Stationary states and phase diagram for a model of the Gunn effect under realistic boundary conditions

A general formulation of boundary conditions for semiconductor-metal contacts follows from a phenomenological procedure sketched here. The resulting boundary conditions, which incorporate only physically well-defined parameters, are used to study the classical unipolar drift-diffusion model for the Gunn effect. The analysis of its stationary solutions reveals the presence of bistability and hysteresis for a certain range of contact parameters. Several types of Gunn effect are predicted to occur in the model, when no stable stationary solution exists, depending on the value of the parameters of the injecting contact appearing in the boundary condition. In this way, the critical role played by contacts in the Gunn effect is clearly established.

Mitochondrial DNA variation along an altitudinal gradient in the greater white-toothed shrew, Crocidura russula.

The distribution of mitochondrial control region-sequence polymorphism was investigated in 15 populations of Crocidura russula along an altitudinal gradient in western Switzerland. High-altitude populations are smaller, sparser and appear to undergo frequent bottlenecks. Accordingly, they showed a loss of rare haplotypes, but unexpectedly, were less differentiated than lowland populations. Furthermore, the major haplotypes segregated significantly with altitude. The results were inconsistent with a simple model of drift and dispersal. They suggested instead a role for historical patterns of colonization, or, alternatively, present-day selective forces acting on one of the mitochondrial genes involved in metabolic pathways.

Tree and Brush Control For County Road Right-of-Way, Ocotober 2002

This manual summarizes the roadside tree and brush control methods used by all of Iowa's 99 counties. It is based on interviews conducted in Spring 2002 with county engineers, roadside managers and others. The target audience of this manual is the novice county engineer or roadside manager. Iowa law is nearly silent on roadside tree and brush control, so individual counties have been left to decide on the level of control they want to achieve and maintain. Different solutions have been developed but the goal of every county remains the same: to provide safe roads for the traveling public. Counties in eastern and southern Iowa appear to face the greatest brush control challenge. Most control efforts can be divided into two categories: mechanical and chemical. Mechanical control includes cutting tools and supporting equipment. A chain saw is the most widely used cutting tool. Tractor mounted boom mowers and brush cutters are used to prune miles of brush but have significant safety and aesthetic limitations and boom mowers are easily broken by inexperienced operators. The advent of tree shears and hydraulic thumbs offer unprecedented versatility. Bulldozers are often considered a method of last resort since they reduce large areas to bare ground. Any chipper that violently grabs brush should not be used. Chemical control is the application of herbicide to different parts of a plant: foliar spray is applied to leaves; basal bark spray is applied to the tree trunk; a cut stump treatment is applied to the cambium ring of a cut surface. There is reluctance by many to apply herbicide into the air due to drift concerns. One-third of Iowa counties do not use foliar spray. By contrast, several accepted control methods are directed toward the ground. Freshly cut stumps should be treated to prevent resprouting. Basal bark spray is highly effective in sensitive areas such as near houses. Interest in chemical control is slowly increasing as herbicides and application methods are refined. Fall burning, a third, distinctly separate technique is underused as a brush control method and can be effective if timed correctly. In all, control methods tend to reflect agricultural patterns in a county. The use of chain saws and foliar sprays tends to increase in counties where row crops predominate, and boom mowing tends to increase in counties where grassland predominates. For counties with light to moderate roadside brush, rotational maintenance is the key to effective control. The most comprehensive approach to control is to implement an integrated roadside vegetation management (IRVM) program. An IRVM program is usually directed by a Roadside Manager whose duties may be shared with another position. Funding for control programs comes from the Rural Services Basic portion of a county's budget. The average annual county brush control budget is about $76,000. That figure is thought not to include shared expenses such as fuel and buildings. Start up costs for an IRVM program are less if an existing control program is converted. In addition, IRVM budgets from three different northeastern Iowa counties are offered for comparison in this manual. The manual also includes a chapter on temporary traffic control in rural work zones, a summary of the Iowa Code as it relates to brush control, and rules on avoiding seasonal disturbance of the endangered Indiana bat. Appendices summarize survey and forest cover data, an equipment inventory, sample forms for record keeping, a sample brush control policy, a few legal opinions, a literature search, and a glossary.

Joint evolution of dispersal and inbreeding load.

Inbreeding avoidance is often invoked to explain observed patterns of dispersal, and theoretical models indeed point to a possibly important role. However, while inbreeding load is usually assumed constant in these models, it is actually bound to vary dynamically under the combined influences of mutation, drift, and selection and thus to evolve jointly with dispersal. Here we report the results of individual-based stochastic simulations allowing such a joint evolution. We show that strongly deleterious mutations should play no significant role, owing to the low genomic mutation rate for such mutations. Mildly deleterious mutations, by contrast, may create enough heterosis to affect the evolution of dispersal as an inbreeding-avoidance mechanism, but only provided that they are also strongly recessive. If slightly recessive, they will spread among demes and accumulate at the metapopulation level, thus contributing to mutational load, but not to heterosis. The resulting loss of viability may then combine with demographic stochasticity to promote population fluctuations, which foster indirect incentives for dispersal. Our simulations suggest that, under biologically realistic parameter values, deleterious mutations have a limited impact on the evolution of dispersal, which on average exceeds by only one-third the values expected from kin-competition avoidance.

Simulations of electrophoretic collisions of DNA knots with gel obstacles

Gel electrophoresis can be used to separate nicked circular DNA molecules of equal length but forming different knot types. At low electric fields, complex knots drift faster than simpler knots. However, at high electric field the opposite is the case and simpler knots migrate faster than more complex knots. Using Monte Carlo simulations we investigate the reasons of this reversal of relative order of electrophoretic mobility of DNA molecules forming different knot types. We observe that at high electric fields the simulated knotted molecules tend to hang over the gel fibres and require passing over a substantial energy barrier to slip over the impeding gel fibre. At low electric field the interactions of drifting molecules with the gel fibres are weak and there are no significant energy barriers that oppose the detachment of knotted molecules from transverse gel fibres.

Dynamics of domain walls in pattern formation under traveling-wave forcing

We study dynamics of domain walls in pattern forming systems that are externally forced by a moving space-periodic modulation close to 2:1 spatial resonance. The motion of the forcing induces nongradient dynamics, while the wave number mismatch breaks explicitly the chiral symmetry of the domain walls. The combination of both effects yields an imperfect nonequilibrium Ising-Bloch bifurcation, where all kinks (including the Ising-like one) drift. Kink velocities and interactions are studied within the generic amplitude equation. For nonzero mismatch, a transition to traveling bound kink-antikink pairs and chaotic wave trains occurs.

Accuracy in the experimental calorimetric study of the crystallization kinetics and predicitve transformation diagrams: Application to a Ga-Te amorphous alloy

The uncertainties inherent to experimental differential scanning calorimetric data are evaluated. A new procedure is developed to perform the kinetic analysis of continuous heating calorimetric data when the heat capacity of the sample changes during the crystallization. The accuracy of isothermal calorimetric data is analyzed in terms of the peak-to-peak noise of the calorimetric signal and base line drift typical of differential scanning calorimetry equipment. Their influence in the evaluation of the kinetic parameters is discussed. An empirical construction of the time-temperature and temperature heating rate transformation diagrams, grounded on the kinetic parameters, is presented. The method is applied to the kinetic study of the primary crystallization of Te in an amorphous alloy of nominal composition Ga20Te80, obtained by rapid solidification.

Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl.

Gradients of variation-or clines-have always intrigued biologists. Classically, they have been interpreted as the outcomes of antagonistic interactions between selection and gene flow. Alternatively, clines may also establish neutrally with isolation by distance (IBD) or secondary contact between previously isolated populations. The relative importance of natural selection and these two neutral processes in the establishment of clinal variation can be tested by comparing genetic differentiation at neutral genetic markers and at the studied trait. A third neutral process, surfing of a newly arisen mutation during the colonization of a new habitat, is more difficult to test. Here, we designed a spatially explicit approximate Bayesian computation (ABC) simulation framework to evaluate whether the strong cline in the genetically based reddish coloration observed in the European barn owl (Tyto alba) arose as a by-product of a range expansion or whether selection has to be invoked to explain this colour cline, for which we have previously ruled out the actions of IBD or secondary contact. Using ABC simulations and genetic data on 390 individuals from 20 locations genotyped at 22 microsatellites loci, we first determined how barn owls colonized Europe after the last glaciation. Using these results in new simulations on the evolution of the colour phenotype, and assuming various genetic architectures for the colour trait, we demonstrate that the observed colour cline cannot be due to the surfing of a neutral mutation. Taking advantage of spatially explicit ABC, which proved to be a powerful method to disentangle the respective roles of selection and drift in range expansions, we conclude that the formation of the colour cline observed in the barn owl must be due to natural selection.

Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields.

Gel electrophoresis allows one to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots, being more compact, drift faster than simpler knots. Recent experiments have shown that the drift velocity dependence on the knot type is inverted when changing from low to high electric fields. We present a computer simulation on a lattice of a closed, knotted, charged DNA chain drifting in an external electric field in a topologically restricted medium. Using a Monte Carlo algorithm, the dependence of the electrophoretic migration of the DNA molecules on the knot type and on the electric field intensity is investigated. The results are in qualitative and quantitative agreement with electrophoretic experiments done under conditions of low and high electric fields.

Stationary states and phase diagram for a model of the Gunn effect under realistic boundary conditions

A general formulation of boundary conditions for semiconductor-metal contacts follows from a phenomenological procedure sketched here. The resulting boundary conditions, which incorporate only physically well-defined parameters, are used to study the classical unipolar drift-diffusion model for the Gunn effect. The analysis of its stationary solutions reveals the presence of bistability and hysteresis for a certain range of contact parameters. Several types of Gunn effect are predicted to occur in the model, when no stable stationary solution exists, depending on the value of the parameters of the injecting contact appearing in the boundary condition. In this way, the critical role played by contacts in the Gunn effect is clearly established.

On a class of exact solutions to the Fokker-Planck equations

In this paper we study under which circumstances there exists a general change of gross variables that transforms any FokkerPlanck equation into another of the OrnsteinUhlenbeck class that, therefore, has an exact solution. We find that any FokkerPlanck equation will be exactly solvable by means of a change of gross variables if and only if the curvature tensor and the torsion tensor associated with the diffusion is zero and the transformed drift is linear. We apply our criteria to the Kubo and Gompertz models.

Exact temporal evolution for some non-linear diffusion process

Exact solutions to FokkerPlanck equations with nonlinear drift are considered. Applications of these exact solutions for concrete models are studied. We arrive at the conclusion that for certain drifts we obtain divergent moments (and infinite relaxation time) if the diffusion process can be extended without any obstacle to the whole space. But if we introduce a potential barrier that limits the diffusion process, moments converge with a finite relaxation time.

Parrondo-like behavior in continuous-time random walks with memory

The continuous-time random walk (CTRW) formalism can be adapted to encompass stochastic processes with memory. In this paper we will show how the random combination of two different unbiased CTRWs can give rise to a process with clear drift, if one of them is a CTRW with memory. If one identifies the other one as noise, the effect can be thought of as a kind of stochastic resonance. The ultimate origin of this phenomenon is the same as that of the Parrondo paradox in game theory.

Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura

Background: Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes throughout 40 generations of adaptation to a common laboratory environment. Specifically, genetic variability, population differentiation and demographic structure were compared in two replicated groups of Drosophila subobscura populations recently sampled from different wild sources. Results: We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied. The observed decline in genetic variability was higher during the first 14 generations of laboratory adaptation. The two groups of replicated populations showed overall similarity in variability patterns. Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process. One of the ten microsatellites analyzed showed a clearly distinct temporal pattern of allele frequency change, suggesting the occurrence of positive selection affecting the region around that particular locus. Conclusion: Genetic drift was responsible for most of the divergence and loss of variability between and within replicates, with most changes occurring during the first generations of laboratory adaptation. We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed. Overall, there was a similarity of evolutionary dynamics at the molecular level in our laboratory populations, despite distinct genetic backgrounds and some differences in phenotypic evolution.

Distribution of the transposable elements bilbo and gypsy in original and colonizing populations of Drosophila subobscura

Background: Transposable elements (TEs) constitute a substantial amount of all eukaryotic genomes. They induce an important proportion of deleterious mutations by insertion into genes or gene regulatory regions. However, their mutational capabilities are not always adverse but can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution and activity in the genomes of populations under different environmental and demographic regimes, is important to understand their role in species evolution. In this work we study the chromosomaldistribution of two TEs, gypsy and bilbo, in original and colonizing populations of Drosophilasubobscura to reveal the putative effect of colonization on their insertion profile.Results: Chromosomal frequency distribution of two TEs in one original and three colonizingpopulations of D. subobscura, is different. Whereas the original population shows a low insertionfrequency in most TE sites, colonizing populations have a mixture of high (frequency ¿ 10%) andlow insertion sites for both TEs. Most highly occupied sites are coincident among colonizingpopulations and some of them are correlated to chromosomal arrangements. Comparisons of TEcopy number between the X chromosome and autosomes show that gypsy occupancy seems to becontrolled by negative selection, but bilbo one does not. Conclusion: These results are in accordance that TEs in Drosophila subobscura colonizing populations are submitted to a founder effect followed by genetic drift as a consequence of colonization. This would explain the high insertion frequencies of bilbo and gypsy in coincident sites of colonizing populations. High occupancy sites would represent insertion events prior to colonization. Sites of low frequency would be insertions that occurred after colonization and/orcopies from the original population whose frequency is decreasing in colonizing populations. Thiswork is a pioneer attempt to explain the chromosomal distribution of TEs in a colonizing specieswith high inversion polymorphism to reveal the putative effect of arrangements in TE insertionprofiles. In general no associations between arrangements and TE have been found, except in a fewcases where the association is very strong. Alternatively, founder drift effects, seem to play aleading role in TE genome distribution in colonizing populations.