Operator Spectrum and Exact Exponents of the Fully Packed Loop Model

We develop a Coulomb gas description of the critical fluctuations in the fully packed loop model on the honeycomb lattice. We identify the complete operator spectrum of this model in terms of electric and magnetic {\em vector}-charges, and we calculate the scaling dimensions of these operators exactly. We also study the geometrical properties of loops in this model, and we derive exact results for the fractal dimension and the loop size distribution function. A review of the many different representations of this model that have recently appeared in the literature, is given.Comment: 17 pages latex, 3 postscript figures, IOP style files include

Landau theory of glassy dynamics

An exact solution of a Landau model of an order-disorder transition with activated critical dynamics is presented. The model describes a funnel-shaped topography of the order parameter space in which the number of energy lowering trajectories rapidly diminishes as the ordered ground-state is approached. This leads to an asymmetry in the effective transition rates which results in a non-exponential relaxation of the order-parameter fluctuations and a Vogel-Fulcher-Tammann divergence of the relaxation times, typical of a glass transition. We argue that the Landau model provides a general framework for studying glassy dynamics in a variety of systems.Comment: 4 pages, 2 figure

A First Exposure to Statistical Mechanics for Life Scientists

Statistical mechanics is one of the most powerful and elegant tools in the quantitative sciences. One key virtue of statistical mechanics is that it is designed to examine large systems with many interacting degrees of freedom, providing a clue that it might have some bearing on the analysis of the molecules of living matter. As a result of data on biological systems becoming increasingly quantitative, there is a concomitant demand that the models set forth to describe biological systems be themselves quantitative. We describe how statistical mechanics is part of the quantitative toolkit that is needed to respond to such data. The power of statistical mechanics is not limited to traditional physical and chemical problems and there are a host of interesting ways in which these ideas can be applied in biology. This article reports on our efforts to teach statistical mechanics to life science students and provides a framework for others interested in bringing these tools to a nontraditional audience in the life sciences.Comment: 27 pages, 16 figures. Submitted to American Journal of Physic

Force steps during viral DNA packaging?

Biophysicists and structural biologists increasingly acknowledge the role played by the mechanical properties of macromolecules as a critical element in many biological processes. This change has been brought about, in part, by the advent of single molecule biophysics techniques that have made it possible to exert piconewton forces on key macromolecules and observe their deformations at nanometer length scales, as well as to observe the mechanical action of macromolecules such as molecular motors. This has opened up immense possibilities for a new generation of mechanical investigations that will respond to such measurements in an attempt to develop a coherent theory for the mechanical behavior of macromolecules under conditions where thermal and chemical effects are on an equal footing with deterministic forces. This paper presents an application of the principles of mechanics to the problem of DNA packaging, one of the key events in the life cycle of bacterial viruses with special reference to the nature of the internal forces that are built up during the DNA packaging process

Kac-Moody Symmetries of Critical Ground States

The symmetries of critical ground states of two-dimensional lattice models are investigated. We show how mapping a critical ground state to a model of a rough interface can be used to identify the chiral symmetry algebra of the conformal field theory that describes its scaling limit. This is demonstrated in the case of the six-vertex model, the three-coloring model on the honeycomb lattice, and the four-coloring model on the square lattice. These models are critical and they are described in the continuum by conformal field theories whose symmetry algebras are the $su(2)_{k=1}$, $su(3)_{k=1}$, and the $su(4)_{k=1}$ Kac-Moody algebra, respectively. Our approach is based on the Frenkel--Kac--Segal vertex operator construction of level one Kac--Moody algebras.Comment: 42 pages, RevTex, 14 ps figures, Submitted to Nucl. Phys. B. [FS

Stretching short biopolymers by fields and forces

We study the mechanical properties of semiflexible polymers when the contour length of the polymer is comparable to its persistence length. We compute the exact average end-to-end distance and shape of the polymer for different boundary conditions, and show that boundary effects can lead to significant deviations from the well-known long-polymer results. We also consider the case of stretching a uniformly charged biopolymer by an electric field, for which we compute the average extension and the average shape, which is shown to be trumpetlike. Our results also apply to long biopolymers when thermal fluctuations have been smoothed out by a large applied field or force.Comment: 10 pages, 7 figure

Secondary Structures in Long Compact Polymers

Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform numerical calculations is generating a sufficiently large number of randomly sampled configurations. We present a Monte-Carlo algorithm which uniformly samples compact polymer configurations in an efficient manner allowing investigations of chains much longer than previously studied. Chain configurations generated by the algorithm are used to compute statistics of secondary structures in compact polymers. We determine the fraction of monomers participating in secondary structures, and show that it is self averaging in the long chain limit and strictly less than one. Comparison with results for lattice models of open polymer chains shows that compact chains are significantly more likely to form secondary structure.Comment: 14 pages, 14 figure

A First Exposure to Statistical Mechanics for Life Scientists: Applications to Binding

Statistical mechanics is one of the most powerful and elegant tools in the quantitative sciences. One key virtue of statistical mechanics is that it is designed to examine large systems with many interacting degrees of freedom, providing a clue that it might have some bearing on the analysis of the molecules of living matter. As a result of data on biological systems becoming increasingly quantitative, there is a concomitant demand that the models set forth to describe biological systems be themselves quantitative. We describe how statistical mechanics is part of the quantitative toolkit that is needed to respond to such data. The power of statistical mechanics is not limited to traditional physical and chemical problems and there are a host of interesting ways in which these ideas can be applied in biology. This article reports on our efforts to teach statistical mechanics to life science students with special reference to binding problems in biology and provides a framework for others interested in bringing these tools to a nontraditional audience in the life sciences. 1 1 Does Statistical Mechanics Matter in Biology

Conformational Entropy of Compact Polymers

Exact results for the scaling properties of compact polymers on the square lattice are obtained from an effective field theory. The entropic exponent \gamma=117/112 is calculated, and a line of fixed points associated with interacting chains is identified; along this line \gamma varies continuously. Theoretical results are checked against detailed numerical transfer matrix calculations, which also yield a precise estimate for the connective constant \kappa=1.47280(1).Comment: 4 pages, 1 figur

Correlated quantum percolation in the lowest Landau level

Our understanding of localization in the integer quantum Hall effect is informed by a combination of semi-classical models and percolation theory. Motivated by the effect of correlations on classical percolation we study numerically electron localization in the lowest Landau level in the presence of a power-law correlated disorder potential. Careful comparisons between classical and quantum dynamics suggest that the extended Harris criterion is applicable in the quantum case. This leads to a prediction of new localization quantum critical points in integer quantum Hall systems with power-law correlated disorder potentials. We demonstrate the stability of these critical points to addition of competing short-range disorder potentials, and discuss possible experimental realizations.Comment: 15 pages, 12 figure