arXiv subjects

David A. Kessler

Publications and source records attributed to David A. Kessler.

At least 109 records · Page 6Linked to original sources

arXiv2007

Singularities in Speckled Speckle

Speckle patterns produced by random optical fields with two (or more) widely different correlation lengths exhibit speckle spots that are themselves highly speckled. Using computer simulations and analytic theory we present results for the point singularities of speckled speckle fields: optical vortices in scalar (one polarization component) fields; C points in vector (two polarization component) fields. In single correlation length fields both types of singularities tend to be more{}-or{}-less uniformly distributed. In contrast, the singularity structure of speckled speckle is anomalous: for some sets of source parameters vortices and C points tend to form widely separated giant clusters, for other parameter sets these singularities tend to form chains that surround large empty regions. The critical point statistics of speckled speckle is also anomalous. In scalar (vector) single correlation length fields phase (azimuthal) extrema are always outnumbered by vortices (C points). In contrast, in speckled speckle fields, phase extrema can outnumber vortices, and azimuthal extrema can outnumber C points, by factors that can easily exceed $10^{4}$ for experimentally realistic source parameters.

physics.optics↗

arXiv2007

Short and Long Range Screening of Optical Singularities

Screening of topological charges (singularities) is discussed for paraxial optical fields with short and with long range correlations. For short range screening the charge variance in a circular region with radius $R$ grows linearly with $R$, instead of with $R^{2}$ as expected in the absence of screening; for long range screening it grows faster than $R$: for a field whose autocorrelation function is the zero order Bessel function J_{0}, the charge variance grows as R ln R$. A J_{0} correlation function is not attainable in practice, but we show how to generate an optical field whose correlation function closely approximates this form. The charge variance can be measured by counting positive and negative singularities inside the region A, or more easily by counting signed zero crossings on the perimeter of A. \For the first method the charge variance is calculated by integration over the charge correlation function C(r), for the second by integration over the zero crossing correlation function Gamma(r). Using the explicit forms of C(r) and of Gamma(r) we show that both methods of calculation yield the same result. We show that for short range screening the zero crossings can be counted along a straight line whose length equals P, but that for long range screening this simplification no longer holds. We also show that for realizable optical fields, for sufficiently small R, the charge variance goes as R^2, whereas for sufficiently large R, it grows as R. These universal laws are applicable to both short and pseudo-long range correlation functions.

physics.optics↗

arXiv2007

Epidemic Size in the Sis Model of Endemic Infec- Tions

We study the Susceptible-Infected-Susceptible model of the spread of an endemic infection. We calculate an exact expression for the mean number of transmissions for all values of the population and the infectivity. We derive the large-N asymptotic behavior for the infectivitiy below, above, and in the critical region. We obtain an analytical expression for the probability distribution of the number of transmissions, n, in the critical region. We show that this distribution has a $n^3/2$ singularity for small n and decays exponentially for large n. The exponent decreases with the distance from threshold, diverging to infinity far below and approaching zero far above.

q-bio.PE↗

arXiv2007

Solution of an infection model near threshold

We study the Susceptible-Infected-Recovered model of epidemics in the vicinity of the threshold infectivity. We derive the distribution of total outbreak size in the limit of large population size $N$. This is accomplished by mapping the problem to the first passage time of a random walker subject to a drift that increases linearly with time. We recover the scaling results of Ben-Naim and Krapivsky that the effective maximal size of the outbreak scales as $N^{2/3}$, with the average scaling as $N^{1/3}$, with an explicit form for the scaling function.

q-bio.PE↗

arXiv2006

Extinction Rates for Fluctuation-Induced Metastabilities : A Real-Space WKB Approach

The extinction of a single species due to demographic stochasticity is analyzed. The discrete nature of the individual agents and the Poissonian noise related to the birth-death processes result in local extinction of a metastable population, as the system hits the absorbing state. The Fokker-Planck formulation of that problem fails to capture the statistics of large deviations from the metastable state, while approximations appropriate close to the absorbing state become, in general, invalid as the population becomes large. To connect these two regimes, a master equation based on a real space WKB method is presented, and is shown to yield an excellent approximation for the decay rate and the extreme events statistics all the way down to the absorbing state. The details of the underlying microscopic process, smeared out in a mean field treatment, are shown to be crucial for an exact determination of the extinction exponent. This general scheme is shown to reproduce the known results in the field, to yield new corollaries and to fit quite precisely the numerical solutions. Moreover it allows for systematic improvement via a series expansion where the small parameter is the inverse of the number of individuals in the metastable state.

q-bio.PE↗

arXiv2006

Fluctuation Induced Instabilities in Front Propagation up a Co-Moving Reaction Gradient in Two Dimensions

We study 2D fronts propagating up a co-moving reaction rate gradient in finite number reaction-diffusion systems. We show that in a 2D rectangular channel, planar solutions to the deterministic mean-field equation are stable with respect to deviations from planarity. We argue that planar fronts in the corresponding stochastic system, on the other hand, are unstable if the channel width exceeds a critical value. Furthermore, the velocity of the stochastic fronts is shown to depend on the channel width in a simple and interesting way, in contrast to fronts in the deterministic MFE. Thus, fluctuations alter the behavior of these fronts in an essential way. These affects are shown to be partially captured by introducing a density cutoff in the reaction rate. Some of the predictions of the cutoff mean-field approach are shown to be in quantitative accord with the stochastic results.

cond-mat.stat-mech↗

arXiv2005

Analytic approach to the evolutionary effects of genetic exchange

We present an approximate analytic study of our previously introduced model of evolution including the effects of genetic exchange. This model is motivated by the process of bacterial transformation. We solve for the velocity, the rate of increase of fitness, as a function of the fixed population size, $N$. We find the velocity increases with $\ln N$, eventually saturated at an $N$ which depends on the strength of the recombination process. The analytical treatment is seen to agree well with direct numerical simulations of our model equations.

q-bio.PE↗

arXiv2005

Front Propagation up a Reaction Rate Gradient

We expand on a previous study of fronts in finite particle number reaction-diffusion systems in the presence of a reaction rate gradient in the direction of the front motion. We study the system via reaction-diffusion equations, using the expedient of a cutoff in the reaction rate below some critical density to capture the essential role of fl uctuations in the system. For large density, the velocity is large, which allows for an approximate analytic treatment. We derive an analytic approximation for the front velocity depe ndence on bulk particle density, showing that the velocity indeed diverge s in the infinite density limit. The form in which diffusion is impleme nted, namely nearest-neighbor hopping on a lattice, is seen to have an essential impact on the nature of the divergence.

cond-mat.stat-mech↗

arXiv2005

Front Propagation Dynamics with Exponentially-Distributed Hopping

We study reaction-diffusion systems where diffusion is by jumps whose sizes are distributed exponentially. We first study the Fisher-like problem of propagation of a front into an unstable state, as typified by the A+B $\to$ 2A reaction. We find that the effect of fluctuations is especially pronounced at small hopping rates. Fluctuations are treated heuristically via a density cutoff in the reaction rate. We then consider the case of propagating up a reaction rate gradient. The effect of fluctuations here is pronounced, with the front velocity increasing without limit with increasing bulk particle density. The rate of increase is faster than in the case of a reaction-gradient with nearest-neighbor hopping. We derive analytic expressions for the front velocity dependence on bulk particle density. Compute simulations are performed to confirm the analytical results.

cond-mat.stat-mech↗

arXiv2005

Equation-free Dynamic Renormalization of a KPZ-type Equation

In the context of equation-free computation, we devise and implement a procedure for using short-time direct simulations of a KPZ type equation to calculate the self-similar solution for its ensemble averaged correlation function. The method involves "lifting" from candidate pair-correlation functions to consistent realization ensembles, short bursts of KPZ-type evolution, and appropriate rescaling of the resulting averaged pair correlation functions. Both the self-similar shapes and their similarity exponents are obtained at a computational cost significantly reduced to that required to reach saturation in such systems.

cond-mat.stat-mech↗

arXiv2004

Recombination dramatically speeds up evolution of finite populations

We study the role of recombination, as practiced by genetically-competent bacteria, in speeding up Darwinian evolution. This is done by adding a new process to a previously-studied Markov model of evolution on a smooth fitness landscape; this new process allows alleles to be exchanged with those in the surrounding medium. Our results, both numerical and analytic, indicate that for a wide range of intermediate population sizes, recombination dramatically speeds up the evolutionary advance.

q-bio.PE↗

arXiv2004

Crack (Non)Propagation in Amorphous Media

We study Mode I crack propagation in amorphous material via a molecular dynamics simulation of a binary alloy with pairwise central-force interactions. We find that when the system is subjected to constant displacement after introduction of a seed crack, the crack does not propagate. This was found to be true both for the modified Lennard-Jones potential of Falk and a shorter-range potential of our own devising. Crystalline samples prepared with these potentials exhibit normal brittle fracture, with running cracks. Only when subjected to a constantly increasing strain did the crack in the glasses lengthen. Even here, once the strain stopped increasing, the crack tip stopped moving. We examined the stress-strain curve for our model materials, and found that they did not exhibit the saturated stress plateau characteristic of ductile materials. We attribute the failure of crack propagation in this system to the availability of many meta-stable configurations available to the crack tip which serve to soak up the energy which would otherwise drive the crack. We conclude that this class of models is inadequate to describe crack propagation in brittle glasses.

cond-mat.mtrl-sci↗

arXiv2004

Fluctuation-regularized Front Propagation Dynamics

We introduce and study a new class of fronts in finite particle number reaction-diffusion systems, corresponding to propagating up a reaction rate gradient. We show that these systems have no traditional mean-field limit, as the nature of the long-time front solution in the stochastic process differs essentially from that obtained by solving the mean-field deterministic reaction-diffusion equations. Instead, one can incorporate some aspects of the fluctuations via introducing a density cutoff. Using this method, we derive analytic expressions for the front velocity dependence on bulk particle density and show self-consistently why this cutoff approach can get the correct leading-order physics.

cond-mat.stat-mech↗

arXiv2003

Analytical study of the effect of recombination on evolution via DNA shuffling

We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations. The simplicity of the model allows us to obtain a full analytical treatment of both its dynamical and equilibrium properties, for the case of an infinite population. We also briefly discuss finite population size corrections.

physics.bio-ph↗

arXiv2003

Fluctuating Filaments Under Tension - From Flexible Chains to Rigid Rods

We develop a novel biased Monte-Carlo simulation technique to measure the force-extension curves and the distribution function of the extension of fluctuating filaments stretched by external force. The method is applicable for arbitrary ratio of the persistence length to the contour length and for arbitrary forces. The simulation results agree with analytic expressions for the force-extension curves and for the renormalized length-scale-dependent elastic moduli, derived in the rigid rod and in the strong force limits. We find that orientational fluctuations and wall effects produce non-Gaussian distributions for nearly rigid filaments in the small to intermediate force regime. We compare our results to the predictions of previous investigators and propose new experiments on nearly rigid rods such as actin filaments.

cond-mat.soft↗

arXiv2003

Equilibrium state of molecular breeding

We investigate the equilibrium state of the model of Peng, \textit{et al.} for molecular breeding. In the model, a population of DNA sequences is successively culled by removing the sequences with the lowest binding affinity to a particular target sequence. The remaining sequences are then amplified to restore the original population size, undergoing some degree of point-substitution of nucleotides in the process. Working in the infinite population size limit, we derive an equation for the equilibrium distribution of binding affinity, here modeled by the number of matches to the target sequence. The equation is then solved approximately in the limit of large sequence length, in the three regimes of strong, intermediate and weak selection. The approximate solutions are verified via comparison to exact numerical results.

cond-mat.stat-mech↗

arXiv2002

Does the continuum theory of dynamic fracture work?

We investigate the validity of the Linear Elastic Fracture Mechanics approach to dynamic fracture. We first test the predictions in a lattice simulation, using a formula of Eshelby for the time-dependent Stress Intensity Factor. Excellent agreement with the theory is found. We then use the same method to analyze the experiment of Sharon and Fineberg. The data here is not consistent with the theoretical expectation.

cond-mat.mtrl-sci↗

arXiv2002

Stretching Instability of Helical Spring

We show that when a gradually increasing tensile force is applied to the ends of a helical spring with sufficiently large ratios of radius to pitch and twist to bending rigidity, the end-to-end distance undergoes a sequence of discontinuous stretching transitions. Subsequent decrease of the force leads to step-like contraction and hysteresis is observed. For finite helices, the number of these transitions increases with the number of helical turns but only one stretching and one contraction instability survive in the limit of an infinite helix. We calculate the critical line that separates the region of parameters in which the deformation is continuous from that in which stretching instabilities occur, and propose experimental tests of our predictions.

cond-mat.soft↗