Related papers: Cross-linker mediated compaction and local morphol…
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is…
We investigate the kinetics of a polymer collapse due to the formation of irreversible crosslinks between its monomers. Using the contact probability $P(s)$ as a scale-dependent order parameter depending on the chemical distance $s$, our…
Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures…
Within self-consistent field theory we study the phase behaviour of a symmetric binary AB polymer blend confined into a thin film. The film surfaces interact with the monomers via short range potentials. One surface attracts the A component…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
Polymer translocation in crowded environments is a ubiquitous phenomenon in biological systems. We studied polymer translocation through a pore in free, one-sided (asymmetric), and two-sided (symmetric) crowded environments. Extensive…
Despite their considerable practical and biological applications, the link between molecular properties, assembly conditions and self-organized structure in confined polymer solutions remains elusive. Here, we explore the lyotropic nematic…
In polymer science, cross-linking of polymer chains yields a substantially modified system compared to the one-dimensional constituent chains, due to the increase of dimensionality and effective seeding by defects (cross-linking sites).…
We examine the mechanism of bundling of cytoskeletal actin filaments by two representative bundling proteins, fascin and espin. Small-angle X-ray studies show that increased binding from linkers drives a systematic \textit{overtwist} of…
Molecular dynamic simulation enables one to correlate the evolution of the micro-structure with anisotropic stress when a material is subject to strain. The anisotropic stress due to a constant strain-rate load in a cross-linked polymer is…
We study a lattice model of a single magnetic polymer chain, where Ising spins are located on the sites of a lattice self-avoiding walk in $d=2$. We consider the regime where both conformations and magnetic degrees of freedom are dynamic,…
The cell nucleus houses the chromosomes, which are linked to a soft shell of lamin filaments. Experiments indicate that correlated chromosome dynamics and nuclear shape fluctuations arise from motor activity. To identify the physical…
The idea of creating magnetically controllable colloids whose rheological properties can be finely tuned on the nano- or micro-scale has caused a lot of experimental and theoretical effort. The latter resulted in systems whose building…
We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes and the vertical distance $d$…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…
The selective solute partitioning within a polymeric network is of key importance to applications in which controlled release or uptake of solutes in a responsive hydrogel is required. In this work we investigate the impact of cross-links…
Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…
We present simulations on a binary blend of bead-spring polymer chains. The introduction of monomer size disparity yields very different relaxation times for each component of the blend. Competition between two different arrest mechanisms,…