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Lattice models of directed and semiflexible polymers in anisotropic environment  [PDF]
K. Haydukivska,V. Blavatska
Physics , 2015, DOI: 10.1088/1751-8113/48/42/425002
Abstract: We study the conformational properties of polymers in presence of extended columnar defects of parallel orientation. Two classes of macromolecules are considered: the so-called partially directed polymers with preferred orientation along direction of the external stretching field and semiflexible polymers. We are working within the frames of lattice models: partially directed self-avoiding walks (PDSAWs) and biased self-avoiding walks (BSAWs). Our numerical analysis of PDSAWs reveals, that competition between the stretching field and anisotropy caused by presence of extended defects leads to existing of three characteristic length scales in the system. At each fixed concentration of disorder we found a transition point, where the influence of extended defects is exactly counterbalanced by the stretching field. Numerical simulations of BSAWs in anisotropic environment reveal an increase of polymer stiffness. In particular, the persistence length of semiflexible polymers increases in presence of disorder.
Exact Solution of Semi-Flexible and Super-Flexible Interacting Partially Directed Walks  [PDF]
A. L. Owczarek,T. Prellberg
Mathematics , 2007, DOI: 10.1088/1742-5468/2007/11/P11010
Abstract: We provide the exact generating function for semi-flexible and super-flexible interacting partially directed walks and also analyse the solution in detail. We demonstrate that while fully flexible walks have a collapse transition that is second order and obeys tricritical scaling, once positive stiffness is introduced the collapse transition becomes first order. This confirms a recent conjecture based on numerical results. We note that the addition of an horizontal force in either case does not affect the order of the transition. In the opposite case where stiffness is discouraged by the energy potential introduced, which we denote the super-flexible case, the transition also changes, though more subtly, with the crossover exponent remaining unmoved from the neutral case but the entropic exponents changing.
Stretching of polymers in a turbulent environment  [PDF]
Bruno Eckhardt,Jochen Kronjaeger,Joerg Schumacher
Physics , 2002, DOI: 10.1016/S0010-4655(02)00339-9
Abstract: The interaction of polymers with small-scale velocity gradients can trigger a coil-stretch transition in the polymers. We analyze this transition within a direct numerical simulation of shear turbulence with an Oldroyd-B model for the polymer. In the coiled state the lengths of polymers are distributed algebraically with an exponent alpha=2 gamma-1/De, where gamma is a characteristic stretching rate of the flow and De the Deborah number. In the stretched state we demonstrate that the length distribution of the polymers is limited by the feedback to the flow.
Theory and Monte Carlo simulations for the stretching of flexible and semi-flexible single polymer chains under external fields  [PDF]
Fabio Manca,Stefano Giordano,Pier Luca Palla,Fabrizio Cleri,Luciano Colombo
Physics , 2012, DOI: 10.1063/1.4772656
Abstract: Recent developments of microscopic mechanical experiments allow the manipulation of individual polymer molecules in two main ways: \textit{uniform} stretching by external forces and \textit{non-uniform} stretching by external fields. Many results can be thereby obtained for specific kinds of polymers and specific geometries. In this work we describe the non-uniform stretching of a single, non-branched polymer molecule by an external field (e.g. fluid in uniform motion, or uniform electric field) by a universal physical framework which leads to general conclusions on different types of polymers. We derive analytical results both for the freely-jointed chain and the worm-like chain models based on classical statistical mechanics. Moreover, we provide a Monte Carlo numerical analysis of the mechanical properties of flexible and semi-flexible polymers anchored at one end. The simulations confirm the analytical achievements, and moreover allow to study the situations where the theory can not provide explicit and useful results. In all cases we evaluate the average conformation of the polymer and its fluctuation statistics as a function of the chain length, bending rigidity and field strength.
Directed polymers and Randomness  [PDF]
Somendra M. Bhattacharjee
Physics , 2005,
Abstract: The effects of two types of randomness on the behaviour of directed polymers are discussed in this chapter. The first part deals with the effect of randomness in medium so that a directed polymer feels a random external potential. The second part deals with the RANI model of two directed polymers with heterogeneity along the chain such that the interaction is random. The random medium problem is better understood compared to the RANI model.
Stretching dynamics of semiflexible polymers  [PDF]
B. Obermayer,O. Hallatschek,E. Frey,K. Kroy
Quantitative Biology , 2006, DOI: 10.1140/epje/i2006-10221-y
Abstract: We analyze the nonequilibrium dynamics of single inextensible semiflexible biopolymers as stretching forces are applied at the ends. Based on different (contradicting) heuristic arguments, various scaling laws have been proposed for the propagation speed of the backbone tension which is induced in response to stretching. Here, we employ a newly developed unified theory to systematically substantiate, restrict, and extend these approaches. Introducing the practically relevant scenario of a chain equilibrated under some prestretching force $f_\text{pre}$ that is suddenly exposed to a different external force $f_\text{ext}$ at the ends, we give a concise physical explanation of the underlying relaxation processes by means of an intuitive blob picture. We discuss the corresponding intermediate asymptotics, derive results for experimentally relevant observables, and support our conclusions by numerical solutions of the coarse-grained equations of motion for the tension.
Thermodynamics of tubelike flexible polymers  [PDF]
Thomas Vogel,Thomas Neuhaus,Michael Bachmann,Wolfhard Janke
Physics , 2009, DOI: 10.1103/PhysRevE.80.011802
Abstract: In this work we present the general phase behavior of short tubelike flexible polymers. The geometric thickness constraint is implemented through the concept of the global radius of curvature. We use sophisticated Monte Carlo sampling methods to simulate small bead-stick polymer models with Lennard-Jones interaction among non-bonded monomers. We analyze energetic fluctuations and structural quantities to classify conformational pseudophases. We find that the tube thickness influences the thermodynamic behavior of simple tubelike polymers significantly, i.e., for given temperature, the formation of secondary structures strongly depends on the tube thickness.
Partially Directed Snake Polyominoes  [PDF]
Alain Goupil,Marie-Eve Pellerin,Jér?me de Wouters d'Oplinter
Mathematics , 2013,
Abstract: The goal of this paper is to study the family of snake polyominoes. More precisely, we focus our attention on the class of partially directed snakes. We establish functional equations and length generating functions of two dimensional, three dimensional and then $N$ dimensional partially directed snake polyominoes. We then turn our attention to partially directed snakes inscribed in a $b\times k$ rectangle and we establish two-variable generating functions, with respect to height $k$ and length $n$ of the snakes. We include observations on the relationship between snake polyominoes and self-avoiding walks. We conclude with a discussion on inscribed snakes polyominoes of maximal length which lead us to the formulation of a conjecture encountered in the course of our investigations.
Directed polymers in high dimensions  [PDF]
Ralf Bundschuh,Michael Lassig
Physics , 1996, DOI: 10.1103/PhysRevE.54.304
Abstract: We study directed polymers subject to a quenched random potential in d transversal dimensions. This system is closely related to the Kardar-Parisi-Zhang equation of nonlinear stochastic growth. By a careful analysis of the perturbation theory we show that physical quantities develop singular behavior for d to 4. For example, the universal finite size amplitude of the free energy at the roughening transition is proportional to (4-d)^(1/2). This shows that the dimension d=4 plays a special role for this system and points towards d=4 as the upper critical dimension of the Kardar-Parisi-Zhang problem.
Local Energy Statistics in Directed Polymers  [PDF]
Irina Kourkova
Mathematics , 2007,
Abstract: Recently, Bauke and Mertens conjectured that the local statistics of energies in random spin systems with discrete spin space should, in most circumstances, be the same as in the random energy model. We show that this conjecture holds true as well for directed polymers in random environment. We also show that, under certain conditions, this conjecture holds for directed polymers even if energy levels that grow moderately with the volume of the system are considered.
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