cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Temperature-induced reversible conformational change in the first 100 residues of α-synuclein
Creators: name: Pielak, Gary J.
name: Young, Gregory B.
name: Charlton, Lisa M.
name: Tripathy, Ashutosh
name: McNulty, Brian C.
name: Orans, Jillian
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Natively disordered proteins are a growing class of anomalies to the structure–function paradigm. The natively disordered protein α-synuclein is the primary component of Lewy bodies, the cellular hallmark of Parkinson’s disease. We noticed a dramatic difference in dilute solution 1H-15N Heteronuclear Single Quantum Coherence (HSQC) spectra of wild-type α-synuclein and two disease-related mutants (A30P and A53T), with spectra collected at 35°C showing fewer cross-peaks than spectra acquired at 10°C. Here, we show the change to be the result of a reversible conformational exchange linked to an increase in hydrodynamic radius and secondary structure as the temperature is raised. Combined with analytical ultracentrifugation data showing α-synuclein to be monomeric at both temperatures, we conclude that the poor quality of the 1H-15N HSQC spectra obtained at 35°C is due to conformational fluctuations that occur on the proton chemical shift time scale. Using a truncated variant of α-synuclein, we show the conformational exchange occurs in the first 100 amino acids of the protein. Our data illustrate a key difference between globular and natively disordered proteins. The properties of globular proteins change little with solution conditions until they denature cooperatively, but the properties of natively disordered proteins can vary dramatically with solution conditions.
Dynamics of Gauge Field Inflation
Creators: name: Alexander, Stephon
name: Jyoti, Dhrubo
name: Kosowsky, Arthur
name: Marciano, Antonino
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We analyze the existence and stability of dynamical attractor solutions for cosmological inflation driven by the coupling between fermions and a gauge field. Assuming a spatially homogeneous and isotropic gauge field and fermion current, the interacting fermion equation of motion reduces to that of a free fermion up to a phase shift. Consistency of the model is ensured via the Stuckelberg mechanism. We prove the existence of exactly one stable solution, and demonstrate the stability numerically. Inflation arises without fine tuning, and does not require postulating any effective potential or non-standard coupling.
description: 17 pages, 2 figures; version 2; minor revisions; submitted to JCAP 10-29-14
title: Auswahlkriterien für agile timeboxed und non-timeboxed Ansätze
Creators: name: El-Kormany, Akram
Publisher: name: FH CAMPUS 02 (CAMPUS 02 Fachhochschule der Wirtschaft)
Year: 2023
Subjects: subject: 658 Allgemeines Management

description: Agile Entwicklungsmethoden haben schon seit vielen Jahren ihren Einsatz in der Wirtschaft gefunden. Unternehmen haben den Bedarf von solchen agilen Entwicklungsprozessen entdeckt und haben schnelle Maßnahmen getroffen, um weiter am Markt zu existieren und die Kundenwünsche mit Hilfe von agilen Prozessen zu erfüllen. Jedoch gibt es einen wesentlichen Faktor, der alle agilen Entwicklungsprozesse betrifft, dieser Faktor ist die Zeit. Die Zeit spielt eine wesentliche Rolle für alle Auftraggeber und Auftragnehmer. Unter den agilen Entwicklungsprozessen gibt es zwei unterschiedliche Ansätze, timeboxed und non-timeboxed. Da stellt sich die interessante Frage: „Welche Auswahlkriterien sind entscheidend für agile Timeboxed und Nontimeboxed Ansätze?“, mit der sich diese Arbeit beschäftigt. Aufgrund dessen, dass es in der vorhandenen Literatur kaum Antworten auf diese Fragestellung gibt, wurden im Rahmen dieser Masterarbeit mithilfe der qualitativen Inhaltsanalyse „Interview“, einige Experten Interviews durchgeführt, um diese Frage zu beantworten. Die Ergebnisse dieser Arbeit stellen einen Software-Manager einige Auswahlkriterien zur Verfügung, anhand dessen entschieden werden kann, ob man einen Timeboxing oder einen Non-Timeboxing Ansatz bevorzugt.
description: Agile development methods have been used in business for many years. Companies have discovered the need for such agile development processes and have taken swift action to continue to exist in the marketplace and to meet customer needs through agile processes. However, there is an essential factor that affects all agile development processes, this factor is time. Time plays an essential role for all clients and contractors. Among the agile development processes, there are some that are timeboxed and others that are nontimeboxed. This raises the interesting question: "Which selection criteria are crucial for timeboxed and non-timeboxed approaches?", which is the subject of this master's thesis. Due to the fact that there are hardly any answers to this question in the existing literature, interviews were conducted in the context of this master thesis with the help of the qualitative content analysis "Interview", in order to answer this question. The results of this master’s thesis provide a software manager with a few selection criteria that can be used to decide whether to apply a timebox or a non-timeboxing approach.
On the scattering of entropy waves at sudden area expansions
Creators: name: Guzmán-Iñigo, Juan
name: Yang, Dong
name: Gaudron, Renaud
name: Morgans, Aimee S.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: In this work, we investigate both numerically and theoretically the sound generated by entropy waves passing through sudden area expansions. The numerical approach is based on a triple decomposition of the flow variables into a steady mean, a small-amplitude coherent part, and a stochastic turbulent part. The mean flow is obtained as the solution of the Reynolds-Averaged Navier-Stokes (RANS) equations. The equations governing the coherent perturbations are linearised and solved in the frequency domain. To account for the effect of turbulence on the coherent perturbations, a frozen eddy viscosity model is employed. When entropy fluctuations pass through the area expansion, the generated entropy noise behaves as a low-pass filter. The numerical predictions of the noise at low frequencies are compared to the predictions of compact, quasi-one-dimensional, and isentropic theory and large discrepancies are observed. An alternative model for the generated entropy noise tailored for area expansions is then proposed. Such model is based on the conservation of mass, momentum, and energy written in integral form. The model assumes zero frequency and the one-dimensionality of the flow variables far upstream and downstream of the expansion. The predictions of this model agree well with the numerical simulations across a range of finite subsonic Mach numbers including low, intermediate, and high Mach numbers.
description: 35 pages, 16 figures
3D Radiative Transfer in $η$ Carinae: Application of the SimpleX Algorithm to 3D SPH Simulations of Binary Colliding Winds
Creators: name: Clementel, N.
name: Madura, T. I.
name: Kruip, C. J. H.
name: Icke, V.
name: Gull, T. R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Eta Carinae is an ideal astrophysical laboratory for studying massive binary interactions and evolution, and stellar wind-wind collisions. Recent three-dimensional (3D) simulations set the stage for understanding the highly complex 3D flows in $η$ Car. Observations of different broad high- and low-ionization forbidden emission lines provide an excellent tool to constrain the orientation of the system, the primary's mass-loss rate, and the ionizing flux of the hot secondary. In this work we present the first steps towards generating synthetic observations to compare with available and future HST/STIS data. We present initial results from full 3D radiative transfer simulations of the interacting winds in $η$ Car. We use the SimpleX algorithm to post-process the output from 3D SPH simulations and obtain the ionization fractions of hydrogen and helium assuming three different mass-loss rates for the primary star. The resultant ionization maps of both species constrain the regions where the observed forbidden emission lines can form. Including collisional ionization is necessary to achieve a better description of the ionization states, especially in the areas shielded from the secondary's radiation. We find that reducing the primary's mass-loss rate increases the volume of ionized gas, creating larger areas where the forbidden emission lines can form. We conclude that post processing 3D SPH data with SimpleX is a viable tool to create ionization maps for $η$ Car.
description: 18 pages, 11 figures, accepted for publication in MNRAS
title: Impacts of ocean acidification
Creators: name: Williamson, Phil
name: Turley, Carol
name: Brownlee, Colin
name: Findlay, Helen S.
name: Ridgwell, Andy
name: Schmidt, Daniela N.
name: Schroeder, Declan C.
name: Blackford, Jerry
name: Tyrrell, Toby
name: Pinnegar, John K.
Publisher: name: Marine Climate Change Impacts Partnership (MCCIP), Lowestoft, UK
Year: 2013

description: MCCIP Science Review 2013, 34-48
Dynamics of entanglement of a three-level atom in motion interacting with two coupled modes including parametric down conversion
Creators: name: Faghihi, M. J.
name: Tavassoly, M. K.
name: Hatami, M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In this paper, a model by which we study the interaction between a motional three-level atom and two-mode field injected simultaneously in a bichromatic cavity is considered; the three-level atom is assumed to be in a $Λ$-type configuration. As a result, the atom-field and the field-field interaction (parametric down conversion) will be appeared. It is shown that, by applying a canonical transformation, the introduced model can be reduced to a well-known form of the generalized Jaynes-Cummings model. Under particular initial conditions, which may be prepared for the atom and the field, the time evolution of state vector of the entire system is analytically evaluated. Then, the dynamics of atom by considering `atomic population inversion' and two different measures of entanglement, i.e., `von Neumann entropy' and `idempotency defect' is discussed, in detail. It is deduced from the numerical results that, the duration and the maximum amount of the considered physical quantities can be suitably tuned by selecting the proper field-mode structure parameter $p$ and the detuning parameters.
description: 12 pages. arXiv admin note: text overlap with arXiv:1407.7716, arXiv:1407.7690
Computational study of the putative active form of protein Z (PZa): Sequence design and structural modeling
Creators: name: Chandrasekaran, Vasu
name: Pedersen, Lee G.
name: Lee, Chang Jun
name: Duke, Robert E.
name: Perera, Lalith
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Although protein Z (PZ) has a domain arrangement similar to the essential coagulation proteins FVII, FIX, FX, and protein C, its serine protease (SP)-like domain is incomplete and does not exhibit proteolytic activity. We have generated a trial sequence of putative activated protein Z (PZa) by identifying amino acid mutations in the SP-like domain that might reasonably resurrect the serine protease catalytic activity of PZ. The structure of the activated form was then modeled based on the proposed sequence using homology modeling and solvent-equilibrated molecular dynamics simulations. In silico docking of inhibitors of FVIIa and FXa to the putative active site of equilibrated PZa, along with structural comparison with its homologous proteins, suggest that the designed PZa can possibly act as a serine protease.
The physics of Lyman-alpha escape from disc-like galaxies
Creators: name: Smith, Aaron
name: Kannan, Rahul
name: Tacchella, Sandro
name: Vogelsberger, Mark
name: Hernquist, Lars
name: Marinacci, Federico
name: Sales, Laura V.
name: Torrey, Paul
name: Li, Hui
name: Yeh, Yuan-Chen
name: Qi, Jia
Publisher: name: arXiv
Year: 2021
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Hydrogen emission lines can provide extensive information about star-forming galaxies in both the local and high-redshift Universe. We present a detailed Lyman continuum (LyC), Lyman-alpha (Lyα), and Balmer line (Hα and H\b{eta}) radiative transfer study of a high-resolution isolated Milky-Way simulation using the Arepo-RT radiation hydrodynamics code with the SMUGGLE galaxy formation model. The realistic framework includes stellar feedback, non-equilibrium thermochemistry, and dust grain evolution in the interstellar medium (ISM). We extend our Cosmic Lyα Transfer (COLT) code with photoionization equilibrium Monte Carlo radiative transfer for self-consistent end-to-end (non-)resonant line predictions. Accurate LyC reprocessing to recombination emission requires modelling pre-absorption by dust (27.5%), helium ionization (8.7%), and anisotropic escape fractions (7.9%), as these reduce the available budget for hydrogen line emission (55.9%). We investigate the role of the multiphase dusty ISM, disc geometry, gas kinematics, and star formation activity in governing the physics of emission and escape, focusing on the time variability, gas phase structure, and spatial, spectral, and viewing angle dependence of the emergent photons. Isolated disc simulations are well-suited for comprehensive observational comparisons with local Hα surveys, but would require a proper cosmological circumgalactic medium (CGM) environment as well as less dust absorption and rotational broadening to serve as analogs for high-redshift Lyα emitting galaxies. Future applications of our framework to next-generation cosmological simulations of galaxy formation including radiation-hydrodynamics that resolve <10 pc multiphase ISM and <1 kpc CGM structures will provide crucial insights and predictions for current and upcoming Lyα observations.
description: 28 pages, 32 figures, MNRAS, in press
On monads and warpings
Creators: name: Lack, Stephen
name: Street, Ross
Publisher: name: arXiv
Year: 2014
Subjects: subject: Category Theory (math.CT)
subject: FOS: Mathematics
subject: 18C15, 18D05, 18D10

description: We explain the sense in which a warping on a monoidal category is the same as a pseudomonad on the corresponding one-object bicategory, and we describe extensions of this to the setting of skew monoidal categories: these are a generalization of monoidal categories in which the associativity and unit maps are not required to be invertible. Our analysis leads us to describe a normalization process for skew monoidal categories, which produces a universal skew monoidal category for which the right unit map is invertible.
description: 15 pages. Version 2: revised based on a very helpful report from the referee. To appear in the Cahiers de Topologie and Geometrie Differentielle Categoriques
19 F NMR studies of α-synuclein-membrane interactions: α-Synuclein-Membrane Interactions
Creators: name: Pielak, Gary J.
name: Li, Conggang
name: Wang, Gui-Fang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: α-Synuclein function is thought to be related to its membrane binding ability. Solution NMR studies have identified several α-synuclein-membrane interaction modes in small unilamellar vesicles (SUVs), but how membrane properties affect binding remains unclear. Here, we use 19F NMR to study α-synuclein-membrane interactions by using 3-fluoro-L-tyrosine (3FY) and trifluoromethyl-L-phenylalanine (tfmF) labeled proteins. Our results indicate that the affinity is affected by both the head group and the acyl chain of the SUV. Negatively charged head groups have higher affinity, but different head groups with the same charge also affect binding. We show that the saturation of the acyl chain has a dramatic effect on the α-synuclein-membrane interactions by studying lipids with the same head group but different chains. Taken together, the data show that α-synuclein's N-terminal region is the most important determinate of SUV binding, but its C-terminal region also modulates the interactions. Our data support the existence of multiple tight phospholipid-binding modes, a result incompatible with the model that α-synuclein lies solely on the membrane surface.
Oblique transition in hypersonic double-wedge flow
Creators: name: Dwivedi, Anubhav
name: Sidharth, G. S.
name: Jovanović, Mihailo R.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Analysis of PDEs (math.AP)
subject: Dynamical Systems (math.DS)
subject: Optimization and Control (math.OC)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We utilize resolvent and weakly nonlinear analyses in combination with direct numerical simulations (DNS) to identify mechanisms for oblique transition in a Mach 5 hypersonic flow over an adiabatic slender double-wedge. Even though the laminar separated flow is globally stable, resolvent analysis demonstrates significant amplification of unsteady external disturbances to the linearized flow equations. These disturbances are introduced upstream of the separation zone and they lead to the appearance of oblique waves further downstream. We demonstrate that large amplification of oblique waves arises from the growth of fluctuation shear stress due to streamline curvature of the laminar base flow in the separated shear layer. This is in contrast to the attached boundary layers, where no such mechanism exists. We also use a weakly nonlinear analysis to show that the resolvent operator associated with linearization around the laminar base flow governs the evolution of steady reattachment streaks that arise from quadratic interactions of unsteady oblique waves. These quadratic interactions generate vortical excitations in the reattaching shear layer which lead to the formation of streaks in the recirculation zone and their subsequent amplification, breakdown, and transition to turbulence downstream. Our analysis of the energy budget shows that deceleration of the base flow near reattachment is primarily responsible for amplification of steady streaks. Finally, we employ DNS to examine latter stages of transition to turbulence and demonstrate the predictive power of a weakly nonlinear input-output framework in uncovering triggering mechanisms for oblique transition in separated high-speed boundary layer flows.
description: 36 pages, 26 figures
Activation of the human nuclear xenobiotic receptor PXR by the reverse transcriptase-targeted anti-HIV drug PNU-142721
Creators: name: Cheng, Yuan
name: Redinbo, Matthew R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The human pregnane X receptor (PXR) is a member of the nuclear receptor superfamily of ligand-regulated transcription factors. PXR responds to a structurally diverse variety of endogenous and xenobiotic compounds, and coordinates the expression of genes central to the metabolism and excretion of potentially harmful chemicals, including human therapeutics. The reverse transcriptase inhibitor PNU-142721 has been designed to treat human immunodeficiency virus (HIV) infection. Although this compound has anti-HIV activity, it was established using cell-based assays that PNU-142721 is an efficacious PXR agonist. We present here the 2.8 Å resolution crystal structure of the human PXR ligand-binding domain in complex with PNU-142721. PXR employs one hydrogen bond and fourteen van der Waals contacts to interact with the ligand, but allows two loops adjacent to the ligand-binding pocket to remain disordered in the structure. These observations highlight the role structural flexibility plays in PXR's promiscuous responses to xenobiotics. The crystal structure also explains why PNU-173575, a thiomethyl metabolite of PNU-142721, exhibits enhanced PXR activation relative to the unmodified compound and why PNU-142721 can also activate rat PXR. Taken together, the results presented here elucidate the structural basis for PXR activation by PNU-142721 and related chemicals.
Consimilarity of Split Quaternion Matrices and a Solution of the Split Quaternion Matrix Equation X-AX_B=C
Creators: name: Kosal, Hidayet Huda
name: Akyigit, Mahmut
name: Tosun, Murat
Publisher: name: arXiv
Year: 2014
Subjects: subject: Commutative Algebra (math.AC)
subject: FOS: Mathematics

description: In this paper, the consimilarity of complex matrices is generalized for the split quaternions. In this regard, coneigenvalue and coneigenvector are defined for split quaternion matrices. Also, the existence of solution to the split quaternion matrix equation X-AXB = C is characterized and the solution of the equation in the explicit form are derived via its real representation.
description: 12 page
The interface of protein structure, protein biophysics, and molecular evolution
Creators: name: Echave, Julian
name: Regan, Lynne
name: Thorne, Jeffrey L.
name: de Koning, A. P. Jason
name: Thornton, Joseph W.
name: Teufel, Ashley I.
name: Bahar, Ivet
name: Bornberg-Bauer, Erich
name: Teichmann, Sarah A.
name: Roger, Andrew
name: Liberles, David A.
name: Holder, Mark T.
name: Pollock, David D.
name: Sunyaev, Shamil
name: Shakhnovich, Eugene
name: Grahnen, Johan A.
name: Rubinstein, Nimrod
name: Bloom, Jesse
name: Elofsson, Arne
name: Goldstein, Richard A.
name: Bastolla, Ugo
name: Colwell, Lucy J.
name: Lartillot, Nicholas
name: Weinreich, Daniel M.
name: Lakner, Clemens
name: Naylor, Gavin
name: Pupko, Tal
name: Gerloff, Dietlind L.
name: Lovell, Simon C.
name: Dokholyan, Nikolay V.
name: Perica, Tina
name: Sjölander, Kimmen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction.
Effect of $TiO_{2}$ nanoparticles on the thermal stability of native DNA under UV irradiation
Creators: name: Usenko, Evgeniya
name: Glamazda, Alexander
name: Valeev, Vladimir
name: Karachevtsev, Victor
Publisher: name: arXiv
Year: 2021
Subjects: subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences

description: $TiO_{2}$ nanoparticles (NPs) are widely used in the environmental engineering, medicine, chemical and food industries due to their unique photocatalytic and biocidal properties. NPs may generate reactive oxygen species and, hence, have the toxic effect on the living cells via oxidative stress. An external UV irradiation may magnify the photocatalytic properties of $TiO_{2}$ NPs. In this regard, we have analyzed the influence of $TiO_{2}$ NPs on the conformation and thermal stability of native DNA in a buffer solution without and under UV irradiation exploiting absorption spectroscopy with DNA thermal denaturation in the range of 20-94 degrees Celsius. Upon DNA heating from about 25 to 44 degrees Celsius, we have observed the stabilization of DNA duplex in the presence of $TiO_{2}$ NPs. This additional biopolymer stabilization indicates that partial DNA unwinding appears as a result of the direct binding of the biopolymer to NPs. We showed that the performed UV treatment of DNA during 3 hours leads to partial unwinding of the biopolymer structure. The NPs injection to the biopolymer solution induced the additional effect on the DNA thermal stability under UV irradiation. The performed analysis of the experimental data suggests that the nature of the impact of NPs on the biopolymer is complex.
description: Preprint submitted to The European Physical Journal E
Proposing Conceptual Model for National Research and Scientific Spatial Information System
Creators: name: Pournaghi, Roya
Publisher: name: Iranian Research Institute for Information Science and Technology (IranDoc)
Year: 2015
Subjects: Spatial Information System

description: "This research aims to develop a conceptual model for the national system of scientific and research information resource management in the country, using effective indicators and determining the effective indicators in the management of scientific research information resources (human, financial, scientific resources, etc.). It also identifies the components influencing each of the indicators related to the management of scientific research information resources in the country, employing a documentary study and model design approach. The research stages can be summarized as follows: a review of theoretical foundations and previous research to determine the indicators and components (library study); extraction of indicators and components, and studying texts to determine the appropriate structure for the conceptual model and design the model. 

In summary, in terms of the time frame of the research coverage, this study is classified as a cross-sectional study. Regarding the type and method of data collection, it is a combination of documentary studies and text surveys, and due to the nature of the research, it falls under developmental-applied research. The indicators used in the model development are based on conducted studies and analysis and comparison with other existing research indicators in the country. The national research indicators include budget, human resources, articles, journals, books, awards, conferences, etc. 

The conceptual model of the national system for managing scientific and research information resources serves as a guide for establishing and constructing a system that can oversee the management of scientific and research information resources in the country. This system will assist policymakers and decision-makers in the research sector in monitoring spatial distributions and examining the allocation of research facilities across the country for future planning. It can conduct spatial analysis of scientific and research information from organizations and educational institutions in various fields and, with a comprehensive collection of scientific and research information at the national level, enables the monitoring of the country's scientific and research growth. Additionally, the optimal and efficient management of resources will be the main advantage of this system."
description: https://en.irandoc.ac.ir/research/48
Reaction-diffusion-advection equation in binary tree networks and optimal size ratio
Creators: name: Sakaguchi, Hidetsugu
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: Tissues and Organs (q-bio.TO)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: A simple reaction-diffusion-advection equation is proposed in a dichotomous tree network to discuss an optimal network. An optimal size ratio r is evaluated by the principle of maximization of total reaction rate. In the case of reaction-limited conditions, the optimal ratio can be larger than (1/2)^{1/3} for a fixed value of branching number, which is consistent with observations in mammalian lungs. We find furthermore that there is an optimal branching number when the Peclet number is large. Under the doubly optimal conditions with respect to the size ratio and branching number, the optimal value of r is close to (1/2)^{1/3}.
description: 5 pages, 4 figures
The circumgalactic medium of high redshift galaxies
Creators: name: Pallottini, Andrea
name: Gallerani, Simona
name: Ferrara, Andrea
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We study the properties of the circumgalactic medium (CGM) of high-$z$ galaxies in the metal enrichment simulations presented in Pallottini et al. 2014. At $z=4$, we find that the simulated CGM gas density profiles are self-similar, once scaled with the virial radius of the parent dark matter halo. We also find a simple analytical expression relating the neutral hydrogen equivalent width (${\rm EW}_{\rm HI}$) of CGM absorbers as a function of the line of sight impact parameter ($b$). We test our predictions against mock spectra extracted from the simulations, and show that the model reproduces the ${\rm EW}_{\rm HI}(b)$ profile extracted from the synthetic spectra analysis. When compared with available data, our CGM model nicely predicts the observed ${\rm EW}_{\rm HI}(b)$ in $z\lesssim2$ galaxies, and supports the idea that the CGM profile does not evolve with redshift.
description: 5 pages, 4 figures, accepted for publication in MNRAS Letters
Entanglement harvesting from conformal vacuums between two Unruh-DeWitt detectors moving along null paths
Creators: name: Barman, Subhajit
name: Barman, Dipankar
name: Majhi, Bibhas Ranjan
Publisher: name: arXiv
Year: 2021
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: It is well-known that the $(1+1)$ dimensional Schwarzschild and spatially flat FLRW spacetimes are conformally flat. This work examines entanglement harvesting from the conformal field vacuums in these spacetimes between two Unruh-DeWitt detectors, moving along outgoing null trajectories. In $(1+1)$ dimensional Schwarzschild spacetime, we considered the Boulware and Unruh vacuums for our investigations. In this analysis, one observes that while entanglement harvesting is possible in $(1+1)$ dimensional Schwarzschild and $(1+3)$ dimensional de Sitter spacetimes, it is not possible in the $(1+1)$ dimensional de Sitter background for the same set of parameters when the detectors move along the same outgoing null trajectory. The qualitative results from the Boulware and the Unruh vacuums are alike. Furthermore, we observed that the concurrence depends on the distance $d$ between the two null paths of the detectors periodically, and depending on the parameter values, there could be entanglement harvesting shadow points or regions. We also observe that the mutual information does not depend on $d$ in $(1+1)$ dimensional Schwarzschild and de Sitter spacetimes but periodically depends on it in $(1+3)$ dimensional de Sitter background. We also provide elucidation on the origin of the harvested entanglement.
description: Comments added, published in JHEP
title: Ethnische und religiöse Vertreibungen im Irak am Beispiel der christlichen und der jesidischen Minderheit / Karte: Frank Schemmerling ; Text: Stefan Brenner
Creators: name: Brenner, Stefan
Publisher: name: ZMSBw
Year: 2023

description: Die aktuelle Karte : historische Ereignisse in Kartenansicht / Zentrum für Militärgeschichte und Sozialwissenschaften der Bundeswehr; [17]
Initial data for binary neutron stars with adjustable eccentricity
Creators: name: Moldenhauer, Niclas
name: Markakis, Charalampos M.
name: Johnson-McDaniel, Nathan K.
name: Tichy, Wolfgang
name: Bruegmann, Bernd
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Binary neutron stars in circular orbits can be modeled as helically symmetric, i.e., stationary in a rotating frame. This symmetry gives rise to a first integral of the Euler equation, often employed for constructing equilibrium solutions via iteration. For eccentric orbits, however, the lack of helical symmetry has prevented the use of this method, and the numerical relativity community has often resorted to constructing initial data by superimposing boosted spherical stars without solving the Euler equation. The spuriously excited neutron star oscillations seen in evolutions of such data arise because such configurations lack the appropriate tidal deformations and are stationary in a linearly comoving---rather than rotating---frame. We consider eccentric configurations at apoapsis that are instantaneously stationary in a rotating frame. We extend the notion of helical symmetry to eccentric orbits, by approximating the elliptical orbit of each companion as instantaneously circular, using the ellipse's inscribed circle. The two inscribed helical symmetry vectors give rise to approximate instantaneous first integrals of the Euler equation throughout each companion. We use these integrals as the basis of a self-consistent iteration of the Einstein constraints to construct conformal thin-sandwich initial data for eccentric binaries. We find that the spurious stellar oscillations are reduced by at least an order of magnitude, compared with those found in evolutions of superposed initial data. The tidally induced oscillations, however, are physical and qualitatively similar to earlier evolutions. Finally, we show how to incorporate radial velocity due to radiation reaction in our inscribed helical symmetry vectors, which would allow one to obtain truly non-eccentric initial data when our eccentricity parameter $e$ is set to zero.
description: 23 pages, 10 figures
CMB hemispherical asymmetry from non-linear isocurvature perturbations
Creators: name: Assadullahi, Hooshyar
name: Firouzjahi, Hassan
name: Namjoo, Mohammad Hossein
name: Wands, David
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We investigate whether non-adiabatic perturbations from inflation could produce an asymmetric distribution of temperature anisotropies on large angular scales in the cosmic microwave background (CMB). We use a generalised non-linear $δN$ formalism to calculate the non-Gaussianity of the primordial density and isocurvature perturbations due to the presence of non-adiabatic, but approximately scale-invariant field fluctuations during multi-field inflation. This local-type non-Gaussianity leads to a correlation between very long wavelength inhomogeneities, larger than our observable horizon, and smaller scale fluctuations in the radiation and matter density. Matter isocurvature perturbations contribute primarily to low CMB multipoles and hence can lead to a hemispherical asymmetry on large angular scales, with negligible asymmetry on smaller scales. In curvaton models, where the matter isocurvature perturbation is partly correlated with the primordial density perturbation, we are unable to obtain a significant asymmetry on large angular scales while respecting current observational constraints on the observed quadrupole. However in the axion model, where the matter isocurvature and primordial density perturbations are uncorrelated, we find it may be possible to obtain a significant asymmetry due to isocurvature modes on large angular scales. Such an isocurvature origin for the hemispherical asymmetry would naturally give rise to a distinctive asymmetry in the CMB polarisation on large scales.
description: 15 pages, 5 figures
title: Henner Fürtig, Geschichte des Irak / Text von Christian Jentzsch ; gelesen von Andreas Eichner
Creators: name: Jentzsch, Christian
Publisher: name: ZMSBw
Year: 2023

description: Buchjournal: Angelesen. : das Buchjournal des ZMSBw / Zentrum für Militärgeschichte und Sozialwissenschaften der Bundeswehr; [44]
title: In kind : the enactive poem and the co-creative response
Creators: name: Errington, Patrick
Publisher: name: University of St Andrews
publisherIdentifier: https://ror.org/02wn5qz54
publisherIdentifierScheme: ROR
Year: 2019

description: 	How we approach a poem changes it. Recently, it has been suggested that one readerly approach – a bodily orientation characterised by distance, suspicion, and resistance – risks becoming reflexive, pre-conscious, and predominant. This use-oriented reading allows us to destabilise, denaturalise, dissect, defend, and define poetic texts through its manifestation in contemporary literary critique, yet it is coming to be regarded as the sole manner and mood of intelligent, intellectual engagement. In this thesis, I demonstrate the need to pluralise this attentive orientation, particularly when it comes to contemporary lyric poetry. I suggest how an overlooked mode of response might foster a more receptive mode of approach: the ‘co-creative’ response. Lyric poems mean to move us, and they come to mean by moving us. Recent ‘simulation theories of language comprehension’, from the field of cognitive neuroscience, provide empirical evidence that language processing is not a product of a-modal symbol manipulation but rather involves ‘simulations’ by certain classes of neurons in areas used for real-world action and perception. As habituation and abstraction increase, however, these embodied simulations ‘streamline’, becoming narrow schematic ‘shadows’ of once broad, qualitatively rich simulations. Poems, I suggest, seek to reverse this process by situationally novel variations of language, coming to mean in the broadly embodied sense in which real-world experiences ‘mean’. Readers are asked to ‘enact’ the poem, to ‘co-create’ its meaning. Where critique traditionally requires that readers resist enactive participation in the aim of objective analysis, the co-creative response – a response ‘in kind’ by imitation, versioning, or hommage – asks readers to receive and carry forward the enactive unfolding of a poem with a composition of their own. I assert that, by thus responding with – rather than to – poems, we might foster an attentive stance of active receptivity, thereby coming to understand poems as the enactive phenomena they are.
Descent of tautological sheaves from Hilbert schemes to Enriques manifolds
Creators: name: Reede, Fabian
Publisher: name: Berlin ; Heidelberg [u.a.] : Springer
Year: 2024
Subjects: subject: 14D20
subject: 14J28
subject: Enriques manifolds
subject: Moduli spaces
subject: Primary: 14F06
subject: Secondary: 14F08
subject: Stable sheaves
subject: Dewey Decimal Classification::500 | Naturwissenschaften::510 | Mathematik

description: Let X be a K3 surface which doubly covers an Enriques surface S. If n∈N is an odd number, then the Hilbert scheme of n-points X[n] admits a natural quotient S[n]. This quotient is an Enriques manifold in the sense of Oguiso and Schröer. In this paper we construct slope stable sheaves on S[n] and study some of their properties.
The quantum UV-IR map for line defects in $\mathfrak{gl}(3)$-type class $S$ theories
Creators: name: Neitzke, Andrew
name: Yan, Fei
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Geometric Topology (math.GT)
subject: Quantum Algebra (math.QA)
subject: Representation Theory (math.RT)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We consider the quantum UV-IR map for line defects in class $S$ theories of $\mathfrak{gl}(3)$-type. This map computes the protected spin character which counts framed BPS states with spin for the bulk-defect system. We give a geometric method of computing this map motivated by the physics of five-dimensional $\mathcal{N}=2$ supersymmetric Yang-Mills theory, and compute it explicitly in various examples. As a spin-off we propose a new way of computing a certain specialization of the HOMFLY polynomial for links in $\mathbb{R}^3$, as a sum over BPS webs attached to the link.
description: Mathematica and Python code included as auxiliary files, 55 pages, 51 figures
A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds
Creators: name: Kuhlman, Brian
name: Stranges, P. Benjamin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The accurate design of new protein–protein interactions is a longstanding goal of computational protein design. However, most computationally designed interfaces fail to form experimentally. This investigation compares five previously described successful de novo interface designs with 158 failures. Both sets of proteins were designed with the molecular modeling program Rosetta. Designs were considered a success if a high-resolution crystal structure of the complex closely matched the design model and the equilibrium dissociation constant for binding was less than 10 μM. The successes and failures represent a wide variety of interface types and design goals including heterodimers, homodimers, peptide-protein interactions, one-sided designs (i.e., where only one of the proteins was mutated) and two-sided designs. The most striking feature of the successful designs is that they have fewer polar atoms at their interfaces than many of the failed designs. Designs that attempted to create extensive sets of interface-spanning hydrogen bonds resulted in no detectable binding. In contrast, polar atoms make up more than 40% of the interface area of many natural dimers, and native interfaces often contain extensive hydrogen bonding networks. These results suggest that Rosetta may not be accurately balancing hydrogen bonding and electrostatic energies against desolvation penalties and that design processes may not include sufficient sampling to identify side chains in preordered conformations that can fully satisfy the hydrogen bonding potential of the interface.
Homogeneous Photometry VI: Variable Stars in the Leo I Dwarf Spheroidal Galaxy
Creators: name: Stetson, Peter B.
name: Fiorentino, Giuliana
name: Bono, Giuseppe
name: Bernard, Edouard J.
name: Monelli, Matteo
name: Iannicola, Giacinto
name: Gallart, Carme
name: Ferraro, Ivan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We have characterized the pulsation properties of 164 candidate RR Lyrae variables (RRLs) and 55 candidate Anomalous and/or short-period Cepheids in Leo I dwarf spheroidal galaxy. On the basis of its RRLs Leo I is confirmed to be an Oosterhoff-intermediate type galaxy, like several other dwarfs. We show that in their pulsation properties, the RRLs representing the oldest stellar population in the galaxy are not significantly different from those of five other nearby, isolated dwarf spheroidal galaxies. A similar result is obtained when comparing them to RR Lyrae stars in recently discovered ultra-faint dwarf galaxies. We are able to compare the period distributions and period-amplitude relations for a statistically significant sample of ab type RR Lyrae stars in dwarf galaxies (~1300stars) with those in the Galactic halo field (~14,000stars) and globular clusters (~1000stars). Field RRLs show a significant change in their period distribution when moving from the inner (dG<14 kpc) to the outer (dG>14kpc) halo regions. This suggests that the halo formed from (at least) two dissimilar progenitors or types of progenitor. Considered together, the RRLs in classical dwarf spheroidal and ultra-faint dwarf galaxies-as observed today-do not appear to follow the well defined pulsation properties shown by those in either the inner or the outer Galactic halo, nor do they have the same properties as RRLs in globular clusters. In particular, the samples of fundamental-mode RRLs in dwarfs seem to lack High Amplitudes and Short Periods ("HASP":AV>1.0mag and P <0.48d) when compared with those observed in the Galactic halo field and globular clusters. The observed properties of RRLs do not support the idea that currently existing classical dwarf spheroidal and ultra-faint dwarf galaxies are surviving representative examples of the original building blocks of the Galactic halo.
description: 49 pages in referee format, 12 figures
Survey of charging scheduling, fleet management, and location planning of charging stations for electrified demand-responsive transport systems: methodologies and recent developments
Creators: name: Ma, Tai-Yu
name: Fang, Yumeng
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computational Engineering, Finance, and Science (cs.CE)
subject: Systems and Control (eess.SY)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: The accelerated electrification of transport systems with EVs has brought new challenges for charging scheduling, fleet management, and charging infrastructure location and configuration planning. In this review, we have provided a systematic review of the recent development in strategic, tactical, and operational decisions for demand responsive transport system planning using electric vehicles (EV-DRT). We have summarized recent developments in mathematical modeling approaches and identified future research directions. A list of existing open-access datasets, numerical test instances, and software are provided for future research in EV-DRT and related problems.
How to extract a spectrum from hydrodynamic equations
Creators: name: Gibbon, John D.
name: Vincenzi, Dario
Publisher: name: arXiv
Year: 2021
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: Practical results gained from statistical theories of turbulence usually appear in the form of an inertial range energy spectrum $\mathcal{E}(k)\sim k^{-q}$ and a cut-off wave-number $k_{c}$. For example, the values $q=5/3$ and $\ell k_{c}\sim \mathit{Re}^{3/4}$ are intimately associated with Kolmogorov's 1941 theory. To extract such spectral information from the Navier-Stokes equations, Doering and Gibbon (2002) introduced the idea of forming a set of dynamic wave-numbers $κ_n(t)$ from ratios of norms of solutions. The time averages of the $κ_n(t)$ can be interpreted as the 2$n$th-moments of the energy spectrum. They found that $1 < q \leqslant 8/3$, thereby confirming the earlier work of Sulem and Frisch (1975) who showed that when spatial intermittency is included, no inertial range can exist in the limit of vanishing viscosity unless $q \leqslant 8/3$. Since the $κ_n(t)$ are based on Navier-Stokes weak solutions, this approach connects empirical predictions of the energy spectrum with the mathematical analysis of the Navier-Stokes equations. This method is developed to show how it can be applied to many hydrodynamic models such as the two dimensional Navier--Stokes equations (in both the direct- and inverse-cascade regimes), the forced Burgers equation and shell models.
description: 22 pages