cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Quasiparticle self-consistent $GW$ band structures and high-pressure phase transitions of LiGaO$_2$ and NaGaO$_2
Creators: name: Radha, Santosh Kumar
name: Ratnaparkhe, Amol
name: Lambrecht, Walter R. L.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Quasi-particle self-consistent $GW$ calculations are presented for the band structures of LiGaO2 and NaGaO2 in the orthorhombic $Pna2_1$ tetrahedrally coordinated crystal structures. Symmetry labeling of the bands near the gap is carried out and effective mass tensors are extracted for the conduction band minimum and crystal field split valence band maxima at $Γ$. The gap is found to be direct at $Γ$ and is 5.81 eV in LiGaO2 and 5.46 eV in NaGaO2. Electron-phonon coupling zero-point normalization is estimated to lower these gaps by about 0.2 eV. Optical response functions are calculated within the independent particle long wavelength limit and show the expected anisotropy of the absorption onsets due to the crystal field splitting of the VBM. The results show that both materials are promising candidates as ultrawide gap semiconductors with wurtzite based tetrahedrally bonded crystal structures. Direct transitions from the lowest conduction band to higher bands, relevant to n-type doped material and transparent conduction applications are found to start only above 3.9 eV and are allowed for only one polarization, and several higher band transitions are forbidden by symmetry. Alternative crystal structures, such as $R\bar{3}m$ and a rocksalt type phase with tetragonally distorted $P4/mmm$ spacegroup, both with octahedral coordination of the cations are also investigated. They are found to have higher energy but about 20 \% smaller volume per formula unit. The transition pressures to these phases are determined and for LiGaO2 found to be in good agreement with experimental studies. The $R\bar{3}m$phase also has a comparably high but slightly indirect band gap while the rocksalt type phase if found to have a considerably smaller gap of about 3.1 eV in LiGaO2 and 1.0 eV in NaGaO2.
description: 15 pages, 18 figures, 14 tables
Activated sampling in complex materials at finite temperature: the properly-obeying-probability activation-relaxation technique
Creators: name: Vocks, Henk
name: Chubynsky, M. V.
name: Barkema, G. T.
name: Mousseau, Normand
Publisher: name: arXiv
Year: 2005
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: While the dynamics of many complex systems is dominated by activated events, there are very few simulation methods that take advantage of this fact. Most of these procedures are restricted to relatively simple systems or, as with the activation-relaxation technique (ART), sample the conformation space efficiently at the cost of a correct thermodynamical description. We present here an extension of ART, the properly-obeying-probability ART (POP-ART), that obeys detailed balance and samples correctly the thermodynamic ensemble. Testing POP-ART on two model systems, a vacancy and an interstitial in crystalline silicon, we show that this method recovers the proper thermodynamical weights associated with the various accessible states and is significantly faster than MD in the diffusion of a vacancy below 700 K.
description: 10 pages, 3 figures
On the Erdős-Sloane and Shifted Sloane Persistence Problems
Creators: name: Bonuccelli, Gabriel
name: Colucci, Lucas
name: de Faria, Edson
Publisher: name: arXiv
Year: 2020
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 11A63 (Primary), 11A67 (Secondary)

description: In this paper, we investigate two variations on the so-called persistence problem of Sloane: the shifted version, which was introduced by Wagstaff; and the nonzero version, proposed by Erdős. We explore connections between these problems and a recent conjecture of de Faria and Tresser regarding equidistribution of the digits of some integer sequences and some of its natural generalizations.
description: 30 pages
Scattering data and bound states of a squeezed double-layer structure
Creators: name: Zolotaryuk, Alexander V.
name: Zolotaryuk, Yaroslav
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: A heterostructure composed of two parallel homogeneous layers is studied in the limit as their widths $l_1$ and $l_2$, and the distance between them $r$ shrinks to zero simultaneously. The problem is investigated in one dimension and the squeezing potential in the Schrödinger equation is given by the strengths $V_1$ and $V_2$ depending on the layer thickness. A whole class of functions $V_1(l_1)$ and $V_2(l_2)$ is specified by certain limit characteristics as $l_1$ and $l_2$ tend to zero. The squeezing limit of the scattering data $a(k)$ and $b(k)$ derived for the finite system is shown to exist only if some conditions on the system parameters $V_j$, $l_j$, $j=1,2$, and $r$ take place. These conditions appear as a result of an appropriate cancellation of divergences. Two ways of this cancellation are carried out and the corresponding two resonance sets in the system parameter space are derived. On one of these sets, the existence of non-trivial bound states is proven in the squeezing limit, including the particular example of the squeezed potential in the form of the derivative of Dirac's delta function, contrary to the widespread opinion on the non-existence of bound states in $δ'$-like systems. The scenario how a single bound state survives in the squeezed system from a finite number of bound states in the finite system is described in detail.
description: 7 figures, 35 pages. To appear in Journal of Physics A: Mathematical and Theoretical; https://iopscience.iop.org/article/10.1088/1751-8121/abd156
Second-harmonic generation and linear electro-optical coefficients of BN nanotubes
Creators: name: Guo, G. Y.
name: Lin, J. C.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: A systematic {\it ab initio} study of the second-order nonlinear optical properties of BN nanotubes within density functional theory in the local density approximation has been performed. Highly accurate full-potential projector augmented-wave method was used. Specifically, the second-harmonic generation ($χ_{abc}^{(2)}$) and linear electro-optical ($r_{abc}$) coefficients of a large number of the single-walled zigzag, armchair and chiral BN nanotubes (BN-NT) as well as the double-walled zigzag (12,0)@(20,0) BN nanotube and the single-walled zigzag (12,0) BN-NT bundle have been calculated. Importantly, unlike carbon nanotubes, both the zigzag and chiral BN-NTs are found to exhibit large second-order nonlinear optical behavior with the $χ_{abc}^{(2)}$ and $r_{abc}$ coefficients being up to thirty times larger than that of bulk BN in both zinc-blende and wurtzite structures, indicating that BN-NTs are promising materials for nonlinear optical and opto-electric applications. Though the interwall interaction in the double-walled BN-NTs is found to reduce the second-order nonlinear optical coefficients significantly, the interwall interaction in the single-walled BN-NT bundle has essentially no effect on the nonlinear optical properties. The prominant features in the spectra of $χ_{abc}^{(2)}(-2ω,ω,ω)$ of the BN-NTs are suscessfully correlated with the features in the linear optical dielectric function $ε(ω)$ in terms of single-photon and two-photon resonances.
description: Phys. Rev. B (accepted)
Constructing Turing complete Euler flows in dimension $3$
Creators: name: Cardona, Robert
name: Miranda, Eva
name: Peralta-Salas, Daniel
name: Presas, Francisco
Publisher: name: arXiv
Year: 2020
Subjects: subject: Dynamical Systems (math.DS)
subject: Computational Complexity (cs.CC)
subject: Analysis of PDEs (math.AP)
subject: Symplectic Geometry (math.SG)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: Can every physical system simulate any Turing machine? This is a classical problem which is intimately connected with the undecidability of certain physical phenomena. Concerning fluid flows, Moore asked in [15] if hydrodynamics is capable of performing computations. More recently, Tao launched a programme based on the Turing completeness of the Euler equations to address the blow up problem in the Navier-Stokes equations. In this direction, the undecidability of some physical systems has been studied in recent years, from the quantum gap problem [7] to quantum field theories [11]. To the best of our knowledge, the existence of undecidable particle paths of 3D fluid flows has remained an elusive open problem since Moore's works in the early 1990's. In this article we construct a Turing complete stationary Euler flow on a Riemannian $S^3$ and speculate on its implications concerning Tao's approach to the blow up problem in the Navier-Stokes equations.
description: minor changes, 16 pages, 2 figures
Using parameter elimination to solve discrete linear Chebyshev approximation problems
Creators: name: Krivulin, Nikolai
Publisher: name: arXiv
Year: 2020
Subjects: subject: Optimization and Control (math.OC)
subject: Numerical Analysis (math.NA)
subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: 41A50 (Primary), 90C47, 62J05 (Secondary)

description: We consider discrete linear Chebyshev approximation problems in which the unknown parameters of linear function are fitted by minimizing the maximum absolute deviation of errors. Such problems find application in the solution of overdetermined systems of linear equations that appear in many practical contexts. The least maximum absolute deviation estimator is used in regression analysis in statistics when the distribution of errors has bounded support. To derive a direct solution of the problem, we propose an algebraic approach based on a parameter elimination technique. As a key component of the approach, an elimination lemma is proved to handle the problem by reducing it to a problem with one parameter eliminated, together with a box constraint imposed on this parameter. We demonstrate the application of the lemma to the direct solution of linear regression problems with one and two parameters. We develop a procedure to solve multidimensional approximation (multiple linear regression) problems in a finite number of steps. The procedure follows a method that comprises two phases: backward elimination and forward substitution of parameters. We describe the main components of the procedure and estimate its computational complexity. We implement symbolic computations in MATLAB to obtain exact solutions for two numerical examples.
description: 23 pages
Coverage analysis for conformance testing of communication protocols
Creators: name: Zhu, Jinsong
Publisher: name: University of British Columbia
Year: 2009

description: Generation of effective test suite and the evaluation of any given test suite are two of the most essential issues in conformance testing. We combine these two aspects and propose quantitative coverage measures that are subsequently used as the basis for generating test suites with any test coverage requirement. Two criteria for coverage measure are studied: a) fault coverage which measures the effectiveness by examining the fault detecting ability of a test suite under a certain fault model, and b) behavior coverage which measures the effectiveness by computing the amount of protocol behavior space that are exercised by a test suite. In the realm of fault coverage, we propose a coverage measure that targets on finite state specifications, typically in the form of I /O Finite State Machines (FSMs). A formal definition and algorithms that compute the measure are given. The computation of the measure is hard in general (no better than NP-complete); however, with search optimization techniques, the performance of our algorithm has been shown to be high and practical for some large protocols. The measure is then utilized to generate additional test cases to a "weak" test suite, thereby producing test suites with better coverage. The enhancement of a test suite can be done incrementally to satisfy a particular coverage requirement. The application of the measure in fault localization is also explored. The above coverage measure is further extended to the case of testing embedded modules of a composite system modeled as a set of communicating FSMs. The problem differs from the isolated module case in that the module under test has limited observability and controllability due to the presence of the test context. We propose an approach that reduces the problem to the case of isolated modules while maintaining observational equivalence at the composite system level. We prove that the calculation of the coverage measure is no better than NP-complete. However, application of the measure to a real life protocol, the protocol that supports the Universal Personal Computing on the Internet, shows that at a higher level of abstraction, the approach remains effective. As a last contribution of the thesis, we studied the coverage measure for behavior coverage based on Labeled Transition System (LTS). We use the basic metric based method [100] as our theoretical foundation. We generalize the basic method to handle protocols extended with data storage in the model of extended LTS. This results in a metric characterization that incorporates the testing distance contribution from data variations. We proved that this generalized metric space possesses the total boundedness and completeness properties, which allows for a test generation and selection process that can approximate the entire protocol space with arbitrary precision.
Invariable mobility edge in a quasiperiodic lattice
Creators: name: Liu, Tong
name: Zhu, Yufei
name: Cheng, Shujie
name: Li, Feng
name: Guo, Hao
name: Pu, Yong
Publisher: name: arXiv
Year: 2021
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: In this paper, we study a one-dimensional tight-binding model with tunable incommensurate potentials. Through the analysis of the inverse participation rate, we uncover that the wave functions corresponding to the energies of the system exhibit different properties. There exists a critical energy under which the wave functions corresponding to all energies are extended. On the contrary, the wave functions corresponding to all energies above the critical energy are localized. However, we are surprised to find that the critical energy is a constant independent of the potentials. We use the self-dual relation to solve the critical energy, namely the mobility edge, and then we verify the analytical results again by analyzing the spatial distributions of the wave functions. Finally, we give a brief discussion on the possible experimental observation of the invariable mobility edge in the system of ultracold atoms in optical lattices.
description: This paper is not published or submitted to a journal.There was an error in the proof of analysis
Peylo, Jürgen: Leben zum Lob Gottes
Creators: name: Basdekis, Athanasios
Publisher: name: Ökumenische Rundschau
Year: 2025

description: Ökumenische Rundschau, Bd. 38 Nr. 3 (1989): Ökumenische Rundschau, Band 38, Heft 3
EUV spectra of highly-charged ions W$^{54+}$-W$^{63+}$ relevant to ITER diagnostics
Creators: name: Ralchenko, Yu.
name: Draganic, I. N.
name: Tan, J. N.
name: Gillaspy, J. D.
name: Pomeroy, J. M.
name: Reader, J.
name: Feldman, U.
name: Holland, G. E.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: We report the first measurements and detailed analysis of extreme ultraviolet (EUV) spectra (4 nm to 20 nm) of highly-charged tungsten ions W$^{54+}$ to W$^{63+}$ obtained with an electron beam ion trap (EBIT). Collisional-radiative modelling is used to identify strong electric-dipole and magnetic-dipole transitions in all ionization stages. These lines can be used for impurity transport studies and temperature diagnostics in fusion reactors, such as ITER. Identifications of prominent lines from several W ions were confirmed by measurement of isoelectronic EUV spectra of Hf, Ta, and Au. We also discuss the importance of charge exchange recombination for correct description of ionization balance in the EBIT plasma.
description: 11 pages, 4 figures
Towards the Gravituhedron: New Expressions for NMHV Gravity Amplitudes
Creators: name: Trnka, Jaroslav
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper, we present new expressions for n-point NMHV tree-level gravity amplitudes. We introduce a method of factorization diagrams which is a simple graphical representation of R-invariants in Yang-Mills theory. We define the gravity analogues which we call G-invariants, and expand the NMHV gravity amplitudes in terms of these objects. We provide explicit formulas of NMHV gravity amplitudes up to eight points in terms of G-invariants, and give the general definition for any number of points. We discuss the connection to BCFW representation, special behavior under large momentum shift, the role of momentum twistors and the intricate web of spurious poles cancelation. Because of the close connection between R-invariants and the (tree-level) Amplituhedron for Yang-Mills amplitudes, we speculate that the new expansion for gravity amplitudes should correspond to the triangulation of the putative Gravituhedron geometry.
description: 72 pages, 50 figures
Quantum Simulations of SARS-CoV-2 Main Protease Mpro Enable Accurate Scoring of Diverse Ligands
Creators: name: Wang, Yuhang
name: Murlidaran, Sruthi
name: Pearlman, David A.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Biomolecules (q-bio.BM)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: The COVID-19 pandemic has led to unprecedented efforts to identify drugs that can reduce its associated morbidity/mortality rate. Computational chemistry approaches hold the potential for triaging potential candidates far more quickly than their experimental counterparts. These methods have been widely used to search for small molecules that can inhibit critical proteins involved in the SARS-CoV-2 replication cycle. An important target is the SARS-CoV-2 main protease Mpro, an enzyme that cleaves the viral polyproteins into individual proteins required for viral replication and transcription. Unfortunately, standard computational screening methods face difficulties in ranking diverse ligands to a receptor due to disparate ligand scaffolds and varying charge states. Here, we describe full density functional quantum mechanical (DFT/QM) simulations of Mpro in complex with various ligands to obtain absolute ligand binding energies. Our calculations are enabled by a new cloud-native parallel DFT/QM implementation running on computational resources from Amazon Web Services (AWS). The results we obtain are promising: the approach is quite capable of scoring a very diverse set of existing drug compounds for their affinities to Mpro and suggest the DFT/QM approach is potentially more broadly applicable to repurpose screening against this target. In addition, each DFT/QM simulation required only ~1 hour (wall clock time) per ligand. The fast turnaround time raises the practical possibility of a broad application of large-scale quantum mechanics in the drug discovery pipeline at stages where ligand diversity is essential.
description: Updated reference (7) from pre-print to PNSA publication Fix some capitalization issues 8 pages, 6 figures
Geometry and superfluidity of the flat band in a non-Hermitian optical lattice
Creators: name: He, Peng
name: Ding, Hai-Tao
name: Zhu, Shi-Liang
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Superconductivity (cond-mat.supr-con)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We propose an ultracold-atom setting where a fermionic superfluidity with attractive s-wave interaction is uploaded in a non-Hermitian Lieb optical lattice. The existence of a real-energy flat band solution is revealed. We show that the interplay between the skin effect and flat-band localization leads to exotic localization properties. We develop a multiband mean-field description of this system and use both order parameters and superfluid weight to describe the phase transition. A relation between the superfluid weight and non-Hermitian quantum metric of the quantum states manifold is built. We find non-monotone criticality depending on the non-Hermiticity, and the non-reciprocity prominently enhances the phase coherence of the pairing field, suggesting ubiquitous critical behavior of the non-Hermitian fermionic superfluidity.
description: 10 pages, 4 figures
Electron quasi-itinerancy intertwined with quantum order by disorder in pyrochlore iridate magnetism
Creators: name: Chen, Gang
name: Wang, Xiaoqun
Publisher: name: arXiv
Year: 2020
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We point out the emergence of magnetism from the interplay of electron quasi-itinerancy and quantum order by disorder in pyrochlore iridates. Like other Mott insulating iridates, the Ir$^{4+}$ ion in pyrochlore iridates develops an effective ${J=1/2}$ moment from the on-site spin-orbit coupling. We consider the generic symmetry-allowed exchange between these local moments on a pyrochlore lattice and obtain the mean-field phase diagram. Assuming the superexchange is mediated by direct and/or indirect electron hopping via intermediate oxygens, we derive the exchange interactions in the strong coupling regime from the Hubbard model. This exchange has a degenerate classical ground state manifold and quantum fluctuation selects a non-coplanar ground state, known as quantum order by disorder. Extending to the intermediate coupling regime, the same non-coplanar order is selected from the degenerate manifold by the kinetic energy, which is dubbed "electron quasi-itinerancy". We discuss the experimental relevance of our results and electron quasi-itinerancy among other iridates and $4d/5d$ magnets.
description: 10 pages, 8 figures. correct typos. Initially written 9 years ago
Thermal conductivity of R2CuO4, with R = La, Pr and Gd
Creators: name: Berggold, K.
name: Lorenz, T.
name: Baier, J.
name: Kriener, M.
name: Senff, D.
name: Barilo, S.
name: Freimuth, A.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We present measurements of the in-plane kappa_ab and out-of-plane kappa_c thermal conductivity of Pr2CuO4 and Gd2CuO4 single crystals. The anisotropy gives strong evidence for a large contribution of magnetic excitations to kappa_ab i.e. for a heat current within the CuO2 planes. However, the absolute values of kappa_mag are lower than previous results on La2CuO4. These differences probably arise from deviations from the nominal oxygen stoichiometry. This has a drastic influence on kappa_mag, which is shown by an investigation of a La2CuO4+delta polycrystal.
description: 2 pages, 1 figure; presented at SCES2005
Na Induced Correlations in Na$_x$CoO$_2$
Creators: name: Marianetti, C. A.
name: Kotliar, G.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Increasing experimental evidence is building which indicates that signatures of strong correlations are present in the Na rich region of Na$_x$CoO$_2$ (ie. $x\approx0.7$) and absent in the Na poor region (ie. $x\approx0.3$). This is unexpected given that NaCoO$_2$ is a band insulator and CoO$_2$ has an integer filled open shell making it a candidate for strong correlations. We explain these experimental observations by presenting a minimal low-energy Hamiltonian for the cobaltates and solving it within LDA+DMFT. The Na potential is shown to be a key element in understanding correlations in this material. Furthermore, LDA calculations for the realistic Na ordering predict a \emph{binary} perturbation of the Co sites which correlates with the Na$_1$ sites (ie. Na sites above/below Co sites).
EXPLORATION OF THE CHLAMYDOMONAS REINHARDTII CPH1 CRYPTOCHROME AS A POTENTIAL PHYTOCHROME-LIKE PHOTORECEPTOR BINDING PARTNER
Creators: name: Anguiano Arreguin, Pedro Cesareo
Publisher: name: Zenodo
Year: 2021
Subjects: Chlamydomonas reinhardtii
cryptochrome
phytochrome
CPH1
interaction
photoreceptor

description: Light signals are mediated in plants by photoreceptors, including the blue-light cryptochrome and the red/far-red light phytochrome. A phytochrome has yet to be isolated in Chlamydomonas reinhardtii, despite the green alga possessing genes regulated by red light, calcium and calmodulin, all of which are involved in red-light signaling. As cryptochromes have been observed to physically interact with unstimulated phytochromes in Arabidopsis thaliana, we hypothesized that a novel phytochrome-like photoreceptor could be isolated in C. reinhardtii through a pull-down assay using the C. reinhardtii plant-type cryptochrome CPH1 as bait under far-red light or dark conditions. The cDNA encoding the 504AA Photolyase Homology Region (PHR) of the C. reinhardtii plant cryptochrome CPH1 was subcloned into the pET28a expression vector and expressed in E. coli BL21(DE3) cells. The expressed CPH1PHR protein was purified using Immobilized Metal Affinity Chromatography and pull-down assays were performed using CPH1PHR mixed with C. reinhardtii or etiolated pea (Pisum sativum) protein under green, red, far-red, or blue light. SDS-PAGE analysis revealed CPH1PHR interacted with six C. reinhardtii proteins ranging from ~40 to ~52 kDa in a light-independent manner. These proteins may represent the COP1/SPA1 E3 ligase complex-related transcription factor CrCo, a putative PIF homolog, two homologs of the brassinosteroid BIN2 receptor, or the brassinosteroid-related transcription factor NSG17. While CPH1PHR was unable to bind a potential C. reinhardtii phytochrome-like photoreceptor or the pea phytochrome, these results may help elucidate the various roles that the CPH1 photoreceptor plays in this green alga.
Using dimensionality reduction and clustering techniques to classify space plasma regimes
Creators: name: Bakrania, Mayur R.
name: Rae, I. Jonathan
name: Walsh, Andrew P.
name: Verscharen, Daniel
name: Smith, Andy W.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Collisionless space plasma environments are typically characterised by distinct particle populations. Although moments of their velocity distribution functions help in distinguishing different plasma regimes, the distribution functions themselves provide more comprehensive information about the plasma state, especially at times when the distribution function includes non-thermal effects. Unlike moments, however, distribution functions are not easily characterised by a small number of parameters, making their classification more difficult to achieve. In order to perform this classification, we propose to distinguish between the different plasma regions by applying dimensionality reduction and clustering methods to electron distributions in pitch angle and energy space. We utilise four separate algorithms to achieve our plasma classifications: autoencoders, principal component analysis, mean shift, and agglomerative clustering. We test our classification algorithms by applying our scheme to data from the Cluster-PEACE instrument measured in the Earth's magnetotail. Traditionally, it is thought that the Earth's magnetotail is split into three different regions (the plasma sheet, the plasma sheet boundary layer, and the lobes), that are primarily defined by their plasma characteristics. Starting with the ECLAT database with associated classifications based on the plasma parameters, we identify 8 distinct groups of distributions, that are dependent upon significantly more complex plasma and field dynamics. By comparing the average distributions as well as the plasma and magnetic field parameters for each region, we relate several of the groups to different plasma sheet populations, and the rest we attribute to the plasma sheet boundary layer and the lobes. We find clear distinctions between each of our classified regions and the ECLAT results.
description: Published in Frontiers in Astronomy and Space Sciences, 20 pages, 7 figures
Molecular Correlation Functions for Uniaxial Ellipsoids in the Isotropic State
Creators: name: De Michele, Cristiano
name: Scala, Antonio
name: Schilling, Rolf
name: Sciortino, Francesco
Publisher: name: arXiv
Year: 2005
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We perform event-driven molecular dynamics simulations of a system composed by uniaxial hard ellipsoids for different values of the aspect-ratio and packing fraction . We compare the molecular orientational-dependent structure factors previously calculated within the Percus-Yevick approximation with the numerical results. The agreement between theoretical and numerical results is rather satisfactory. We also show that, for specific orientational quantities, the molecular structure factors are sensitive to the particle shape and can be used to distinguish prolate from oblate ellipsoids. A first-order theoretical expansion around the spherical shape and a geometrical analysis of the configurations confirms and explains such an observation.
Potential of graphene oxide as a drug delivery system for Sumatriptan: a detailed density functional theory study
Creators: name: Jafari, Zahra
name: Robabeh Baharfar
name: Rad, Ali Shokuhi
name: Asghari, Sakineh
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified

description: The adsorption property of Sumatriptan drug onto graphene oxide (GO) was studied using density functional theory (DFT) calculations. All possible initial positions of drug adsorption were considered to find out which one is energetically favorable. According to the achieved findings, the stronger interactions occurred between the positively polarized parts of the Sumatriptan (i.e. hydrogen atoms of the–OH and –NH parts) and negatively polarized oxygen atoms of the GO. The presence of non-covalent interactions of GO and Sumatriptan was confirmed based on the determined geometrical parameters, electronic structure analysis results, and adsorption energies. Different parameters such as frontier molecular orbital (FMO), natural bond orbital (NBO), dipole moment, and solation energy were investigated. Global indices such as hardness, softness, chemical potential, and electrophilicity of all systems were calculated and compared. The adsorption energy values were determined within the range of −8.39 to –10.59 kcal/mol (–1.87 to –5.67 BSSE corrected) in the water solvent for different adsorption geometries. The obtained results show that GO can act as a promising carrier/sensor for Sumatriptan drug in practical application. Communicated by Ramaswamy H. Sarma
Beam Energy dependence of Light Nuclei Production in Au+Au Collisions
Creators: name: Zhao, Wenbin
name: Shen, Chun
name: Ko, Che Ming
name: Liu, Quansheng
name: Song, Huichao
Publisher: name: arXiv
Year: 2020
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: We study the collision energy dependence of (anti-)deuteron and (anti-)triton production in the most central Au+Au collisions at $\sqrt{s_\mathrm{NN}}=$ 7.7, 11.5, 19.6, 27, 39, 62.4 and 200 GeV, using the nucleon coalescence model. The needed phase-space distribution of nucleons at the kinetic freeze-out is generated from a new 3D hybrid dynamical model (\texttt{iEBE-MUSIC}) by using a smooth crossover equation of state (EoS) without a QCD critical point. Our model calculations predict that the coalescence parameters of (anti-)deuteron ($B_2(d)$ and $B_2(\bar{d})$) decrease monotonically as the collision energy increases, and the light nuclei yield ratio $N_t N_p/N_d^2$ remains approximately a constant with respect to the collision energy. These calculated observables fail to reproduce the non-monotonic behavior of the corresponding data from the STAR Collaboration. Without including any effects of the critical point in our model, our results serve as the baseline predictions for the yields of light nuclei in the search for the possible QCD critical points from the experimental beam energy scan of heavy ion collisions.
description: 10 pages, 5 figures
Potential of graphene oxide as a drug delivery system for Sumatriptan: A detailed Density Functional Theory study
Creators: name: Jafari, Zahra
name: Robabeh Baharfar
name: Rad, Ali Shokuhi
name: Asghari, Sakineh
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified

description: The adsorption property of Sumatriptan drug onto graphene oxide (GO) was studied using density functional theory (DFT) calculations. All possible initial positions of drug adsorption were considered to find out which one is energetically favorable. According to the achieved findings, the stronger interactions occurred between the positively polarized parts of the Sumatriptan (i.e. hydrogen atoms of the–OH and –NH parts) and negatively polarized oxygen atoms of the GO. The presence of non-covalent interactions of GO and Sumatriptan was confirmed based on the determined geometrical parameters, electronic structure analysis results, and adsorption energies. Different parameters such as frontier molecular orbital (FMO), natural bond orbital (NBO), dipole moment, and solation energy were investigated. Global indices such as hardness, softness, chemical potential, and electrophilicity of all systems were calculated and compared. The adsorption energy values were determined within the range of -8.39 to -10.59 kCal/mol (-1.87 to -5.67 BSSE corrected) in the water solvent for different adsorption geometries. The obtained results show that GO can act as a promising carrier/sensor for Sumatriptan drug in practical application.
Progress in the Glauber model at collider energies
Creators: name: d'Enterria, David
name: Loizides, Constantin
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Experiment (nucl-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We review the theoretical and experimental progress in the Glauber model of multiple nucleon and/or parton scatterings, after the last 10--15 years of operation with proton and nuclear beams at the CERN Large Hadron Collider (LHC) and with various light and heavy colliding ions at the BNL Relativistic Heavy Ion Collider (RHIC). The main developments and the state-of-the-art of the field are summarized. These encompass measurements of the inclusive inelastic proton and nuclear cross sections, advances in the description of the proton and nuclear density profiles and their fluctuations, inclusion of subnucleonic degrees of freedom, experimental procedures and issues related to the determination of the collision centrality, validation of the binary scaling prescription for hard scattering cross sections, and constraints on transport properties of quark-gluon matter from varying initial-state conditions in relativistic hydrodynamics calculations. These advances confirm the validity and usefulness of the Glauber formalism for quantitative studies of QCD matter produced in high-energy collisions of systems, from protons to uranium nuclei, of vastly different size.
description: 37 pages; 14 figures. Invited report for 'Annual Review Nucl. & Part. Science'. (Minor text modifications. 1 figure updated. Appendix and refs. added)
Alerta sobre Raiva Humana: Norte-Nordeste, 2024-2025
Creators: name: Ibiapina, Andressa Barros
name: Silva Catenacci, Lilian
name: Guedes Alcoforado Aguiar, Bruno
name: Costa, Dorcas Lamounier
Publisher: name: Zenodo
Year: 2025

description: O alerta sobre raiva humana Norte-Nordeste, 2024-2025, emitido pelo Centro de Inteligência e Agravos Tropicais Emergentes e Negligenciados (CIATEN).
Characterization of VopJ by modelling, docking and molecular dynamics simulation with reference to its role in infection of enteropathogen Vibrio parahaemolyticus
Creators: name: Ishan H. Raval
name: Labala, Rajendra K.
name: Raval, Krishna H.
name: Chatterjee, Shruti
name: Soumya Haldar
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Vibrio parahaemolyticus is a renowned enteropathogen known for infecting humans. The infection usually involves various genes which help bacterium bypass the immune system of the host. Type III secretion system (T3SS) is an essential factor for the infection. The present study introduces the probable structure of VopJ, a T3SS effector of V. parahaemolyticus. The vopJ gene was amplified and sequenced from V. parahaemolyticus. The model generated through homology modelling showed a Z score of around 2.5, which fits quite near in the standard model available in the databases. The model has only a couple of outlier amino acids, which indicate a good fit of the model. Docking studies with small molecules like Acetyl-CoA, Inositol hexakisphosphate, GTP, and AMP have shown negative ΔG − 10.49, −52.80, −8.36 and −9.02, respectively, which indicates spontaneous binding. The molecular simulation studies have also supported the binding with a low RMSD value of less than 0.5 nm. The RMSF values obtained using the modelling were also quite low (>0.35 nm), which indicates the consistency achieved using the docking studies. These small molecules are very crucial in the MAPK pathways, which is essential for the immune response from the host cell. This effector can thus have an ability to highjack the immune system and help the bacterium in the potent infection. Up to our understanding, this is the first report which describes the in-silico model to understand the mode of infection of T3SS in enteropathogen V. parahaemolyticus. Communicated by Ramaswamy H. Sarma
A Multi-wavelength Study of the X-ray Sources in NGC 5018
Creators: name: Ghosh, Kajal K.
name: Swartz, Douglas A.
name: Tennant, Allyn F.
name: Wu, Kinwah
name: Saripalli, Lakshmi
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The E3 giant elliptical galaxy NGC5018 was observed with the Chandra X-ray Observatory on 14 April 2001. Results of analysis of these X-ray data as well as of complementary optical, infrared, and radio data are reported. Seven X-ray point sources, including the nucleus, were detected.If they are intrinsic to NGC5018, then all six non-nuclear sources have luminosities exceeding E+39 ergs/s in the 0.5-8.0 keV energy band; placing them in the class of Ultra-luminous X-ray sources. Comparison of X-ray source positions to archival HST/WFPC2 images reveal four of the six non-nuclear sources are spatially-coincident with bright, absolute-magnitude (V) around -8.6 mag, objects. These four objects have optical magnitudes and (V-I) colors consistent with globular clusters in NGC5018 but they also have X-ray-to-optical flux ratios consistent with background active galactic nuclei. Strong, unpolarized, radio emission has been detected from one of the optically-bright counterparts. Another optically-bright counterpart was observed to vary by one mag in optical observations taken 28 July 1997 and 04 Feb 1999. Extended X-ray emission is detected within a 15"radius of the galaxy center at a luminosity of E+40 ergs/s in the X-ray band. Its thermal X-ray spectrum (kT around 0.4 keV) and its spatial coincidence with strong H_alpha emission are consistent with a hot gas origin. The nucleus itself may be a weak X-ray source, around E+39 ergs/s, that displays a radio spectrum typical of AGN.
description: Text with 15 figures and 5 Tables. To appear in the 10 May 2005, issue of The Astrophysical Journal
A parametrized Kalman filter for fast track fitting at LHCb
Creators: name: Billoir, Pierre
name: De Cian, Michel
name: Günther, Paul André
name: Stemmle, Simon
Publisher: name: arXiv
Year: 2021
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We present an alternative implementation of the Kalman filter employed for track fitting within the LHCb experiment. It uses simple parametrizations for the extrapolation of particle trajectories in the field of the LHCb dipole magnet and for the effects of multiple scattering in the detector material. A speedup of more than a factor of four is achieved while maintaining the quality of the estimated track quantities. This Kalman filter implementation could be used in the purely software-based trigger of the LHCb upgrade.
Spectra of W$^{39+}$-W$^{47+}$ in the 12 nm to 20 nm region observed with an EBIT light source
Creators: name: Ralchenko, Yu.
name: Reader, J.
name: Pomeroy, J. M.
name: Tan, J. N.
name: Gillaspy, J. D.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: We observed spectra of highly ionized tungsten in the extreme ultraviolet with an electron beam ion trap (EBIT) and a grazing incidence spectrometer at the National Institute of Standards and Technology. Stages of ionization were distinguished by varying the energy of the electron beam between 2.1 keV and 4.3 keV and correlating the energies with spectral line emergence. The spectra were calibrated by reference lines of highly ionized iron produced in the EBIT. Identification of the observed lines was aided by collisional-radiative modeling of the EBIT plasma. Good quantitative agreement was obtained between the modeling results and the experimental observations. Our line identifications complement recent results for W$^{40+}$-W$^{45+}$ observed in a tokamak plasma by Pütterich {\it et al} (\jpb {\bf 38}, 3071, 2005). For most lines we agree with their assignment of ionization stage. Additionally, we present new identifications for some allowed and forbidden lines of W$^{39+}$, W$^{44+}$, W$^{46+}$, and W$^{47+}$. The uncertainties of our wavelengths range from 0.002 nm to 0.010 nm.
description: 19 pages, 8 figures
Resveratrol binding to human complement fragment 5a (hC5a) may modulate the C5aR signaling axes
Creators: name: Mishra, Richa
name: Aurosikha Das
name: Soumendra Rana
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Resveratrol (RSV), the active pharmaceutical ingredient (API) found in several fruits, nuts and marketed nutraceuticals is one of the promiscuous phytoalexin known to promote good health. The health benefits of RSV could be due to its antioxidant activity or its direct interaction with target proteins, resulting modulation of several cells signaling and inflammatory pathways. Among many of its disease preventing activities, RSV has been shown to ameliorate inflammation by directly binding the COX-1 and COX-2 enzymes, the established targets of common non-steroidal anti-inflammatory drugs (NSAIDs). As a follow up to our recent study, we have now identified that RSV can also directly target hC5a, a pro-inflammatory glycoprotein of the complement system, whose upregulation has been linked to exacerbate the chronic inflammation induced diseases, by recruitment of C5a receptor (C5aR) expressed in both immune and non-immune cells. The data derived from the molecular dynamics, automated docking and binding free energy calculation as well as from the circular dichroism, and steady state fluorescence studies indicate that glycosylation of hC5a may not alter its structure significantly and further confirms that RSV strongly bind to the hC5a, which may be responsible for the anti-inflammatory activity demonstrated by RSV in hC5a-C5aR induced inflammatory pathways. Communicated by Ramaswamy H. Sarma
IRIS observations of the low-atmosphere counterparts of active region outflows
Creators: name: Polito, Vanessa
name: De Pontieu, Bart
name: Testa, Paola
name: Brooks, David H.
name: Hansteen, Viggo
Publisher: name: arXiv
Year: 2020
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Active region (AR) outflows have been studied in detail since the launch of \textit{Hinode}/EIS and are believed to provide a possible source of mass and energy to the slow solar wind. In this work, we investigate the lower atmospheric counterpart of AR outflows using observations from the \textit{Interface Region Imaging Spectrograph} (\textit{IRIS}). We find that the \textit{IRIS} \siiv, \cii\ and \mgii\ transition region (TR) and chromospheric lines exhibit different spectral features in the outflows as compared to neighboring regions at the footpoints ("moss") of hot AR loops. The average redshift of \siiv\ in the outflows region ($\approx$ 5.5~km s$^{-1}$) is smaller than typical moss ($\approx$ 12--13 km~s$^{-1}$) and quiet Sun ($\approx$ 7.5 km~s$^{-1}$) values, while the \cii~line is blueshifted ($\approx$ -1.1--1.5 km~s$^{-1}$), in contrast to the moss where it is observed to be redshifted by about $\approx$ 2.5 km~s$^{-1}$. Further, we observe that the low atmosphere underneath the coronal outflows is highly structured, with the presence of blueshifts in \siiv\ and positive \mgii\ k2 asymmetries (which can be interpreted as signatures of chromospheric upflows) which are mostly not observed in the moss. These observations show a clear correlation between the coronal outflows and the chromosphere and TR underneath, which has not been shown before. Our work strongly suggests that these regions are not separate environments and should be treated together, and that current leading theories of AR outflows, such as the interchange reconnection model, need to take into account the dynamics of the low atmosphere.