Determining a reasonable range of relative numerical tolerance values for simulating deterministic models of biochemical reactions

What values of relative numerical tolerance should be chosen in simulation of a deterministic model of a biochemical reaction is unclear, which impairs the modeling effort since the simulation outcomes of a model may depend on the relative numerical tolerance values. In an attempt to provide a guideline to selecting appropriate numerical tolerance values in simulation of in vivo biochemical reactions, reasonable numerical tolerance values were estimated based on the uncertainty principle and assumptions of related cellular parameters. The calculations indicate that relative numerical tolerance values can be reasonably set at or around 10^4 for the concentrations expressed in ng/L. This work also suggests that further reducing relative numerical values may result in erroneous simulation results.Plant Biology, Ecology, and Evolutio

Effects of Fermi energy, dot size and leads width on weak localization in chaotic quantum dots

Magnetotransport in chaotic quantum dots at low magnetic fields is investigated by means of a tight binding Hamiltonian on L x L clusters of the square lattice. Chaoticity is induced by introducing L bulk vacancies. The dependence of weak localization on the Fermi energy, dot size and leads width is investigated in detail and the results compared with those of previous analyses, in particular with random matrix theory predictions. Our results indicate that the dependence of the critical flux Phi_c on the square root of the number of open modes, as predicted by random matrix theory, is obscured by the strong energy dependence of the proportionality constant. Instead, the size dependence of the critical flux predicted by Efetov and random matrix theory, namely, Phi_c ~ sqrt{1/L}, is clearly illustrated by the present results. Our numerical results do also show that the weak localization term significantly decreases as the leads width W approaches L. However, calculations for W=L indicate that the weak localization effect does not disappear as L increases.Comment: RevTeX, 8 postscript figures include

Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group

Previous comparative genomic studies of genes involved in olfactory behavior in Drosophila focused only on particular gene families such as odorant receptor and/or odorant binding proteins. However, olfactory behavior has a complex genetic architecture that is orchestrated by many interacting genes. In this paper, we present a comparative genomic study of olfactory behavior in Drosophila including an extended set of genes known to affect olfactory behavior. We took advantage of the recent burst of whole genome sequences and the development of powerful statistical tools to analyze genomic data and test evolutionary and functional hypotheses of olfactory genes in the six species of the Drosophila melanogaster species group for which whole genome sequences are available. Our study reveals widespread purifying selection and limited incidence of positive selection on olfactory genes. We show that the pace of evolution of olfactory genes is mostly independent of the life cycle stage, and of the number of life cycle stages, in which they participate in olfaction. However, we detected a relationship between evolutionary rates and the position that the gene products occupy in the olfactory system, genes occupying central positions tend to be more constrained than peripheral genes. Finally, we demonstrate that specialization to one host does not seem to be associated with bursts of adaptive evolution in olfactory genes in D. sechellia and D. erecta, the two specialists species analyzed, but rather different lineages have idiosyncratic evolutionary histories in which both historical and ecological factors have been involved

Population Genetics of Duplicated Alternatively Spliced Exons of the Dscam Gene in Daphnia and Drosophila

In insects and crustaceans, the Down syndrome cell adhesion molecule (Dscam) occurs in many different isoforms. These are produced by mutually exclusive alternative splicing of dozens of tandem duplicated exons coding for parts or whole immunoglobulin (Ig) domains of the Dscam protein. This diversity plays a role in the development of the nervous system and also in the immune system. Structural analysis of the protein suggested candidate epitopes where binding to pathogens could occur. These epitopes are coded by regions of the duplicated exons and are therefore diverse within individuals. Here we apply molecular population genetics and molecular evolution analyses using Daphnia magna and several Drosophila species to investigate the potential role of natural selection in the divergence between orthologs of these duplicated exons among species, as well as between paralogous exons within species. We found no evidence for a role of positive selection in the divergence of these paralogous exons. However, the power of this test was low, and the fact that no signs of gene conversion between paralogous exons were found suggests that paralog diversity may nonetheless be maintained by selection. The analysis of orthologous exons in Drosophila and in Daphnia revealed an excess of non-synonymous polymorphisms in the epitopes putatively involved in pathogen binding. This may be a sign of balancing selection. Indeed, in Dr. melanogaster the same derived non-synonymous alleles segregate in several populations around the world. Yet other hallmarks of balancing selection were not found. Hence, we cannot rule out that the excess of non-synonymous polymorphisms is caused by segregating slightly deleterious alleles, thus potentially indicating reduced selective constraints in the putative pathogen binding epitopes of Dscam

Measurement of Muon Neutrino Quasi-Elastic Scattering on Carbon

The observation of neutrino oscillations is clear evidence for physics beyond the standard model. To make precise measurements of this phenomenon, neutrino oscillation experiments, including MiniBooNE, require an accurate description of neutrino charged current quasi-elastic (CCQE) cross sections to predict signal samples. Using a high-statistics sample of muon neutrino CCQE events, MiniBooNE finds that a simple Fermi gas model, with appropriate adjustments, accurately characterizes the CCQE events observed in a carbon-based detector. The extracted parameters include an effective axial mass, M_A^eff = 1.23+/-0.20 GeV, that describes the four-momentum dependence of the axial-vector form factor of the nucleon; and a Pauli-suppression parameter, kappa = 1.019+/-0.011. Such a modified Fermi gas model may also be used by future accelerator-based experiments measuring neutrino oscillations on nuclear targets.Comment: 5 pages, 3 figure

Measurement of the \nu_\mu charged current \pi^+ to quasi-elastic cross section ratio on mineral oil in a 0.8 GeV neutrino beam

Using high statistics samples of charged current $\nu_\mu$ interactions, MiniBooNE reports a measurement of the single charged pion production to quasi-elastic cross section ratio on mineral oil (CH$_2$), both with and without corrections for hadron re-interactions in the target nucleus. The result is provided as a function of neutrino energy in the range 0.4 GeV $< E_\nu <$ 2.4 GeV with 11% precision in the region of highest statistics. The results are consistent with previous measurements and the prediction from historical neutrino calculations.Comment: 4 pages, 2 figure

First Observation of Coherent π0\pi^0 Production in Neutrino Nucleus Interactions with Eν<E_{\nu}< 2 GeV

The MiniBooNE experiment at Fermilab has amassed the largest sample to date of $\pi^0$s produced in neutral current (NC) neutrino-nucleus interactions at low energy. This paper reports a measurement of the momentum distribution of $\pi^0$s produced in mineral oil (CH$_2$) and the first observation of coherent $\pi^0$ production below 2 GeV. In the forward direction, the yield of events observed above the expectation for resonant production is attributed primarily to coherent production off carbon, but may also include a small contribution from diffractive production on hydrogen. Integrated over the MiniBooNE neutrino flux, the sum of the NC coherent and diffractive modes is found to be (19.5 $\pm$1.1 (stat) $\pm$2.5 (sys))% of all exclusive NC $\pi^0$ production at MiniBooNE. These measurements are of immediate utility because they quantify an important background to MiniBooNE's search for $\nu_{\mu} \to \nu_e$ oscillations.Comment: Submitted to Phys. Lett.

Design and construction of the MicroBooNE Cosmic Ray Tagger system

The MicroBooNE detector utilizes a liquid argon time projection chamber (LArTPC) with an 85 t active mass to study neutrino interactions along the Booster Neutrino Beam (BNB) at Fermilab. With a deployment location near ground level, the detector records many cosmic muon tracks in each beam-related detector trigger that can be misidentified as signals of interest. To reduce these cosmogenic backgrounds, we have designed and constructed a TPC-external Cosmic Ray Tagger (CRT). This sub-system was developed by the Laboratory for High Energy Physics (LHEP), Albert Einstein center for fundamental physics, University of Bern. The system utilizes plastic scintillation modules to provide precise time and position information for TPC-traversing particles. Successful matching of TPC tracks and CRT data will allow us to reduce cosmogenic background and better characterize the light collection system and LArTPC data using cosmic muons. In this paper we describe the design and installation of the MicroBooNE CRT system and provide an overview of a series of tests done to verify the proper operation of the system and its components during installation, commissioning, and physics data-taking