Helix coil mixing in twist-storing polymers

Twist-storing polymers respond with elastic energy penalty to coherent or random twisting along the local chain axis away from its equilibrium, which can be straight (as in “ribbons”) or helical (as in DNA and other biopolymers). Here we study the equilibrium conformation of such polymers, focusing on the thermodynamic balance between twist and writhe, resulting from the competition between the random coil entropy and the potential energy stored in superhelical portions of the polymer chain. Two macroscopic variables characterise such a chain, the end-to-end distance R and the link number Lk, which is a topological invariant of a given polymer with clamped ends. We find that with increasing link number Lk, the chain accommodates its excess twist in growing plectonemes, unless forced out of this state by stretching its end-to-end distance R. We calculate the force-extension relation, which exhibits crossovers between different deformation regimes. Received 16 November 2000 and Received in final form 6 February 2001     

Generalizing Ribbons and the Twist of the Lattice Ribbon

For a standard or canonical ribbon from differential geometry the topological White’s theorem connects the linking number, writhe and total twist of the ribbon. Here we provide an integral expression, analog to the total twist of a canonical ribbon, that connects linking number and writhe of two curves that do not necessarily form a canonical ribbon. First, we apply this integral expression to derive an expression for the writhe of a polygonal curve. Second, but importantly, we revisit the lattice ribbon. Lattice ribbons were introduced some time ago to enable simulation of physical systems modeled by double stranded polymers. Application of the integral expression yields an algorithm for determining the twist of the lattice ribbon. An interesting relation between writhe of the center line of a lattice ribbon and its linking number follows.     

Region Graph Partition Function Expansion and Approximate Free Energy Landscapes: Theory and Some Numerical Results

Graphical models for finite-dimensional spin glasses and real-world combinatorial optimization and satisfaction problems usually have an abundant number of short loops. The cluster variation method and its extension, the region graph method, are theoretical approaches for treating the complicated short-loop-induced local correlations. For graphical models represented by non-redundant or redundant region graphs, approximate free energy landscapes are constructed in this paper through the mathematical framework of region graph partition function expansion. Several free energy functionals are obtained, each of which use a set of probability distribution functions or functionals as order parameters. These probability distribution function/functionals are required to satisfy the region graph belief-propagation equation or the region graph survey-propagation equation to ensure vanishing correction contributions of region subgraphs with dangling edges. As a simple application of the general theory, we perform region graph belief-propagation simulations on the square-lattice ferromagnetic Ising model and the Edwards-Anderson model. Considerable improvements over the conventional Bethe-Peierls approximation are achieved. Collective domains of different sizes in the disordered and frustrated square lattice are identified by the message-passing procedure. Such collective domains and the frustrations among them are responsible for the low-temperature glass-like dynamical behaviors of the system.     

Entanglement complexity of lattice ribbons

We consider a discrete ribbon model for double-stranded polymers where the ribbon is constrained to lie in a three-dimensional lattice. The ribbon can be open or closed, and closed ribbons can be orientable or nonorientable. We prove some results about the asymptotic behavior of the numbers of ribbons withn plaquettes, and a theorem about the frequency of occurrence of certain patterns in these ribbons. We use this to derive results about the frequency of knots in closed ribbons, the linking of the boundary curves of orientable closed ribbons, and the twist and writhe of ribbons. We show that the centerline and boundary of a closed ribbon are both almost surely knotted in the infinite-n limit. For an orientable ribbon, the expectation of the absolute value of the linking number of the two boundary curves increases at least as fast as n, and similar results hold for the twist and writhe.     

Form Factors of Branch-Point Twist Fields in Quantum Integrable Models and Entanglement Entropy

In this paper we compute the leading correction to the bipartite entanglement entropy at large sub-system size, in integrable quantum field theories with diagonal scattering matrices. We find a remarkably universal result, depending only on the particle spectrum of the theory and not on the details of the scattering matrix. We employ the “replica trick” whereby the entropy is obtained as the derivative with respect to n of the trace of the nth power of the reduced density matrix of the sub-system, evaluated at n=1. The main novelty of our work is the introduction of a particular type of twist fields in quantum field theory that are naturally related to branch points in an n-sheeted Riemann surface. Their two-point function directly gives the scaling limit of the trace of the nth power of the reduced density matrix. Taking advantage of integrability, we use the expansion of this two-point function in terms of form factors of the twist fields, in order to evaluate it at large distances in the two-particle approximation. Although this is a well-known technique, the new geometry of the problem implies a modification of the form factor equations satisfied by standard local fields of integrable quantum field theory. We derive the new form factor equations and provide solutions, which we specialize both to the Ising and sinh-Gordon models.     

Permutation orbifolds

A general theory of permutation orbifolds is developed for arbitrary twist groups. Explicit expressions for the number of primaries, the partition function, the genus one characters, the matrix elements of modular transformations and for fusion rule coefficients are presented, together with the relevant mathematical concepts, such as Λ-matrices and twisted dimensions. The arithmetic restrictions implied by the theory for the allowed modular representations in CFT are discussed. The simplest nonabelian example with twist group S₃ is described to illustrate the general theory.     

Quark-hadron duality in electron-pion scattering

We explore the relationship between exclusive and inclusive electromagnetic scattering from the pion, focusing on the transition region at intermediate Q². Combining Drell-Yan data on the leading twist quark distribution in the pion with a model for the resonance region at large x, we calculate QCD moments of the pion structure function over a range of Q², and quantify the role of higher twist corrections. Using a parameterization of the pion elastic form factor and phenomenological models for the π↦ρ transition form factor, we further test the extent to which local duality may be valid for the pion. Received: 10 February 2003 / Accepted: 12 March 2003 / Published online: 27 May 2003     

Quasi-quantization of writhe in ideal knots

The values of writhe of the tightest conformations, found by the SONO algorithm, of all alternating prime knots with up to 10 crossings are analysed. The distribution of the writhe values is shown to be concentrated around the equally spaced levels. The “writhe quantum” is shown to be close to the rational 4/7 value. The deviation of the writhe values from the n(4/7) writhe levels scheme is analysed quantitatively. Received 29 February 2001 and Received in final form 17 August 2001     

Twist and writhe dynamics of stiff polymers

I consider the dynamics of a stiff filament, in particular the coupling of twist and bend via writhe. The time dependence of the writhe of a filament of length L is ([Wr(t) - Wr(0)]2) > approximately Lt(1/4). Simulations, on a simple model of a stiff polymer, are used to confirm scaling arguments. Fuller's theorem, and its relation with geometric phases, is reconsidered for open filaments.     

Correlation Functions for MN/SN Orbifolds

We develop a method for computing correlation functions of twist operators in the bosonic 2-d CFT arising from orbifolds M ^N /S _N , where M is an arbitrary manifold. The path integral with twist operators is replaced by a path integral on a covering space with no operator insertions. Thus, even though the CFT is defined on the sphere, the correlators are expressed in terms of partition functions on Riemann surfaces with a finite range of genus g. For large N, this genus expansion coincides with a 1/N expansion. The contribution from the covering space of genus zero is “universal” in the sense that it depends only on the central charge of the CFT. For 3-point functions we give an explicit form for the contribution from the sphere, and for the 4-point function we do an example which has genus zero and genus one contributions. The condition for the genus zero contribution to the 3-point functions to be non-vanishing is similar to the fusion rules for an SU(2) WZW model. We observe that the 3-point coupling becomes small compared to its large N limit when the orders of the twist operators become comparable to the square root of N – this is a manifestation of the stringy exclusion principle. Received: 20 July 2000 / Accepted: 17 December 2000     

The Elliptic Genus and Hidden Symmetry

We study the elliptic genus (a partition function) in certain interacting, twist quantum field theories. Without twists, these theories have N=2 supersymmetry. The twists provide a regularization, and also partially break the supersymmetry. In spite of the regularization, one can establish a homotopy of the elliptic genus in a coupling parameter. Our construction relies on a priori estimates and other methods from constructive quantum field theory; this mathematical underpinning allows us to justify evaluating the elliptic genus at one endpoint of the homotopy. We obtain a version of Witten's proposed formula for the elliptic genus in terms of classical theta functions. As a consequence, the elliptic genus has a hidden SL(2, ℤ) symmetry characteristic of conformal theory, even though the underlying theory is not conformal. Received: 7 January 2000 / Accepted: 10 April 2000     

Matrix models as CFT: Genus expansion

We show how the formulation of the matrix models as conformal field theories on a Riemann surfaces can be used to compute the genus expansion of the observables. Here we consider the simplest example of the Hermitian matrix model, where the classical solution is described by a hyperelliptic Riemann surface. To each branch point of the Riemann surface we associate an operator which represents a twist field dressed by the modes of the twisted boson. The partition function of the matrix model is computed as a correlation function of such dressed twist fields. The perturbative construction of the dressing operators yields a set of Feynman rules for the genus expansion, which involve vertices, propagators and tadpoles. The vertices are universal, the propagators and the tadpoles depend on the Riemann surface. As a demonstration we evaluate the genus-two free energy using the Feynman rules.     

Spin and Abelian Electromagnetic Duality¶on Four-Manifolds

We investigate the electromagnetic duality properties of an Abelian gauge theory on a compact oriented four-manifold by analysing the behaviour of a generalised partition function under modular transformations of the dimensionless coupling constants. The true partition function is invariant under the full modular group but the generalised partition function exhibits more complicated behaviour depending on topological properties of the four-manifold concerned. It is already known that there may be “modular weights” which are linear combinations of the Euler number and Hirzebruch signature of the four-manifold. But sometimes the partition function transforms only under a subgroup of the modular group (the Hecke subgroup). In this case it is impossible to define real spinor wave-functions on the four-manifold. But complex spinors are possible provided the background magnetic fluxes are appropriately fractional rather than integral. This gives rise to a second partition function which enables the full modular group to be realised by permuting the two partition functions, together with a third. Thus the full modular group is realised in all cases. The demonstration makes use of various constructions concerning integral lattices and theta functions that seem to be of intrinsic interest. Received: 5 June 2000 / Accepted: 9 October 2000     

On the magnetically induced cholesteric to nematic phase transition

This Letter is concerned with the theoretical investigation of the application of a magnetic field perpendicular to the axis of twist in an infinite sample of cholesteric liquid crystal. We use the continuum theory for cholesterics to determine the forms that the sample may take and distinguish between these by use of energy comparisons. A rigorous mathematical justification of the result by de Gennes is then presented.     

Elliptic dynamical reflection algebra and partition function of SOS model with reflecting end

In this paper we introduce an elliptic dynamical reflection algebra describing an SOS model with a reflecting end. Using a factorizing Drinfel’d twist, we compute the partition function of this model with domain wall boundary conditions. We show that it can be represented in the form of a single Izergin determinant.     

Scaling of Linking and Writhing Numbers for Spherically Confined and Topologically Equilibrated Flexible Polymers

Scaling laws for Gauss linking number Ca and writhing number Wr for spherically confined flexible polymers with thermally fluctuating topology are analyzed. For ideal (phantom) polymers each of N segments of length unity confined to a spherical pore of radius R there are two scaling regimes: for sufficiently weak confinement (R≫N ^1/3) each chain has |Wr|≈N ^1/2, and each pair of chains has average |Ca|≈N/R ^3/2; alternately for sufficiently tight confinement (N ^1/3≫R), |Wr|≈|Ca|≈N/R ^3/2. Adding segment-segment avoidance modifies this result: for n chains with excluded volume interactions |Ca|≈(N/n)^1/2 f(φ) where f is a scaling function that depends approximately linearly on the segment concentration φ=nN/R ³. Scaling results for writhe are used to estimate the maximum writhe of a polymer; this is demonstrated to be realizable through a writhing instability that occurs for a polymer which is able to change knotting topology and which is subject to an applied torque. Finally, scaling results for linking are used to estimate bounds on the entanglement complexity of long chromosomal DNA molecules inside cells, and to show how “lengthwise” chromosome condensation can suppress DNA entanglement.     

A geometrical template for toroidal aggregates of chiral macromolecules

The formation of toroidal aggregates by long chiral molecules of biological origin, as collagen, f-actin and DNA, or by chiral synthetic polypeptides has been observed in specific ionic environments. Such aggregates have received considerable attention in order to identify the various physical factors susceptible to contribute to this original morphogenesis, particularly in the case of those formed by DNA. We consider here the eventual role of a spontaneous uniform twist of micrometric pitch whose possible occurrence is suggested by some observations and by recent studies of DNA dense phases exhibiting cholesteric and “blue” phase structures. Following an approach inspired by the geometry and topology of fiber bundles, we show that the necessity to propagate such a twist in a dense bundle of fibers leads to the formation of aggregates having a toroidal shape and, in the case of the nanometric aggregates of DNA, characteristic sizes similar to those observed.     

Space-time geometry of topological phases

The 2 + 1 dimensional lattice models of Levin and Wen (2005) [1] provide the most general known microscopic construction of topological phases of matter. Based heavily on the mathematical structure of category theory, many of the special properties of these models are not obvious. In the current paper, we present a geometrical space-time picture of the partition function of the Levin-Wen models which can be described as doubles (two copies with opposite chiralities) of underlying anyon theories. Our space-time picture describes the partition function as a knot invariant of a complicated link, where both the lattice variables of the microscopic Levin-Wen model and the terms of the Hamiltonian are represented as labeled strings of this link. This complicated link, previously studied in the mathematical literature, and known as Chain-Mail, can be related directly to known topological invariants of 3-manifolds such as the so-called Turaev-Viro invariant and the Witten-Reshitikhin-Turaev invariant. We further consider quasi-particle excitations of the Levin-Wen models and we see how they can be understood by adding additional strings to the Chain-Mail link representing quasi-particle world-lines. Our construction gives particularly important new insight into how a doubled theory arises from these microscopic models.     

Light-cone QCD sum rules for the Λ baryon electromagnetic form factors and its magnetic moment

We present the light-cone QCD sum rules up to twist 6 for the electromagnetic form factors of the Λ baryon. To estimate the magnetic moment of the baryon, the magnetic form factor is fitted by the dipole formula. The numerical value of our estimation is μ _Λ =−(0.64±0.04)μ _N , which is in accordance with the experimental data and the existing theoretical results. We find that it is twist 4 but not the leading twist distribution amplitudes that dominate the results.     

Twist in an exactly solvable directed lattice ribbon

We investigate the transition between a twisted regime and a disordered regime in a directed ribbon model on a cubic lattice. A fugacity corresponding to an interaction which models half-twists in the ribbon is introduced and the interacting model is solved exactly. Our results suggest that conformational entropy and a local interaction which induces twist are key ingredients to model qualitatively the crossover behavior between a twisted (helical) regime and a denatured regime in duplex biopolymers such as DNA.