distance λ apart of each other. Within a formally exact approach based on Gardiner’s Poisson representation method we show that the asymptotic t=∞ state attained by such diffusion-limited reactions is generally not a true thermodynamic equilibrium, but rather a nonequilibrium steady state, and that the law of mass action is invalid. The classical concepts hold only in case when the ratio k+(μ)/k-(μ) does not depend on μ for any μ. [ABSTRACT FROM AUTHOR]

We investigate theoretically the physics of diffusion-limited intramolecular polymer reactions. The present work completes and goes beyond a previous study [T. Guérin, O. Bénichou, and R. Voituriez, Nat. Chem. 4, 568 (2012)] that showed that the distribution of the polymer conformations at the very instant of reaction plays a key role in the cyclization kinetics, and takes explicitly into account the non-Markovian nature of the reactant motion. Here, we present in detail this non-Markovian theory, and compare it explicitly with existing Markovian theories and with numerical stochastic simulations. A large focus is made on the description of the non-equilibrium reactive conformations, with both numerical and analytical tools. We show that the reactive conformations are elongated and are characterized by a spectrum with a slowly decreasing tail, implying that the monomers that neighbor the reactive monomers are significantly shifted at the instant of reaction. We complete the study by deriving explicit formulas for the reaction rates in the Markovian Wilemski-Fixman theory when the reactants are located in arbitrary positions in the chain. We also give a simple scaling argument to understand the existence of two regimes in the reaction time, that come from two possible behaviors of monomer motion, which can be either diffusive or subdiffusive. [ABSTRACT FROM AUTHOR]

Semiflexible polymer rings whose bonds obey both angular and dihedral restrictions [M. Dolgushev and A. Blumen, J. Chem. Phys. 138, 204902 (2013)], are treated under exact closure constraints. This allows us to obtain semianalytic results for their dynamics, based on sets of Langevin equations. The dihedral restrictions clearly manifest themselves in the behavior of the mean-square monomer displacement. The determination of the equilibrium ring conformations shows that the dihedral constraints influence the ring curvature, leading to compact folded structures. The method for imposing such constraints in Gaussian systems is very general and it allows to account for heterogeneous (site-dependent) restrictions. We show it by considering rings in which one site differs from the others.