Related papers: Topological interactions between ring polymers: Im…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
Semi-flexible polymers in crowded environments exhibit complex dynamics that play a crucial role in various biological and material design processes. Based on the classic reptation theory, it is generally believed that semiflexible polymers…
We present a scheme comprised of a one-dimensional system with repulsive interactions, in which the formation of bound pairs can take place in an easily tunable fashion.By capacitively coupling a primary electronic quantum wire of interest…
The work in this article is inspired by a classical problem: the statistical physical properties of a closed polymer loop that is wound around a rod. Historically the preserved topology of this system has been addressed through…
Topological band theory has transformed our understanding of crystalline materials by classifying the connectivity and crossings of electronic energy levels. Extending these concepts to molecular systems has therefore attracted significant…
We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
The Mott transition, a metal-insulator transition due to strong electronic interaction, is observed in many materials without an accompanying change of system symmetry. An important open question in Mott's proposal is the role of long-range…
Polymer-related materials exhibit rich glassy behaviors at different length scales due to their various molecular structures and topological constraints. Recent studies have identified transient interpenetration of the long-chain rings…
We propose a simple mean-field theory for the structure of ring polymer melts. By combining the notion of topological volume fraction and a classical van der Waals theory of fluids, we take into account many body effects of topological…
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with…
Rotors are common in nature - from rotating membrane-proteins to superfluid-vortices. Yet, little is known about the collective dynamics of heterogeneous populations of rotors. Here, we show experimentally, numerically, and analytically…
We perform simulations to compute the effective potential between the centers-of-mass of two polymers with reversible bonds. We investigate the influence of the topology of the unbonded precursor (linear or ring) and the specific sequence…
The effect of topology on the collapse transition and instantaneous shape of an energy polydisperse polymer (a model heteropolymer) is studied by means of computer simulations. In particular, we consider three different chain topology,…
The principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to play a role in mammalian gene regulation. We investigated the 3-dimensional…
Simulations and Mode-Coupling Theory calculations, for a large range of the arm number $f$ and packing fraction $\eta$ have shown that the structural arrest and the dynamics of star polymers in a good solvent are extremely rich: the systems…
Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and…
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polymer simulations, microscopy and mass spectrometry to dissect…
We perform computer simulations of mechanically linked (poly[2]catenanes, PC) and chemically bonded (bonded rings, BR) pairs of self-avoiding ring polymers in steady shear. We find that BR's develop a novel motif, termed gradient tumbling,…
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…