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Register a new userTopological signatures of globular polymers
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Simulations in which a globular ring polymer with delocalized knots is separated in two interacting loops by a slipping link, or in two non-interacting globuli by a wall with a hole, show how the minimal crossing number of the knots controls the equilibrium statistics. With slipping link the ring length is divided between the loops according to a simple law, but with unexpectedly large fluctuations. These are suppressed only for unknotted loops, whose length distribution shows always a fast power law decay. We also discover and explain a topological effect interfering with that of surface tension in the globule translocation through a membrane nanopore.
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In the first part of this work a summary is provided of some recent experiments and theoretical results which are relevant in the research of systems of polymer rings in nontrivial topological conformations. Next, some advances in modeling the behavior of single polymer knots are presented. The numerical simulations are performed with the help of the Wang-Landau Monte Carlo algorithm. To sample the polymer conformation a set of random transformations called pivot moves is used. The crucial problem of preserving the topology of the knots after each move is tackled with the help of two new techniques which are briefly explained. As an application, the results of an investigation of the effects of topology on the thermal properties of polymer knots is reported. In the end, original results are discussed concerning the use of parallelized codes to study polymers knots composed by a large number of segments within the Wang-Landau approach.
Soft topological surface phonons in idealized ball-and-spring lattices with coordination number $z=2d$ in $d$ dimensions become finite-frequency surface phonons in physically realizable superisostatic lattices with $z>2d$. We study these finite-frequency modes in model lattices with added next-nearest-neighbor springs or bending forces at nodes with an eye to signatures of the topological surface modes that are retained in the physical lattices. Our results apply to metamaterial lattices, prepared with modern printing techniques, that closely approach isostaticity.
Molecular dynamics simulations confirm recent extensional flow experiments showing ring polymer melts exhibit strong extension-rate thickening of the viscosity at Weissenberg numbers $Wi<<1$. Thickening coincides with the extreme elongation of a minority population of rings that grows with $Wi$. The large susceptibility of some rings to extend is due to a flow-driven formation of topological links that connect multiple rings into supramolecular chains. Links form spontaneously with a longer delay at lower $Wi$ and are pulled tight and stabilized by the flow. Once linked, these composite objects experience larger drag forces than individual rings, driving their strong elongation. The fraction of linked rings generated by flow depends non-monotonically on $Wi$, increasing to a maximum when $Wisim1$ before rapidly decreasing when the strain rate approaches the relaxation rate of the smallest ring loops $sim 1/tau_e$.
We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by a special three body interaction and impacts on the behaviour both locally and non-locally. When thick polymers undergo compaction due to an attractive self-interaction, we find a new type of phase transition between a compact phase and a swollen phase at zero temperature on increasing the thickness. In the vicinity of this transition, short tubes form space filling helices and sheets as observed in protein native state structures. Upon increasing the chain length, or the number of chains, we numerically find a crossover from secondary structure motifs to a quite distinct class of structures akin to the semi-crystalline phase of polymers or amyloid fibers in polypeptides.
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the absence of hydrodynamic interactions. The dsDNA is modelled with one bead-spring element per basepair, and the polymer dynamics is described by the Langevin equation. The key to efficiency is that we describe the equations of motion for the polymer in terms of the amplitudes of the polymers fluctuation modes, as opposed to the use of the physical positions of the beads. We show that, within an accuracy tolerance level of $5%$ of several key observables, the model allows for single Langevin time steps of $approx1.6$, 8, 16 and 16 ps for a dsDNA model-chain consisting of 64, 128, 256 and 512 basepairs (i.e., chains of 0.55, 1.11, 2.24 and 4.48 persistence lengths) respectively. Correspondingly, in one hour, a standard desktop computer can simulate 0.23, 0.56, 0.56 and 0.26 ms of these dsDNA chains respectively. We compare our results to those obtained from other methods, in particular, the (inextensible discretised) WLC model. Importantly, we demonstrate that at the same level of discretisation, i.e., when each discretisation element is one basepair long, our algorithm gains about 5-6 orders of magnitude in the size of time steps over the inextensible WLC model. Further, we show that our model can be mapped one-on-one to a discretised version of the extensible WLC model; implying that the speed-up we achieve in our model must hold equally well for the latter. We also demonstrate the use of the method by simulating efficiently the tumbling behaviour of a dsDNA segment in a shear flow.
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