Fluctuations in models of biological macroevolution

Fluctuations in diversity and extinction sizes are discussed and compared for two different, individual-based models of biological coevolution. Both models display power-law distributions for various quantities of evolutionary interest, such as the lifetimes of individual species, the quiet periods between evolutionary upheavals larger than a given cutoff, and the sizes of extinction events. Time series of the diversity and measures of the size of extinctions give rise to flicker noise. Surprisingly, the power-law behaviors of the probability densities of quiet periods in the two models differ, while the distributions of the lifetimes of individual species are the same.Comment: 7 pages, 5 figure

Computational Lattice-Gas Modeling of the Electrosorption of Small Molecules and Ions

We present two recent applications of lattice-gas modeling techniques to electrochemical adsorption on catalytically active metal substrates: urea on Pt(100) and (bi)sulfate on Rh(111). Both involve the specific adsorption of small molecules or ions on well-characterized single-crystal electrodes, and they provide a particularly good fit between the adsorbate geometry and the substrate structure. The close geometric fit facilitates the formation of ordered submonolayer adsorbate phases in a range of electrode potential positive of the range in which an adsorbed monolayer of hydrogen is stable. In both systems the ordered-phase region is separated from the adsorbed- hydrogen region by a phase transition, signified in cyclic voltammograms by a sharp current peak. Based on data from {\it in situ\/} radiochemical surface concentration measurements, cyclic voltammetry, and scanning tunneling micro- scopy, and {\it ex situ\/} Auger electron spectroscopy and low-energy electron diffraction, we have developed specific lattice-gas models for the two systems. These models were studied by group-theoretical ground-state calcu- lations and numerical Monte Carlo simulations, and effective lattice-gas inter- action parameters were determined so as to provide agreement with experiments.Comment: 17 pp. uuencoded postscript, FSU-SCRI-94C-9

Field-driven solid-on-solid interfaces moving under a stochastic Arrhenius dynamic: effects of the barrier height

We present analytical results and kinetic Monte Carlo simulations for the mobility and microscopic structure of solid-on-solid (SOS) interfaces driven far from equilibrium by an external force, such as an applied field or (electro)chemical potential difference. The interfaces evolve under a specific stochastic dynamic with a local energy barrier (an Arrhenius dynamic), known as the transition dynamics approximation (TDA). We calculate the average height of steps on the interface, the average interface velocity, and the skewness of the interface as functions of the driving force and the height of the energy barrier. We find that the microscopic interface structure depends quite strongly on the barrier height. As the barrier becomes higher, the local interface width decreases and the skewness increases, suggesting increasing short-range correlations between the step heights.Comment: 6 pages, 5 figs. RevTe

Discrete-Event Analytic Technique for Surface Growth Problems

We introduce an approach for calculating non-universal properties of rough surfaces. The technique uses concepts of distinct surface-configuration classes, defined by the surface growth rule. The key idea is a mapping between discrete events that take place on the interface and its elementary local-site configurations. We construct theoretical probability distributions of deposition events at saturation for surfaces generated by selected growth rules. These distributions are then used to compute measurable physical quantities. Despite the neglect of temporal correlations, our approximate analytical results are in very good agreement with numerical simulations. This discrete-event analytic technique can be particularly useful when applied to quantification problems, which are known to not be suited to continuum methods.Comment: 4 pages, 7 figures, published 17 Feb. 200

Kinetic Monte Carlo simulations of electrodeposition: Crossover from continuous to instantaneous homogeneous nucleation within Avrami's law

The influence of lateral adsorbate diffusion on the dynamics of the first-order phase transition in a two-dimensional Ising lattice gas with attractive nearest-neighbor interactions is investigated by means of kinetic Monte Carlo simulations. For example, electrochemical underpotential deposition proceeds by this mechanism. One major difference from adsorption in vacuum surface science is that under control of the electrode potential and in the absence of mass-transport limitations, local adsorption equilibrium is approximately established. We analyze our results using the theory of Kolmogorov, Johnson and Mehl, and Avrami (KJMA), which we extend to an exponentially decaying nucleation rate. Such a decay may occur due to a suppression of nucleation around existing clusters in the presence of lateral adsorbate diffusion. Correlation functions prove the existence of such exclusion zones. By comparison with microscopic results for the nucleation rate I and the interface velocity of the growing clusters v, we can show that the KJMA theory yields the correct order of magnitude for Iv^2. This is true even though the spatial correlations mediated by diffusion are neglected. The decaying nucleation rate causes a gradual crossover from continuous to instantaneous nucleation, which is complete when the decay of the nucleation rate is very fast on the time scale of the phase transformation. Hence, instantaneous nucleation can be homogeneous, producing negative minima in the two-point correlation functions. We also present in this paper an n-fold way Monte Carlo algorithm for a square lattice gas with adsorption/desorption and lateral diffusion.Comment: minor modifications; accepted for publication in Surface Scienc

Absorbing Random Walks Interpolating Between Centrality Measures on Complex Networks

Centrality, which quantifies the "importance" of individual nodes, is among the most essential concepts in modern network theory. As there are many ways in which a node can be important, many different centrality measures are in use. Here, we concentrate on versions of the common betweenness and it closeness centralities. The former measures the fraction of paths between pairs of nodes that go through a given node, while the latter measures an average inverse distance between a particular node and all other nodes. Both centralities only consider shortest paths (i.e., geodesics) between pairs of nodes. Here we develop a method, based on absorbing Markov chains, that enables us to continuously interpolate both of these centrality measures away from the geodesic limit and toward a limit where no restriction is placed on the length of the paths the walkers can explore. At this second limit, the interpolated betweenness and closeness centralities reduce, respectively, to the well-known it current betweenness and resistance closeness (information) centralities. The method is tested numerically on four real networks, revealing complex changes in node centrality rankings with respect to the value of the interpolation parameter. Non-monotonic betweenness behaviors are found to characterize nodes that lie close to inter-community boundaries in the studied networks

Complex dynamics in coevolution models with ratio-dependent functional response

We explore the complex dynamical behavior of two simple predator-prey models of biological coevolution that on the ecological level account for interspecific and intraspecific competition, as well as adaptive foraging behavior. The underlying individual-based population dynamics are based on a ratio-dependent functional response [W.M. Getz, J. Theor. Biol. 108, 623 (1984)]. Analytical results for fixed-point population sizes in some simple communities are derived and discussed. In long kinetic Monte Carlo simulations we find quite robust, approximate 1/f noise in species diversity and population sizes, as well as power-law distributions for the lifetimes of individual species and the durations of periods of relative evolutionary stasis. Adaptive foraging enhances coexistence of species and produces a metastable low-diversity phase and a stable high-diversity phase.Comment: 19 page