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Chromatin and associated proteins constitute the highly folded structure of chromosomes. We consider a self-avoiding polymer model of the chromatin, segments of which may get cross-linked via protein binders that repel each other. The…
Kinetic-transport equations are, by now, standard models to describe the dynamics of populations of bacteria moving by run-and-tumble. Experimental observations show that bacteria increase their run duration when encountering an increasing…
We have studied the aging effect on the dynamics of unbinding of a double stranded directed polymer in a random medium. By using the Monte Carlo dynamics of a lattice model in two dimensions, for which disorder is known to be relevant, the…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
This paper is a follow-up work of arxiv.org/abs/2101.05949. We study a non-directed polymer model in random environments. The polymer is represented by a simple symmetric random walk $S$ on $\mathbb{Z}^d$ with $d\geq2$ and the random…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
Unconcatenated, unknotted polymer rings in the melt are subject to strong interactions with neighboring chains due to the presence of topological constraints. We study this by computer simulation using the bond-fluctuation algorithm for…
Soft glassy materials often consist of deformable objects. Here, we use a two-dimensional assembly of semi-flexible ring polymers as a model system to investigate how polydispersity in particle stiffness or size influences the onset of…
In many important cellular processes, including mRNA translation, gene transcription, phosphotransfer, and intracellular transport, biological "particles" move along some kind of "tracks". The motion of these particles can be modeled as a…
Star polymers can exhibit a heterogeneous dynamical behavior due to their internal structure. In this work we employ atomistic molecular dynamics simulations to study translational motion in non-entangled polystyrene and poly(ethylene…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
A system of two self and mutual interacting ring polymers, close together in space, can display several competing equilibrium phases and phase transitions. Using Monte Carlo simulations and combinatorial arguments on a corresponding lattice…
Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…
The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the Random Energy Model…
We investigate, using numerical simulations, the conformations of isolated active ring polymers. We find that the their behaviour depends crucially on their size: short rings ($N \lesssim$ 100) are swelled whereas longer rings ($N \gtrsim$…
We study the survival probability and the growth rate for branching random walks in random environment (BRWRE). The particles perform simple symmetric random walks on the $d$-dimensional integer lattice, while at each time unit, they split…
Non-spherical particles transported by an anisotropic turbulent flow preferentially align with the mean shear and intermittently tumble when the local strain fluctuates. Such an intricate behaviour is here studied for inertialess,…
The role of active stress on the conformational dynamics of a polymer has drawn significant interest due to its potential applications in understanding the energy landscape of protein structures, buckling of biopolymers, genomic spatial…
We propose a general class of co-evolving tree network models driven by local exploration where new vertices attach to the current network via randomly sampling a vertex and then exploring the graph for a random number of steps in the…