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Fernando Haas, Shahzad Mahmood
Nonlinear ion-acoustic waves are analyzed in a nonrelativistic magnetized quantum plasma with arbitrary degeneracy of electrons. Quantum statistics is taken into account by means of the equation of state for ideal fermions at arbitrary temperature. Quantum diffraction is described by a modified Bohm potential consistent with finite-temperature quantum kinetic theory in the long-wavelength limit. The dispersion relation of the obliquely propagating electrostatic waves in magnetized quantum plasma with arbitrary degeneracy of electrons is obtained...
September 2016: Physical Review. E
Alberto Fabrizio, François P Rotzinger
The water exchange reaction of the americyl(VI) aqua ion was investigated with quantum chemical methods, density functional theory (DFT), and wave function theory (WFT). Associative and dissociative substitution mechanisms were studied, whereby DFT produced inaccurate results for the associative mechanism in contrast to WFT. The Gibbs activation energies (ΔG(‡)) for the dissociative (D) and the associative interchange (Ia) mechanisms, computed with WFT taking into account static and dynamic electron correlation, near-degeneracy, and spin-orbit coupling, are equal within the error limits of the calculations...
October 14, 2016: Inorganic Chemistry
Andrew F May, Stuart Calder, David S Parker, Brian C Sales, Michael A McGuire
Identifying and characterizing systems with coupled and competing interactions is central to the development of physical models that can accurately describe and predict emergent behavior in condensed matter systems. This work demonstrates that the metallic compound CuFe2Ge2 has competing magnetic ground states, which are shown to be strongly coupled to the lattice and easily manipulated using temperature and applied magnetic fields. Temperature-dependent magnetization M measurements reveal a ferromagnetic-like onset at 228 (1) K and a broad maximum in M near 180 K...
October 14, 2016: Scientific Reports
Megan Breski, Debasis Dey, Sara Obringer, Babu Sudhamalla, Kabirul Islam
Oxidative C-H hydroxylation of methyl groups, followed by their removal from DNA, RNA or histones, is an epigenetic process critical to transcriptional reprogramming and cell fate determination. This reaction is catalyzed by Fe(II)-dependent dioxygenases using the essential metabolite 2-ketoglutarate (2KG) as a cofactor. Given that the human genome encodes for more than 60 2KG-dependent dioxygenases, assigning their individual functions remains a significant challenge. Here we describe a protein-ligand interface engineering approach to break the biochemical degeneracy of these enzymes...
October 6, 2016: Journal of the American Chemical Society
Duarte Araújo, Keith Davids
Individual players act as a coherent unit during team sports performance, forming a team synergy. A synergy is a collective property of a task-specific organization of individuals, such that the degrees of freedom of each individual in the system are coupled, enabling the degrees of freedom of different individuals to co-regulate each other. Here, we present an explanation for the emergence of such collective behaviors, indicating how these can be assessed and understood through the measurement of key system properties that exist, considering the contribution of each individual and beyond These include: to (i) dimensional compression, a process resulting in independent degree of freedom being coupled so that the synergy has fewer degrees of freedom than the set of components from which it arises; (ii) reciprocal compensation, if one element do not produce its function, other elements should display changes in their contributions so that task goals are still attained; (iii) interpersonal linkages, the specific contribution of each element to a group task; and (iv), degeneracy, structurally different components performing a similar, but not necessarily identical, function with respect to context...
2016: Frontiers in Psychology
Faustino Sánchez-Garduño, Judith Pérez-Velázquez
This paper deals with the analysis of existence of traveling wave solutions (TWS) for a diffusion-degenerate (at D(0) = 0) and advection-degenerate (at h'(0) = 0) reaction-diffusion-advection (RDA) equation. Diffusion is a strictly increasing function and the reaction term generalizes the kinetic part of the Fisher-KPP equation. We consider different forms of the convection term h(u): (1)  h'(u) is constant k, (2)  h'(u) = ku with k > 0, and (3) it is a quite general form which guarantees the degeneracy in the advective term...
2016: TheScientificWorldJournal
Roman Sloutsky, Kristen M Naegle
Since the advent of large-scale genomic sequencing, and the consequent availability of large numbers of homologous protein sequences, there has been burgeoning development of methods for extracting functional information from multiple sequence alignments (MSAs). One type of analysis seeks to identify specificity determining positions (SDPs) based on the assumption that such positions are highly conserved within groups of sequences sharing functional specificity, but conserved to different amino acids in different specificity groups...
2016: PloS One
Chen-Rong Liu, Yao-Wu Guo, Zhuo-Jun Li, Wei Li, Yan Chen
The quest for exotic quantum states of matter has become one of the most challenging tasks in modern condensed matter communications. Interplay between topology and strong electron-electron interactions leads to lots of fascinating effects since the discovery of the fractional quantum Hall effect. Here, we theoretically study the Rashba-type spin-orbit coupling effect on a fractional quantum spin Hall system by means of finite size exact diagonalization. Numerical evidences from the ground degeneracies, states evolutions, entanglement spectra, and static structure factor calculations demonstrate that non-trivial fractional topological Tao-Thouless-like quantum state can be realized in the fractional quantum spin Hall effect in a thin torus geometric structure by tuning the strength of spin-orbit coupling...
2016: Scientific Reports
Zin Lin, Adi Pick, Marko Lončar, Alejandro W Rodriguez
We formulate and exploit a computational inverse-design method based on topology optimization to demonstrate photonic crystal structures supporting complex spectral degeneracies. In particular, we discover photonic crystals exhibiting third-order Dirac points formed by the accidental degeneracy of monopolar, dipolar, and quadrupolar modes. We show that, under suitable conditions, these modes can coalesce and form a third-order exceptional point, leading to strong modifications in the spontaneous emission (SE) of emitters, related to the local density of states...
September 2, 2016: Physical Review Letters
Dongliang Zhang, H T Quan, Biao Wu
After a brief historical review of ergodicity and mixing in dynamics, particularly in quantum dynamics, we introduce definitions of quantum ergodicity and mixing using the structure of the system's energy levels and spacings. Our definitions are consistent with the usual understanding of ergodicity and mixing. Two parameters concerning the degeneracy in energy levels and spacings are introduced. They are computed for right triangular billiards and the results indicate a very close relation between quantum ergodicity (mixing) and quantum chaos...
August 2016: Physical Review. E
Stephen Wilson, Jianfei Qi, Fabian V Filipp
Sequence motifs are short, recurring patterns in DNA that can mediate sequence-specific binding for proteins such as transcription factors or DNA modifying enzymes. The androgen response element (ARE) is a palindromic, dihexameric motif present in promoters or enhancers of genes targeted by the androgen receptor (AR). Using chromatin immunoprecipitation sequencing (ChIP-Seq) we refined AR-binding and AREs at a genome-scale in androgen-insensitive and androgen-responsive prostate cancer cell lines. Model-based searches identified more than 120,000 ChIP-Seq motifs allowing for expansion and refinement of the ARE...
2016: Scientific Reports
Gina Webster, Audrey Y-H Teh, Julian K-C Ma
Degeneracy in the genetic code allows multiple codon sequences to encode the same protein. Codon usage bias in genes is the term given to the preferred use of particular synonymous codons. Synonymous codon substitutions had been regarded as "silent" as the primary structure of the protein was not affected; however, it is now accepted that synonymous substitutions can have a significant effect on heterologous protein expression. Codon optimization, the process of altering codons within the gene sequence to improve recombinant protein expression, has become widely practised...
September 12, 2016: Biotechnology and Bioengineering
Maissam Barkeshli
It has been recently shown that non-Abelian defects with localized parafermion zero modes can arise in conventional Abelian fractional quantum Hall (FQH) states. Here we propose an alternate route to creating, manipulating, and measuring topologically protected degeneracies in bilayer FQH states coupled to superconductors, without the creation of localized parafermion zero modes. We focus mainly on electron-hole bilayers, with a ±1/3 Laughlin FQH state in each layer, with boundaries that are proximity coupled to a superconductor...
August 26, 2016: Physical Review Letters
Ramona Kositzki, Stefan Mebs, Jennifer Marx, Julia J Griese, Nils Schuth, Martin Högbom, Volker Schünemann, Michael Haumann
Enzymes with a dimetal-carboxylate cofactor catalyze reactions among the top challenges in chemistry such as methane and dioxygen (O2) activation. Recently described proteins bind a manganese-iron cofactor (MnFe) instead of the classical diiron cofactor (FeFe). Determination of atomic-level differences of homo- versus hetero-bimetallic cofactors is crucial to understand their diverse redox reactions. We studied a ligand-binding oxidase from the bacterium Geobacillus kaustophilus (R2lox) loaded with a FeFe or MnFe cofactor, which catalyzes O2 reduction and an unusual tyrosine-valine ether cross-link formation, as revealed by X-ray crystallography...
October 3, 2016: Inorganic Chemistry
G D Belletti, S D Dalosto, S Tinte
The interface between a zigzag graphene nanoribbon (zGNR) and the ferroelectric PbTiO3 (0 0 1) surface is studied through first-principles calculations. We investigate how the electric polarization normal to the surface tunes the zGNR electronic and magnetic properties. A ferroelectric single-domain configuration with polarization up and down is considered including explicitly a bottom metallic electrode. Our results show how not only the ferroelectric polarization direction determines the doping in zGNR-the downward polarization induces a p-type doping in a planar zGNR whereas the upward polarization keeps it intrinsic-but also the features of the clean ferroelectric surface, such as the atomic relaxation and the electronic distribution...
November 2, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Michael G Napolitano, Matthieu Landon, Christopher J Gregg, Marc J Lajoie, Lakshmi Govindarajan, Joshua A Mosberg, Gleb Kuznetsov, Daniel B Goodman, Oscar Vargas-Rodriguez, Farren J Isaacs, Dieter Söll, George M Church
The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as noncoding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU codons, but the remaining 13 "recalcitrant" AGRs required diversification to identify viable alternatives...
September 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
Elizabeth C Cropper, Andrew M Dacks, Klaudiusz R Weiss
Often distinct elements serve similar functions within a network. However, it is unclear whether this network degeneracy is beneficial, or merely a reflection of tighter regulation of overall network performance relative to individual neuronal properties. We review circumstances where data strongly suggest that degeneracy is beneficial in that it makes network function more robust. Importantly, network degeneracy is likely to have functional consequences that are not widely appreciated. This is likely to be true when network activity is configured by modulators with persistent actions, and the history of network activity potentially impacts subsequent functioning...
August 30, 2016: Current Opinion in Neurobiology
G Siracusano, R Tomasello, A Giordano, V Puliafito, B Azzerboni, O Ozatay, M Carpentieri, G Finocchio
Solitons are very promising for the design of the next generation of ultralow power devices for storage and computation. The key ingredient to achieving this goal is the fundamental understanding of their stabilization and manipulation. Here, we show how the interfacial Dzyaloshinskii-Moriya Interaction (IDMI) is able to lift the energy degeneracy of a magnetic vortex state by stabilizing a topological soliton with radial chirality, hereafter called radial vortex. It has a noninteger Skyrmion number S (0.5<|S|<1) due to both the vortex core polarity and the magnetization tilting induced by the IDMI boundary conditions...
August 19, 2016: Physical Review Letters
Gangjian Tan, Li-Dong Zhao, Mercouri G Kanatzidis
There has been a renaissance of interest in exploring highly efficient thermoelectric materials as a possible route to address the worldwide energy generation, utilization, and management. This review describes the recent advances in designing high-performance bulk thermoelectric materials. We begin with the fundamental stratagem of achieving the greatest thermoelectric figure of merit ZT of a given material by carrier concentration engineering, including Fermi level regulation and optimum carrier density stabilization...
October 12, 2016: Chemical Reviews
Georg W Winkler, QuanSheng Wu, Matthias Troyer, Peter Krogstrup, Alexey A Soluyanov
Superconductor proximitized one-dimensional semiconductor nanowires with strong spin-orbit interaction (SOI) are, at this time, the most promising candidates for the realization of topological quantum information processing. In current experiments the SOI originates predominantly from extrinsic fields, induced by finite size effects and applied gate voltages. The dependence of the topological transition in these devices on microscopic details makes scaling to a large number of devices difficult unless a material with dominant intrinsic bulk SOI is used...
August 12, 2016: Physical Review Letters
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