相关论文: Emergent helicity in free-standing semiflexible, c…
Generic interactions e.g. the Coulomb or other long ranged radially symmetric repulsive interactions between monomers of bead-spring model of a semi-flexible polymer induce instabilities in a initially straight polymer chain to form long…
The presence of ordered structures such as helices in collapsed states of polymer chains is still an open question challenging physics and biology. In this work, we present a potential model for polymer chains with monomers that are not…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
Biological molecules can form hydrogen bonds between nearby residues, leading to helical secondary structures. The associated reduction of configurational entropy leads to a temperature dependence of this effect: the "helix-coil…
Helices are not generic outcomes of polymer collapse. Collapsed conformations of semiflexible polymers with isotropic attractions typically form globules, toroids, or rod-like structures, as seen in simulations and described by…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
The conformations of semiflexible (bio)polymers are studied in flow through geometrically structured microchannels. Using mesoscale hydrodynamics simulations, we show that the polymer undergoes a rod-to-helix transition as it moves from the…
Using Langevin simulations, we find that simple 'generic' bead-and-spring homopolymer chains in a sufficiently bad solvent spontaneously develop helical order during the process of collapsing from an initially stretched conformation. The…
The helix is a ubiquitous motif for biopolymers. We propose a heuristic, entropically based model that predicts helix formation in a system of hard spheres and semiflexible tubes. We find that the entropy of the spheres is maximized when…
Inspired by recent experiments on the spatial organization of bacterial chromosomes, we consider a type of "bottle brush" polymer consisting of a flexible backbone chain, to which flexible side loops are connected. We show that such a model…
Configurations of a single semiflexible polymer is studied when it is pushed into a nanochannel in the case where the polymer persistence length $l_p$ is much longer than the channel diameter $D$, i.e. $l_p/D \gg 1$. Using numerical…
The field of synthetic active matter has, thus far, been led by efforts to create point-like, isolated (yet interacting) self-propelled objects (\emph{e.g.} colloids, droplets, microrobots) and understanding their collective dynamics. The…
The equations for strands of rigid charge configurations interacting nonlocally are formulated on the special Euclidean group, SE(3), which naturally generates helical conformations. Helical stationary shapes are found by minimizing the…
Helices of increased electron density can spontaneously form in materials containing multiple, interacting density waves. Although a macroscopic order parameter theory describing this behaviour has been proposed and experimentally tested, a…
We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters we…
Polymer chains decorated with a fraction of monomers capable of forming reversible bonds form transient polymer networks that are important in soft and biological systems. If chains are flexible and the attractive monomers are all of the…
Emergent behaviors occur in a vast array of systems across many scales, and are of fundamental physical importance because of the intrinsic difficulty in linking microscopic system properties to macroscopic behaviors. Here we study the…
We investigate a system of equally charged Coulomb-interacting particles confined to a toroidal helix in the presence of an external electric field. Due to the confinement, the particles experience an effective interaction that oscillates…
Autonomous locomotion is a ubiquitous phenomenon in biology and in physics of active systems at microscopic scale. This includes prokaryotic, eukaryotic cells (crawling and swimming) and artificial swimmers. An outstanding feature is the…
A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from…