Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.Comment: 9 pages, 2 figure

From Majorana theory of atomic autoionization to Feshbach resonances in high temperature superconductors

The Ettore Majorana paper - Theory of incomplete P triplets- published in 1931, focuses on the role of selection rules for the non-radiative decay of two electron excitations in atomic spectra, involving the configuration interaction between discrete and continuum channels. This work is a key step for understanding the 1935 work of Ugo Fano on the asymmetric lineshape of two electron excitations and the 1958 Herman Feshbach paper on the shape resonances in nuclear scattering arising from configuration interaction between many different scattering channels. The Feshbach resonances are today of high scientific interest in many different fields and in particular for ultracold gases and high Tc superconductivity.Comment: 13 pages, 7 figures. Journal of Superconductivity and Novel Magnetism to be publishe

In-Situ Infrared Transmission Study of Rb- and K-Doped Fullerenes

We have measured the four IR active $C_{60}$ molecular vibrations in $M_{x}C_{60}$ $(M = K, Rb)$ as a function of doping $x$. We observe discontinuous changes in the vibrational spectra showing four distinct phases (presumably $x = 0, 3, 4$, and 6). The $1427cm^{-1}$ and $576cm^{-1}$ modes show the largest changes shifting downward in frequency in four steps as the doping increases. Several new very weak modes are visible in the $x=6$ phase and are possibly Raman modes becoming weakly optically active. We present quantitative fits of the data and calculate the electron-phonon coupling of the $1427cm^{-1}$ IR mode.Comment: 3 pages, Figure 1 included, 3 more figures available by request. REVTEX v3.0 IRC60DO

Energy landscape, two-level systems and entropy barriers in Lennard-Jones clusters

We develop an efficient numerical algorithm for the identification of a large number of saddle points of the potential energy function of Lennard- Jones clusters. Knowledge of the saddle points allows us to find many thousand adjacent minima of clusters containing up to 80 argon atoms and to locate many pairs of minima with the right characteristics to form two-level systems (TLS). The true TLS are singled out by calculating the ground-state tunneling splitting. The entropic contribution to all barriers is evaluated and discussed.Comment: 4 pages, RevTex, 2 PostScript figure

Simultaneous alignment and folding of protein sequences

Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We presentpartiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm’s complexity is polynomial in time and space. Algorithmically,partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments,partiFold-Align significantly outperforms state-of-the-art pairwise sequence alignment tools in the most difficult low sequence homology case and improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families. partiFold-Align is available at http://partiFold.csail.mit.edu

Beyond equilibrium: Re-evaluating physical modelling of fluvial systems to represent climate changes

© 2018 Elsevier B.V. The interactions between water, sediment and biology in fluvial systems are complex and driven by multiple forcing mechanisms across a range of spatial and temporal scales. In a changing climate, some meteorological drivers are expected to become more extreme with, for example, more prolonged droughts or more frequent flooding. Such environmental changes will potentially have significant consequences for the human populations and ecosystems that are dependent on riverscapes, but our understanding of fluvial system response to external drivers remains incomplete. As a consequence, many of the predictions of the effects of climate change have a large uncertainty that hampers effective management of fluvial environments. Amongst the array of methodological approaches available to scientists and engineers charged with improving that understanding, is physical modelling. Here, we review the role of physical modelling for understanding both biotic and abiotic processes and their interactions in fluvial systems. The approaches currently employed for scaling and representing fluvial processes in physical models are explored, from 1:1 experiments that reproduce processes at real-time or time scales of 10 −1 -10 0 years, to analogue models that compress spatial scales to simulate processes over time scales exceeding 10 2 –10 3 years. An important gap in existing capabilities identified in this study is the representation of fluvial systems over time scales relevant for managing the immediate impacts of global climatic change; 10 1 – 10 2 years, the representation of variable forcing (e.g. storms), and the representation of biological processes. Research to fill this knowledge gap is proposed, including examples of how the time scale of study in directly scaled models could be extended and the time scale of landscape models could be compressed in the future, through the use of lightweight sediments, and innovative approaches for representing vegetation and biostabilisation in fluvial environments at condensed time scales, such as small-scale vegetation, plastic plants and polymers. It is argued that by improving physical modelling capabilities and coupling physical and numerical models, it should be possible to improve understanding of the complex interactions and processes induced by variable forcing within fluvial systems over a broader range of time scales. This will enable policymakers and environmental managers to help reduce and mitigate the risks associated with the impacts of climate change in rivers

Dynamics of earthquake nucleation process represented by the Burridge-Knopoff model

Dynamics of earthquake nucleation process is studied on the basis of the one-dimensional Burridge-Knopoff (BK) model obeying the rate- and state-dependent friction (RSF) law. We investigate the properties of the model at each stage of the nucleation process, including the quasi-static initial phase, the unstable acceleration phase and the high-speed rupture phase or a mainshock. Two kinds of nucleation lengths L_sc and L_c are identified and investigated. The nucleation length L_sc and the initial phase exist only for a weak frictional instability regime, while the nucleation length L_c and the acceleration phase exist for both weak and strong instability regimes. Both L_sc and L_c are found to be determined by the model parameters, the frictional weakening parameter and the elastic stiffness parameter, hardly dependent on the size of an ensuing mainshock. The sliding velocity is extremely slow in the initial phase up to L_sc, of order the pulling speed of the plate, while it reaches a detectable level at a certain stage of the acceleration phase. The continuum limits of the results are discussed. The continuum limit of the BK model lies in the weak frictional instability regime so that a mature homogeneous fault under the RSF law always accompanies the quasi-static nucleation process. Duration times of each stage of the nucleation process are examined. The relation to the elastic continuum model and implications to real seismicity are discussed.Comment: Title changed. Changes mainly in abstract and in section 1. To appear in European Physical Journal

Large-scale pharmacogenomic study of sulfonylureas and the QT, JT and QRS intervals: CHARGE Pharmacogenomics Working Group

Sulfonylureas, a commonly used class of medication used to treat type 2 diabetes, have been associated with an increased risk of cardiovascular disease. Their effects on QT interval duration and related electrocardiographic phenotypes are potential mechanisms for this adverse effect. In 11 ethnically diverse cohorts that included 71 857 European, African-American and Hispanic/Latino ancestry individuals with repeated measures of medication use and electrocardiogram (ECG) measurements, we conducted a pharmacogenomic genome-wide association study of sulfonylurea use and three ECG phenotypes: QT, JT and QRS intervals. In ancestry-specific meta-analyses, eight novel pharmacogenomic loci met the threshold for genome-wide significance (P<5 × 10−8), and a pharmacokinetic variant in CYP2C9 (rs1057910) that has been associated with sulfonylurea-related treatment effects and other adverse drug reactions in previous studies was replicated. Additional research is needed to replicate the novel findings and to understand their biological basis