Escalation of error catastrophe for enzymatic self-replicators

It is a long-standing question in origin-of-life research whether the information content of replicating molecules can be maintained in the presence of replication errors. Extending standard quasispecies models of non-enzymatic replication, we analyze highly specific enzymatic self-replication mediated through an otherwise neutral recognition region, which leads to frequency-dependent replication rates. We find a significant reduction of the maximally tolerable error rate, because the replication rate of the fittest molecules decreases with the fraction of functional enzymes. Our analysis is extended to hypercyclic couplings as an example for catalytic networks.Comment: 6 pages, 4 figures; accepted at Europhys. Let

Records and sequences of records from random variables with a linear trend

We consider records and sequences of records drawn from discrete time series of the form $X_{n}=Y_{n}+cn$, where the $Y_{n}$ are independent and identically distributed random variables and $c$ is a constant drift. For very small and very large drift velocities, we investigate the asymptotic behavior of the probability $p_n(c)$ of a record occurring in the $n$th step and the probability $P_N(c)$ that all $N$ entries are records, i.e. that $X_1 < X_2 < ... < X_N$. Our work is motivated by the analysis of temperature time series in climatology, and by the study of mutational pathways in evolutionary biology.Comment: 21 pages, 7 figure

Bottleneck-induced transitions in a minimal model for intracellular transport

We consider the influence of disorder on the non-equilibrium steady state of a minimal model for intracellular transport. In this model particles move unidirectionally according to the \emph{totally asymmetric exclusion process} (TASEP) and are coupled to a bulk reservoir by \emph{Langmuir kinetics}. Our discussion focuses on localized point defects acting as a bottleneck for the particle transport. Combining analytic methods and numerical simulations, we identify a rich phase behavior as a function of the defect strength. Our analytical approach relies on an effective mean-field theory obtained by splitting the lattice into two subsystems, which are effectively connected exploiting the local current conservation. Introducing the key concept of a carrying capacity, the maximal current which can flow through the bulk of the system (including the defect), we discriminate between the cases where the defect is irrelevant and those where it acts as a bottleneck and induces various novel phases (called {\it bottleneck phases}). Contrary to the simple TASEP in the presence of inhomogeneities, many scenarios emerge and translate into rich underlying phase-diagrams, the topological properties of which are discussed.Comment: 14 pages, 15 figures, 1 tabl

Kinetic roughening of surfaces: Derivation, solution and application of linear growth equations

We present a comprehensive analysis of a linear growth model, which combines the characteristic features of the Edwards--Wilkinson and noisy Mullins equations. This model can be derived from microscopics and it describes the relaxation and growth of surfaces under conditions where the nonlinearities can be neglected. We calculate in detail the surface width and various correlation functions characterizing the model. In particular, we study the crossover scaling of these functions between the two limits described by the combined equation. Also, we study the effect of colored and conserved noise on the growth exponents, and the effect of different initial conditions. The contribution of a rough substrate to the surface width is shown to decay universally as $w_i(0) (\xi_s/\xi(t))^{d/2}$, where $\xi(t) \sim t^{1/z}$ is the time--dependent correlation length associated with the growth process, $w_i(0)$ is the initial roughness and $\xi_s$ the correlation length of the substrate roughness, and $d$ is the surface dimensionality. As a second application, we compute the large distance asymptotics of the height correlation function and show that it differs qualitatively from the functional forms commonly used in the intepretation of scattering experiments.Comment: 28 pages with 4 PostScript figures, uses titlepage.sty; to appear in Phys. Rev.

Coarsening of Sand Ripples in Mass Transfer Models with Extinction

Coarsening of sand ripples is studied in a one-dimensional stochastic model, where neighboring ripples exchange mass with algebraic rates, $\Gamma(m) \sim m^\gamma$, and ripples of zero mass are removed from the system. For $\gamma < 0$ ripples vanish through rare fluctuations and the average ripples mass grows as \avem(t) \sim -\gamma^{-1} \ln (t). Temporal correlations decay as $t^{-1/2}$ or $t^{-2/3}$ depending on the symmetry of the mass transfer, and asymptotically the system is characterized by a product measure. The stationary ripple mass distribution is obtained exactly. For $\gamma > 0$ ripple evolution is linearly unstable, and the noise in the dynamics is irrelevant. For $\gamma = 1$ the problem is solved on the mean field level, but the mean-field theory does not adequately describe the full behavior of the coarsening. In particular, it fails to account for the numerically observed universality with respect to the initial ripple size distribution. The results are not restricted to sand ripple evolution since the model can be mapped to zero range processes, urn models, exclusion processes, and cluster-cluster aggregation.Comment: 10 pages, 8 figures, RevTeX4, submitted to Phys. Rev.

Epitaxial Growth of Thin Films -- a Statistical Mechanical Model

A theoretical framework is developed to describe experiments on the structure of epitaxial thin films, particularly niobium on sapphire. We extend the hypothesis of dynamical scaling to apply to the structure of thin films from its conventional application to simple surfaces. We then present a phenomenological continuum theory that provides a good description of the observed scattering and the measured exponents. Finally the results of experiment and theory are compared.Comment: 10 pages, 3 figures, minor revisions. accepted for publication in J Phys Condense Matte

Stretched exponentials and power laws in granular avalanching

We introduce a model for granular avalanching which exhibits both stretched exponential and power law avalanching over its parameter range. Two modes of transport are incorporated, a rolling layer consisting of individual particles and the overdamped, sliding motion of particle clusters. The crossover in behaviour observed in experiments on piles of rice is attributed to a change in the dominant mode of transport. We predict that power law avalanching will be observed whenever surface flow is dominated by clustered motion. Comment: 8 pages, more concise and some points clarified

Evolutionary trajectories in rugged fitness landscapes

We consider the evolutionary trajectories traced out by an infinite population undergoing mutation-selection dynamics in static, uncorrelated random fitness landscapes. Starting from the population that consists of a single genotype, the most populated genotype \textit{jumps} from a local fitness maximum to another and eventually reaches the global maximum. We use a strong selection limit, which reduces the dynamics beyond the first time step to the competition between independent mutant subpopulations, to study the dynamics of this model and of a simpler one-dimensional model which ignores the geometry of the sequence space. We find that the fit genotypes that appear along a trajectory are a subset of suitably defined fitness \textit{records}, and exploit several results from the record theory for non-identically distributed random variables. The genotypes that contribute to the trajectory are those records that are not \textit{bypassed} by superior records arising further away from the initial population. Several conjectures concerning the statistics of bypassing are extracted from numerical simulations. In particular, for the one-dimensional model, we propose a simple relation between the bypassing probability and the dynamic exponent which describes the scaling of the typical evolution time with genome size. The latter can be determined exactly in terms of the extremal properties of the fitness distribution.Comment: Figures in color; minor revisions in tex

Dynamic Scaling in a 2+1 Dimensional Limited Mobility Model of Epitaxial Growth

We study statistical scale invariance and dynamic scaling in a simple solid-on-solid 2+1 - dimensional limited mobility discrete model of nonequilibrium surface growth, which we believe should describe the low temperature kinetic roughening properties of molecular beam epitaxy. The model exhibits long-lived ``transient'' anomalous and multiaffine dynamic scaling properties similar to that found in the corresponding 1+1 - dimensional problem. Using large-scale simulations we obtain the relevant scaling exponents, and compare with continuum theories.Comment: 5 pages, 4 ps figures included, RevTe