Related papers: Entropy-driven phase behaviour of all-DNA associat…
By using the transfer matrix approach, we investigate the asymptotic behavior of the entropy of flexible chains with $M$ monomers each placed on stripes. In the limit of high density of monomers, we study the behavior of the entropy as a…
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 perform numerical simulations of isolated, partially active polymers, driven out-of-equilibrium by a fraction of their monomers. We show that, if the active beads are all gathered in a contiguous block, the position of the section along…
We study theoretically the replication of Kinetoplast DNA consisting of several thousands separate mini-circles found in organisms of the class Kinetoplastida. When the cell is not actively dividing these are topologically connected in a…
Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…
We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor…
Entangled states are ubiquitous amongst fibrous materials, whether naturally occurring (keratin, collagen, DNA) or synthetic (nanotube assemblies, elastane). A key mechanical characteristic of these systems is their ability to reorganise in…
Active systems are characterized by a continuous production of entropy at steady state. We study the statistics of entropy production within a lattice-based model of interacting active particles that is capable of motility-induced phase…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
Recently developed linker-mediated vitrimers based on metathesis of dioxaborolanes with various commercially available polymers have shown both good processability and outstanding performance, such as mechanical, thermal, and chemical…
In many biopolymer solutions, attractive interactions that stabilize finite-sized clusters at low concentrations also promote phase separation at high concentrations. Here we study a model biopolymer system that exhibits the opposite…
Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
We develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes…
The electrical conductance of molecular junctions may strongly depend on the temperature, and weakly on molecular length, under two distinct mechanisms: phase-coherent resonant conduction, with charges proceeding via delocalized molecular…
Graphyne is a generic name for a carbon allotrope family of 2D structures, where acetylenic groups connect benzenoid rings, with the coexistence of sp and sp2 hybridized carbon atoms. In this work we have investigated, through fully…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
Reactive dopant atoms embedded in inert host metal surfaces define the active sites in single-atom alloys (SAAs), yet SAA synthesis remains challenging. To address this, we elucidate how dopant adatoms deposited on Cu and Ag surfaces become…
Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific…