Experimental Measurement of the Persistence Exponent of the Planar Ising Model

Using a twisted nematic liquid crystal system exhibiting planar Ising model dynamics, we have measured the scaling exponent $\theta$ which characterizes the time evolution, $p(t) \sim t^{-\theta}$, of the probability p(t) that the local order parameter has not switched its state by the time t. For 0.4 seconds to 200 seconds following the phase quench, the system exhibits scaling behavior and, measured over this interval, $\theta = 0.19 \pm 0.031$, in good agreement with theoretical analysis and numerical simulations.Comment: 4 pages RevTeX (multicol.sty and epsf.sty needed): 1 EPS figure. Introduction and reference list modifie

Phase ordering in bulk uniaxial nematic liquid crystals

The phase-ordering kinetics of a bulk uniaxial nematic liquid crystal is addressed using techniques that have been successfully applied to describe ordering in the O(n) model. The method involves constructing an appropriate mapping between the order-parameter tensor and a Gaussian auxiliary field. The mapping accounts both for the geometry of the director about the dominant charge 1/2 string defects and biaxiality near the string cores. At late-times t following a quench, there exists a scaling regime where the bulk nematic liquid crystal and the three-dimensional O(2) model are found to be isomorphic, within the Gaussian approximation. As a consequence, the scaling function for order-parameter correlations in the nematic liquid crystal is exactly that of the O(2) model, and the length characteristic of the strings grows as $t^{1/2}$. These results are in accord with experiment and simulation. Related models dealing with thin films and monopole defects in the bulk are presented and discussed.Comment: 21 pages, 3 figures, REVTeX, submitted to Phys. Rev.

Dynamical Scaling: the Two-Dimensional XY Model Following a Quench

To sensitively test scaling in the 2D XY model quenched from high-temperatures into the ordered phase, we study the difference between measured correlations and the (scaling) results of a Gaussian-closure approximation. We also directly compare various length-scales. All of our results are consistent with dynamical scaling and an asymptotic growth law $L \sim (t/\ln[t/t_0])^{1/2}$, though with a time-scale $t_0$ that depends on the length-scale in question. We then reconstruct correlations from the minimal-energy configuration consistent with the vortex positions, and find them significantly different from the ``natural'' correlations --- though both scale with $L$. This indicates that both topological (vortex) and non-topological (``spin-wave'') contributions to correlations are relevant arbitrarily late after the quench. We also present a consistent definition of dynamical scaling applicable more generally, and emphasize how to generalize our approach to other quenched systems where dynamical scaling is in question. Our approach directly applies to planar liquid-crystal systems.Comment: 10 pages, 10 figure

Nonequilibrium Dynamics in the Complex Ginzburg-Landau Equation

We present results from a comprehensive analytical and numerical study of nonequilibrium dynamics in the 2-dimensional complex Ginzburg-Landau (CGL) equation. In particular, we use spiral defects to characterize the domain growth law and the evolution morphology. An asymptotic analysis of the single-spiral correlation function shows a sequence of singularities -- analogous to those seen for time-dependent Ginzburg-Landau (TDGL) models with O(n) symmetry, where $n$ is even.Comment: 11 pages, 5 figure

How Efficient Is The Langacker-Pi Mechanism of Monopole Annihilation?

We investigate the dynamics of monopole annihilation by the Langacker-Pi mechanism. We find taht considerations of causality, flux-tube energetics and the friction from Aharonov-Bohm scatteering suggest that the monopole annihilation is most efficient if electromagnetism is spontaneously broken at the lowest temperature ($T_{em} \approx 10^6 GeV$) consistent with not having the monopoles dominate the energy density of the universe.Comment: 10 page

The Energy-Scaling Approach to Phase-Ordering Growth Laws

We present a simple, unified approach to determining the growth law for the characteristic length scale, $L(t)$, in the phase ordering kinetics of a system quenched from a disordered phase to within an ordered phase. This approach, based on a scaling assumption for pair correlations, determines $L(t)$ self-consistently for purely dissipative dynamics by computing the time-dependence of the energy in two ways. We derive growth laws for conserved and non-conserved $O(n)$ models, including two-dimensional XY models and systems with textures. We demonstrate that the growth laws for other systems, such as liquid-crystals and Potts models, are determined by the type of topological defect in the order parameter field that dominates the energy. We also obtain generalized Porod laws for systems with topological textures.Comment: LATeX 18 pages (REVTeX macros), one postscript figure appended, REVISED --- rearranged and clarified, new paragraph on naive dimensional analysis at end of section I

Phase-ordering dynamics of the Gay-Berne nematic liquid crystal

Phase-ordering dynamics in nematic liquid crystals has been the subject of much active investigation in recent years in theory, experiments and simulations. With a rapid quench from the isotropic to nematic phase a large number of topological defects are formed and dominate the subsequent equilibration process. We present here the results of a molecular dynamics simulation of the Gay-Berne model of liquid crystals after such a quench in a system with 65536 molecules. Twist disclination lines as well as type-1 lines and monopoles were observed. Evidence of dynamical scaling was found in the behavior of the spatial correlation function and the density of disclination lines. However, the behavior of the structure factor provides a more sensitive measure of scaling, and we observed a crossover from a defect dominated regime at small values of the wavevector to a thermal fluctuation dominated regime at large wavevector.Comment: 18 pages, 16 figures, animations available at http://www.physics.brown.edu/Users/faculty/pelcovits/lc/coarsening.htm

Growth Laws for Phase Ordering

We determine the characteristic length scale, $L(t)$, in phase ordering kinetics for both scalar and vector fields, with either short- or long-range interactions, and with or without conservation laws. We obtain $L(t)$ consistently by comparing the global rate of energy change to the energy dissipation from the local evolution of the order parameter. We derive growth laws for O(n) models, and our results can be applied to other systems with similar defect structures.Comment: 12 pages, LaTeX, second tr

Intermittency in Dynamics of Two-Dimensional Vortex-like Defects

We examine high-order dynamical correlations of defects (vortices, disclinations etc) in thin films starting from the Langevin equation for the defect motion. We demonstrate that dynamical correlation functions $F_{2n}$ of vorticity and disclinicity behave as $F_{2n}\sim y^2/r^{4n}$ where $r$ is the characteristic scale and $y$ is the fugacity. As a consequence, below the Berezinskii-Kosterlitz-Thouless transition temperature $F_{2n}$ are characterized by anomalous scaling exponents. The behavior strongly differs from the normal law $F_{2n}\sim F_2^n$ occurring for simultaneous correlation functions, the non-simultaneous correlation functions appear to be much larger. The phenomenon resembles intermittency in turbulence.Comment: 30 pages, 11 figure

Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints: interaction cliffs.

This is the original submitted version, before peer review. The final peer-reviewed version is available from ACS at http://pubs.acs.org/doi/abs/10.1021/ci500721x.Activity landscape modeling is mostly a descriptive technique that allows rationalizing continuous and discontinuous SARs. Nevertheless, the interpretation of some landscape features, especially of activity cliffs, is not straightforward. As the nature of activity cliffs depends on the ligand and the target, information regarding both should be included in the analysis. A specific way to include this information is using protein-ligand interaction fingerprints (IFPs). In this paper we report the activity landscape modeling of 507 ligand-kinase complexes (from the KLIFS database) including IFP, which facilitates the analysis and interpretation of activity cliffs. Here we introduce the structure-activity-interaction similarity (SAIS) maps that incorporate information on ligand-target contact similarity. We also introduce the concept of interaction cliffs defined as ligand-target complexes with high structural and interaction similarity but have a large potency difference of the ligands. Moreover, the information retrieved regarding the specific interaction allowed the identification of activity cliff hot spots, which help to rationalize activity cliffs from the target point of view. In general, the information provided by IFPs provides a structure-based understanding of some activity landscape features. This paper shows examples of analyses that can be carried out when IFPs are added to the activity landscape model.M-L is very grateful to CONACyT (No. 217442/312933) and the Cambridge Overseas Trust for funding. AB thanks Unilever for funding and the European Research Council for a Starting Grant (ERC-2013- StG-336159 MIXTURE). J.L.M-F. is grateful to the School of Chemistry, Department of Pharmacy of the National Autonomous University of Mexico (UNAM) for support. This work was supported by a scholarship from the Secretariat of Public Education and the Mexican government