Non-Markovian closure kinetics of flexible polymers with hydrodynamic interactions.

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.

Contact Kinetics in Fractal Macromolecules.

We consider the kinetics of first contact between two monomers of the same macromolecule. Relying on a fractal description of the macromolecule, we develop an analytical method to compute the mean first contact time for various molecular sizes. In our theoretical description, the non-Markovian feature of monomer motion, arising from the interactions with the other monomers, is captured by accounting for the nonequilibrium conformations of the macromolecule at the very instant of first contact.

Cyclization kinetics of Gaussian semiflexible polymer chains.

We consider the dynamics and the cyclization kinetics of Gaussian semiflexible chains, in which the interaction potential tends to align successive bonds. We provide asymptotic expressions for the cyclization time, for the eigenvalues and eigenfunctions, and for the mean square displacement at all time and length scales, with explicit dependence on the capture radius, on the positions of the reactive monomers in the chain, and on the finite number of beads. For the cyclization kinetics, we take into account non-Markovian effects by calculating the distribution of reactive conformations of the polymer, which are not taken into account in the classical Wilemski-Fixman theory.

Slow encounters of particle pairs in branched structures.

On infinite homogeneous structures, two random walkers meet with certainty if and only if the structure is recurrent; i.e., a single random walker returns to its starting point with probability 1.

Transport properties of continuous-time quantum walks on Sierpinski fractals.

We model quantum transport, described by continuous-time quantum walks (CTQWs), on deterministic Sierpinski fractals, differentiating between Sierpinski gaskets and Sierpinski carpets, along with their dual structures. The transport efficiencies are defined in terms of the exact and the average return probabilities, as well as by the mean survival probability when absorbing traps are present. In the case of gaskets, localization can be identified already for small networks (generations).