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Register a new userOn the size of knots in ring polymers
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We give two different, statistically consistent definitions of the length l of a prime knot tied into a polymer ring. In the good solvent regime the polymer is modelled by a self avoiding polygon of N steps on cubic lattice and l is the number of steps over which the knot ``spreads in a given configuration. An analysis of extensive Monte Carlo data in equilibrium shows that the probability distribution of l as a function of N obeys a scaling of the form p(l,N) ~ l^(-c) f(l/N^D), with c ~ 1.25 and D ~ 1. Both D and c could be independent of knot type. As a consequence, the knot is weakly localized, i.e. <l> ~ N^t, with t=2-c ~ 0.75. For a ring with fixed knot type, weak localization implies the existence of a peculiar characteristic length l^(nu) ~ N^(t nu). In the scaling ~ N^(nu) (nu ~0.58) of the radius of gyration of the whole ring, this length determines a leading power law correction which is much stronger than that found in the case of unrestricted topology. The existence of such correction is confirmed by an analysis of extensive Monte Carlo data for the radius of gyration. The collapsed regime is studied by introducing in the model sufficiently strong attractive interactions for nearest neighbor sites visited by the self-avoiding polygon. In this regime knot length determinations can be based on the entropic competition between two knotted loops separated by a slip link. These measurements enable us to conclude that each knot is delocalized (t ~ 1).
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The exact solution of directed self-avoiding walks confined to a slit of finite width and interacting with the walls of the slit via an attractive potential has been calculated recently. The walks can be considered to model the polymer-induced steric stabilisation and sensitised floculation of colloidal dispersions. The large width asymptotics led to a phase diagram different to that of a polymer attached to, and attracted to, a single wall. The question that arises is: can one interpolate between the single wall and two wall cases? In this paper we calculate the exact scaling functions for the partition function by considering the two variable asymptotics of the partition function for simultaneous large length and large width. Consequently, we find the scaling functions for the force induced by the polymer on the walls. We find that these scaling functions are given by elliptic theta-functions. In some parts of the phase diagram there is more a complex crossover between the single wall and two wall cases and we elucidate how this happens.
The Rouse-Zimm equation for the position vectors of beads mapping the polymer is generalized by taking into account the viscous aftereffect and the hydrodynamic noise. For the noise, the random fluctuations of the hydrodynamic tensor of stresses are responsible. The preaveraging of the Oseen tensor for the nonstationary Navier-Stokes equation allowed us to relate the time correlation functions of the Fourier components of the bead position to the correlation functions of the hydrodynamic field created by the noise. The velocity autocorrelation function of the center of inertia of the polymer coil is considered in detail for both the short and long times when it behaves according to the t^(-3/2) law and does not depend on any polymer parameters. The diffusion coefficient of the polymer is close to that from the Zimm theory, with corrections depending on the ratio between the size of the bead and the size of the whole coil.
In this paper in terms of the replica method we consider the high temperature limit of (2+1) directed polymers in a random potential and propose an approach which allows to compute the scaling exponent $theta$ of the free energy fluctuations as well as the left tail of its probability distribution function. It is argued that $theta = 1/2$ which is different from the zero-temperature numerical value which is close to 0.241. This result implies that unlike the $(1+1)$ system in the two-dimensional case the free energy scaling exponent is non-universal being temperature dependent.
We analyze the statistics of the shortest and fastest paths on the road network between randomly sampled end points. To a good approximation, these optimal paths are found to be directed in that their lengths (at large scales) are linearly proportional to the absolute distance between them. This motivates comparisons to universal features of directed polymers in random media. There are similarities in scalings of fluctuations in length/time and transverse wanderings, but also important distinctions in the scaling exponents, likely due to long-range correlations in geographic and man-made features. At short scales the optimal paths are not directed due to circuitous excursions governed by a fat-tailed (power-law) probability distribution.
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible polymers has not been explored much. Here, via extensive replica exchange Monte Carlo simulation we investigate the same for a bead-stick and a bead-spring homopolymer model that covers the whole range from flexible to stiff. We establish the fact that the presence of stable knotted phases in the phase diagram is dependent on the ratio $r_b/r_{rm{min}}$ where $r_b$ is the equilibrium bond length and $r_{rm{min}}$ is the distance for the strongest nonbonded contacts. Our results provide evidence for both models that if the ratio $r_b/r_{rm{min}}$ is outside a small window around unity then depending on the bending stiffness one always encounters stable knotted phases along with the usual frozen and bent-like structures at low temperatures. These findings prompt us to conclude that knots are generic stable phases in semiflexible polymers.
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