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Modeling of polymer chains has received a lot of attention in mathematics. In fact, probabilistic models that naturally arise in statistical mechanics have been widely studied by mathematicians for the very challenging and novel problems…
We consider the passage of long polymers of length N through a hole in a membrane. If the process is slow, it is in principle possible to focus on the dynamics of the number of monomers s on one side of the membrane, assuming that the two…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
Random walks are a fundamental model in applied mathematics and are a common example of a Markov chain. The limiting stationary distribution of the Markov chain represents the fraction of the time spent in each state during the stochastic…
Motivated by experiments in which a polynucleotide is driven through a proteinaceous pore by an electric field, we study the diffusive motion of a polymer threaded through a narrow channel with which it may have strong interactions. We show…
We consider the translocation dynamics of a polymer chain forced through a nanopore by an external force on its head monomer on the trans side. For a proper theoretical treatment we generalize the iso-flux tension propagation (IFTP) theory…
We explore the dynamics of a tracer in an active particle harmonic chain, investigating the influence of interactions. Our analysis involves calculating mean-squared displacements (MSD) and space-time correlations through Green's function…
We present a Markov-chain analysis of blockwise-stochastic algorithms for solving partially block-separable optimization problems. Our main contributions to the extensive literature on these methods are statements about the Markov operators…
A probabilistic method for solving time-dependent load-transfer models of fracture is developed. It is applicable to any rule of load redistribution, i.e, local, hierarchical, etc. In the new method, the fluctuations are generated during…
It has been established that the entangled polymer dynamics can be reasonably described by single chain models such as tube and slip-link models. Although the entanglement effect is a result of the hard-core interaction between chains,…
We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of external driving force, we consider a polymer which is initially placed in the middle of the pore…
We introduce an efficient, scalable Monte Carlo algorithm to simulate cross-linked architectures of freely-jointed and discrete worm-like chains. Bond movement is based on the discrete tractrix construction, which effects conformational…
We investigate the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. An attractive interaction can greatly improve translocation probability. At the same time, it also increases…
In this study, an efficient reanalysis strategy for dynamic topology optimization is proposed. Compared with other related studies, an online successive dynamic reanalysis method and POD-based approximate dynamic displacement strategy are…
A recently proposed generalised continuum theory of curved dislocations describes the spatial and temporal evolution of statistically stored and geometrically necessary dislocation densities as well as the curvature. The dynamics follow…
This work explores a synchronization-like phenomenon induced by common noise for continuous-time Markov jump processes given by chemical reaction networks. A corresponding random dynamical system is formulated in a two-step procedure, at…
We theoretically investigate the looping dynamics of a linear polymer immersed in a viscoelastic fluid. The dynamics of the chain is governed by a Rouse model with a fractional memory kernel recently proposed by Weber et al. (S. C. Weber,…
Information transfer is an essential factor in determining the robustness of collective behaviour in biological systems with distributed control. The most direct way to study the information transfer mechanisms is to experimentally detect…
A fundamental theory is presented for the mechanical response of polymer networks undergoing large deformation which seamlessly integrates statistical mechanical principles with macroscopic thermodynamic constitutive theory. Our formulation…
We investigate an intermittent stochastic process, in which the diffusive motion with time-dependent diffusion coefficient $D(t)\sim t^{\alpha-1}$, $\alpha>0$ (scaled Brownian motion), is stochastically reset to its initial position and…