Corrections to scaling in 2--dimensional polymer statistics

Writing $= AN^{2\nu}(1+BN^{-\Delta_1}+CN^{-1}+ ...)$ for the mean square end--to--end length $$ of a self--avoiding polymer chain of $N$ links, we have calculated $\Delta_1$ for the two--dimensional {\em continuum} case from a new {\em finite} perturbation method based on the ground state of Edwards self consistent solution which predicts the (exact) $\nu=3/4$ exponent. This calculation yields $\Delta_1=1/2$. A finite size scaling analysis of data generated for the continuum using a biased sampling Monte Carlo algorithm supports this value, as does a re--analysis of exact data for two--dimensional lattices.Comment: 10 pages of RevTex, 5 Postscript figures. Accepted for publication in Phys. Rev. B. Brief Reports. Also submitted to J. Phys.

Motion of Bound Domain Walls in a Spin Ladder

The elementary excitation spectrum of the spin-$\frac{1}{2}$ antiferromagnetic (AFM) Heisenberg chain is described in terms of a pair of freely propagating spinons. In the case of the Ising-like Heisenberg Hamiltonian spinons can be interpreted as domain walls (DWs) separating degenerate ground states. In dimension $d>1$, the issue of spinons as elementary excitations is still unsettled. In this paper, we study two spin-$\frac{1}{2}$ AFM ladder models in which the individual chains are described by the Ising-like Heisenberg Hamiltonian. The rung exchange interactions are assumed to be pure Ising-type in one case and Ising-like Heisenberg in the other. Using the low-energy effective Hamiltonian approach in a perturbative formulation, we show that the spinons are coupled in bound pairs. In the first model, the bound pairs are delocalized due to a four-spin ring exchange term in the effective Hamiltonian. The appropriate dynamic structure factor is calculated and the associated lineshape is found to be almost symmetric in contrast to the 1d case. In the case of the second model, the bound pair of spinons lowers its kinetic energy by propagating between chains. The results obtained are consistent with recent theoretical studies and experimental observations on ladder-like materials.Comment: 12 pages, 7 figure

Speckle from phase ordering systems

The statistical properties of coherent radiation scattered from phase-ordering materials are studied in detail using large-scale computer simulations and analytic arguments. Specifically, we consider a two-dimensional model with a nonconserved, scalar order parameter (Model A), quenched through an order-disorder transition into the two-phase regime. For such systems it is well established that the standard scaling hypothesis applies, consequently the average scattering intensity at wavevector _k and time t' is proportional to a scaling function which depends only on a rescaled time, t ~ |_k|^2 t'. We find that the simulated intensities are exponentially distributed, with the time-dependent average well approximated using a scaling function due to Ohta, Jasnow, and Kawasaki. Considering fluctuations around the average behavior, we find that the covariance of the scattering intensity for a single wavevector at two different times is proportional to a scaling function with natural variables mt = |t_1 - t_2| and pt = (t_1 + t_2)/2. In the asymptotic large-pt limit this scaling function depends only on z = mt / pt^(1/2). For small values of z, the scaling function is quadratic, corresponding to highly persistent behavior of the intensity fluctuations. We empirically establish a connection between the intensity covariance and the two-time, two-point correlation function of the order parameter. This connection allows sensitive testing, either experimental or numerical, of existing theories for two-time correlations in systems undergoing order-disorder phase transitions. Comparison between theory and our numerical results requires no adjustable parameters.Comment: 18 pgs RevTeX, to appear in PR

Subcellular heterogeneity of ryanodine receptor properties in ventricular myocytes with low T-tubule density

Rationale: In ventricular myocytes of large mammals, not all ryanodine receptor (RyR) clusters are associated with T-tubules (TTs); this fraction increases with cellular remodeling after myocardial infarction (MI). Objective: To characterize RyR functional properties in relation to TT proximity, at baseline and after MI. Methods: Myocytes were isolated from left ventricle of healthy pigs (CTRL) or from the area adjacent to a myocardial infarction (MI). Ca2+ transients were measured under whole-cell voltage clamp during confocal linescan imaging (fluo-3) and segmented according to proximity of TTs (sites of early Ca2+ release, F>F50 within 20 ms) or their absence (delayed areas). Spontaneous Ca2+ release events during diastole, Ca2+ sparks, reflecting RyR activity and properties, were subsequently assigned to either category. Results: In CTRL, spark frequency was higher in proximity of TTs, but spark duration was significantly shorter. Block of Na+/Ca2+ exchanger (NCX) prolonged spark duration selectively near TTs, while block of Ca2+ influx via Ca2+ channels did not affect sparks properties. In MI, total spark mass was increased in line with higher SR Ca2+ content. Extremely long sparks (>47.6 ms) occurred more frequently. The fraction of near-TT sparks was reduced; frequency increased mainly in delayed sites. Increased duration was seen in near-TT sparks only; Ca2+ removal by NCX at the membrane was significantly lower in MI. Conclusion: TT proximity modulates RyR cluster properties resulting in intracellular heterogeneity of diastolic spark activity. Remodeling in the area adjacent to MI differentially affects these RyR subpopulations. Reduction of the number of sparks near TTs and reduced local NCX removal limit cellular Ca2+ loss and raise SR Ca2+ content, but may promote Ca2+ waves

Decay of isolated surface features driven by the Gibbs-Thomson effect in analytic model and simulation

A theory based on the thermodynamic Gibbs-Thomson relation is presented which provides the framework for understanding the time evolution of isolated nanoscale features (i.e., islands and pits) on surfaces. Two limiting cases are predicted, in which either diffusion or interface transfer is the limiting process. These cases correspond to similar regimes considered in previous works addressing the Ostwald ripening of ensembles of features. A third possible limiting case is noted for the special geometry of "stacked" islands. In these limiting cases, isolated features are predicted to decay in size with a power law scaling in time: A is proportional to (t0-t)^n, where A is the area of the feature, t0 is the time at which the feature disappears, and n=2/3 or 1. The constant of proportionality is related to parameters describing both the kinetic and equilibrium properties of the surface. A continuous time Monte Carlo simulation is used to test the application of this theory to generic surfaces with atomic scale features. A new method is described to obtain macroscopic kinetic parameters describing interfaces in such simulations. Simulation and analytic theory are compared directly, using measurements of the simulation to determine the constants of the analytic theory. Agreement between the two is very good over a range of surface parameters, suggesting that the analytic theory properly captures the necessary physics. It is anticipated that the simulation will be useful in modeling complex surface geometries often seen in experiments on physical surfaces, for which application of the analytic model is not straightforward.Comment: RevTeX (with .bbl file), 25 pages, 7 figures from 9 Postscript files embedded using epsf. Submitted to Phys. Rev. B A few minor changes made on 9/24/9

Pulsar Timing and its Application for Navigation and Gravitational Wave Detection

Pulsars are natural cosmic clocks. On long timescales they rival the precision of terrestrial atomic clocks. Using a technique called pulsar timing, the exact measurement of pulse arrival times allows a number of applications, ranging from testing theories of gravity to detecting gravitational waves. Also an external reference system suitable for autonomous space navigation can be defined by pulsars, using them as natural navigation beacons, not unlike the use of GPS satellites for navigation on Earth. By comparing pulse arrival times measured on-board a spacecraft with predicted pulse arrivals at a reference location (e.g. the solar system barycenter), the spacecraft position can be determined autonomously and with high accuracy everywhere in the solar system and beyond. We describe the unique properties of pulsars that suggest that such a navigation system will certainly have its application in future astronautics. We also describe the on-going experiments to use the clock-like nature of pulsars to "construct" a galactic-sized gravitational wave detector for low-frequency (f_GW ~1E-9 - 1E-7 Hz) gravitational waves. We present the current status and provide an outlook for the future.Comment: 30 pages, 9 figures. To appear in Vol 63: High Performance Clocks, Springer Space Science Review

Characterization of complex networks: A survey of measurements

Each complex network (or class of networks) presents specific topological features which characterize its connectivity and highly influence the dynamics of processes executed on the network. The analysis, discrimination, and synthesis of complex networks therefore rely on the use of measurements capable of expressing the most relevant topological features. This article presents a survey of such measurements. It includes general considerations about complex network characterization, a brief review of the principal models, and the presentation of the main existing measurements. Important related issues covered in this work comprise the representation of the evolution of complex networks in terms of trajectories in several measurement spaces, the analysis of the correlations between some of the most traditional measurements, perturbation analysis, as well as the use of multivariate statistics for feature selection and network classification. Depending on the network and the analysis task one has in mind, a specific set of features may be chosen. It is hoped that the present survey will help the proper application and interpretation of measurements.Comment: A working manuscript with 78 pages, 32 figures. Suggestions of measurements for inclusion are welcomed by the author

Application of Graphene within Optoelectronic Devices and Transistors

Scientists are always yearning for new and exciting ways to unlock graphene's true potential. However, recent reports suggest this two-dimensional material may harbor some unique properties, making it a viable candidate for use in optoelectronic and semiconducting devices. Whereas on one hand, graphene is highly transparent due to its atomic thickness, the material does exhibit a strong interaction with photons. This has clear advantages over existing materials used in photonic devices such as Indium-based compounds. Moreover, the material can be used to 'trap' light and alter the incident wavelength, forming the basis of the plasmonic devices. We also highlight upon graphene's nonlinear optical response to an applied electric field, and the phenomenon of saturable absorption. Within the context of logical devices, graphene has no discernible band-gap. Therefore, generating one will be of utmost importance. Amongst many others, some existing methods to open this band-gap include chemical doping, deformation of the honeycomb structure, or the use of carbon nanotubes (CNTs). We shall also discuss various designs of transistors, including those which incorporate CNTs, and others which exploit the idea of quantum tunneling. A key advantage of the CNT transistor is that ballistic transport occurs throughout the CNT channel, with short channel effects being minimized. We shall also discuss recent developments of the graphene tunneling transistor, with emphasis being placed upon its operational mechanism. Finally, we provide perspective for incorporating graphene within high frequency devices, which do not require a pre-defined band-gap.Comment: Due to be published in "Current Topics in Applied Spectroscopy and the Science of Nanomaterials" - Springer (Fall 2014). (17 pages, 19 figures

Optimality of mutation and selection in germinal centers

The population dynamics theory of B cells in a typical germinal center could play an important role in revealing how affinity maturation is achieved. However, the existing models encountered some conflicts with experiments. To resolve these conflicts, we present a coarse-grained model to calculate the B cell population development in affinity maturation, which allows a comprehensive analysis of its parameter space to look for optimal values of mutation rate, selection strength, and initial antibody-antigen binding level that maximize the affinity improvement. With these optimized parameters, the model is compatible with the experimental observations such as the ~100-fold affinity improvements, the number of mutations, the hypermutation rate, and the "all or none" phenomenon. Moreover, we study the reasons behind the optimal parameters. The optimal mutation rate, in agreement with the hypermutation rate in vivo, results from a tradeoff between accumulating enough beneficial mutations and avoiding too many deleterious or lethal mutations. The optimal selection strength evolves as a balance between the need for affinity improvement and the requirement to pass the population bottleneck. These findings point to the conclusion that germinal centers have been optimized by evolution to generate strong affinity antibodies effectively and rapidly. In addition, we study the enhancement of affinity improvement due to B cell migration between germinal centers. These results could enhance our understandings to the functions of germinal centers.Comment: 5 figures in main text, and 4 figures in Supplementary Informatio

Recurrence quantification analysis as a tool for the characterization of molecular dynamics simulations

A molecular dynamics simulation of a Lennard-Jones fluid, and a trajectory of the B1 immunoglobulin G-binding domain of streptococcal protein G (B1-IgG) simulated in water are analyzed by recurrence quantification, which is noteworthy for its independence from stationarity constraints, as well as its ability to detect transients, and both linear and nonlinear state changes. The results demonstrate the sensitivity of the technique for the discrimination of phase sensitive dynamics. Physical interpretation of the recurrence measures is also discussed.Comment: 7 pages, 8 figures, revtex; revised for review for Phys. Rev. E (clarifications and expansion of discussion)-- addition of the 8 postscript figures previously omitted, but unchanged from version