Charge transfer in DNA: hole charge is confined to a single base pair due to solvation effects

We include solvation effects in tight-binding Hamiltonians for hole states in DNA. The corresponding linear-response parameters are derived from accurate estimates of solvation energy calculated for several hole charge distributions in DNA stacks. Two models are considered: (A) the correction to a diagonal Hamiltonian matrix element depends only on the charge localized on the corresponding site and (B) in addition to this term, the reaction field due to adjacent base pairs is accounted for. We show that both schemes give very similar results. The effects of the polar medium on the hole distribution in DNA are studied. We conclude that the effects of polar surroundings essentially suppress charge delocalization in DNA, and hole states in (GC)n sequences are localized on individual guanines

Simulation methods with extended stability for stiff biochemical kinetics

Background: With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (bio)chemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA). The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows. Results: In this paper we extend Poisson τ-leap methods to a general class of Runge-Kutta (RK) τ-leap methods. We show that with the proper selection of the coefficients, the variance of the extended τ-leap can be well-behaved, leading to significantly larger step sizes.Conclusions: The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original τ-leap method. The approach paves the way to explore new multiscale methods to simulate (bio)chemical systems.

Antireflection coatings from analogy between electron scattering and spin precession

We use the analogy between scattering of a wave from a potential, and the precession of a spin-half particle in a magnetic field, to gain insight into the design of an antireflection coating for electrons in a semiconductor superlattice. It is shown that the classic recipes derived for optics are generally not applicable due to the different dispersion law for electrons. Using the stability conditions we show that a Poisson distribution of impedance steps is a better approximation than is a Gaussian distribution. Examples are given of filters with average transmissivity exceeding 95% over an allowed band.

An extension of the Marsden-Ratiu reduction for Poisson manifolds

We propose a generalization of the reduction of Poisson manifolds by distributions introduced by Marsden and Ratiu. Our proposal overcomes some of the restrictions of the original procedure, and makes the reduced Poisson structure effectively dependent on the distribution. Different applications are discussed, as well as the algebraic interpretation of the procedure and its formulation in terms of Dirac structures.

On an asymptotic formula for the maximum voltage drop in a on-chip power distribution network

We present a new asymptotic formula for the maximum static voltage in a simplified model for on-chip power distribution networks of array bonded integrated circuits. In this model the voltage is the solution of a Poisson equation in an infinite planar domain whose boundary is an array of circular pads of radius ", and we deal with the singular limit Ɛ → 0 case. In comparison with approximations that appear in the electronic engineering literature, our formula is more complete since we have obtained terms up to order Ɛ15. A procedure will be presented to compute all the successive terms, which can be interpreted as using multipole solutions of equations involving spatial derivatives of functions. To deduce the formula we use the method of matched asymptotic expansions. Our results are completely analytical and we make an extensive use of special functions and of the Gauss constant G

Wave-height hazard analysis in Eastern Coast of Spain : Bayesian approach using generalized Pareto distribution

Standard practice of wave-height hazard analysis often pays little attention to the uncertainty of assessed return periods and occurrence probabilities. This fact favors the opinion that, when large events happen, the hazard assessment should change accordingly. However, uncertainty of the hazard estimates is normally able to hide the effect of those large events. This is illustrated using data from the Mediterranean coast of Spain, where the last years have been extremely disastrous. Thus, it is possible to compare the hazard assessment based on data previous to those years with the analysis including them. With our approach, no significant change is detected when the statistical uncertainty is taken into account. The hazard analysis is carried out with a standard model. Time-occurrence of events is assumed Poisson distributed. The wave-height of each event is modelled as a random variable which upper tail follows a Generalized Pareto Distribution (GPD). Moreover, wave-heights are assumed independent from event to event and also independent of their occurrence in time. A threshold for excesses is assessed empirically. The other three parameters (Poisson rate, shape and scale parameters of GPD) are jointly estimated using Bayes' theorem. Prior distribution accounts for physical features of ocean waves in the Mediterranean sea and experience with these phenomena. Posterior distribution of the parameters allows to obtain posterior distributions of other derived parameters like occurrence probabilities and return periods. Predictives are also available. Computations are carried out using the program BGPE v2.0

Metabolic profiles of countries and ecological distribution conflicts.

"Social metabolism" is a notion that links up the natural sciences and the social sciences, and also human history. Work has been done by some groups in Europe in order to operationalize the old idea of looking at the economy from the point of view of "social metabolism". This paper is an attempt to consider the links between each society’s characteristic metabolic profile and the ecological distribution conflicts, at different scales (international, national, regional).

Distribution center consolidation games

We study the location-inventory model as introduced by Teo et al. (2001) to analyze the impact of consolidation of distribution centers on facility and inventory costs. We extend their result on profitability of consolidation. We associate a cooperative game with each location-inventory situation and prove that this game has a non-empty core for identical and independent demand processes. This illustrates that consolidation does not only lower joint costs (which was shown by Teo et al. (2001)), but it allows for a stable division of the minimal costs as well.

Recent trends in Spanish income distribution: a robust picture of falling income inequality

Income distribution in Spain has experienced a substantial improvement towards equalisation during the second half of the seventies and the eighties; a period during which most OECD countries experienced the opposite trend. In spite of the many recent papers on the Spanish income distribution, the period covered by those stops in 1990. The aim of this paper is to extent the analysis to 1996 employing the same methodology and the same data set (ECPF). Our results not only corroborate the (decreasing inequality) trend found by others during the second half of the eighties, but also suggest that this trend extends over the first half of the nineties. We also show that our main conclusions are robust to changes in the equivalence scale, to changes in the definition of income and to potential data contamination. Finally, we analyse some of the causes which may be driving the overall picture of income inequality using two decomposition techniques. From this analyses three variables emerge as the major responsible factors for the observed improvement in the income distribution: education, household composition and socioeconomic situation of the household head.

The Proposals for a European tax on CO2 and their implications for intercountry distribution

This paper analyzes the advantages and implications of the implementation of a European tax on carbon dioxide emissions as an own resource of the European Union. In contrast to a harmonized tax, which would only have distributive effects within each member state, a tax collected at European scale would also have important distributive effects among different countries. These effects would also depend on the use of tax revenues. The paper investigates the distributive effects among the member states of three tax models: a pure CO2

Equity and CO2 emissions distribution in climate change integrated assessment

Emissions distribution is a focus variable for the design of future international agreements to tackle global warming. This paper specifically analyses the future path of emissions distribution and its determinants in different scenarios. Whereas our analysis is driven by tools which are typically applied in the income distribution literature and which have recently been applied to the analysis of CO2 emissions distribution, a new methodological approach is that our study is driven by simulations run with a popular regionalised optimal growth climate change model over the 1995-2105 period. We find that the architecture of environmental policies, the implementation of flexible mechanisms and income concentration are key determinants of emissions distribution over time. In particular we find a robust positive relationship between measures of inequalities.

Formal deformations of Poisson structures in low dimensions

In this paper, we study formal deformations of Poisson structures, especially for three families of Poisson varieties in dimensions two and three. For these families of Poisson structures, using an explicit basis of the second Poisson cohomology space, we solve the deformation equations at each step and obtain a large family of formal deformations for each Poisson structure which we consider. With the help of an explicit formula, we show that this family contains, modulo equivalence, all possible formal eformations. We show moreover that, when the Poisson structure is generic, all members of the family are non-equivalent.

A priori ratemaking using bivariate poisson regression models

In automobile insurance, it is useful to achieve a priori ratemaking by resorting to gene- ralized linear models, and here the Poisson regression model constitutes the most widely accepted basis. However, insurance companies distinguish between claims with or without bodily injuries, or claims with full or partial liability of the insured driver. This paper exa- mines an a priori ratemaking procedure when including two di®erent types of claim. When assuming independence between claim types, the premium can be obtained by summing the premiums for each type of guarantee and is dependent on the rating factors chosen. If the independence assumption is relaxed, then it is unclear as to how the tari® system might be a®ected. In order to answer this question, bivariate Poisson regression models, suitable for paired count data exhibiting correlation, are introduced. It is shown that the usual independence assumption is unrealistic here. These models are applied to an automobile insurance claims database containing 80,994 contracts belonging to a Spanish insurance company. Finally, the consequences for pure and loaded premiums when the independence assumption is relaxed by using a bivariate Poisson regression model are analysed.

Modelling of bird distribution under complex mediterranean landscape dynamics: open habitat birds and fire (MEDFIRE)

Report for the scientific sojourn at the Simon Fraser University, Canada, from July to September 2007. General context: landscape change during the last years is having significant impacts on biodiversity in many Mediterranean areas. Land abandonment, urbanisation and specially fire are profoundly transforming large areas in the Western Mediterranean basin and we know little on how these changes influence species distribution and in particular how these species will respond to further change in a context of global change including climate. General objectives: integrate landscape and population dynamics models in a platform allowing capturing species distribution responses to landscape changes and assessing impact on species distribution of different scenarios of further change. Specific objective 1: develop a landscape dynamic model capturing fire and forest succession dynamics in Catalonia and linked to a stochastic landscape occupancy (SLOM) (or spatially explicit population, SEPM) model for the Ortolan bunting, a species strongly linked to fire related habitat in the region. Predictions from the occupancy or spatially explicit population Ortolan bunting model (SEPM) should be evaluated using data from the DINDIS database. This database tracks bird colonisation of recently burnt big areas (&50 ha). Through a number of different SEPM scenarios with different values for a number of parameter, we should be able to assess different hypothesis in factors driving bird colonisation in new burnt patches. These factors to be mainly, landscape context (i.e. difficulty to reach the patch, and potential presence of coloniser sources), dispersal constraints, type of regenerating vegetation after fire, and species characteristics (niche breadth, etc).