arXiv subjects

David R. Nelson

Publications and source records attributed to David R. Nelson.

At least 91 records · Page 5Linked to original sources

arXiv2009

Fisher equation with turbulence in one dimension

We investigate the dynamics of the Fisher equation for the spreading of micro-organisms in one dimension subject to both turbulent convection and diffusion. We show that for strong enough turbulence, bacteria, for example, track in a quasilocalized fashion (with remakably long persistance times) sinks in the turbulent field. An important consequence is a large reduction in the carrying capacity of the fluid medium. We determine analytically the regimes where this quasi-localized behavior occurs and test our predictions by numerical simulations.

q-bio.PE↗

arXiv2008

Life at the front of an expanding population

Recent microbial experiments suggest that enhanced genetic drift at the frontier of a two-dimensional range expansion can cause genetic sectoring patterns with fractal domain boundaries. Here, we propose and analyze a simple model of asexual biological evolution at expanding frontiers to explain these neutral patterns and predict the effect of natural selection. Our model attributes the observed gradual decrease in the number of sectors at the leading edge to an unbiased random walk of sector boundaries. Natural selection introduces a deterministic bias in the wandering of domain boundaries that renders beneficial mutations more likely to escape genetic drift and become established in a sector. We find that the opening angle of those sectors and the rate at which they become established depend sensitively on the selective advantage of the mutants. Deleterious mutations, on the other hand, are not able to establish a sector permanently. They can, however, temporarily "surf" on the population front, and thereby reach unusual high frequencies. As a consequence, expanding frontiers are susceptible to deleterious mutations as revealed by the high fraction of mutants at mutation-selection balance. Numerically, we also determine the condition at which the wild type is lost in favor of deleterious mutants (genetic meltdown) at a growing front. Our prediction for this error threshold differs qualitatively from existing well-mixed theories, and sets tight constraints on sustainable mutation rates for populations that undergo frequent range expansions.

q-bio.PE↗

arXiv2008

Genetic drift at expanding frontiers promotes gene segregation

Competition between random genetic drift and natural selection plays a central role in evolution: Whereas non-beneficial mutations often prevail in small populations by chance, mutations that sweep through large populations typically confer a selective advantage. Here, however, we observe chance effects during range expansions that dramatically alter the gene pool even in large microbial populations. Initially well-mixed populations of two fluorescently labeled strains of Escherichia coli develop well-defined, sector-like regions with fractal boundaries in expanding colonies. The formation of these regions is driven by random fluctuations that originate in a thin band of pioneers at the expanding frontier. A comparison of bacterial and yeast colonies (Saccharomyces cerevisiae) suggests that this large-scale genetic sectoring is a generic phenomenon that may provide a detectable footprint of past range expansions.

q-bio.PE↗

arXiv2008

Collapse and folding of pressurized rings in two dimensions

Hydrostatically pressurized circular rings confined to two dimensions (or cylinders constrained to have only z-independent deformations) undergo Euler type buckling when the outside pressure exceeds a critical value. We perform a stability analysis of rings with arc-length dependent bending moduli and determine how weakened bending modulus segments affect the buckling critical pressure. Rings with a 4-fold symmetric modulation are particularly susceptible to collapse. In addition we study the initial post-buckling stages of the pressurized rings to determine possible ring folding patterns.

cond-mat.soft↗

arXiv2008

Defect-Mediated Emulsification in Two Dimensions

We consider two dimensional dispersions of droplets of isotropic phase in a liquid with an XY-like order parameter, tilt, nematic, and hexatic symmetries being included. Strong anchoring boundary conditions are assumed. Textures for a single droplet and a pair of droplets are calculated and a universal droplet-droplet pair potential is obtained. The interaction of dispersed droplets via the ordered phase is attractive at large distances and repulsive at short distances, which results in a well defined preferred separation for two droplets and topological stabilization of the emulsion. This interaction also drives self-assembly into chains. Preferred separations and energy barriers to coalescence are calculated, and effects of thermal fluctuations and film thickness are discussed.

cond-mat.soft↗

arXiv2008

Vortices in Superfluid Films on Curved Surfaces

We present a systematic study of how vortices in superfluid films interact with the spatially varying Gaussian curvature of the underlying substrate. The Gaussian curvature acts as a source for a geometric potential that attracts (repels) vortices towards regions of negative (positive) Gaussian curvature independently of the sign of their topological charge. Various experimental tests involving rotating superfluid films and vortex pinning are first discussed for films coating gently curved substrates that can be treated in perturbation theory from flatness. An estimate of the experimental regimes of interest is obtained by comparing the strength of the geometrical forces to the vortex pinning induced by the varying thickness of the film which is in turn caused by capillary effects and gravity. We then present a non-perturbative technique based on conformal mappings that leads an exact solution for the geometric potential as well as the geometric correction to the interaction between vortices. The conformal mapping approach is illustrated by means of explicit calculations of the geometric effects encountered in the study of some strongly curved surfaces and by deriving universal bounds on their strength.

cond-mat.soft↗

arXiv2007

Effects of kinked linear defects on planar flux line arrays

In the hard core limit, interacting vortices in planar type II superconductors can be modeled as non-interacting one dimensional fermions propagating in imaginary time. We use this analogy to derive analytical expressions for the probability density and imaginary current of vortex lines interacting with an isolated bent line defect and to understand the pinning properties of such systems. When there is an abrupt change of the direction of the pinning defect, we find a sinusoidal modulation of the vortex density in directions both parallel and perpendicular to the defect.

cond-mat.supr-con↗

arXiv2007

Genome landscapes and bacteriophage codon usage

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa and L. lactis as their primary host. We introduce the concept of a `genome landscape,' which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such a GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.

q-bio.GN↗

arXiv2007

Interstitial Fractionalization and Spherical Crystallography

Finding the ground states of identical particles packed on spheres has relevance for stabilizing emulsions and a venerable history in the literature of theoretical physics and mathematics. Theory and experiment have confirmed that defects such as disclinations and dislocations are an intrinsic part of the ground state. Here we discuss the remarkable behavior of vacancies and interstitials in spherical crystals. The strain fields of isolated disclinations forced in by the spherical topology literally rip interstitials and vacancies apart, typically into dislocation fragments that combine with the disclinations to create small grain boundary scars. The fractionation is often into three charge-neutral dislocations, although dislocation pairs can be created as well. We use a powerful, freely available computer program to explore interstitial fractionalization in some detail, for a variety of power law pair potentials. We investigate the dependence on initial conditions and the final state energies, and compare the position dependence of interstitial energies with the predictions of continuum elastic theory on the sphere. The theory predicts that, before fragmentation, interstitials are repelled from 5-fold disclinations and vacancies are attracted. We also use vacancies and interstitials to study low energy states in the vicinity of "magic numbers" that accommodate regular icosadeltahedral tessellations.

cond-mat.soft↗

arXiv2007

Unzipping Vortices in Type-II Superconductors

The unzipping of vortex lines using magnetic-force microscopy from extended defects is studied theoretically. We study both the unzipping isolated vortex from common defects, such as columnar pins and twin-planes, and the unzipping of a vortex from a plane in the presence of other vortices. We show, using analytic and numerical methods, that the universal properties of the unzipping transition of a single vortex depend only on the dimensionality of the defect in the presence and absence of disorder. For the unzipping of a vortex from a plane populated with many vortices is shown to be very sensitive to the properties of the vortices in the two-dimensional plane. In particular such unzipping experiments can be used to measure the ``Luttinger liquid parameter'' of the vortices in the plane. In addition we suggest a method for measuring the line tension of the vortex directly using the experiments.

cond-mat.stat-mech↗

arXiv2007

Gene surfing

Spatially resolved genetic data is increasingly used to reconstruct the migrational history of species. To assist such inference, we study, by means of simulations and analytical methods, the dynamics of neutral gene frequencies in a population undergoing a continual range expansion in one dimension. During such a colonization period, lineages can fix at the wave front by means of a ``surfing'' mechanism [Edmonds C.A., Lillie A.S. & Cavalli-Sforza L.L. (2004) Proc Natl Acad Sci USA 101: 975-979]. We quantify this phenomenon in terms of (i) the spatial distribution of lineages that reach fixation and, closely related, (ii) the continual loss of genetic diversity (heterozygosity) at the wave front, characterizing the approach to fixation. Our simulations show that an effective population size can be assigned to the wave that controls the (observable) gradient in heterozygosity left behind the colonization process. This effective population size is markedly higher in pushed waves than in pulled waves, and increases only sub-linearly with deme size. To explain these and other findings, we develop a versatile analytical approach, based on the physics of reaction-diffusion systems, that yields simple predictions for any deterministic population dynamics.

q-bio.PE↗

arXiv2007

Geometric Theory of Columnar Phases on Curved Substrates

We study thin self-assembled columns constrained to lie on a curved, rigid substrate. The curvature presents no local obstruction to equally spaced columns in contrast to curved crystals for which the crystalline bonds are frustrated. Instead, the vanishing compressional strain of the columns implies that their normals lie on geodesics which converge (diverge) in regions of positive (negative) Gaussian curvature, in analogy to the focussing of light rays by a lens. We show that the out of plane bending of the cylinders acts as an effective ordering field.

cond-mat.soft↗

arXiv2006

Conditions for extreme sensitivity of protein diffusion in membranes to cell environments

We study protein diffusion in multicomponent lipid membranes close to a rigid substrate separated by a layer of viscous fluid. The large-distance, long-time asymptotics for Brownian motion are calculated using a nonlinear stochastic Navier-Stokes equation including the effect of friction with the substrate. The advective nonlinearity, neglected in previous treatments, gives only a small correction to the renormalized viscosity and diffusion coefficient at room temperature. We find, however, that in realistic multicomponent lipid mixtures, close to a critical point for phase separation, protein diffusion acquires a strong power-law dependence on temperature and the distance to the substrate $H$, making it much more sensitive to cell environment, unlike the logarithmic dependence on $H$ and very small thermal correction away from the critical point.

cond-mat.soft↗

arXiv2006

Transverse Meissner Physics of Planar Superconductors with Columnar Pins

The statistical mechanics of thermally excited vortex lines with columnar defects can be mapped onto the physics of interacting quantum particles with quenched random disorder in one less dimension. The destruction of the Bose glass phase in Type II superconductors, when the external magnetic field is tilted sufficiently far from the column direction, is described by a poorly understood non-Hermitian quantum phase transition. We present here exact results for this transition in (1+1)-dimensions, obtained by mapping the problem in the hard core limit onto one-dimensional fermions described by a non-Hermitian tight binding model. Both site randomness and the relatively unexplored case of bond randomness are considered. Analysis near the mobility edge and near the band center in the latter case is facilitated by a real space renormalization group procedure used previously for Hermitian quantum problems with quenched randomness in one dimension.

cond-mat.dis-nn↗

arXiv2006

Nematic textures in spherical shells

The equilibrium texture of nematic shells is studied as a function of their thickness. For ultrathin shells the ground state has four short 1/2 disclination lines but, as the thickness of the film increases, a three dimensional escaped configuration composed of two pairs of half-hedgehogs becomes energetically favorable. We derive an exact solution for the nematic ground state in the one Frank constant approximation and study the stability of the corresponding texture against thermal fluctuations.

cond-mat.soft↗

arXiv2006

Crystallography on Curved Surfaces

We study static and dynamical properties that distinguish two dimensional crystals constrained to lie on a curved substrate from their flat space counterparts. A generic mechanism of dislocation unbinding in the presence of varying Gaussian curvature is presented in the context of a model surface amenable to full analytical treatment. We find that glide diffusion of isolated dislocations is suppressed by a binding potential of purely geometrical origin. Finally, the energetics and biased diffusion dynamics of point defects such as vacancies and interstitials is explained in terms of their geometric potential.

cond-mat.soft↗

arXiv2006

Vortex pinning by meandering line defects in planar superconductors

To better understand vortex pinning in thin superconducting slabs, we study the interaction of a single fluctuating vortex filament with a curved line defect in (1+1) dimensions. This problem is also relevant to the interaction of scratches with wandering step edges in vicinal surfaces. The equilibrium probability density for a fluctuating line attracted to a particular fixed defect trajectory is derived analytically by mapping the problem to a straight line defect in the presence of a space and time-varying external tilt field. The consequences of both rapid and slow changes in the frozen defect trajectory, as well as finite size effects are discussed. A sudden change in the defect direction leads to a delocalization transition, accompanied by a divergence in the trapping length, near a critical angle.

cond-mat.stat-mech↗

arXiv2005

Crystalline Particle Packings on a Sphere with Long Range Power Law Potentials

The original Thomson problem of "spherical crystallography" seeks the ground state of electron shells interacting via the Coulomb potential; however one can also study crystalline ground states of particles interacting with other potentials. We focus here on long range power law interactions of the form 1/r^gamma (0 < γ< 2), with the classic Thomson problem given by gamma=1. At large R/a, where R is the sphere radius and a is the particle spacing, the problem can be reformulated as a continuum elastic model that depends on the Young's modulus of particles packed in the plane and the universal (independent of the pair potential) geometrical interactions between disclination defects. The energy of the continuum model can be expressed as an expansion in powers of the total number of particles, M sim (R/a)^2, with coefficients explicitly related to both geometric and potential-dependent terms. For icosahedral configurations of twelve 5-fold disclinations, the first non-trivial coefficient of the expansion agrees with explicit numerical evaluation for discrete particle arrangements to 4 significant digits; the discrepancy in the 5th digit arises from a contribution to the energy that is sensitive to the particular icosadeltahedral configuration and that is neglected in the continuum calculation. In the limit of a very large number of particles, an instability toward grain boundaries can be understood in terms of a "Debye{--}Huckel" solution, where dislocations have continuous Burgers' vector "charges". Discrete dislocations in grain boundaries for intermediate particle numbers are discussed as well.

cond-mat.soft↗