Nonlinear Sigma Model for Disordered Media: Replica Trick for Non-Perturbative Results and Interactions

In these lectures, given at the NATO ASI at Windsor (2001), applications of the replicas nonlinear sigma model to disordered systems are reviewed. A particular attention is given to two sets of issues. First, obtaining non-perturbative results in the replica limit is discussed, using as examples (i) an oscillatory behaviour of the two-level correlation function and (ii) long-tail asymptotes of different mesoscopic distributions. Second, a new variant of the sigma model for interacting electrons in disordered normal and superconducting systems is presented, with demonstrating how to reduce it, under certain controlled approximations, to known ``phase-only'' actions, including that of the ``dirty bosons'' model.Comment: 25 pages, Proceedings of the NATO ASI "Field Theory of Strongly Correlated Fermions and Bosons in Low - Dimensional Disordered Systems", Windsor, August, 2001; to be published by Kluwe

Dynamics of localization in a waveguide

This is a review of the dynamics of wave propagation through a disordered N-mode waveguide in the localized regime. The basic quantities considered are the Wigner-Smith and single-mode delay times, plus the time-dependent power spectrum of a reflected pulse. The long-time dynamics is dominated by resonant transmission over length scales much larger than the localization length. The corresponding distribution of the Wigner-Smith delay times is the Laguerre ensemble of random-matrix theory. In the power spectrum the resonances show up as a 1/t^2 tail after N^2 scattering times. In the distribution of single-mode delay times the resonances introduce a dynamic coherent backscattering effect, that provides a way to distinguish localization from absorption.Comment: 18 pages including 8 figures; minor correction

Keldysh technique and non-linear sigma-model: basic principles and applications

The purpose of this review is to provide a comprehensive pedagogical introduction into Keldysh technique for interacting out-of-equilibrium fermionic and bosonic systems. The emphasis is placed on a functional integral representation of underlying microscopic models. A large part of the review is devoted to derivation and applications of the non-linear sigma-model for disordered metals and superconductors. We discuss such topics as transport properties, mesoscopic effects, counting statistics, interaction corrections, kinetic equation, etc. The sections devoted to disordered superconductors include Usadel equation, fluctuation corrections, time-dependent Ginzburg-Landau theory, proximity and Josephson effects, etc. (This review is a substantial extension of arXiv:cond-mat/0412296.)Comment: Review: 103 pages, 19 figure

Functional impact and evolution of a novel human polymorphic inversion that disrupts a gene and creates a fusion transcript

Since the discovery of chromosomal inversions almost 100 years ago, how they are maintained in natural populations has been a highly debated issue. One of the hypotheses is that inversion breakpoints could affect genes and modify gene expression levels, although evidence of this came only from laboratory mutants. In humans, a few inversions have been shown to associate with expression differences, but in all cases the molecular causes have remained elusive. Here, we have carried out a complete characterization of a new human polymorphic inversion and determined that it is specific to East Asian populations. In addition, we demonstrate that it disrupts the ZNF257 gene and, through the translocation of the first exon and regulatory sequences, creates a previously nonexistent fusion transcript, which together are associated to expression changes in several other genes. Finally, we investigate the potential evolutionary and phenotypic consequences of the inversion, and suggest that it is probably deleterious. This is therefore the first example of a natural polymorphic inversion that has position effects and creates a new chimeric gene, contributing to answer an old question in evolutionary biology

Genomics meets HIV-1

Genomics is now a core element in the effort to develop a vaccine against HIV-1. Thanks to unprecedented progress in high-throughput genotyping and sequencing, in knowledge about genetic variation in humans, and in evolutionary genomics, it is finally possible to systematically search the genome for common genetic variants that influence the human response to HIV-1. The identification of such variants would help to determine which aspects of the response to the virus are the most promising targets for intervention. However, a key obstacle to progress remains the scarcity of appropriate human cohorts available for genomic research

Ca2+ monitoring in Plasmodium falciparum using the yellow cameleon-Nano biosensor

Calcium (Ca2+)-mediated signaling is a conserved mechanism in eukaryotes, including the human malaria parasite, Plasmodium falciparum. Due to its small size (300?nM). We determined that the mammalian SERCA inhibitor thapsigargin and antimalarial dihydroartemisinin did not perturb SERCA activity. The change of the cytosolic Ca2+ level in P. falciparum was additionally detectable by flow cytometry. Thus, we propose that the developed YC-Nano-based system is useful to study Ca2+ signaling in P. falciparum and is applicable for drug screening.We are grateful to Japanese Red Cross Blood Society for providing human RBC and plasma. We also thank Tanaka R, Ogoshi (Sakura) M and Matsumoto N for technical assistance and Templeton TJ for critical reading. This study was conducted at the Joint Usage / Research Center on Tropical Disease, Institute of Tropical Medicine, Nagasaki University, Japan. KP was a Tokyo Biochemical Research Foundation (TBRF, http://www.tokyobrf.or.jp) post-doctoral fellow and PEF was a Japanese Society of Promotion Sciences (JSPS) post-doctoral fellow. This work was supported in part by the TBRF (K.P.), JSPS (P.E.F.), Takeda Science Foundation (K.Y.), Grants-in-Aids for Scientific Research 24590509 (K.Y.), 22390079 (O.K.), and for Scientific Research on Innovative Areas 23117008 (O.K.), MEXT, Japan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Pseudogap in a thin film of a conventional superconductor

A superconducting state is characterized by the gap in the electronic density of states which vanishes at the superconducting transition temperature Tc. It was discovered that in high temperature superconductors a noticeable depression in the density of states still remains even at temperatures above Tc; this feature being called pseudogap. Here we show that a pseudogap exists in a conventional superconductor: ultrathin titanium nitride films over a wide range of temperatures above Tc. Our study reveals that this pseudogap state is induced by superconducting fluctuations and favored by two-dimensionality and by the proximity to the transition to the insulating state. A general character of the observed phenomenon provides a powerful tool to discriminate between fluctuations as the origin of the pseudogap state, and other contributions in the layered high temperature superconductor compounds.Comment: 26 pages, 4 figure

Grammatical evolution decision trees for detecting gene-gene interactions

<p>Abstract</p> <p>Background</p> <p>A fundamental goal of human genetics is the discovery of polymorphisms that predict common, complex diseases. It is hypothesized that complex diseases are due to a myriad of factors including environmental exposures and complex genetic risk models, including gene-gene interactions. Such epistatic models present an important analytical challenge, requiring that methods perform not only statistical modeling, but also variable selection to generate testable genetic model hypotheses. This challenge is amplified by recent advances in genotyping technology, as the number of potential predictor variables is rapidly increasing.</p> <p>Methods</p> <p>Decision trees are a highly successful, easily interpretable data-mining method that are typically optimized with a hierarchical model building approach, which limits their potential to identify interacting effects. To overcome this limitation, we utilize evolutionary computation, specifically grammatical evolution, to build decision trees to detect and model gene-gene interactions. In the current study, we introduce the Grammatical Evolution Decision Trees (GEDT) method and software and evaluate this approach on simulated data representing gene-gene interaction models of a range of effect sizes. We compare the performance of the method to a traditional decision tree algorithm and a random search approach and demonstrate the improved performance of the method to detect purely epistatic interactions.</p> <p>Results</p> <p>The results of our simulations demonstrate that GEDT has high power to detect even very moderate genetic risk models. GEDT has high power to detect interactions with and without main effects.</p> <p>Conclusions</p> <p>GEDT, while still in its initial stages of development, is a promising new approach for identifying gene-gene interactions in genetic association studies.</p

Kinematic Plasticity during Flight in Fruit Bats: Individual Variability in Response to Loading

All bats experience daily and seasonal fluctuation in body mass. An increase in mass requires changes in flight kinematics to produce the extra lift necessary to compensate for increased weight. How bats modify their kinematics to increase lift, however, is not well understood. In this study, we investigated the effect of a 20% increase in mass on flight kinematics for Cynopterus brachyotis, the lesser dog-faced fruit bat. We reconstructed the 3D wing kinematics and how they changed with the additional mass. Bats showed a marked change in wing kinematics in response to loading, but changes varied among individuals. Each bat adjusted a different combination of kinematic parameters to increase lift, indicating that aerodynamic force generation can be modulated in multiple ways. Two main kinematic strategies were distinguished: bats either changed the motion of the wings by primarily increasing wingbeat frequency, or changed the configuration of the wings by increasing wing area and camber. The complex, individual-dependent response to increased loading in our bats points to an underappreciated aspect of locomotor control, in which the inherent complexity of the biomechanical system allows for kinematic plasticity. The kinematic plasticity and functional redundancy observed in bat flight can have evolutionary consequences, such as an increase potential for morphological and kinematic diversification due to weakened locomotor trade-offs