Related papers: Manipulating a single adsorbed DNA for a critical …
A universality class describing the statistics of the merging of two single polymer strands to a double polymer strand and the reverse process is examined. The polymers can have an intrinsic direction, and the simpler case, where only…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
We describe some recent results concerning the statistical properties of a self-interacting polymer stretched by an external force. We concentrate mainly on the cases of purely attractive or purely repulsive self-interactions, but our…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
We examine the statistics of conformations of a linear polymer in a solvent. The polymer is allowed to form double polymers. We closely follow a classical technique to derive a field theory for the problem from an $O\left(n\right)$…
We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the…
The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates…
The critical point of the condensation transition for linear molecules adsorbed on square lattices, was studied by using an adaptation of the Histogram Reweighting technique. The results were obtained by means of grand canonical Monte Carlo…
Applying a force to certain supramolecular bonds may initially stabilize them, manifested by a lower dissociation rate. We show that this behavior, known as catch bonding and by now broadly reported in numerous biophysics bonds, is…
We use a phenomenological field theory, reflecting the symmetries and conservation laws of sandpiles, to compare the driven dissipative sandpile, widely studied in the context of self-organized criticality, with the corresponding…
Monte Carlo simulations using an explicit solvent model indicate a new pathway for translocation of a polymer chain through a lipid bilayer. We consider a polymer chain composed of repeat units with a given hydrophobicity and a…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
In biological cells, DNA replication is carried out by the replisome, a protein complex encompassing multiple DNA polymerases. DNA replication is semi-discontinuous: a DNA polymerase synthesizes one (leading) strand of the DNA continuously,…
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
It is shown that hadronic matter formed at high temperatures, according to the prescription of the statistical bootstrap principle, develops a critical point at nonzero baryon chemical potential. The location of the critical point in the…
We study the growth of slip line in a plastically deforming crystal by numerical simulation of a double-ended pile-up model with a dislocation source at one end, and an absorbing wall at the other end. In presence of defects, the pile-up…