cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Methods development and applications for ultrafast protein crystallography
Creators: name: Fadini, Alisia
Publisher: name: Imperial College London
Year: 2023

description: Time-resolved crystallography follows the structural rearrangements that underlie protein functionality in real space and time. X-ray free electron lasers (XFELs) enable the temporal resolution of these experiments to extend to the ultrafast regime. Through time resolved serial femtosecond crystallography (TR-SFX), atomic motions in proteins on timescales that are relevant for chemical bond isomerization and breaking, or for electron movement, can now be visualized. My thesis employs these properties of time-resolved crystallography and explores methodological developments that can improve on its current capabilities, with the focus on understanding protein photochemistry: a complete study of photon-induced protein dynamics requires the ability to confidently identify the formation of transient species and photoproducts in protein electron density starting at ultrafast timescales. The first results presented characterize mapping of time to energy in protein diffraction patterns simulated with an energy-chirped polychromatic XFEL pulse. TR-SFX is next employed to resolve a photoisomerization pathway, the hula twist, in a fluorescent protein; tracking the reaction from femtoseconds to microseconds yields the first experimental structural evidence of a hula twist mechanism in a protein on its femtosecond-to-picosecond timescale and insight on how chromophore isomerization and twisting lead to secondary protein structure rearrangements. New tools are developed to identify time-evolving species in electron densities. Gaussianity statistics, cross-validation, and denoising procedures find crystallographic map generation parameters that maximize signal and reveal new structural details in existing data. Finally, orientation-dependent merging of TR-SFX intensities is proposed: birefringent decomposition of an optical laser field used for photoexcitation leads to an effective power density titration across protein crystal orientations. This can be analyzed to understand the effect of high intensity photoexcitation in recorded signals. Populations modeling is implemented for a model system to assess the magnitude of the birefringent effect and determine the data collection conditions that would enable this type of analysis.
Experimental observation and computational analysis of striations in electronegative capacitively coupled radio-frequency plasmas
Creators: name: Liu, Yong-Xin
name: Schuengel, Edmund
name: Korolov, Ihor
name: Donko, Zoltan
name: Wang, You-Nian
name: Schulze, Julian
Publisher: name: arXiv
Year: 2016
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Self-organized spatial structures in the light emission from the ion-ion capacitive RF plasma of a strongly electronegative gas (CF4) are observed experimentally for the first time. Their formation is analyzed and understood based on particle-based kinetic simulations. These "striations" are found to be generated by the resonance between the driving radio-frequency and the eigenfrequency of the ion-ion plasma (derived from an analytical model) that establishes a modulation of the electric field, the ion densities, as well as the energy gain and loss processes of electrons in the plasma. The growth of the instability is followed by the numerical simulations.
Wegner estimate for Landau-breather Hamiltonians
Creators: name: Täufer, Matthias
name: Veselic, Ivan
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mathematical Physics (math-ph)
subject: Analysis of PDEs (math.AP)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We consider Landau Hamiltonians with a weak coupling random electric potential of breather type. Under appropriate assumptions we prove a Wegner estimate. It implies the Hoelder continuity of the integrated density of states. The main challenge is the problem how to deal with non-linear dependence on the random parameters.
Additional file 4 of Regenerative potential of multinucleated cells: bone marrow adiponectin-positive multinucleated cells take the lead
Creators: name: Moein, Shiva
name: Ahmadbeigi, Naser
name: Adibi, Rezvan
name: Kamali, Sara
name: Moradzadeh, Kobra
name: Nematollahi, Pardis
name: Nardi, Nance Beyer
name: Gheisari, Yousof
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
classificationCode: 59999
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 4. Fig. S2: Average size of BM-LMCs A. Size determination of BM-isolated LMCs. Values are mean ± SD. B. A representative image of a cultured LMC at 24 h after isolation.
Additional file 1 of Eosinophil-independent IL-5 levels are increased in critically ill COVID-19 patients who survive
Creators: name: Ju, Xiaotian
name: Son, Kiho
name: Jamil, Rameen
name: Culgin, Sarah
name: Salter, Brittany
name: Miyasaki, Kate
name: Fard, Nahal Emami
name: Xiao, Maria
name: Patel, Zil
name: Zhang, Kayla
name: Cowbrough, Braeden
name: Kjarsgaard, Melanie
name: Radford, Katherine
name: Dvorkin-Gheva, Anna
name: Richards, Carl D.
name: Cox, Gerard
name: Chagla, Zain
name: Smieja, Marek
name: Tunks, Marcel
name: Alhazzani, Waleed
name: Bowdish, Dawn M.E.
name: Perri, Dan
name: Nair, Parameswaran K.
name: Sehmi, Roma
name: Mukherjee, Manali
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 29999
subject: Physical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Science Policy

description: Supplementary Material
Causes of Irregular Energy Density in $f(R,T)$ Gravity
Creators: name: Yousaf, Z.
name: Bamba, Kazuharu
name: Bhatti, M. Zaeem ul Haq
Publisher: name: arXiv
Year: 2016
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We investigate irregularity factors for a self-gravitating spherical star evolving in the presence of imperfect fluid. We explore the gravitational field equations and the dynamical equations with the systematic construction in $f(R,T)$ gravity, where $T$ is the trace of the energy-momentum tensor. Furthermore, we analyze two well-known differential equations (which occupy principal importance in the exploration of causes of energy density inhomogeneities) with the help of the Weyl tensor and the conservation laws. The irregularity factors for a spherical star are examined for particular cases of dust, isotropic and anisotropic fluids in dissipative and non-dissipative regimes in the framework of $f(R,T)$ gravity. It is found that as the complexity in the matter with the anisotropic stresses increases, the inhomogeneity factor has more correspondences to one of the structure scalars.
description: 25 pages, no figure, version accepted for publication in Physical Review D
Higgs phase in a gauge $\mathbf{U}(1)$ non-linear $\mathbf{CP}^1$-model. Two species of BPS vortices and their zero modes
Creators: name: Alonso-Izquierdo, Alberto
name: Mateos-Guilarte, Juan
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper zero modes of fluctuation are dissected around the two species of BPS vortices existing in the critical Higgs phase, where the scalar and vector meson masses are equal, of a gauged $\mathbb{U}(1)$ nonlinear $\mathbb{CP}^1$-model. If $2πn$, $n\in \mathbb{Z}$, is the quantized magnetic flux of the two species of BPS vortex solutions, $2n$ linearly independent vortex zero modes for each species are found and described. The existence of two species of moduli spaces of dimension $2n$ of these stringy topological defects is thus locally shown.
description: 17 pages, 28 figures
Micromachining structured optical fibers using focused ion beam milling
Creators: name: Martelli, C.
name: Olivero, P.
name: Canning, J.
name: Groothoff, N.
name: Gibson, B.
name: Huntington, S.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: A focused ion beam is used to mill side holes in air-silica structured fibres. By way of example, side holes are introduced in two types of air-structured fibres (1) a photonic crystal four-ring fibre and (2) a 6-hole single ring step index structured fibre.
description: 15 pages, 4 figures
Deep mutational scanning to understand the evolution of SARS-CoV-2 spike.
Creators: name: Kugathasan, Ruthiran
Publisher: name: Imperial College London
Year: 2023

description: SARS-CoV-2 emerged as a zoonosis in 2019, causing a pandemic that led to significant global mortality, and devastating economic impact. SARS-CoV-2’s pathogenicity was related to its novelty in an immunologically naïve population. With increasing population immunity through vaccination and/or natural infection attenuating the disease, societies have been able to return to a semblance of normality, however SARS-CoV-2 has persisted to become endemic. With endemicity SARS-CoV-2 has continued to adapt and evolve, initially to optimise transmission and latterly to escape immune responses. To predict the future evolution, a deep mutagenesis scanning platform was developed. Deep mutagenesis scanning allows the phenotypic effects of thousands of mutations to be explored in a high-throughput manner. Using whole trimeric Alpha spike displayed on mammalian cells provided a physiologically relevant model and allowed the identification of mutations that increase ACE2 binding (the receptor for SARS-CoV-2 spike) and immune escape, which subsequently appeared in the Omicron lineages. Using this novel deep mutagenesis platform, the evolutionary trajectory of the SARS-CoV-2 receptor-binding domain can be seen to be restricted by epistasis. Vaccine induced immune responses against the receptor binding-domain are found to be remarkably focused on one or two residues despite being polyclonal and these residues have been repeatedly selected for in a variety of variants. From work exploring the antigenic effects of receptor-binding domain mutations, it becomes apparent the N-terminal domain contributes significantly to the immune escape seen with Delta and BA.1. This effect of the N-terminal domain does not appear to be mediated by escape from N-terminal domain directed antibodies, but by making the receptor-binding domain more difficult to neutralise. The plasticity of and focused immune response on the receptor-binding domain make further SARS-CoV-2 antigenic drift inevitable. Work described here suggests the most dramatic changes in antigenicity requires changes in both the N-terminal domain and receptor-binding domain.
Additional file 6 of Regenerative potential of multinucleated cells: bone marrow adiponectin-positive multinucleated cells take the lead
Creators: name: Moein, Shiva
name: Ahmadbeigi, Naser
name: Adibi, Rezvan
name: Kamali, Sara
name: Moradzadeh, Kobra
name: Nematollahi, Pardis
name: Nardi, Nance Beyer
name: Gheisari, Yousof
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
classificationCode: 59999
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 6. Fig. S3: Time-lapse imaging of budding cells. In the top panel, the derivation of a mononucleated cell from an LMC is shown during 10 h. The bottom panel represents the occasional dividing of an LMC into polyploid progenies. Scale bar: 100 µm.
Bender-Wu singularities
Creators: name: Giachetti, Riccardo
name: Grecchi, Vincenzo
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We consider a family of quantum Hamiltonians $H_\hbar=-\hbar^2\,(d^2\!/dx^2) +V(x)$, $x\in\mathbb{R},$ $\hbar>0,$ where $V(x)=i(x^3-x)$ is an imaginary double well potential. We prove the existence of infinite eigenvalue crossings with the selection rules of the eigenvalue pairs taking part in a crossing. This is a semiclassical localization effect. The eigenvalues at the crossings accumulate at a critical energy for some of the Stokes lines.
Random graph approach to multifunctional molecular networks
Creators: name: Kryven, Ivan
name: Duivenvoorden, Jorien
name: Hermans, Joen
name: Iedema, Piet D.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences
subject: 82D60

description: Formation of a molecular network from multifunctional precursors is modelled with a random graph process. The random graph model favours reactivity for monomers that are positioned close in the network topology, and disfavours reactivity for those that are obscured by the surrounding. The phenomena of conversion-dependant reaction rates, gelation, and micro-gelation are thus naturally predicted by the model and do not have to be imposed. Resulting non-homogeneous network topologies are analysed to extract such descriptors as: size distribution, crosslink distances, and gel-point conversion. Furthermore, new to the molecular simulation community descriptors are invented. These descriptors are especially useful for understanding evolution of pure gel, amongst them: cluster coefficient, network modularity, cluster size distribution.
description: 39 pages, 18 figures
Worldline approach for numerical computation of electromagnetic Casimir energies. I. Scalar field coupled to magnetodielectric media
Creators: name: Mackrory, Jonathan B.
name: Bhattacharya, Tanmoy
name: Steck, Daniel A.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We present a worldline method for the calculation of Casimir energies for scalar fields coupled to magnetodielectric media. The scalar model we consider may be applied in arbitrary geometries, and it corresponds exactly to one polarization of the electromagnetic field in planar layered media. Starting from the field theory for electromagnetism, we work with the two decoupled polarizations in planar media and develop worldline path integrals, which represent the two polarizations separately, for computing both Casimir and Casimir-Polder potentials. We then show analytically that the path integrals for the transverse-electric (TE) polarization coupled to a dielectric medium converge to the proper solutions in certain special cases, including the Casimir-Polder potential of an atom near a planar interface, and the Casimir energy due to two planar interfaces. We also evaluate the path integrals numerically via Monte-Carlo path-averaging for these cases, studying the convergence and performance of the resulting computational techniques. While these scalar methods are only exact in particular geometries, they may serve as an approximation for Casimir energies for the vector electromagnetic field in other geometries.
description: 22 pages, 8 figures
CO$_2$ Infrared Phonon Modes in Interstellar Ice Mixtures
Creators: name: Cooke, Ilsa R.
name: Fayolle, Edith C.
name: Öberg, Karin I.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: CO$_2$ ice is an important reservoir of carbon and oxygen in star and planet forming regions. Together with water and CO, CO$_2$ sets the physical and chemical characteristics of interstellar icy grain mantles, including desorption and diffusion energies for other ice constituents. A detailed understanding of CO$_2$ ice spectroscopy is a prerequisite to characterize CO$_2$ interactions with other volatiles both in interstellar ices and in laboratory experiments of interstellar ice analogs. We report laboratory spectra of the CO$_2$ longitudinal optical (LO) phonon mode in pure CO$_2$ ice and in CO$_2$ ice mixtures with H$_2$O, CO, O$_2$ components. We show that the LO phonon mode position is sensitive to the mixing ratio of various ice components of astronomical interest. In the era of JWST, this characteristic could be used to constrain interstellar ice compositions and morphologies. More immediately, LO phonon mode spectroscopy provides a sensitive probe of ice mixing in the laboratory and should thus enable diffusion measurements with higher precision than has been previously possible.
Analytic Evaluation of some 2-, 3- and 4- Electron Atomic Integrals Containing Exponentially Correlated Functions of $r_{ij}$
Creators: name: Padhy, Bholanath
Publisher: name: arXiv
Year: 2016
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: A simple method is outlined for analytic evaluation of the basic 2-electron atomic integral with integrand containing products of atomic s-type Slater orbitals and exponentially correlated function of the form $r_{ij} exp(-λ_{ij}r_{ij})$, by employing the Fourier representation of $exp(-λ_{ij}r_{ij})/r_{ij}$ without the use of either the spherical harmonic addition theorem or the Feynman technique. This method is applied to obtain closed-form expressions, in a simple manner, for certain other 2-,3- and 4-electron atomic integrals with integrands which are products of exponentially correlated functions and atomic s-type Slater orbitals.
description: 9 pages
Equidistribution of curves in homogeneous spaces and Dirichlet's approximation theorem for matrices
Creators: name: Shah, Nimish
name: Yang, Lei
Publisher: name: arXiv
Year: 2016
Subjects: subject: Dynamical Systems (math.DS)
subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 22E40, 11J83

description: In this paper, we study an analytic curve $φ: I=[a,b]\rightarrow \mathrm{M}(m\times n, \mathbb{R})$ in the space of $m$ by $n$ real matrices, and show that if $φ$ satisfies certain geometric condition, then for almost every point on the curve, the Diophantine approximation given by Dirichlet's Theorem can not be improved. To do this, we embed the curve into some homogeneous space $G/Γ$, and prove that under the action of some expanding diagonal subgroup $A= \{a(t): t \in \mathbb{R}\}$, the translates of the curve tend to be equidistributed in $G/Γ$, as $t \rightarrow +\infty$.
description: 29 pages
Additional file 9 of Regenerative potential of multinucleated cells: bone marrow adiponectin-positive multinucleated cells take the lead
Creators: name: Moein, Shiva
name: Ahmadbeigi, Naser
name: Adibi, Rezvan
name: Kamali, Sara
name: Moradzadeh, Kobra
name: Nematollahi, Pardis
name: Nardi, Nance Beyer
name: Gheisari, Yousof
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
classificationCode: 59999
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 9. Fig. S4: Spontaneous differentiation of LMCs into adipocytes. Even in the absence of an adipogenic induction, LMCs could differentiate to adipocytes as revealed by Oil Red O staining of lipid vacuoles. The cells are counterstained with hematoxylin in the right panel. Scale bar: 100 µm.
Comparing the Locking Threshold for Rings and Chains of Oscillators
Creators: name: Ottino-Loffler, Bertrand
name: Strogatz, Steven
Publisher: name: arXiv
Year: 2016
Subjects: subject: Dynamical Systems (math.DS)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 37F99

description: We present a case study of how topology can affect synchronization. Specifically, we consider arrays of phase oscillators coupled in a ring or a chain topology. Each ring is perfectly matched to a chain with the same initial conditions and the same random natural frequencies. The only difference is their boundary conditions: periodic for a ring, and open for a chain. For both topologies, stable phase-locked states exist if and only if the spread or "width" of the natural frequencies is smaller than a critical value called the locking threshold (which depends on the boundary conditions and the particular realization of the frequencies). The central question is whether a ring synchronizes more readily than a chain. We show that it usually does, but not always. Rigorous bounds are derived for the ratio between the locking thresholds of a ring and its matched chain, for a variant of the Kuramoto model that also includes a wider family of models.
description: 9 pages, 4 figures
On the effect of the cosmological expansion on the gravitational lensing by a point mass
Creators: name: Piattella, Oliver F.
Publisher: name: arXiv
Year: 2016
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We analyze the effect of the cosmological expansion on the deflection of light caused by a point mass, adopting the McVittie metric as the geometrical description of a pointlike lens embedded in an expanding universe. In the case of a generic, non-constant Hubble parameter $H$ we derive and approximately solve the null geodesic equations, finding an expression for the bending angle $δ$, which we expand in powers of the mass-to-closest approach distance ratio and of the impact parameter-to-lens distance ratio. It turns out that the leading order of the aforementioned expansion is the same as the one calculated for the Schawarzschild metric and that cosmological corrections contribute to $δ$ only at sub-dominant orders. We explicitly calculate these cosmological corrections for the case of $H$ constant and find that they provide a correction of order $10^{-11}$ on the lens mass estimate.
description: 10 pages, 7 figures (created with tikz)
Simulating confined particles with a flat density profile
Creators: name: Korolkovas, Airidas
Publisher: name: arXiv
Year: 2016
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Particle simulations confined by sharp walls usually develop an oscillatory density profile. For some applications, most notably soft matter liquids, this behavior is often unrealistic and one expects a monotonic density climb instead. To reconcile simulations with experiments, we propose mirror-and-shift boundary conditions where each interface is mapped to a distant part of itself. The main result is that the particle density increases almost monotonically from zero to bulk, over a short distance of about one particle diameter. The method is applied to simulate a polymer brush in explicit solvent, grafted on a flat silicon substrate. The simulated density profile agrees favorably with neutron reflectometry measurements and self-consistent field theory results.
Thermal expansion and magneto-volume studies of the itinerant helical magnet MnSi
Creators: name: Petrova, A. E.
name: Stishov, S. M.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Thermal expansion and forced magnetostriction of MnSi were measured as a function of temperature down to 5 K and magnetic field to 3 T. The small length (volume) discontinuity at the magnetic phase transition in MnSi decreases with application of magnetic field to a value $ΔL/L \sim 10^{-7}$, and then suddenly the discontinuity seemingly jumps to zero. Thermal expansivity peaks strongly deteriorate with magnetic fields. No specific features identifying a tricritical point were observed. We propose that the Frenkel concept of heterophase fluctuations may be relevant in the current case. Therefore, we suggest that the magnetic phase transition in MnSi always remains first order at any temperature and magnetic field, but the transition is progressively smoothed by heterophase fluctuations. These results question the applicability of a model of a fluctuation-induced first order phase transition for MnSi. Probably a model of coupling of an order parameter with other degrees of freedom is more appropriate.
description: 6 figures, 5 pages
Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates
Creators: name: Cendagorta, Joseph R.
name: Powers, Anna
name: Hele, Timothy J. H.
name: Marsalek, Ondrej
name: Bačić, Zlatko
name: Tuckerman, Mark E.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Clathrate hydrates hold considerable promise as safe and economical materials for hydrogen storage. Here we present a quantum mechanical study of H$_2$ and D$_2$ diffusion through a hexagonal face shared by two large cages of clathrate hydrates over a wide range of temperatures. Path integral molecular dynamics simulations are used to compute the free-energy profiles for the diffusion of H$_2$ and D$_2$ as a function of temperature. Ring polymer molecular dynamics rate theory, incorporating both exact quantum statistics and approximate quantum dynamical effects, is utilized in the calculations of the H$_2$ and D$_2$ diffusion rates in a broad temperature interval. We find that the shape of the quantum free-energy profiles and their height relative to the classical free energy barriers at a given temperature, as well as the rate of diffusion, are profoundly affected by competing quantum effects: above 25 K, zero-point energy (ZPE) perpendicular to the reaction path for diffusion between cavities decreases the quantum rate compared to the classical rate, whereas at lower temperatures tunneling outcompetes the ZPE and as result the quantum rate is greater than the classical rate.
description: 9 pages, 4 figures
Photometry of some neglected bright cataclysmic variables and candidates
Creators: name: Bruch, Albert
Publisher: name: arXiv
Year: 2016
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: As part of an effort to better characterize bright cataclysmic variables (CVs) which have received little attention in the past light curves of four confirmed systems (CZ Aql, BO Cet, V380 Oph and EF Tuc) and one candidate (Lib 3) are analyzed. For none of these stars time resolved photometry has been published previously. While no variability was found in the case of Lib 3, which thus cannot be confirmed as a CV, the light curves of all other targets are dominated by strong flickering. Modulations on hourly time scales superimposed on the flickering can probably be related to orbital variations in BO Cet and V380 Oph, but not in CZ Aql and EF Tuc. Variations on the time scale of 10 minutes in CZ Aql, while not yet constituting convincing evidence, together with previous suspicions of a magnetically channeled accretion flow may point at an intermediate polar nature of this star. Some properties of the flickering are quantified in an effort to enlarge the data base for future comparative flickering studies in CVs and to refine the classification of the target stars.
Dynamics of trapped interacting vortices in Bose-Einstein condensates: Role of breathing degree of freedom
Creators: name: Nakamura, Katsuhiro
name: Babajanov, Doniyor
name: Matrasulov, Davron
name: Kobayashi, Michikazu
name: Muruganandam, Paulsamy
Publisher: name: arXiv
Year: 2016
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: With use of a variational principle, we investigate a role of breathing width degree of freedom in the effective theory of interacting vortices in a trapped single-component Bose-Einstein condensates in 2 dimensions under the strong repulsive cubic nonlinearity. As for the trial function, we choose a product of two vortex functions assuming a pair interaction and employ the amplitude form of each vortex function in the Padé approximation which accommodates a hallmark of the vortex core. We have obtained Lagrange equation for the interacting vortex-core coordinates coupled with the time-derivative of width and also its Hamilton formalism by having recourse to a non-standard Poisson bracket. By solving the Hamilton equation, we find rapid radial breathing oscillations superposed on the slower rotational motion of vortex cores, consistent with numerical solutions of Gross-Pitaevskii equation. In higher-energy states of 2 vortex systems, the breathing width degree of freedom plays role of a kicking in the kicked rotator and generates chaos with a structure of sea-urchin needles. Byproduct of the present variational approach includes: (1) the charge-dependent logarithmic inter-vortex interaction multiplied with a pre-factor which depends on the scalar product of a pair of core-position vectors; (2) the charge-independent short-range repulsive inter-vortex interaction and spring force.
Alkali doping of graphene: the crucial role of high temperature annealing
Creators: name: Khademi, Ali
name: Sajadi, Ebrahim
name: Dosanjh, Pinder
name: Bonn, Doug
name: Folk, Joshua A.
name: Stöhr, Alexander
name: Forti, Stiven
name: Starke, Ulrich
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The doping efficiency of lithium deposited at cryogenic temperatures on epitaxial and CVD monolayer graphene has been investigated under ultra-high vacuum conditions. Change of charge carrier density was monitored by gate voltage shift of the Dirac point and by Hall measurements, in low and high doping regimes. It was found that pre-annealing the graphene greatly enhanced the maximum levels of doping that could be achieved: doping saturated at $Δn = 2\times 10^{13}$ e$^-$/cm$^2$ without annealing, independent of sample type or previous processing; after a 900 K anneal, the saturated doping rose one order of magnitude to $Δn = 2\times 10^{14}$ e$^-$/cm$^2$.
High harmonic generation in Landau-quantized graphene subjected to a strong electromagnetic radiation
Creators: name: Avetissian, H. K.
name: Ghazaryan, A. G.
name: Mkrtchian, G. F.
name: Sedrakian, Kh. V.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study nonlinear optical response of Landau quantized graphene to an intense electromagnetic wave. In particular, we consider high harmonic generation process. It is shown that one can achieve efficient generation of high harmonics with strong radiation fields -- when the work of the wave electric field on the magnetic length is larger than pump photon energy. At that high harmonics generation process takes place for a wide range of the pump wave frequencies and intensities even for significant broadening of Landau levels because of impurities in graphene.
description: 13 pages, 5 figures. arXiv admin note: text overlap with arXiv:1604.06250
Additional file 10 of Regenerative potential of multinucleated cells: bone marrow adiponectin-positive multinucleated cells take the lead
Creators: name: Moein, Shiva
name: Ahmadbeigi, Naser
name: Adibi, Rezvan
name: Kamali, Sara
name: Moradzadeh, Kobra
name: Nematollahi, Pardis
name: Nardi, Nance Beyer
name: Gheisari, Yousof
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
classificationCode: 59999
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 10. Fig. S5: Negative controls for the immunocytochemistry assay. LMCs stained with the isotype control antibodies were completely negative for the fluorescence signals. This observation validates the immunocytochemistry data demonstrated in Fig. 3.
Dusty tails of evaporating exoplanets. II. Physical modelling of the KIC 12557548b light curve
Creators: name: van Lieshout, R.
name: Min, M.
name: Dominik, C.
name: Brogi, M.
name: de Graaff, T.
name: Hekker, S.
name: Kama, M.
name: Keller, C. U.
name: Ridden-Harper, A.
name: van Werkhoven, T. I. M.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Evaporating rocky exoplanets, such as KIC 12557548b, eject large amounts of dust grains, which can trail the planet in a comet-like tail. When such objects occult their host star, the resulting transit signal contains information about the dust in the tail. We aim to use the detailed shape of the Kepler light curve of KIC 12557548b to constrain the size and composition of the dust grains that make up the tail, as well as the mass loss rate of the planet. Using a self-consistent numerical model of the dust dynamics and sublimation, we calculate the shape of the tail by following dust grains from their ejection from the planet to their destruction due to sublimation. From this dust cloud shape, we generate synthetic light curves (incorporating the effects of extinction and angle-dependent scattering), which are then compared with the phase-folded Kepler light curve. We explore the free-parameter space thoroughly using a Markov chain Monte Carlo method. Our physics-based model is capable of reproducing the observed light curve in detail. Good fits are found for initial grain sizes between 0.2 and 5.6 micron and dust mass loss rates of 0.6 to 15.6 M_earth/Gyr (2-sigma ranges). We find that only certain combinations of material parameters yield the correct tail length. These constraints are consistent with dust made of corundum (Al2O3), but do not agree with a range of carbonaceous, silicate, or iron compositions. Using a detailed, physically motivated model, it is possible to constrain the composition of the dust in the tails of evaporating rocky exoplanets. This provides a unique opportunity to probe to interior composition of the smallest known exoplanets.
description: 18 pages, 11 figures, A&A accepted
Transport, shot noise, and topology in AC-driven dimer arrays
Creators: name: Niklas, Michael
name: Benito, Mónica
name: Kohler, Sigmund
name: Platero, Gloria
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We analyze an AC-driven dimer chain connected to a strongly biased electron source and drain. It turns out that the resulting transport exhibits fingerprints of topology. They are particularly visible in the driving-induced current suppression and the Fano factor. Thus, shot noise measurements provide a topological phase diagram as a function of the driving parameters. The observed phenomena can be explained physically by a mapping to an effective time-independent Hamiltonian and the emergence of edge states. Moreover, by considering quantum dissipation, we determine the requirements for the coherence properties in a possible experimental realization. For the computation of the zero-frequency noise, we develop an efficient method based on matrix-continued fractions.
description: 8 pages, 6 figures
The Nature of Electron Transport and visible light absorption in Strontium Niobate -- A Plasmonic Water Splitter
Creators: name: Wan, Dongyang
name: Zhao, Yongliang
name: Cai, Yao
name: Asmara, Teguh Citra
name: Huang, Zhen
name: Chen, Jianqiang
name: Hong, Jindui
name: Nelson, Christopher T.
name: Motapothula, Mallikarjuna Rao
name: Yan, Bixing
name: Xu, Rong
name: Zheng, Haimei
name: Ariando
name: Rusydi, Andrivo
name: Minor, Andrew
name: Breese, Mark B. H.
name: Asta, Mark
name: Xu, Qinghua
name: Venkatesan, T.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Semiconductor compounds are widely used for water splitting applications, where photo-generated electron-hole pairs are exploited to induce catalysis. Recently, powders of a metallic oxide (Sr$_{1-x}$NbO$_3$, 0.03 < x < 0.20) have shown competitive photocatalytic efficiency, opening up the material space available for finding optimizing performance in water-splitting applications. The origin of the visible light absorption in these powders was reported to be due to an interband transition and the charge carrier separation was proposed to be due to the high carrier mobility of this material. In the current work we have prepared epitaxial thin films of Sr$_{0.94}$NbO$_{3+δ}$ and found that the bandgap of this material is ~4.1 eV, which is very large. Surprisingly the carrier density of the conducting phase reaches 10$^{22}$ cm$^{-3}$, which is only one order smaller than that of elemental metals and the carrier mobility is only 2.47 cm$^2$/(V$\cdot$s). Contrary to earlier reports, the visible light absorption at 1.8 eV (~688 nm) is due to the bulk plasmon resonance, arising from the large carrier density, instead of an interband transition. Excitation of the plasmonic resonance results in a multifold enhancement of the lifetime of charge carriers. Thus we propose that the hot charge carriers generated from decay of plasmons produced by optical absorption is responsible for the water splitting efficiency of this material under visible light irradiation.
Einsatz von mobil Augmented Reality zur Evaluation von Mehr-Geräte-Systemen
Creators: name: Lindner, Emily
Publisher: name: Zenodo
Year: 2023
Subjects: usability-test, augmented reality, AR

description: Die aufgeführten Dateien, dienen zur Vollständigkeit der Bachelor-Arbeit mit dem Thema "Einsatz von mobil Augmented Reality zur Evaluation von Mehr-Geräte-Systemen".
Additional file 11 of Regenerative potential of multinucleated cells: bone marrow adiponectin-positive multinucleated cells take the lead
Creators: name: Moein, Shiva
name: Ahmadbeigi, Naser
name: Adibi, Rezvan
name: Kamali, Sara
name: Moradzadeh, Kobra
name: Nematollahi, Pardis
name: Nardi, Nance Beyer
name: Gheisari, Yousof
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
classificationCode: 59999
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 11. Fig. S6: The expression of genes related to multinucleation. The bone marrow extracts were passed through a 100-µm pore size filter and then through a 20-µm filter. The cells that attached to the surface of the 20-µm mesh and those that passed through it were separately cultured for 24 h. Non-adherent cells and debris were washed, and the attached cells were used for RNA isolation and cDNA synthesis. Quantitative gene expression analysis on genes related to multinucleation demonstrated that the LMC-rich 20–100 µm fraction has substantially higher expression of Sox2, Cdk1, Chk1, and E2f1 compared to the other population that is rich of mononucleated cells. On the other hand, the genes such as Plk1, Nanog, Oct4, Sycp3, and Rec8 are down-regulated in multinucleated cells.
Additional file 12 of Regenerative potential of multinucleated cells: bone marrow adiponectin-positive multinucleated cells take the lead
Creators: name: Moein, Shiva
name: Ahmadbeigi, Naser
name: Adibi, Rezvan
name: Kamali, Sara
name: Moradzadeh, Kobra
name: Nematollahi, Pardis
name: Nardi, Nance Beyer
name: Gheisari, Yousof
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
classificationCode: 59999
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 12. Fig. S7: Islands of LMCs during BM regeneration. In days 12 and 20 post-sub-lethal irradiation, LMC-rich foci are observed in BM sections.
Eigenstate Thermalization Hypothesis in Conformal Field Theory
Creators: name: Lashkari, Nima
name: Dymarsky, Anatoly
name: Liu, Hong
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We investigate the eigenstate thermalization hypothesis (ETH) in d+1 dimensional conformal field theories by studying reduced density matrices in energy eigenstates. We show that if local probes of high energy primary eigenstates satisfy ETH, then any finite energy observable with support on a subsystem of finite size satisfies ETH. In two dimensions, we discover that if ETH holds locally, the finite size reduced density matrix of states created by heavy primary operators is well-approximated by a projection to the Virasoro identity block.
description: 8 Pages, 3 figures
Thermal Relic Dark Matter Beyond the Unitarity Limit
Creators: name: Harigaya, Keisuke
name: Ibe, Masahiro
name: Kaneta, Kunio
name: Nakano, Wakutaka
name: Suzuki, Motoo
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We discuss a simple model of thermal relic dark matter whose mass can be much larger than the so-called unitarity limit on the mass of point-like particle dark matter. The model consists of new strong dynamics with one flavor of fermions in the fundamental representation which is much heavier than the dynamical scale of the new strong dynamics. Dark matter is identified with the lightest baryonic hadron of the new dynamics. The baryonic hadrons annihilate into the mesonic hadrons of the new strong dynamics when they have large radii. Resultantly, thermal relic dark matter with a mass in the PeV range is possible.
description: 24 pages, 10 figures
Relationalism about mechanics based on a minimalist ontology of matter
Creators: name: Vassallo, Antonio
name: Deckert, Dirk-André
name: Esfeld, Michael
Publisher: name: arXiv
Year: 2016
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: FOS: Physical sciences

description: This paper elaborates on relationalism about space and time as motivated by a minimalist ontology of the physical world: there are only matter points that are individuated by the distance relations among them, with these relations changing. We assess two strategies to combine this ontology with physics, using classical mechanics as example: the Humean strategy adopts the standard, non-relationalist physical theories as they stand and interprets their formal apparatus as the means of bookkeeping of the change of the distance relations instead of committing us to additional elements of the ontology. The alternative theory strategy seeks to combine the relationalist ontology with a relationalist physical theory that reproduces the predictions of the standard theory in the domain where these are empirically tested. We show that, as things stand, this strategy cannot be accomplished without compromising a minimalist relationalist ontology.
description: 25 pages, accepted for publication in European Journal for Philosophy of Science
The Mathematical Intelligencer flunks the Olympics
Creators: name: Gutman, Alexander E.
name: Katz, Mikhail G.
name: Kudryk, Taras S.
name: Kutateladze, Semen S.
Publisher: name: arXiv
Year: 2016
Subjects: subject: History and Overview (math.HO)
subject: Information Theory (cs.IT)
subject: Logic (math.LO)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: 01A60, 01A61, 26E35

description: The Mathematical Intelligencer recently published a note by Y. Sergeyev that challenges both mathematics and intelligence. We examine Sergeyev's claims concerning his purported Infinity computer. We compare his grossone system with the classical Levi-Civita fields and with the hyperreal framework of A. Robinson, and analyze the related algorithmic issues inevitably arising in any genuine computer implementation. We show that Sergeyev's grossone system is unnecessary and vague, and that whatever consistent subsystem could be salvaged is subsumed entirely within a stronger and clearer system (IST). Lou Kauffman, who published an article on a grossone, places it squarely outside the historical panorama of ideas dealing with infinity and infinitesimals.
description: 25 pages, published in Foundations of Science (online first)
Additional file 1 of Non-progressive breast carcinomas detected at mammography screening: a population study
Creators: name: Heggland, Torunn
name: Vatten, Lars Johan
name: Opdahl, Signe
name: Weedon-Fekjær, Harald
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
classificationCode: 19999
subject: Mathematical Sciences not elsewhere classified
subject: Cancer

description: Additional file 1. APC model specification.
Possibility of Combining Ferroelectricity and Rashba-like spin splitting in Monolayers of 1T-type Transition-Metal Dichalcogenides MX2
Creators: name: Bruyer, Emilie
name: Di Sante, Domenico
name: Barone, Paolo
name: Stroppa, Alessandro
name: Whangbo, Myung-Hwan
name: Picozzi, Silvia
Publisher: name: arXiv
Year: 2016
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: First-principles calculations were carried out to explore the possible coupling between spin-polarized electronic states and ferroelectric polarization in monolayers of transition-metal dichalcogenides MX 2 (M = Mo, W; X = S, Se, Te) with distorted octahedrally coordinated 1T structures.For d^2 metal ions, two competing metal clustering effects can take place, where metal ions are arranged in trimers or zigzag chains. Among these, the former structural distortion comes along with an improper ferroelectric phase which persists in the monolayer limit. Switchable Rashba-like spin-polarization features are predicted in the trimerized polytype, which can be permanently tuned by acting on its ferroelectric properties. The polar trimerized structure is found to be stable for 1T-MoS 2 only, while the nonpolar polytype with zigzag metal clustering is predicted to stabilize for other transition-metal dichalcogenides with d 2 metal ions.
description: 7 pages, 4 figures