Diffusive Boundary Layers in the Free-Surface Excitable Medium Spiral

Spiral waves are a ubiquitous feature of the nonequilibrium dynamics of a great variety of excitable systems. In the limit of a large separation in timescale between fast excitation and slow recovery, one can reduce the spiral problem to one involving the motion of a free surface separating the excited and quiescent phases. In this work, we study the free surface problem in the limit of small diffusivity for the slow field variable. Specifically, we show that a previously found spiral solution in the diffusionless limit can be extended to finite diffusivity, without significant alteration. This extension involves the creation of a variety of boundary layers which cure all the undesirable singularities of the aforementioned solution. The implications of our results for the study of spiral stability are briefly discussed.Comment: 6 pages, submitted to PRE Rapid Com

Mechanisms underlying sequence-independent beta-sheet formation

We investigate the formation of beta-sheet structures in proteins without taking into account specific sequence-dependent hydrophobic interactions. To accomplish this, we introduce a model which explicitly incorporates both solvation effects and the angular dependence (on the protein backbone) of hydrogen bond formation. The thermodynamics of this model is studied by comparing the restricted partition functions obtained by "unfreezing" successively larger segments of the native beta-sheet structure. Our results suggest that solvation dynamics together with the aforementioned angular dependence gives rise to a generic cooperativity in this class of systems; this result explains why pathological aggregates involving beta-sheet cores can form from many different proteins. Our work provides the foundation for the construction of phenomenological models to investigate the competition between native folding and non-specific aggregation.Comment: 20 pages, 5 figures, Revtex4, simulation mpeg movie available at http://www-physics.ucsd.edu/~guochin/Images/sheet1.mp

The Universal Gaussian in Soliton Tails

We show that in a large class of equations, solitons formed from generic initial conditions do not have infinitely long exponential tails, but are truncated by a region of Gaussian decay. This phenomenon makes it possible to treat solitons as localized, individual objects. For the case of the KdV equation, we show how the Gaussian decay emerges in the inverse scattering formalism.Comment: 4 pages, 2 figures, revtex with eps

Adinkras From Ordered Quartets of BC4{}_4 Coxeter Group Elements and Regarding 1,358,954,496 Matrix Elements of the Gadget

We examine values of the Adinkra Holoraumy-induced Gadget representation space metric over all possible four-color, four-open node, and four-closed node adinkras. Of the 1,358,954,496 gadget matrix elements, only 226,492,416 are non-vanishing and take on one of three values: $-1/3$, $1/3$, or $1$ and thus a subspace isomorphic to a description of a body-centered tetrahedral molecule emerges.Comment: LaTeX twice, 56pp, 30 tables, 5 figures, latest version includes link to updated code, minor corrections, and additional support about inequivalent representations and tetrahedral geometry comments added along with observations about similarity with results previously found by Nekraso

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

Nonlinear lattice model of viscoelastic Mode III fracture

We study the effect of general nonlinear force laws in viscoelastic lattice models of fracture, focusing on the existence and stability of steady-state Mode III cracks. We show that the hysteretic behavior at small driving is very sensitive to the smoothness of the force law. At large driving, we find a Hopf bifurcation to a straight crack whose velocity is periodic in time. The frequency of the unstable bifurcating mode depends on the smoothness of the potential, but is very close to an exact period-doubling instability. Slightly above the onset of the instability, the system settles into a exactly period-doubled state, presumably connected to the aforementioned bifurcation structure. We explicitly solve for this new state and map out its velocity-driving relation

Microscopic Selection of Fluid Fingering Pattern

We study the issue of the selection of viscous fingering patterns in the limit of small surface tension. Through detailed simulations of anisotropic fingering, we demonstrate conclusively that no selection independent of the small-scale cutoff (macroscopic selection) occurs in this system. Rather, the small-scale cutoff completely controls the pattern, even on short time scales, in accord with the theory of microscopic solvability. We demonstrate that ordered patterns are dynamically selected only for not too small surface tensions. For extremely small surface tensions, the system exhibits chaotic behavior and no regular pattern is realized.Comment: 6 pages, 5 figure

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