A comparison of population types used for QTL mapping in Arabidopsis thaliana

In Arabidopsis, a variety of mapping populations have been used for the detection of quantitative trait loci (QTLs) responsible for natural variation. In this study, we presentan overview of the advantages and disadvantages of the different types of populations used. To do this, we compare the results of both experimental and natural populations for the commonly analysed trait flowering time. It is expected that genome wide association (GWA) mapping will be an increasingly important tool for QTL mapping because of the high allelic richness and mapping resolution in natural populations. In Arabidopsis, GWA mapping becomes ever more facilitated by the increasing availability of re-sequenced genomes of many accessions. However, specifically designed mapping populations such as recombinant inbred lines and near isogenic lines will remain important. The high QTL detection power of such experimental populations can identify spurious GWA associations, and their unique genomic structure is superior for investigating the role of low-frequency alleles. Future QTL studies will therefore benefit from a combined approach of GWA and classical linkage analysis

Towards an Efficient Arc Simulation Framework

Arc simulations require a coupled solution of the flow and electromagnetic equations. Despite of industrial interest, there is no established simulation framework available yet. We assess the usability of STAR-CCM+ for low voltage circuit breaker simulations using a test case of a model arc chamber, since this toolkit allows to define and control the simulation in a single environment. In spite of a partially implemented arc root model, the results agree well with reference data of previous publications

Molecular regimes in ultracold Fermi gases

The use of Feshbach resonances for tuning the interparticle interaction in ultracold Fermi gases has led to remarkable developments, in particular to the creation and Bose-Einstein condensation of weakly bound diatomic molecules of fermionic atoms. These are the largest diatomic molecules obtained so far, with a size of the order of thousands of angstroms. They represent novel composite bosons, which exhibit features of Fermi statistics at short intermolecular distances. Being highly excited, these molecules are remarkably stable with respect to collisional relaxation, which is a consequence of the Pauli exclusion principle for identical fermionic atoms. The purpose of this review is to introduce theoretical approaches and describe the physics of molecular regimes in two-component Fermi gases and Fermi-Fermi mixtures, focusing attention on quantum statistical effects.Comment: Chapter of the book: "Cold Molecules: Theory, Experiment, Applications" edited by R. V. Krems, B. Friedrich and W. C. Stwalley (publication expected in March 2009

Characteristics of First-Order Vortex Lattice Melting: Jumps in Entropy and Magnetization

We derive expressions for the jumps in entropy and magnetization characterizing the first-order melting transition of a flux line lattice. In our analysis we account for the temperature dependence of the Landau parameters and make use of the proper shape of the melting line as determined by the relative importance of electromagnetic and Josephson interactions. The results agree well with experiments on anisotropic Y$_1$Ba$_2$Cu$_3$O$_{7-\delta}$ and layered Bi$_2$Sr$_2$Ca$_1$Cu$_2$O$_8$ materials and reaffirm the validity of the London model.Comment: 4 pages. We have restructured the paper to emphasize that in the London scaling regime (appropriate for YBCO) our results are essentially exact. We have also emphasized that a major controversy over the relevance of the London model to describe VL melting has been settled by this wor

A Review of Progress Towards Simulation of Arc Quenching in Lightning Protection Devices Based on Multi Chamber Systems

Two distinct modes of follow current suppression were observed in multi-chamber systems (MCS) under lightning overvoltage: Zero Quenching (ZQ) and Impulse Quenching (IQ). Sufficiently lower erosion of electrodes and evaporation of discharge chamber walls makes the IQ more preferable as a mechanism of arc quenching. Since experimental search for best MCS design is both difficult and expensive numerical modeling is considered as a prospective method for geometry optimization. Several steps were made towards development of efficient arc model. This article highlights most important results of arc quenching simulation and current status of arc model development

Flux melting in BSCCO: Incorporating both electromagnetic and Josephson couplings

Multilevel Monte Carlo simulations of a BSCCO system are carried out including both Josephson as well as electromagnetic couplings for a range of anisotropies. A first order melting transition of the flux lattice is seen on increasing the temperature and/or the magnetic field. The phase diagram for BSCCO is obtained for different values of the anisotropy parameter $\gamma$. The best fit to the experimental results of D. Majer {\it et al.} [Phys. Rev. Lett. {\bf 75}, 1166 (1995)] is obtained for $\gamma\approx 250$ provided one assumes a temperature dependence $\lambda^2(0)/\lambda^2(T)=1-t$ of the penetration depth with $t=T/T_c$. Assuming a dependence $\lambda^2(0)/\lambda^2(T)=1-t^2$ the best fit is obtained for $\gamma\approx 450$. For finite anisotropy the data is shown to collapse on a straight line when plotted in dimensionless units which shows that the melting transition can be satisfied with a single Lindemann parameter whose value is about 0.3. A different scaling applies to the $\gamma=\infty$ case. The energy jump is measured across the transition and for large values of $\gamma$ it is found to increase with increasing anisotropy and to decrease with increasing magnetic field. For infinite anisotropy we see a 2D behavior of flux droplets with a transition taking place at a temperature independent of the magnetic field. We also show that for smaller values of anisotropy it is reasonable to replace the electromagnetic coupling with an in-plane interaction represented by a Bessel function of the second kind ($K_0$), thus justifying our claim in a previous paper.Comment: 12 figures, revtex

Multiple FLC haplotypes defined by independent cis-regulatory variation underpin life history diversity in Arabidopsis thaliana

Relating molecular variation to phenotypic diversity is a central goal in evolutionary biology. In Arabidopsis thaliana, FLOWERING LOCUS C (FLC) is a major determinant of variation in vernalization—the acceleration of flowering by prolonged cold. Here, through analysis of 1307 A. thaliana accessions, we identify five predominant FLC haplotypes defined by noncoding sequence variation. Genetic and transgenic experiments show that they are functionally distinct, varying in FLC expression level and rate of epigenetic silencing. Allelic heterogeneity at this single locus accounts for a large proportion of natural variation in vernalization that contributes to adaptation of A. thaliana

Universal properties for linelike melting of the vortex lattice

Using numerical results obtained within two models describing vortex matter (interacting elastic lines (Bose model) and uniformly frustrated XY-model) we establish universal properties of the melting transition within the linelike regime. These properties, which are captured correctly by both models, include the scaling of the melting temperature with anisotropy and magnetic field, the effective line tension of vortices in the liquid regime, the latent heat, the entropy jump per entanglement length, and relative jump of Josephson energy at the transition as compared to the latent heat. The universal properties can serve as experimental fingerprints of the linelike regime of melting. Comparison of the models allows us to establish boundaries of the linelike regime in temperature and magnetic field.Comment: Revtex, 12 pages, 2 EPS figure

Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies

With large-scale genomic data becoming the norm in biological studies, the storing, integrating, viewing and searching of such data have become a major challenge. In this article, we describe the development of an Arabidopsis thaliana database that hosts the geographic information and genetic polymorphism data for over 6000 accessions and genome-wide association study (GWAS) results for 107 phenotypes representing the largest collection of Arabidopsis polymorphism data and GWAS results to date. Taking advantage of a series of the latest web 2.0 technologies, such as Ajax (Asynchronous JavaScript and XML), GWT (Google-Web-Toolkit), MVC (Model-View-Controller) web framework and Object Relationship Mapper, we have created a web-based application (web app) for the database, that offers an integrated and dynamic view of geographic information, genetic polymorphism and GWAS results. Essential search functionalities are incorporated into the web app to aid reverse genetics research. The database and its web app have proven to be a valuable resource to the Arabidopsis community. The whole framework serves as an example of how biological data, especially GWAS, can be presented and accessed through the web. In the end, we illustrate the potential to gain new insights through the web app by two examples, showcasing how it can be used to facilitate forward and reverse genetics research. Database URL: http://arabidopsis.usc.edu