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https://www.readbyqxmd.com/read/28208827/on-the-uniqueness-of-the-standard-genetic-code
#1
Gabriel S Zamudio, Marco V José
In this work, we determine the biological and mathematical properties that are sufficient and necessary to uniquely determine both the primeval RNY (purine-any base-pyrimidine) code and the standard genetic code (SGC). These properties are: the evolution of the SGC from the RNY code; the degeneracy of both codes, and the non-degeneracy of the assignments of aminoacyl-tRNA synthetases (aaRSs) to amino acids; the wobbling property; the consideration that glycine was the first amino acid; the topological and symmetrical properties of both codes...
February 13, 2017: Life
https://www.readbyqxmd.com/read/28198863/higher-order-laguerre-gauss-modes-in-non-planar-four-mirror-cavities-for-future-gravitational-wave-detectors
#2
Andreas Noack, Christina Bogan, Benno Willke
One of the limiting noise sources in the current generation of gravitational wave detectors, such as the advanced laser interferometer gravitational wave observatory (aLIGO), is the thermal noise in the interferometer's test mass coatings. One proposed method to reduce the coupling of this noise source to the gravitational wave readout is using a laser beam in the higher-order spatial LG<sub>33</sub> mode within the interferometer. Here we show that the current four-mirror cavities of aLIGO are not compatible with Laguerre-Gauss modes due to astigmatism...
February 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28186785/edge-modes-degeneracies-and-topological-numbers-in-non-hermitian-systems
#3
Daniel Leykam, Konstantin Y Bliokh, Chunli Huang, Y D Chong, Franco Nori
We analyze chiral topological edge modes in a non-Hermitian variant of the 2D Dirac equation. Such modes appear at interfaces between media with different "masses" and/or signs of the "non-Hermitian charge." The existence of these edge modes is intimately related to exceptional points of the bulk Hamiltonians, i.e., degeneracies in the bulk spectra of the media. We find that the topological edge modes can be divided into three families ("Hermitian-like," "non-Hermitian," and "mixed"); these are characterized by two winding numbers, describing two distinct kinds of half-integer charges carried by the exceptional points...
January 27, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28185367/codon-degeneracy-and-amino-acid-abundance-influence-the-measures-of-codon-usage-bias-improved-nc-n%C3%AC-c-and-encprime-n%C3%AC-c-measures
#4
Siddhartha Sankar Satapathy, Ajit Kumar Sahoo, Suvendra Kumar Ray, Tapash Chandra Ghosh
Effective number of codons (N^c) and its variant N^'c (effective number of codons prime) are the two widely used methods for measuring unequal usage of synonymous codons in coding sequences, known as the codon usage bias (CUB). The mathematical formula used in calculating N^c and N^'c values is giving inappropriate measures of CUB in case of low abundance of amino acids. In addition, the magnitude of error also varies according to codon degeneracy. In this study, a modified formula for N^c and N^'c has been developed to measure the CUB more accurately...
February 10, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28177136/degeneracy-rules
#5
Astrid A Prinz
No abstract text is available yet for this article.
February 8, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28157330/low-threshold-multiexciton-optical-gain-in-colloidal-cdse-cdte-core-crown-type-ii-nanoplatelet-heterostructures
#6
Qiuyang Li, Zihao Xu, James R McBride, Tianquan Lian
Colloidal cadmium chalcogenide core/crown type-II nanoplatelet heterostructures, such as CdSe/CdTe, are promising materials for lasing and light-emitting applications. Their rational design and improvement requires the understanding of the nature of single- and multiexciton states. Using pump fluence and wavelength-dependent ultrafast transient absorption spectroscopy, we have identified three spatially and energetically distinct excitons (in the order of increasing energy): interface-localized charge transfer exciton (XCT, with electron in the CdSe core bound to the hole in the CdTe crown), and CdTe crown-localized XCdTe and CdSe core-localized XCdSe excitons...
February 7, 2017: ACS Nano
https://www.readbyqxmd.com/read/28124715/valley-splitting-in-the-transition-metal-dichalcogenide-monolayer-via-atom-adsorption
#7
Xiaofang Chen, Liangshuai Zhong, Xiao Li, Jingshan Qi
In this letter we study the valley degeneracy splitting of the transition-metal dichalcogenide monolayer by first-principles calculations. The local magnetic moments are introduced into the system when the transition-metal atoms are adsorbed on the monolayer surface. The Zeeman effect arising from the local magnetic moment at transition-metal atom sites lifts the valley degeneracy. Anomalous charge, spin and valley Hall effects can be accessed due to valley splitting when we can only excite carriers of one valley...
January 26, 2017: Nanoscale
https://www.readbyqxmd.com/read/28120969/computational-prediction-of-high-thermoelectric-performance-in-p-type-half-heusler-compounds-with-low-band-effective-mass
#8
Teng Fang, Shuqi Zheng, Tian Zhou, Lei Yan, Peng Zhang
Half-Heusler (HH) compounds are important high temperature thermoelectric (TE) materials and have gained ever-increasing popularity. In recent years, p-type FeNbSb-based heavy-band HH compounds have attracted considerable attention with the record-high zT value of 1.5. Here, we use first-principles based methods to predict a very high zT value of 1.54 at 1200 K in p-type RuTaSb alloys. The high band degeneracy and low band effective mass contribute to a high power factor. Although the electrical thermal conductivity is high due to the high carrier mobility and hence electrical conductivity, the total thermal conductivity is moderate because of the low lattice thermal conductivity...
January 25, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28106133/prototypical-topological-orbital-ferromagnet-%C3%AE-femn
#9
Jan-Philipp Hanke, Frank Freimuth, Stefan Blügel, Yuriy Mokrousov
We predict from first principles an entirely topological orbital magnetization in the noncoplanar bulk antiferromagnet γ-FeMn originating in the nontrivial topology of the underlying spin structure, without any reference to spin-orbit interaction. Studying the influence of strain, composition ratio, and spin texture on the topological orbital magnetization and the accompanying topological Hall effect, we promote the scalar spin chirality as key mechanism lifting the orbital degeneracy. The system is thus a prototypical topological orbital ferromagnet, the macroscopic orbital magnetization of which is prominent even without spin-orbit coupling...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28099412/ultrafast-nonthermal-photo-magnetic-recording-in-a-transparent-medium
#10
A Stupakiewicz, K Szerenos, D Afanasiev, A Kirilyuk, A V Kimel
Discovering ways to control the magnetic state of media with the lowest possible production of heat and at the fastest possible speeds is important in the study of fundamental magnetism, with clear practical potential. In metals, it is possible to switch the magnetization between two stable states (and thus to record magnetic bits) using femtosecond circularly polarized laser pulses. However, the switching mechanisms in these materials are directly related to laser-induced heating close to the Curie temperature...
February 2, 2017: Nature
https://www.readbyqxmd.com/read/28094365/adsorbing-the-3d-transition-metal-atoms-to-effectively-modulate-the-electronic-and-magnetic-behaviors-of-zigzag-sic-nanoribbons
#11
Hui Li, Wei Chen, Xiaopeng Shen, Jingwei Liu, Xuri Huang, Guangtao Yu
On the basis of first-principles computations, we propose a simple and effective strategy through surface-adsorbing 3d-transition metal (TM) atoms, including Ti, Cr, Mn, Fe and Co, to modulate the electronic and magnetic behaviors of zigzag SiC nanoribbons (zSiCNRs), in view of the unique d electronic structures and intrinsic magnetic moments of TM atoms. It is revealed that like applying an electric field, the adsorption of these transition metal atoms can induce an evident change in the electrostatic potential of the substrate zSiCNRs owing to the electron transfer from the TM atom to the substrate...
February 1, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28093294/strehler-mildvan-correlation-is-a-degenerate-manifold-of-gompertz-fit
#12
Andrei E Tarkhov, Leonid I Menshikov, Peter O Fedichev
Gompertz empirical law of mortality is often used in practical research to parametrize survival fraction as a function of age with the help of just two quantities: the Initial Mortality Rate (IMR) and the Gompertz exponent, inversely proportional to the Mortality Rate Doubling Time (MRDT). The IMR is often found to be inversely related to the Gompertz exponent, which is the dependence commonly referred to as Strehler-Mildvan (SM) correlation. In this paper, we address fundamental uncertainties of the Gompertz parameters inference from experimental Kaplan-Meier plots and show, that a least squares fit often leads to an ill-defined non-linear optimization problem, which is extremely sensitive to sampling errors and the smallest systematic demographic variations...
January 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28092956/mathematical-analysis-of-a-quorum-sensing-induced-biofilm-dispersal-model-and-numerical-simulation-of-hollowing-effects
#13
Blessing O Emerenini, Stefanie Sonner, Hermann J Eberl
We analyze a mathematical model of quorum sensing induced biofilm dispersal. It is formulated as a system of non-linear, density-dependent, diffusion-reaction equations. The governing equation for the sessile biomass comprises two non-linear diffusion effects, a degeneracy as in the porous medium equation and fast diffusion. This equation is coupled with three semi-linear diffusion-reaction equations for the concentrations of growth limiting nutrients, autoinducers, and dispersed cells. We prove the existence and uniqueness of bounded non-negative solutions of this system and study the behavior of the model in numerical simulations, where we focus on hollowing effects in established biofilms...
June 1, 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/28081013/magneto-photoluminescence-measurements-of-tungsten-disulphide-monolayers
#14
Jan Kuhnert, Arash Rahimi-Iman, Wolfram Heimbrodt
Layered transition-metal dichalcogenides have attracted great interest in the last few years. Thinned down to the monolayer limit they change from an indirect band structure to a direct band gap in the visible region. Due to the monolayer thickness the inversion symmetry of the crystal is broken and spin and valley are coupled to each other. The degeneracy between the two equivalent valleys, K and K', respectively, can be lifted by applying an external magnetic field. Here, we present photoluminescence measurements of CVD-grown tungsten disulphide (WS2) monolayers at temperatures of 2 K...
March 1, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28077404/high-throughput-sequencing-of-the-t-cell-receptor-repertoire-pitfalls-and-opportunities
#15
James M Heather, Mazlina Ismail, Theres Oakes, Benny Chain
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28075136/theoretical-investigation-of-the-interfaces-and-mechanisms-of-induced-spin-polarization-of-1d-narrow-zigzag-graphene-and-h-bn-nanoribbons-on-a-sro-terminated-lsmo-001-surface
#16
Paul Avramov, Alexander A Kuzubov, Artem V Kuklin, Hyosun Lee, Evgenia A Kovaleva, Seiji Sakai, Shiro Entani, Hiroshi Naramoto, Pavel B Sorokin
The structure of the interfaces and the mechanisms of induced spin polarization of 1D infinite and finite narrow graphene- and h-BN zigzag nanoribbons placed on a SrO-terminated La1-xSrxMnO3 (LSMO) (001) surface were studied using density functional theory (DFT) electronic structure calculations. It was found that the π-conjugated nanofragments are bonded to the LSMO(001) surface by weak disperse interactions. The types of coordination of the fragments, the strength of bonding, and the rate of spin polarization depend upon the nature of the fragments...
January 11, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28069767/controlling-light-s-helicity-at-the-source-orbital-angular-momentum-states-from-lasers
#17
REVIEW
Andrew Forbes
Optical modes that carry orbital angular momentum (OAM) are routinely produced external to the laser cavity and have found a variety of applications, thus increasing the demand for integrated solutions for their production. Yet such modes are notoriously difficult to produce from lasers due to the strict symmetry requirements for their creation, together with the need to break the degeneracy in helicity. Here, we review the progress made since 1992 in producing such twisted light modes directly at the source, from gas to solid-state lasers, bulk to integrated on-chip solutions, through to generic devices for on-demand OAM in both scalar and vector forms...
February 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28059339/propagation-characteristics-of-an-extremely-anisotropic-metamaterial-loaded-helical-guide
#18
Dushyant K Sharma, Surya K Pathak
In this study, we report slow wave propagation characteristics of an extremely anisotropic metamaterial loaded helical guide (EAMLHG). An analytical expression has been theoretically derived and numerically computed to get exact solutions of all possible guided modes of propagation. Anisotropy is defined in terms of positive longitudinal permittivity (ϵz > 0) and negatives transverse permittivity value (ϵt < 0). The waveguide supports hybrid (HE) mode propagation and possesses characteristics of backward wave (BW) mode, forward wave (FW) mode, zero-group velocity and mode-degeneracy...
December 26, 2016: Optics Express
https://www.readbyqxmd.com/read/28059069/discovery-of-high-performance-low-cost-n-type-mg3sb2-based-thermoelectric-materials-with-multi-valley-conduction-bands
#19
Jiawei Zhang, Lirong Song, Steffen Hindborg Pedersen, Hao Yin, Le Thanh Hung, Bo Brummerstedt Iversen
Widespread application of thermoelectric devices for waste heat recovery requires low-cost high-performance materials. The currently available n-type thermoelectric materials are limited either by their low efficiencies or by being based on expensive, scarce or toxic elements. Here we report a low-cost n-type material, Te-doped Mg3Sb1.5Bi0.5, that exhibits a very high figure of merit zT ranging from 0.56 to 1.65 at 300-725 K. Using combined theoretical prediction and experimental validation, we show that the high thermoelectric performance originates from the significantly enhanced power factor because of the multi-valley band behaviour dominated by a unique near-edge conduction band with a sixfold valley degeneracy...
January 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28053123/nop9-binds-the-central-pseudoknot-region-of-18s-rrna
#20
Bing Wang, Keqiong Ye
The assembly of eukaryotic ribosomes requires numerous factors that transiently associate with evolving pre-ribosomal particles. The Pumilio repeat-containing protein Nop9 briefly associates with the 90S pre-ribosome during its co-transcriptional assembly. Here, we show that Nop9 specifically binds an 11-nucleotide sequence of 18S rRNA that forms the 3' side of the central pseudoknot and helix 28 in the mature subunit. Crystal structures of Nop9 in the free and RNA-bound states reveal a new type of Pumilio repeat protein with a distinct structure, target sequence and RNA-binding mode...
January 3, 2017: Nucleic Acids Research
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