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Joachim Krug

Publications and source records attributed to Joachim Krug.

At least 73 records · Page 4Linked to original sources
arXiv2010

Bistability in two-locus models with selection, mutation, and recombination

The evolutionary effect of recombination depends crucially on the epistatic interactions between linked loci. A paradigmatic case where recombination is known to be strongly disadvantageous is a two-locus fitness landscape dis- playing reciprocal sign epistasis with two fitness peaks of unequal height. Focusing on the occurrence of bistability in the equilibrium solutions, we consider here the deterministic, haploid two-locus model with reversible mu- tations, selection and recombination. We find analytic formulae for the criti- cal recombination probability rc above which two stable stationary solutions appear which are localized on each of the two fitness peaks. We also derive the stationary genotype frequencies in various parameter regimes. When the recombination rate is close to rc and the fitness difference between the two peaks is small, we obtain a compact description in terms of a cubic polyno- mial which is analogous to the Landau theory of physical phase transitions.

q-bio.PE↗
arXiv2010

Anti-Coarsening and Complex Dynamics of Step Bunches on Vicinal Surfaces during Sublimation

A sublimating vicinal crystal surface can undergo a step bunching instability when the attachment-detachment kinetics is asymmetric, in the sense of a normal Ehrlich-Schwoebel effect. Here we investigate this instability in a model that takes into account the subtle interplay between sublimation and step-step interactions, which breaks the volume-conserving character of the dynamics assumed in previous work. On the basis of a systematically derived continuum equation for the surface profile, we argue that the non-conservative terms pose a limitation on the size of emerging step bunches. This conclusion is supported by extensive simulations of the discrete step dynamics, which show breakup of large bunches into smaller ones as well as arrested coarsening and periodic oscillations between states with different numbers of bunches.

cond-mat.stat-mech↗
arXiv2009

Accurate rate coefficients for models of interstellar gas-grain chemistry

The methodology for modeling grain-surface chemistry has been greatly improved by taking into account the grain size and fluctuation effects. However, the reaction rate coefficients currently used in all practical models of gas-grain chemistry are inaccurate by a significant amount. We provide expressions for these crucial rate coefficients that are both accurate and easy to incorporate into gas-grain models. We use exact results obtained in earlier work, where the reaction rate coefficient was defined by a first-passage problem, which was solved using random walk theory. The approximate reaction rate coefficient presented here is easy to include in all models of interstellar gas-grain chemistry. In contrast to the commonly used expression, the results that it provides are in perfect agreement with detailed kinetic Monte Carlo simulations. We also show the rate coefficient for reactions involving multiple species.

astro-ph.GA↗
arXiv2009

The speed of evolution in large asexual populations

We consider an asexual biological population of constant size $N$ evolving in discrete time under the influence of selection and mutation. Beneficial mutations appear at rate $U$ and their selective effects $s$ are drawn from a distribution $g(s)$. After introducing the required models and concepts of mathematical population genetics, we review different approaches to computing the speed of logarithmic fitness increase as a function of $N$, $U$ and $g(s)$. We present an exact solution of the infinite population size limit and provide an estimate of the population size beyond which it is valid. We then discuss approximate approaches to the finite population problem, distinguishing between the case of a single selection coefficient, $g(s) = δ(s - s_b)$, and a continuous distribution of selection coefficients. Analytic estimates for the speed are compared to numerical simulations up to population sizes of order $10^{300}$.

q-bio.PE↗
arXiv2009

Robustness and epistasis in mutation-selection models

We investigate the fitness advantage associated with the robustness of a phenotype against deleterious mutations using deterministic mutation-selection models of quasispecies type equipped with a mesa shaped fitness landscape. We obtain analytic results for the robustness effect which become exact in the limit of infinite sequence length. Thereby, we are able to clarify a seeming contradiction between recent rigorous work and an earlier heuristic treatment based on a mapping to a Schrödinger equation. We exploit the quantum mechanical analogy to calculate a correction term for finite sequence lengths and verify our analytic results by numerical studies. In addition, we investigate the occurrence of an error threshold for a general class of epistatic landscape and show that diminishing epistasis is a necessary but not sufficient condition for error threshold behavior.

q-bio.PE↗
arXiv2008

Diffusion-limited reactions and mortal random walkers in confined geometries

Motivated by the diffusion-reaction kinetics on interstellar dust grains, we study a first-passage problem of mortal random walkers in a confined two-dimensional geometry. We provide an exact expression for the encounter probability of two walkers, which is evaluated in limiting cases and checked against extensive kinetic Monte Carlo simulations. We analyze the continuum limit which is approached very slowly, with corrections that vanish logarithmically with the lattice size. We then examine the influence of the shape of the lattice on the first-passage probability, where we focus on the aspect ratio dependence: Distorting the lattice always reduces the encounter probability of two walkers and can exhibit a crossover to the behavior of a genuinely one-dimensional random walk. The nature of this transition is also explained qualitatively.

cond-mat.stat-mech↗
arXiv2008

Nonlinear dynamics of surface steps

This is a review of recent theoretical work on complex dynamical behavior of steps on crystal surfaces. The first part of the article is devoted to the electromigration-driven motion of islands and voids, and the second part addresses step bunching on vicinal surfaces.

cond-mat.mtrl-sci↗
arXiv2008

Exploring the effect of sex on an empirical fitness landscape

The nature of epistasis has important consequences for the evolutionary significance of sex and recombination. Recent efforts to find negative epistasis as source of negative linkage disequilibrium and associated long-term sex advantage have yielded little support. Sign epistasis, where the sign of the fitness effects of alleles varies across genetic backgrounds, is responsible for ruggedness of the fitness landscape with implications for the evolution of sex that have been largely unexplored. Here, we describe fitness landscapes for two sets of strains of the asexual fungus \emph{Aspergillus niger} involving all combinations of five mutations. We find that $\sim 30$% of the single-mutation fitness effects are positive despite their negative effect in the wild-type strain, and that several local fitness maxima and minima are present. We then compare adaptation of sexual and asexual populations on these empirical fitness landscapes using simulations. The results show a general disadvantage of sex on these rugged landscapes, caused by the break down by recombination of genotypes escaping from local peaks. Sex facilitates escape from a local peak only for some parameter values on one landscape, indicating its dependence on the landscape's topography. We discuss possible reasons for the discrepancy between our results and the reports of faster adaptation of sexual populations.

q-bio.PE↗
arXiv2007

Evolution in random fitness landscapes: the infinite sites model

We consider the evolution of an asexually reproducing population in an uncorrelated random fitness landscape in the limit of infinite genome size, which implies that each mutation generates a new fitness value drawn from a probability distribution $g(w)$. This is the finite population version of Kingman's house of cards model [J.F.C. Kingman, \textit{J. Appl. Probab.} \textbf{15}, 1 (1978)]. In contrast to Kingman's work, the focus here is on unbounded distributions $g(w)$ which lead to an indefinite growth of the population fitness. The model is solved analytically in the limit of infinite population size $N \to \infty$ and simulated numerically for finite $N$. When the genome-wide mutation probability $U$ is small, the long time behavior of the model reduces to a point process of fixation events, which is referred to as a \textit{diluted record process} (DRP). The DRP is similar to the standard record process except that a new record candidate (a number that exceeds all previous entries in the sequence) is accepted only with a certain probability that depends on the values of the current record and the candidate. We develop a systematic analytic approximation scheme for the DRP. At finite $U$ the fitness frequency distribution of the population decomposes into a stationary part due to mutations and a traveling wave component due to selection, which is shown to imply a reduction of the mean fitness by a factor of $1-U$ compared to the $U \to 0$ limit.

q-bio.PE↗
arXiv2007

Impurity-induced step interactions: a kinetic Monte-Carlo study

A one-dimensional continuum description of growth on vicinal surfaces in the presence of immobile impurities predicts that the impurities can induce step bunching when they suppress the diffusion of adatoms on the surface. In the present communication we verify this prediction by kinetic Monte-Carlo simulations of a two-dimensional solid-on-solid model. We identify the conditions where quasi one-dimensional step flow is stable against island formation or step meandering, and analyse in detail the statistics of the impurity concentration profile. The sign and strength of the impurity-induced step interactions is determined by monitoring the motion of pairs of steps. Assemblies containing up to 20 steps turn out to be unstable towards the emission of single steps. This behavior is traced back to the small value of the effective, impurity-induced attachment asymmetry for adatoms. An analytic estimate for the critical number of steps needed to stabilize a bunch is derived and confirmed by simulations of a one-dimensional model.

cond-mat.stat-mech↗
arXiv2007

Spiral growth, two-dimensional nucleation, and the Ehrlich-Schwoebel effect

Frank's prediction of the spiral growth mode in 1949 defined a pivotal moment in the history of crystal growth. In recent decades the topic has received less attention, and instead we have seen a resurrection of two-dimensional nucleation theory in the context of growth experiments on defect-free homoepitaxial thin films. In particular, the key role of interlayer transport controlled by step edge barriers of the Ehrlich-Schwoebel type in shaping the morphology of multilayer films has been increasingly recognized. After a brief review of the classical theory, this paper reports on a recent study of spiral growth in the presence of step edge barriers. Our key observation is that step edge barriers lead to unconventionally shaped spiral hillocks that display the same characteristic ever-steepening height profiles as wedding cakes formed during growth by two-dimensional nucleation. This prediction was verified experimentally by inducing screw dislocations through ion bombardment of the Pt(111) surface, thus creating a homoepitaxial growth system on which spiral hillocks and wedding cakes coexist.

cond-mat.mtrl-sci↗
arXiv2007

Ehrlich-Schwoebel Effect for Organic Molecules: Direct Calculation of the Step Edge Barrier using Empirical Potentials

The step edge barrier of a prototypical organic semiconductor molecule, 3,4,9,10-perylene-tetracaboxylic-dianhydride (PTCDA) has been analysed by means of calculations based on emperical potentials. The minimum energy path (MEP) has been calculated for a single molecule on a substrate of three molecular layers between equivalent minimum energy positions within two neighboring unit cells. To determine the step edge barrier, we have calculated the MEP over a step to a fourth layer of molecules. We found energy barriers of E_D= 80 meV for in-layer diffusion and E_S = 750 meV for step crossing, indicating a strong Ehrlich-Schwoebel effect for PTCDA.

cond-mat.other↗
arXiv2007

Morphological stability of electromigration-driven vacancy islands

The electromigration-induced shape evolution of two-dimensional vacancy islands on a crystal surface is studied using a continuum approach. We consider the regime where mass transport is restricted to terrace diffusion in the interior of the island. In the limit of fast attachment/detachment kinetics a circle translating at constant velocity is a stationary solution of the problem. In contrast to earlier work [O. Pierre-Louis and T.L. Einstein, Phys. Rev. B 62, 13697 (2000)] we show that the circular solution remains linearly stable for arbitrarily large driving forces. The numerical solution of the full nonlinear problem nevertheless reveals a fingering instability at the trailing end of the island, which develops from finite amplitude perturbations and eventually leads to pinch-off. Relaxing the condition of instantaneous attachment/detachment kinetics, we obtain non-circular elongated stationary shapes in an analytic approximation which compares favorably to the full numerical solution.

cond-mat.mtrl-sci↗
arXiv2007

Records in a changing world

In the context of this paper, a record is an entry in a sequence of random variables (RV's) that is larger or smaller than all previous entries. After a brief review of the classic theory of records, which is largely restricted to sequences of independent and identically distributed (i.i.d.) RV's, new results for sequences of independent RV's with distributions that broaden or sharpen with time are presented. In particular, we show that when the width of the distribution grows as a power law in time $n$, the mean number of records is asymptotically of order $\ln n$ for distributions with a power law tail (the \textit{Fréchet class} of extremal value statistics), of order $(\ln n)^2$ for distributions of exponential type (\textit{Gumbel class}), and of order $n^{1/(ν+1)}$ for distributions of bounded support (\textit{Weibull class}), where the exponent $ν$ describes the behaviour of the distribution at the upper (or lower) boundary. Simulations are presented which indicate that, in contrast to the i.i.d. case, the sequence of record breaking events is correlated in such a way that the variance of the number of records is asymptotically smaller than the mean.

cond-mat.stat-mech↗
arXiv2006

Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapes

We study the adaptation dynamics of an initially maladapted asexual population with genotypes represented by binary sequences of length $L$. The population evolves in a maximally rugged fitness landscape with a large number of local optima. We find that whether the evolutionary trajectory is deterministic or stochastic depends on the effective mutational distance $d_{\mathrm{eff}}$ upto which the population can spread in genotype space. For $d_{\mathrm{eff}}=L$, the deterministic quasispecies theory operates while for $d_{\mathrm{eff}} < 1$, the evolution is completely stochastic. Between these two limiting cases, the dynamics are described by a local quasispecies theory below a crossover time $T_{\times}$ while above $T_{\times}$, the population gets trapped at a local fitness peak and manages to find a better peak either via stochastic tunneling or double mutations. In the stochastic regime $d_\mathrm{eff} < 1$, we identify two subregimes associated with clonal interference and uphill adaptive walks, respectively. We argue that our findings are relevant to the interepretation of evolution experiments with microbial populations.

q-bio.PE↗
arXiv2006

Kinetic Monte Carlo simulations of oscillatory shape evolution for electromigration-driven islands

The shape evolution of two-dimensional islands under electromigration-driven periphery diffusion is studied by kinetic Monte Carlo (KMC) simulations and continuum theory. The energetics of the KMC model is adapted to the Cu(100) surface, and the continuum model is matched to the KMC model by a suitably parametrized choice of the orientation-dependent step stiffness and step atom mobility. At 700 K shape oscillations predicted by continuum theory are quantitatively verified by the KMC simulations, while at 500 K qualitative differences between the two modeling approaches are found.

cond-mat.mtrl-sci↗
arXiv2006

The sweeping rate in diffusion-mediated reactions on dust grain surfaces

A prominent chemical reaction in interstellar clouds is the formation of molecular hydrogen by recombination, which essentially takes place on dust grain surfaces. Analytical approaches to model such a system have hitherto neglected the spatial aspects of the problem by employing a simplistic version of the sweeping rate of reactants. We show how these aspects can be accounted for by a consistent definition of the sweeping rate, and calculate it exactly for a spherical grain. Two regimes can be identified: Small grains, on which two reactants almost surely meet, and large grains, where this is very unlikely. We compare the true sweeping rate to the conventional approximation and find a characteristic reduction in both regimes, most pronounced for large grains. These effects can be understood heuristically using known results from the analysis of two-dimensional random walks. We finally examine the influence of using the true sweeping rate in the calculation of the efficiency of hydrogen recombination: For fixed temperature, the efficiency can be reduced considerably, and relative to that, small grains gain in importance, but the temperature window in which recombination is efficient is not changed substantially.

astro-ph↗