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

Driven Lattice Gases with Quenched Disorder: Exact Results and Different Macroscopic Regimes

We study the effect of quenched spatial disorder on the steady states of driven systems of interacting particles. Two sorts of models are studied: disordered drop-push processes and their generalizations, and the disordered asymmetric simple exclusion process. We write down the exact steady-state measure, and consequently a number of physical quantities explicitly, for the drop-push dynamics in any dimensions for arbitrary disorder. We find that three qualitatively different regimes of behaviour are possible in 1-$d$ disordered driven systems. In the Vanishing-Current regime, the steady-state current approaches zero in the thermodynamic limit. A system with a non-zero current can either be in the Homogeneous regime, chracterized by a single macroscopic density, or the Segregated-Density regime, with macroscopic regions of different densities. We comment on certain important constraints to be taken care of in any field theory of disordered systems.Comment: RevTex, 17pages, 18 figures included using psfig.st

Mutation supply and the repeatability of selection for antibiotic resistance

Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Different sizes of mutant libraries of an antibiotic resistance gene, TEM-1 $\beta$-lactamase in Escherichia coli, were subjected to different antibiotic concentrations. We determined whether populations went extinct or survived, and sequenced the TEM gene of the surviving populations. The distribution of mutations per allele in our mutant libraries- generated by error-prone PCR- followed a Poisson distribution. Extinction patterns could be explained by a simple stochastic model that assumed the sampling of beneficial mutations was key for survival. In most surviving populations, alleles containing at least one known large-effect beneficial mutation were present. These genotype data also support a model which only invokes sampling effects to describe the occurrence of alleles containing large-effect driver mutations. Hence, evolution is largely predictable given cursory knowledge of mutational fitness effects, the mutation rate and population size. There were no clear trends in the repeatability of selected mutants when we considered all mutations present. However, when only known large-effect mutations were considered, the outcome of selection is less repeatable for large libraries, in contrast to expectations. Furthermore, we show experimentally that alleles carrying multiple mutations selected from large libraries confer higher resistance levels relative to alleles with only a known large-effect mutation, suggesting that the scarcity of high-resistance alleles carrying multiple mutations may contribute to the decrease in repeatability at large library sizes.Comment: 31pages, 9 figure

Extremal statistics of curved growing interfaces in 1+1 dimensions

We study the joint probability distribution function (pdf) of the maximum M of the height and its position X_M of a curved growing interface belonging to the universality class described by the Kardar-Parisi-Zhang equation in 1+1 dimensions. We obtain exact results for the closely related problem of p non-intersecting Brownian bridges where we compute the joint pdf P_p(M,\tau_M) where \tau_M is there the time at which the maximal height M is reached. Our analytical results, in the limit p \to \infty, become exact for the interface problem in the growth regime. We show that our results, for moderate values of p \sim 10 describe accurately our numerical data of a prototype of these systems, the polynuclear growth model in droplet geometry. We also discuss applications of our results to the ground state configuration of the directed polymer in a random potential with one fixed endpoint.Comment: 6 pages, 4 figures. Published version, to appear in Europhysics Letters. New results added for non-intersecting excursion

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

The process of irreversible nucleation in multilayer growth. II. Exact results in one and two dimensions

We study irreversible dimer nucleation on top of terraces during epitaxial growth in one and two dimensions, for all values of the step-edge barrier. The problem is solved exactly by transforming it into a first passage problem for a random walker in a higher-dimensional space. The spatial distribution of nucleation events is shown to differ markedly from the mean-field estimate except in the limit of very weak step-edge barriers. The nucleation rate is computed exactly, including numerical prefactors.Comment: 22 pages, 10 figures. To appear in Phys. Rev.

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.

Roughness of Sandpile Surfaces

We study the surface roughness of prototype models displaying self-organized criticality (SOC) and their noncritical variants in one dimension. For SOC systems, we find that two seemingly equivalent definitions of surface roughness yields different asymptotic scaling exponents. Using approximate analytical arguments and extensive numerical studies we conclude that this ambiguity is due to the special scaling properties of the nonlinear steady state surface. We also find that there is no such ambiguity for non-SOC models, although there may be intermediate crossovers to different roughness values. Such crossovers need to be distinguished from the true asymptotic behaviour, as in the case of a noncritical disordered sandpile model studied in [10].Comment: 5 pages, 4 figures. Accepted for publication in Phys. Rev.

Design and fabrication of highly efficient non-linear optical devices for implementing high-speed optical processing

We present the design and fabrication of micro-cavity semiconductor devices for enhanced Two-Photon-Absorption response, and demonstrate the use of these devices for implementing sensitive autocorrelation measurements on pico-second optical pulses