Tradeoff between short-term and long-term adaptation in a changing environment

We investigate the competition dynamics of two microbial or viral strains that live in an environment that switches periodically between two states. One of the strains is adapted to the long-term environment, but pays a short-term cost, while the other is adapted to the short-term environment and pays a cost in the long term. We explore the tradeoff between these alternative strategies in extensive numerical simulations, and present a simple analytic model that can predict the outcome of these competitions as a function of the mutation rate and the time scale of the environmental changes. Our model is relevant for arboviruses, which alternate between different host species on a regular basis.Comment: 9 pages, 3 figures, PRE in pres

Strong coupling isotropization of non-Abelian plasmas simplified

We study the isotropization of a homogeneous, strongly coupled, non-Abelian plasma by means of its gravity dual. We compare the time evolution of a large number of initially anisotropic states as determined, on the one hand, by the full non-linear Einstein's equations and, on the other, by the Einstein's equations linearized around the final equilibrium state. The linear approximation works remarkably well even for states that exhibit large anisotropies. For example, it predicts with a 20% accuracy the isotropization time, which is of the order of t_iso \lesssim 1/T, with T the final equilibrium temperature. We comment on possible extensions to less symmetric situations.Comment: 4 pages, 4 figures; v2: minor changes, matches PRL versio

Strong magnetoresistance induced by long-range disorder

We calculate the semiclassical magnetoresistivity $\rho_{xx}(B)$ of non-interacting fermions in two dimensions moving in a weak and smoothly varying random potential or random magnetic field. We demonstrate that in a broad range of magnetic fields the non-Markovian character of the transport leads to a strong positive magnetoresistance. The effect is especially pronounced in the case of a random magnetic field where $\rho_{xx}(B)$ becomes parametrically much larger than its B=0 value.Comment: REVTEX, 4 pages, 2 eps figure

Zero-frequency anomaly in quasiclassical ac transport: Memory effects in a two-dimensional metal with a long-range random potential or random magnetic field

We study the low-frequency behavior of the {\it ac} conductivity $\sigma(\omega)$ of a two-dimensional fermion gas subject to a smooth random potential (RP) or random magnetic field (RMF). We find a non-analytic $\propto|\omega|$ correction to ${\rm Re} \sigma$, which corresponds to a $1/t^2$ long-time tail in the velocity correlation function. This contribution is induced by return processes neglected in Boltzmann transport theory. The prefactor of this $|\omega|$-term is positive and proportional to $(d/l)^2$ for RP, while it is of opposite sign and proportional to $d/l$ in the weak RMF case, where $l$ is the mean free path and $d$ the disorder correlation length. This non-analytic correction also exists in the strong RMF regime, when the transport is of a percolating nature. The analytical results are supported and complemented by numerical simulations.Comment: 12 pages, RevTeX, 7 figure

Longitudinal Coherence in a Holographic Model of p-Pb Collisions

As a model of the longitudinal structure in heavy ion collisions, we simulate gravitational shock wave collisions in anti-de Sitter space in which each shock is composed of multiple constituents. We find that all constituents act coherently, and their separation leaves no imprint on the resulting plasma, when this separation is $\lesssim 0.26 / T_{hyd}$, with $T_{hyd}$ the temperature of the plasma at the time when hydrodynamics first becomes applicable. In particular, the center-of-mass of the plasma coincides with the center-of-mass of all the constituents participating in the collision, as opposed to the center-of-mass of the individual collisions. We discuss the implications for nucleus-nucleus and proton-nucleus collisions.Comment: 5 pages, 3 figures. v2 matches published versio

Solution of the Quasispecies Model for an Arbitrary Gene Network

In this paper, we study the equilibrium behavior of Eigen's quasispecies equations for an arbitrary gene network. We consider a genome consisting of $N$ genes, so that each gene sequence $\sigma$ may be written as $\sigma = \sigma_1 \sigma_2 ... \sigma_N$. We assume a single fitness peak (SFP) model for each gene, so that gene $i$ has some ``master'' sequence $\sigma_{i, 0}$ for which it is functioning. The fitness landscape is then determined by which genes in the genome are functioning, and which are not. The equilibrium behavior of this model may be solved in the limit of infinite sequence length. The central result is that, instead of a single error catastrophe, the model exhibits a series of localization to delocalization transitions, which we term an ``error cascade.'' As the mutation rate is increased, the selective advantage for maintaining functional copies of certain genes in the network disappears, and the population distribution delocalizes over the corresponding sequence spaces. The network goes through a series of such transitions, as more and more genes become inactivated, until eventually delocalization occurs over the entire genome space, resulting in a final error catastrophe. This model provides a criterion for determining the conditions under which certain genes in a genome will lose functionality due to genetic drift. It also provides insight into the response of gene networks to mutagens. In particular, it suggests an approach for determining the relative importance of various genes to the fitness of an organism, in a more accurate manner than the standard ``deletion set'' method. The results in this paper also have implications for mutational robustness and what C.O. Wilke termed ``survival of the flattest.''Comment: 29 pages, 5 figures, to be submitted to Physical Review

The Error and Repair Catastrophes: A Two-Dimensional Phase Diagram in the Quasispecies Model

This paper develops a two gene, single fitness peak model for determining the equilibrium distribution of genotypes in a unicellular population which is capable of genetic damage repair. The first gene, denoted by $\sigma_{via}$, yields a viable organism with first order growth rate constant $k > 1$ if it is equal to some target ``master'' sequence $\sigma_{via, 0}$. The second gene, denoted by $\sigma_{rep}$, yields an organism capable of genetic repair if it is equal to some target ``master'' sequence $\sigma_{rep, 0}$. This model is analytically solvable in the limit of infinite sequence length, and gives an equilibrium distribution which depends on \mu \equiv L\eps , the product of sequence length and per base pair replication error probability, and \eps_r , the probability of repair failure per base pair. The equilibrium distribution is shown to exist in one of three possible ``phases.'' In the first phase, the population is localized about the viability and repairing master sequences. As \eps_r exceeds the fraction of deleterious mutations, the population undergoes a ``repair'' catastrophe, in which the equilibrium distribution is still localized about the viability master sequence, but is spread ergodically over the sequence subspace defined by the repair gene. Below the repair catastrophe, the distribution undergoes the error catastrophe when $\mu$ exceeds \ln k/\eps_r , while above the repair catastrophe, the distribution undergoes the error catastrophe when $\mu$ exceeds $\ln k/f_{del}$, where $f_{del}$ denotes the fraction of deleterious mutations.Comment: 14 pages, 3 figures. Submitted to Physical Review

Systematic study of the two band/two gap superconductivity in carbon-substituted MgB2 by point-contact spectroscopy

Point-contact measurements on the carbon-substituted Mg(B$_{1-x}$C$_x$)$_2$ filament/powder samples directly reveal a retention of the two superconducting energy gaps in the whole doping range from $x = 0$ to $x \approx 0.1$. The large gap on the $\sigma$-band is decreased in an essentially linear fashion with increasing the carbon concentrations. The changes in the the small gap $\Delta_{\pi}$ up to 3.8 % C are proportionally smaller and are more difficult to detect but for the heavily doped sample with $x \approx 0.1$ and $T_c = 22$ K both gaps are still present, and significantly reduced, consistent with a strong essentially linear, reduction of each gap with the transition temperature.Comment: 5 eps figure

Effects of Neutron Irradiation on Carbon Doped MgB2 Wire Segments

We have studied the evolution of superconducting and normal state properties of neutron irradiated Mg(B$_{.962}$C$_{.038}$)$_2$ wire segments as a function of post exposure annealing time and temperature. The initial fluence fully suppressed superconductivity and resulted in an anisotropic expansion of the unit cell. Superconductivity was restored by post-exposure annealing. The upper critical field, H$_{c2}$(T=0), approximately scales with T$_c$ starting with an undamaged T$_c$ near 37 K and H$_{c2}$(T=0) near 32 T. Up to an annealing temperature of 400 $^ o$C the recovery of T$_c$ tends to coincide with a decrease in the normal state resistivity and a systematic recovery of the lattice parameters. Above 400 $^ o$C a decrease in order along the c- direction coincides with an increase in resistivity, but no apparent change in the evolution of T$_c$ and H$_{c2}$. To first order, it appears that carbon doping and neutron damaging effect the superconducting properties of MgB$_2$ independently