Related papers: The emergent dynamics of double-folded randomly br…
Multifractal properties of the distribution of topological invariants for a model of trajectories randomly entangled with a nonsymmetric lattice of obstacles are investigated. Using the equivalence of the model to random walks on a locally…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
We consider flexible branched polymer, with quenched branch structure, and show that its conformational entropy as a function of its gyration radius $R$, at large $R$, obeys, in the scaling sense, $\Delta S \sim R^2/(a^2L)$, with $a$ bond…
Evolving structure and rheology across Kuhn scale interfaces in entangled polymer fluids under flow play a prominent role in processing of manufactured plastics, and have numerous other applications. Quantitative tracking of chain…
An off-lattice Monte Carlo algorithm for solutions of equilibrium polymers (EP) is proposed. At low and moderate densities this is shown to reproduce faithfully the (static) properties found recently for flexible linear EP using a lattice…
We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries.…
We propose a new toy model of a heteropolymer chain capable of forming planar secondary structures typical for RNA molecules. In this model the sequential intervals between neighboring monomers along a chain are considered as quenched…
The symbiotic branching model describes the dynamics of a spatial two-type population, where locally particles branch at a rate given by the frequency of the other type combined with nearest-neighbour migration. This model generalizes…
We present a mean-field dynamical theory for single semiflexible polymers which can precisely capture, without fitting parameters, recent fluorescence correlation spectroscopy results on single monomer kinetics of DNA strands in solution.…
We consider random walks in dynamic random environments, with an environment generated by the time-reversal of a Markov process from the oriented percolation universality class. If the influence of the random medium on the walk is small in…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
In this work we study the stochastic process of two-species coagulation. This process consists in the aggregation dynamics taking place in a ring. Particles and clusters of particles are set in this ring and they can move either clockwise…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
Branching processes are used to model diverse social and physical scenarios, from extinction of family names to nuclear fission. However, for a better description of natural phenomena, such as viral epidemics in cellular tissues, animal…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
A directed polymer is allowed to branch, with configurations determined by global energy optimization and disorder. A finite size scaling analysis in 2D shows that, if disorder makes branching more and more favorable, a critical transition…
We consider an explicit model of a semiflexible filament moving in two dimensions on a gliding assay of motor proteins, which attach to and detach from filament segments stochastically, with a detachment rate that depends on the local load…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…