Polymers with spatial or topological constraints: theoretical and computational results

DOI10.1016/J.PHYSREP.2011.03.003MaRDI QIDQ535926zbMATH OpenOpenAlexFDO

Authors Cristian Micheletti, Davide Marenduzzo, E. Orlandini

Publication date 15 May 2011

Published in Physics Reports (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1103.4222

zbMATH Keywords

confinementknotspolymersDNA knotting inside viral capsidsknotting of polymer rings undergoing adsorption transitionknotting of polymers under tensionknotting probability in confined geometriespolymers under geometrical confinementsampling at equilibrium by Monte Carlo methods

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Statistical mechanics of polymers (82D60)

Abstract: In this review we provide an organized summary of the theoretical and computational results which are available for polymers subject to spatial or topological constraints. Because of the interdisciplinary character of the topic, we provide an accessible, non-specialist introduction to the main topological concepts, polymer models, and theoretical/computational methods used to investigate dense and entangled polymer systems. The main body of our review deals with: (i) the effect that spatial confinement has on the equilibrium topological entanglement of one or more polymer chains and (ii) the metric and entropic properties of polymer chains with fixed topological state. These problems have important technological applications and implications for the life-sciences. Both aspects, especially the latter, are amply covered. A number of selected open problems are finally highlighted.

Recommendations

• scientific article; zbMATH DE number 1218945
• The statistical mechanics of topological polymers: a field theorist point of view
• Concepts of polymer statistical topology
• Physical knot theory: an introduction to the study of the influence of knotting on the spatial characteristics of polymers
• Field theories and the problem of topological entanglement in polymer physics

Cites work

• scientific article; zbMATH DE number 426371 (Why is no real title available?)
• scientific article; zbMATH DE number 3148803 (Why is no real title available?)
• scientific article; zbMATH DE number 3751923 (Why is no real title available?)
• scientific article; zbMATH DE number 46777 (Why is no real title available?)
• scientific article; zbMATH DE number 3530652 (Why is no real title available?)
• scientific article; zbMATH DE number 1218944 (Why is no real title available?)
• scientific article; zbMATH DE number 1218945 (Why is no real title available?)
• scientific article; zbMATH DE number 1265043 (Why is no real title available?)
• scientific article; zbMATH DE number 1274074 (Why is no real title available?)
• scientific article; zbMATH DE number 1303211 (Why is no real title available?)
• scientific article; zbMATH DE number 1303220 (Why is no real title available?)
• scientific article; zbMATH DE number 1037084 (Why is no real title available?)
• scientific article; zbMATH DE number 201032 (Why is no real title available?)
• scientific article; zbMATH DE number 219013 (Why is no real title available?)
• scientific article; zbMATH DE number 219014 (Why is no real title available?)
• scientific article; zbMATH DE number 1877237 (Why is no real title available?)
• scientific article; zbMATH DE number 1877238 (Why is no real title available?)
• scientific article; zbMATH DE number 2120368 (Why is no real title available?)
• scientific article; zbMATH DE number 791397 (Why is no real title available?)
• scientific article; zbMATH DE number 907055 (Why is no real title available?)
• scientific article; zbMATH DE number 1428888 (Why is no real title available?)
• scientific article; zbMATH DE number 1428892 (Why is no real title available?)
• scientific article; zbMATH DE number 3188477 (Why is no real title available?)
• scientific article; zbMATH DE number 3196612 (Why is no real title available?)
• scientific article; zbMATH DE number 3198429 (Why is no real title available?)
• A new class of stuck unknots in \(\text{Pol}_6\)
• Algebraic invariants of knots and disordered Potts model
• Asymptotics of knotted lattice polygons
• Atmospheres of polygons and knotted polygons
• BIOLOGICAL DISTANCES ON DNA KNOTS AND LINKS: Applications to XER recombination
• Characteristic length of random knotting for cylindrical self-avoiding polygons
• Critical exponents of theN-vector model
• Critical exponents, hyperscaling, and universal amplitude ratios for two- and three-dimensional self-avoiding walks.
• DNA knotting in spooling like conformations in bacteriophages
• ENUMERATING THE PRIME ALTERNATING KNOTS, PART I
• Entanglement complexity of graphs in Z³
• Entanglement complexity of self-avoiding walks
• Entropic exponents of lattice polygons with specified knot type
• FURTHER RESULTS ON THE RATE OF CONVERGENCE TO THE CONNECTIVE CONSTANT OF THE HYPERCUBICAL LATTICE
• Free energy of a semiflexible polymer in a tube and statistics of a randomly-accelerated particle
• Gauge theory for embedded surfaces. I
• Geometry and physics of knots
• Global curvature, thickness, and the ideal shapes of knots
• Implementation and performance analysis of bridging Monte Carlo moves for off-lattice single chain polymers in globular states
• Knot probability for lattice polygons in confined geometries
• Knot probability of polygons subjected to a force: a Monte Carlo study
• Knots in random walks
• Knots in self-avoiding walks
• Knots.
• Knotting in stretched polygons
• LINKING OF RANDOM p-SPHERES IN Z^d
• Lattice Models of Polymers
• Lattice models of branched polymers: effects of geometrical constraints
• Lifting the curtain: Using topology to probe the hidden action of enzymes
• Linking numbers of closed manifolds at random in \(\mathbb{R}^n\), inductances and contacts
• Linking of uniform random polygons in confined spaces
• Linking probabilities of off-lattice self-avoiding polygons and the effects of excluded volume
• Loose, flat knots in collapsed polymers
• Modeling of chromosome intermingling by partially overlapping uniform random polygons
• Monte Carlo explorations of polygonal knot spaces
• Monte Carlo results for projected self-avoiding polygons: a two-dimensional model for knotted polymers
• Monte Carlo simulation in statistical physics. An introduction.
• Monte Carlo study of the interacting self-avoiding walk model in three dimensions.
• NONTRIVIAL EMBEDDINGS OF POLYGONAL INTERVALS AND UNKNOTS IN 3-SPACE
• Neutral and charged polymers at interfaces
• ON RANDOM KNOTS
• On irreducible 3-manifolds which are sufficiently large
• On knots in a model for the adsorption of ring polymers
• On the Alexander polynomial
• On the Braid Index of Alternating Links
• On the Classification of Knots
• On the Number of Self-Avoiding Walks
• On the dominance of trivial knots among SAPs on a cubic lattice
• On the structure and scarcity of alternating links and tangles
• On the topology of a polymer ring
• Polymer entanglement in melts
• Random linking of lattice polygons
• Renormalization of polymer networks and stars
• Rigid curves at random positions and linking numbers
• Scaling behavior of random knots
• Self-Linking and the Gauss Integral in Higher Dimensions
• Self-avoiding walk enumeration via the lace expansion
• Statistical Field Theory
• Statistical mechanics with topological constraints: II
• Statistical topology of closed curves: some applications in polymer physics
• Stochastic Problems in Physics and Astronomy
• Stretched polygons in a lattice tube
• The BFACF algorithm and knotted polygons
• The Knotting of Equilateral Polygons in R³
• The Writhing Number of a Space Curve
• The complexity of lattice knots
• The dimensions of knotted polygons
• The distribution of Alexander polynomials of knots confined to a thin layer
• The first 1,701,936 knots
• The generation of random equilateral polygons
• The growth of the number of prime knots
• The knot probability in lattice polygons
• The linking number and the writhe of uniform random walks and polygons in confined spaces
• The linking probability for 2-component links which span a lattice tube
• The pivot algorithm: a highly efficient Monte Carlo method for the self-avoiding walk.
• The statistical mechanics of interacting walks, polygons, animals and vesicles
• Topology of Closed Random Polygons
• UPPER BOUNDS ON LINKING NUMBERS OF THICK LINKS
• Unknotting number one knots are prime
• Untangling DNA
• What is the length of a knot in a polymer?

Cited in

(23)

• Variational methods for constrained polymer dynamics
• Knotting statistics for polygons in lattice tubes
• Open problems in tube models for concentrated polymers
• Topology in soft and biological matter
• Proving the absence of unbounded polymers in rule-based models
• The second Vassiliev measure of uniform random walks and polygons in confined space
• Topological sum rules in the knotting probabilities of DNA
• Statistical topology of closed curves: some applications in polymer physics
• Inherent features of fractal sets and key attributes of fractal models
• Invariants of random knots and links
• Topological effects on the mechanical properties of polymer knots
• Knot theory realizations in nematic colloids
• A study of polymer knots using a simple knot invariant consisting of multiple contour integrals
• Excluded volume effects in the end-to-end distance of two-generation dendritic polymers: TTT and HH combs
• Models of random knots
• The linking number in systems with periodic boundary conditions
• Relative frequencies of alternating and nonalternating prime knots and composite knots in random knot spaces
• Planar polymers under cylindrical confinement: geometrical approach
• Self-consistent field theory simulations of polymers on arbitrary domains
• Statics and dynamics of DNA knotting
• Linking matrices in systems with periodic boundary conditions
• The effect of angle restriction on the topological characteristics of minicircle networks
• Exact and efficient sampling of conditioned walks

Describes a project that uses

Uses Software

• pKNOT

This page was built for publication: Polymers with spatial or topological constraints: theoretical and computational results

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q535926)