Related papers: Polymer compaction and bridging-induced clustering…
We perform two-dimensional Langevin dynamics simulations of electric-field driven polymer translocation through an attractive nanopore. We investigate the effect of the location of the attractive region using different pore patterns. This…
We analyze the interaction of two conducting, charged polymer chains in solution using a minimal model for their electronic degrees of freedom. We show that a crossing of the two chains in which the polymers pass within Angstroms of each…
Extensive coarse grained molecular dynamics simulations are performed to investigate the conformational phase diagram of a neutral polymer in the presence of attractive crowders. We show that, for low crowded densities, the polymer…
Nano- to micro-sized particles with differently charged surface areas exhibit complex interaction patterns, characterized by both opposite-charge attraction and like-charge repulsion. While several successful models have been proposed in…
We consider a statistical mechanics model for biopolymers. Sophisticated polymer chains, such as DNA, have stiffness when they stretch chains. The Laplacian interaction is used to describe the stiffness. Also, the surface between two media…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring…
Patchy particles are an intriguing subject of study and indeed a model system in the field of soft matter physics. In recent years, patchy particle models have been applied to describe a wide variety of systems, including colloidal…
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show…
We use a coarse grained molecular model of supported lipid bilayers to study the formation of adhesion domains. We find that this process is a first order phase transition, triggered by a combination of pairwise short range attractive…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why…
The phase behaviour of a single large semiflexible polymer immersed in a suspension of spherical particles is studied. All interactions are simple excluded volume interactions and the diameter of the spherical particles is an order of…
Specific lipid environments are necessary for the establishment of protein signalling platforms in membranes, yet their origin has been highly debated. We present a continuum, exactly solvable model of protein induced local demixing of…
Nanoparticle agglomeration in a quiescent fluid is simulated by solving the Langevin equations of motion of a set of interacting monomers in the continuum regime. Monomers interact via a radial, rapidly decaying intermonomer potential. The…
Statistical analysis of protein-protein interactions shows anomalously high frequency of homodimers [Ispolatov, I., et al. (2005) Nucleic Acids Res 33, 3629-35]. Furthermore, recent findings [Wright, C.F., et al. (2005) Nature 438, 878-81]…
We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which…
Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…