cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Clustering of neural codewords revealed by a first-order phase transition
Creators: name: Huang, Haiping
name: Toyoizumi, Taro
Publisher: name: arXiv
Year: 2016
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: A network of neurons in the central nervous system collectively represents information by its spiking activity states. Typically observed states, i.e., codewords, occupy only a limited portion of the state space due to constraints imposed by network interactions. Geometrical organization of codewords in the state space, critical for neural information processing, is poorly understood due to its high dimensionality. Here, we explore the organization of neural codewords using retinal data by computing the entropy of codewords as a function of Hamming distance from a particular reference codeword. Specifically, we report that the retinal codewords in the state space are divided into multiple distinct clusters separated by entropy-gaps, and that this structure is shared with well-known associative memory networks in a recallable phase. Our analysis also elucidates a special nature of the all-silent state. The all-silent state is surrounded by the densest cluster of codewords and located within a reachable distance from most codewords. This codeword-space structure quantitatively predicts typical deviation of a state-trajectory from its initial state. Altogether, our findings reveal a non-trivial heterogeneous structure of the codeword-space that shapes information representation in a biological network.
description: 14 pages, 5 figures in main text plus Supplemental Material (7 pages)
On classification of non-abelian Painlevé type systems
Creators: name: Bobrova, Irina
name: Sokolov, Vladimir
Publisher: name: arXiv
Year: 2023
Subjects: subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences

description: We find all non-abelian generalizations of $\text{P}_1 - \text{P}_6$ Painlevé systems such that the corresponding autonomous system obtained by freezing the independent variable is integrable. All these systems have isomonodromic Lax representations.
Modeling Capabilities with Model-Based Systems Engineering (MBSE)
Creators: name: Shevchenko, Nataliya
Publisher: name: Carnegie Mellon University
Year: 2022
Subjects: subject: 80309 Software Engineering
subject: FOS: Computer and information sciences

description: Model-based Systems Engineering (MBSE) as a methodology does not directly address capabilities, which describes the abilities of a system to achieve or perform a task or a mission. As a part of a problem description, capabilities have a strong connection to system requirements, and can be modeled using similar approaches. In the SEI Blog post Requirements in Model-based Systems Engineering (MBSE), I discussed the requirements domain. In this post, I consider the role of capabilities in system engineering—their purpose, how they are modeled and analyzed using MBSE and SysML, and how they can be associated with business requirements.
Streamlined data analysis in Python
Creators: name: Altenkort, Luis
name: Clarke, David Anthony
name: Goswami, Jishnu
name: Sandmeyer, Hauke
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Python is a particularly appealing language to carry out data analysis, owing in part to its user-friendly character as well as its access to well maintained and powerful libraries like NumPy and SciPy. Still, for the purpose of analyzing data in a lattice QCD context, some desirable functionality is missing from these libraries. Moreover, scripting languages tend to be slower than compiled ones. To help address these points we present the AnalysisToolbox, a collection of Python modules to facilitate lattice QCD data analysis. Some highlighted features include general-purpose jackknife and bootstrap routines; modules for reading in and storing gauge configurations; a module to carry out hadron resonance gas model calculations; and convenience wrappers for SciPy integration, curve fitting, and splines. These features are sped up behind the scenes using parallelization and just-in-time compilation.
description: 9 pages, 1 figure, presented at the 40th International Symposium on Lattice Field Theory
Magnetic Resonance Force Detection using a Membrane Resonator
Creators: name: Scozzaro, Nicolas
name: Ruchotzke, Will
name: Belding, Amanda
name: Cardellino, Jeremy D.
name: Blomberg, Erick C.
name: McCullian, Brendan A.
name: Bhallamudi, Vidya P.
name: Pelekhov, Denis V.
name: Hammel, P. Chris
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The availability of compact, low-cost magnetic resonance imaging instruments would further broaden the substantial impact of this technology. We report highly sensitive detection of magnetic resonance using low-stress silicon nitride (SiN$_x$) membranes. We use these membranes as low-loss, high-frequency mechanical oscillators and find they are able to mechanically detect spin-dependent forces with high sensitivity enabling ultrasensitive magnetic resonance detection. The high force detection sensitivity stems from their high mechanical quality factor $Q\sim10^6$ combined with the low mass of the resonator. We use this excellent mechanical force sensitivity to detect the electron spin magnetic resonance using a SiN$_x$ membrane as a force detector. The demonstrated force sensitivity at 300 K is 4 fN/$\sqrt{\mathrm{Hz}}$, indicating a potential low temperature (4 K) sensitivity of 25 aN/$\sqrt{\mathrm{Hz}}$. Given their sensitivity, robust construction, large surface area and low cost, SiN$_x$ membranes can potentially serve as the central component of a compact room-temperature ESR and NMR instrument that has superior spatial resolution to conventional approaches.
Dynamics near the ground state for the energy critical nonlinear heat equation in large dimensions
Creators: name: Collot, Charles
name: Merle, Frank
name: Raphael, Pierre
Publisher: name: arXiv
Year: 2016
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: Primary 35B35, 35B40, 35K58, Secondary 35B33, 35B44, 35B53

description: We consider the energy critical semilinear heat equation $$\partial_tu=Δu+|u|^{\frac{4}{d-2}}u, \ \ x\in \mathbb R^d$$ and give a complete classification of the flow near the ground state solitary wave $$Q(x)=\frac{1}{\left( 1+\frac{|x|^2}{d(d-2)}\right)^{\frac{d-2}{2}}}$$ in dimension $d\ge 7$, in the energy critical topology and without radial symmetry assumption. Given an initial data $Q+\varepsilon_0$ with $\parallel \nabla \varepsilon_0\parallel_{L^2}\ll 1$, the solution either blows up in the ODE type I regime, or dissipates, and these two open sets are separated by a codimension one set of solutions asymptotically attracted by the solitary wave. In particular, non self similar type II blow up is ruled out in dimension $d\ge 7$ near the solitary wave even though it is known to occur in smaller dimensions. Our proof is based on sole energy estimates deeply and draws a route map for the classification of the flow near the solitary wave in the energy critical setting. A by-product of our method is the classification of minimal elements around $Q$ belonging to the unstable manifold.
description: 81 pages
Homology modeling, docking, molecular dynamics and in vitro studies to identify Rhipicephalus microplus acetylcholinesterase inhibitors
Creators: name: Cerqueira, Amanda Ponce Morais
name: Santana, Isis Bugia
name: Araújo, Janay Stefany Carneiro
name: Lima, Hélimar Gonçalves
name: Batatinha, Maria José Moreira
name: Branco, Alexsandro
name: Junior, Manoelito Coelho dos Santos
name: Botura, Mariana Borges
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology

description: Rhipicephalus microplus is an important ectoparasite of cattle, causing considerable economical losses. Resistance to chemical acaricides has stimulated the search for new antiparasitic drugs, including natural products as an eco-friendly alternative of control. Flavonoids represent a class of natural compounds with many biological activities, such as enzyme inhibitors. Acetylcholinesterase is an essential enzyme for tick survival that stands out as an important target for the development of acaricides. This work aimed to predict this 3D structure by homology modeling and use the model to identify compound with inhibitory activity. The model of R. microplus AChE1 (RmAChE1) was constructed using MODELLER program. The optimization and molecular dynamic investigation were performed in GROMACS program. The model developed was used, by molecular docking, to evaluate the anticholinesterase activity of flavonoids (quercetin, rutin, diosmin, naringin and hesperidin) and an acaricide synthetic (eserine). Additionally, in vitro inhibition of AChE and larval immersion tests were performed. The model of RmAChE1 showed to be sterically and energetically acceptable. In molecular dynamics simulations, the 3D structure remains stable with Root Mean Square Deviation = 3.58 Å and Root Mean Square Fluctuation = 1.43 Å. In molecular docking analyses, only eserine and quercetin show affinity energy to the RmAChE (Gridscore: −52.17 and −39.44 kcal/mol, respectively). Among the flavonoids, quercetin exhibited the best in vitro inhibition of AChE activity (15.8%) and mortality of larvae tick (30.2%). The use of in silico and in vitro techniques has shown that quercetin showed promising anti-tick activity and structural requirements to interact with RmAChE1. Communicated by Ramaswamy H. Sarma
Valley and spin pump by scattering at non-magnetic disorders
Creators: name: An, Xing-Tao
name: Xiao, Jiang
name: Tu, M. W. -Y.
name: Yu, Hongyi
name: Fal'ko, Vladimir I.
name: Yao, Wang
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: In solid, the crystalline structure can endow electron an internal degree of freedom known as valley, which characterizes the degenerate energy minima in momentum space. The recent success in optical pumping of valley polarization in 2D transition metal dichalcogenides (TMDs) has greatly promoted the concept of valley-based informatics and electronics. However, between the demonstrated valley polarization of transient electron-hole pair excitations and practical valleytronic operations, there exist obvious gaps to fill, among which is the valley pump of long-lived charge carriers. Here we discover that the quested valley pump of electrons or holes can be realized simply by scattering at the ubiquitous nonmagnetic disorders, not relying on any specific material property. The mechanism is rooted in the nature of valley as a momentum space index: the intervalley backscattering in general has valley contrasted rate due to the distinct momentum transfers, causing a net transfer of population from one valley to another. As examples, we numerically demonstrate the sizable valley pump effects driven by charge current in nanoribbons of monolayer TMDs, where the spin-orbit scattering by non-magnetic disorders also realizes spin pump for the spin-valley locked holes. Our finding points to an unexpected new opportunity towards valley-spintronics, turning disorders from a deleterious factor to a resource of valley and spin polarization.
description: 14 pages, 3 figures
Extraordinary surface critical behavior induced by symmetry-protected topological state of a two-dimensional quantum magnet
Creators: name: Wang, Zhe
name: Zhang, Fan
name: Guo, Wenan
Publisher: name: arXiv
Year: 2023
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Using Quantum Monte Carlo simulations, we study spin-1/2 diagonal ladders coupled by ferromagnetic Heisenberg interactions. The model can also be viewed as usual ladders with ferromagnetic rung couplings coupled by antiferromagnetic diagonal couplings. We find that the model hosts a striped magnetic ordered phase and two topological nontrivial Haldane phases, separated by two quantum critical points. We show that the two quantum critical points are all in the three-dimensional O(3) universality class irrelevant to the topological properties of the Haldane phases. The properties of the surface formed by ladder ends in the two Haldane phases are studied. We find that the surface states are both gapless due to the symmetry-protected topological bulk states. We further demonstrate that extraordinary surface critical behaviors are realized at both critical points on such gapless surfaces without enhancing the surface coupling. Notably, the surface is not expected to be ordered in the three-dimensional classical O(3) critical point, suggesting that the topological properties of the Haldane phases are responsible for such surface critical behavior.
description: 10 pages, 6 figures
Promoting $p$-based Hall effects by $p$-$d$-$f$ hybridization in Gd-based dichalcogenides
Creators: name: Zeer, Mahmoud
name: Go, Dongwook
name: Schmitz, Peter
name: Saunderson, Tom G.
name: Wang, Hao
name: Ghabboun, Jamal
name: Blügel, Stefan
name: Wulfhekel, Wulf
name: Mokrousov, Yuriy
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We conduct a first-principles study of Hall effects in rare-earth dichalcogenides, focusing on monolayers of the H-phase EuX$_2$ and GdX$_2$, where X = S, Se, and Te. Our predictions reveal that all EuX$_2$ and GdX$_2$ systems exhibit high magnetic moments and wide bandgaps. We observe that while in case of EuX$_2$ the $p$ and $f$ states hybridize directly below the Fermi energy, the absence of $f$ and $d$ states of Gd at the Fermi energy results in $p$-like spin-polarized electronic structure of GdX$_2$, which mediates $p$-based magnetotransport. Notably, these systems display significant anomalous, spin, and orbital Hall conductivities. We find that in GdX$_2$ the strength of correlations controls the relative position of $p$, $d$ and $f$-states and their hybridization which has a crucial impact on $p$-state polarization and the anomalous Hall effect, but not the spin and orbital Hall effect. Moreover, we find that the application of strain can significantly modify the electronic structure of the monolayers, resulting in quantized charge, spin and orbital transport in GdTe$_2$ via a strain-mediated orbital inversion mechanism taking place at the Fermi energy. Our findings suggest that rare-earth dichalcogenides hold promise as a platform for topological spintronics and orbitronics.
description: 12 pages, 5 figures
Germanium Vacancy in Diamond Quantum Memory Exceeding 20 ms
Creators: name: Senkalla, Katharina
name: Genov, Genko
name: Metsch, Mathias H.
name: Siyushev, Petr
name: Jelezko, Fedor
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Negatively charged group-IV defects in diamond show great potential as quantum network nodes due to their efficient spin-photon interface. However, reaching sufficiently long coherence times remains a challenge. In this work, we demonstrate coherent control of germanium vacancy center (GeV) at millikelvin temperatures and extend its coherence time by several orders of magnitude to more than 20 ms. We model the magnetic and amplitude noise as an Ornstein-Uhlenbeck process, reproducing the experimental results well. The utilized method paves the way to optimized coherence times of group-IV defects in various experimental conditions and their successful applications in quantum technologies
Numerical solution of the quantum Lenard-Balescu equation for a one-component plasma
Creators: name: Scullard, Christian R.
name: Belt, Andrew P.
name: Fennell, Susan C.
name: Janković, Marija R.
name: Ng, Nathan
name: Serna, Susana
name: Graziani, Frank R.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We present a numerical solution of the quantum Lenard-Balescu equation using a spectral method, namely an expansion in Laguerre polynomials. This method exactly conserves both particles and energy and facilitates the integration over the dielectric function. To demonstrate the method, we solve the equilibration problem for a spatially homogeneous one-component plasma with various initial conditions. Unlike the more usual Landau/Fokker-Planck system, this method requires no input Coulomb logarithm; the logarithmic terms in the collision integral arise naturally from the equation along with the non-logarithmic order-unity terms. The spectral method can also be used to solve the Landau equation and a quantum version of the Landau equation in which the integration over the wavenumber requires only a lower cutoff. We solve these problems as well and compare them with the full Lenard-Balescu solution in the weak-coupling limit. Finally, we discuss the possible generalization of this method to include spatial inhomogeneity and velocity anisotropy.
Understanding the binding affinities between SFRP1CRD, SFRP1Netrin, Wnt5B and frizzled receptors 2, 3 and 7 using MD simulations
Creators: name: Sunkara, Raghava R.
name: Koulgi, Shruti
name: Jani, Vinod
name: Gadewal, Nikhil
name: Sonavane, Uddhavesh
name: Joshi, Rajendra
name: Waghmare, Sanjeev K.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Cancer

description: cWnt-signalling plays a crucial role in stem cell maintenance and tissue homeostasis. Secreted frizzled-related proteins(SFRP), Wnt inhibitors consist of the N-terminal cysteine rich domain(CRD) and the C-terminal netrin(NTR) domain. SFRP1 binds to the Wnt ligands and frizzled receptors(FZ) either through its SFRP1CRD or through its SFRP1Netrin domains; however, very little is known on these binding affinities. Here, we attempted to understand the interactions and binding affinities of SFRP1-Wnt5B, SFRP1-FZ(2, 3 & 7) and Wnt5B-FZ(2, 3 & 7) that are mainly expressed in murine hair follicle stem cells. SFRP1CRD, SFRP1Netrin, Wnt5B and FZ(2, 3 & 7) structures were built using homology modelling, followed by their molecular dynamics simulations. SFRP1CRD showed lower fluctuation when in complex with FZ2, FZ3 and FZ7 and Wnt5B as compared to SFRP1Netrin using RMSF and RMSD. However, free energy showed SFRP1Netrin was energetically more stable than SFRP1CRD. SFRP1Netrin formed more number of interactions with FZ as compared to SFRP1CRD. Importantly, SFRP1Netrin favoured binding to the FZ receptors(FZ3 > FZ7 > FZ2) as compared to Wnt5B ligand. Conversely, the SFRP1CRD showed more affinity towards the Wnt5B ligand as compared to FZ receptors. Wnt5B showed the best binding affinity with FZ3 followed by SFRP1CRD and SFRP1Netrin. Therefore, SFRP1Netrin can bind to the FZ3 with higher binding affinity and may inhibit non-canonical Wnt-signalling pathway. Our study provides the comprehensive information on the binding affinities among the Wnt5B, SFRP1CRD/Netrin and FZ(2, 3 & 7). Thus, this information might also help in designing novel strategies to inhibit aberrant Wnt-signalling. Communicated by Ramaswamy H. Sarma
On Multi-step MLE-process for Markov Sequences
Creators: name: Kutoyants, Yury A.
name: Motrunich, Anastasia
Publisher: name: arXiv
Year: 2016
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: 62F12, 62M05, 62M10

description: We consider the problem of the construction of the estimator-process of the unknown finite-dimensional parameter in the case of the observations of nonlinear autoregressive process. The estimation is done in two or three steps. First we estimate the unknown parameter by a learning relatively short part of observations and then we use the one-step MLE idea to construct an-estimator process which is asymptotically equivalent to the MLE. To have the learning interval shorter we introduce the two-step procedure which leads to the asymptotically efficient estimator-process too. The presented results are illustrated with the help of two numerical examples.
description: 24 pages, 6 fugures
Janus monolayer ScXY (X$\neq$Y=Cl, Br and I) for piezoelectric and valleytronic application: a first-principle prediction
Creators: name: Guo, San-Dong
name: Guo, Xiao-Shu
name: Si, Shuo-Ning
name: Cheng, Kai
name: Wang, Ke
name: Ang, Yee Sin
Publisher: name: arXiv
Year: 2023
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Coexistence of ferromagnetism, piezoelectricity and valley in two-dimensional (2D) materials is crucial to advance multifunctional electronic technologies. Here, Janus ScXY (X$\neq$Y=Cl, Br and I) monolayers are predicted to be in-plane piezoelectric ferromagnetic (FM) semiconductors with dynamical, mechanical and thermal stabilities. The predicted piezoelectric strain coefficients $d_{11}$ and $d_{31}$ (absolute values) are higher than ones of most 2D materials. Moreover, the $d_{31}$ (absolute value) of ScClI reaches up to 1.14 pm/V, which is highly desirable for ultrathin piezoelectric device application. To obtain spontaneous valley polarization, charge doping are explored to tune the direction of magnetization of ScXY. By appropriate hole doping, their easy magnetization axis can change from in-plane to out-of-plane, resulting in spontaneous valley polarization. Taking ScBrI with 0.20 holes per f.u. as a example, under the action of an in-plane electric field, the hole carriers of K valley turn towards one edge of the sample, which will produce anomalous valley Hall effect (AVHE), and the hole carriers of $Γ$ valley move in a straight line. These findings could pave the way for designing piezoelectric and valleytronic devices.
description: 7 pages,7 figures
Numerical Bifurcation for the Capillary Whitham Equation
Creators: name: Remonato, Filippo
name: Kalisch, Henrik
Publisher: name: arXiv
Year: 2016
Subjects: subject: Pattern Formation and Solitons (nlin.PS)
subject: Analysis of PDEs (math.AP)
subject: Numerical Analysis (math.NA)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: The so-called Whitham equation arises in the modeling of free surface water waves, and combines a generic nonlinear quadratic term with the exact linear dispersion relation for gravity waves on the free surface of a fluid with finite depth. In this work, the effect of incorporating capillarity into the Whitham equation is in focus. The capillary Whitham equation is a nonlocal equation similar to the usual Whitham equation, but containing an additional term with a coefficient depending on the Bond number T which measures the relative strength of capillary and gravity effects on the wave motion. A spectral collocation scheme for computing approximations to periodic traveling waves for the capillary Whitham equation is put forward. Numerical approximations of periodic traveling waves are computed using a bifurcation approach, and a number of bifurcation curves are found. Our analysis uncovers a rich structure of bifurcation patterns, including subharmonic bifurcations, as well as connecting and crossing branches. Indeed, for some values of the Bond number T, the bifurcation diagram features distinct branches of solutions which intersect at a secondary bifurcation point. The same branches may also cross without connecting, and some bifurcation curves feature self-crossings without self-connections.
Galesus (Schizogalesus) magnificus Nixon 1930
Creators: name: Notton, David G.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Diapriidae
Galesus
Galesus magnificus

description: Galesus (Schizogalesus) magnificus Nixon, 1930: 401, 408.
Valid name
Coptera robustior (Silvestri, 1913).
Summary of types
Syntype ♀, BMNH number 9.660. Syntype ♀.
Primary type data
Type; Natal/ Kloof/ 1500ft. / Sept. 1926; S.Africa/ R.E.Turner/ Brit. Mus./ 1926-404; Galesus / magnificus/ ♀ type Nixon/ 1930 (syntype ♀). Paratype; Port St. John/ Pondoland/ 6-25.Feb.1924; S.Africa/ R.E.Turner/ Brit. Mus./ 1924-136.; Galesus / magnificus/ ♀ paratype Nixon/ 1930 (syntype ♀).
Type locality
South Africa, Eastern Cape Province, Port St Johns; KwaZulu-Natal, Kloof.
Remarks
There are two females agreeing with Nixon’s description and labelled by him as Galesus magnificus. Of these, one is labelled as “type” and the other “ paratype ”; however, since neither a unique holotype or lectotype has yet been fixed, all of the type series is syntypic (Article 73.2). Both syntypes are mounted on card points and are entire.
description: Published as part of Notton, David G., 2014, A catalogue of the types of Diapriinae (Hymenoptera, Diapriidae) at the Natural History Museum, London, pp. 1-123 in European Journal of Taxonomy 75 on pages 89-90, DOI: 10.5852/ejt.2014.75, http://zenodo.org/record/3862773
Assessing the Effects of Orbital Relaxation and the Coherent-State Transformation in Quantum Electrodynamics Density Functional and Coupled-Cluster Theories
Creators: name: Liebenthal, Marcus D.
name: Vu, Nam
name: DePrince, A. Eugene
Publisher: name: arXiv
Year: 2023
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: Cavity quantum electrodynamics (QED) generalizations of time-dependent (TD) density functional theory (DFT) and equation-of-motion (EOM) coupled-cluster (CC) theory are used to model small molecules strongly coupled to optical cavity modes. We consider two types of calculations. In the first approach (termed "relaxed"), we use a coherent-state-transformed Hamiltonian within the ground- and excited-state portions of the calculations, and cavity-induced orbital relaxation effects are included at the mean-field level. This procedure guarantees that the energy is origin invariant in post-self-consistent-field calculations. In the second approach (termed "unrelaxed"), we ignore the coherent-state transformation and the associated orbital relaxation effects. In this case, ground-state unrelaxed QED-CC calculations pick up a modest origin dependence but otherwise reproduce relaxed QED-CC results within the coherent-state basis. On the other hand, a severe origin dependence manifests in ground-state unrelaxed QED mean-field energies. For excitation energies computed at experimentally realizable coupling strengths, relaxed and unrelaxed QED-EOM-CC results are similar, while significant differences emerge for unrelaxed and relaxed QED-TDDFT. First, QED-EOM-CC and relaxed QED-TDDFT both predict that electronic states that are not resonant with the cavity mode are nonetheless perturbed by the cavity. Unrelaxed QED-TDDFT, on the other hand, fails to capture this effect. Second, in the limit of large coupling strengths, relaxed QED-TDDFT tends to overestimate Rabi splittings, while unrelaxed QED-TDDFT underestimates them, given splittings from relaxed QED-EOM-CC as a reference, and relaxed QED-TDDFT generally does the better job of reproducing the QED-EOM-CC results.
Discovery of novel heterocyclic amide-based inhibitors: an integrative in-silico approach to targeting soluble epoxide hydrolase
Creators: name: Fakhar, Zeynab
name: Hejazi, Leila
name: Tabatabai, Sayyed Abbas
name: Munro, Orde Q.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Inhibition of soluble epoxide hydrolase (sEH) is considered as an emerging druggable target to reduce blood pressure, improve insulin sensitivity, and decrease inflammation. Despite the availability of different classes of sEH small molecule inhibitors for the potential treatment of hypertension, only a few candidates have reached clinical trials, making the optimal control of blood pressure presently unattainable. This necessity motivated us to explore a series of novel quinazoline-4(3H)-one and 4,6-disubstituted pyridin-2(1H)-one derivatives targeting sEH enzyme. Herein, comprehensive computational investigations were performed to probe the inhibition efficacy of these potent compounds in terms of inhibitor-enzyme interactions against sEH. In this study, the 39 in-house with a focused library comprising 39 in-house synthesized compounds were selected. The structure-based pharmacophore modeling was developed based on the crystal structure of sEH with its co-crystallized biologically active inhibitor. The generated hypotheses were applied for virtual screening-based PHASE fitness scores. Docking-based virtual screening workflows were used to generate lead compounds using HTVS, SP and XP based GLIDE G-score values. The candidate leads were filtered using ADMET pharmacological and physicochemical properties screening. A 100-ns of molecular dynamics simulations with Molecular dynamics simulations (100 ns) were performed to explore the binding affinities of the considered compounds. Our study identified four best candidates from quinazoline-4(3H)-one derivatives, which indicated that a quinazolinone ring serves as a suitable scaffold to develop novel small molecule sEH inhibitors. Communicated by Ramaswamy H. Sarma
Irreversibility of symbolic time series: a cautionary tale
Creators: name: Arola-Fernandez, Lluis
name: Lacasa, Lucas
Publisher: name: arXiv
Year: 2023
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Physical sciences

description: Many empirical time series are genuinely symbolic: examples range from link activation patterns in network science, DNA coding or firing patterns in neuroscience to cryptography or combinatorics on words. In some other contexts, the underlying time series is actually real-valued, and symbolization is applied subsequently, as in symbolic dynamics of chaotic systems. Among several time series quantifiers, time series irreversibility (the difference between forward and backward statistics in stationary time series) is of great relevance. However, the irreversible character of symbolized time series is not always equivalent to the one of the underlying real-valued signal, leading to some misconceptions and confusion on interpretability. Such confusion is even bigger for binary time series (a classical way to encode chaotic trajectories via symbolic dynamics). In this article we aim to clarify some usual misconceptions and provide theoretical grounding for the practical analysis -- and interpretation -- of time irreversibility in symbolic time series. We outline sources of irreversibility in stationary symbolic sequences coming from frequency asymmetries of non-palindromic pairs which we enumerate, and prove that binary time series cannot show any irreversibility based on words of length m < 4, thus discussing the implications and sources of confusion. We also study irreversibility in the context of symbolic dynamics, and clarify why these can be reversible even when the underlying dynamical system is not, such as the case of the fully chaotic logistic map.
Sharing Imaging Data in a Nutshell
Creators: name: Luby-Phelps, Kate
name: Dean, Kevin
Publisher: name: Zenodo
Year: 2023
Subjects: data sharing, image repositories, image file format, image metadata, licensing

description: A brief introduction to the basics of publicly sharing image data. An attempt to demystify the process for those who have never thought much about it before. Disclaimer: this document is not a statement of UT Southwestern policy.
description: This document was developed as a result of discussions with and advice from the following colleagues at UT Southwestern: Dr. Kevin Dean, Ph.D., Lyda Hill Department of Bioinformatics; Dr. Denise Ramirez, Ph.D., Director of the Whole Brain Imaging Facility; Dr. Marcel Mettlen, Ph.D., Director of the Quantitative Light Microscopy Facility; Dr. Reto Fiolka, Ph.D., Lyda Hill Department of Bioinformatics; Dr. Ralph Mason, Ph.D., Director of the Small Animal Imaging Resource; Dr. Elliott Ross, Ph.D., Associate Dean of Basic Research.
The Radial Distribution of H2 and CO in TW Hya as Revealed by Resolved ALMA Observations of CO Isotopologues
Creators: name: Schwarz, Kamber R.
name: Bergin, Edwin A.
name: Cleeves, L. Ilsedore
name: Blake, Geoffrey A.
name: Zhang, Ke
name: Öberg, Karin I.
name: van Dishoeck, Ewine F.
name: Qi, Chunhua
Publisher: name: arXiv
Year: 2016
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: CO is widely used as a tracer of molecular gas. However, there is now mounting evidence that gas phase carbon is depleted in the disk around TW Hya. Previous efforts to quantify this depletion have been hampered by uncertainties regarding the radial thermal structure in the disk. Here we present resolved ALMA observations of 13CO 3-2, C18O 3-2, 13CO 6-5, and C18O 6-5 emission in TW Hya, which allow us to derive radial gas temperature and gas surface density profiles, as well as map the CO abundance as a function of radius. These observations provide a measurement of the surface CO snowline at ~30 AU and show evidence for an outer ring of CO emission centered at 53 AU, a feature previously seen only in less abundant species. Further, the derived CO gas temperature profile constrains the freeze-out temperature of CO in the warm molecular layer to < 21 K. Combined with the previous detection of HD 1-0, these data constrain the surface density of the warm H2 gas in the inner ~30 AU. We find that CO is depleted by two orders of magnitude from R=10-60 AU, with the small amount of CO returning to the gas phase inside the surface CO snowline insufficient to explain the overall depletion. Finally, this new data is used in conjunction with previous modeling of the TW Hya disk to constrain the midplane CO snowline to 17-23 AU.
description: 8 pages, 4 figures, accepted for publication in ApJ
Gravitational waves in $α-$attractors
Creators: name: Kumar, K. Sravan
name: Marto, João
name: Moniz, Paulo Vargas
name: Das, Suratna
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study inflation in the $α-$attractor model under a non-slow-roll dynamics with an ansatz proposed by Gong \& Sasaki \cite{Gong:2015ypa} of assuming $N=N\left(ϕ\right)$. Under this approach, we construct a class of local shapes of inflaton potential that are different from the T-models. We find this type of inflationary scenario predicts an attractor at $n_{s}\sim0.967$ and $r\sim0.00055$. In our approach, the non-slow-roll inflaton dynamics are related to the $α-$parameter which is the curvature of Kähler geometry in the SUGRA embedding of this model.
description: 6 pages, 2 figures. Contribution to the proceedings of "The Fourtheenth Marcel Grossmann Meeting on General Relativity", University of Rome "La Sapienza", Rome, July 12-18, 2015, based on a talk delivered at the ST4 parallel session
Depolarization shift of the superradiant phase transition
Creators: name: Grießer, Tobias
name: Vukics, András
name: Domokos, Peter
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: We investigate the possibility of a Dicke-type superradiant phase transition of an atomic gas with an extended model which takes into account the short-range depolarizing interactions between atoms approaching each other as close as the atomic size scale, which interaction appears in a regularized electric-dipole picture of the QED of atoms. By using a mean field model, we find that a critical density does indeed exist, though the atom-atom contact interaction shifts it to a higher value than it can be obtained from the bare Dicke-model. We argue that the system, at the critical density, transitions to the condensed rather than the "superradiant" phase.
description: 7 pages, 1 figure
Introducing CERT Kaiju: Malware Analysis Tools for Ghidra
Creators: name: Wassermann, Garret
name: Gennari, Jeffrey
Publisher: name: Carnegie Mellon University
Year: 2023
Subjects: subject: 80303 Computer System Security
subject: FOS: Computer and information sciences

description: Since the National Security Agency publicly released the software reverse engineering (SRE) tool suite, we have been working to integrate Ghidra into our Pharos malware analysis tool. Ghidra provides many useful reverse engineering services including disassembly, function partitioning, decompilation, and various other types of program analyses. As this post details, we have been developing a new suite of tools, known as Kaiju, for malware analysis and reverse engineering to take advantage of Ghidra’s capabilities and interface. Ghidra provides a compelling environment for reverse engineering tools that are relatively easy to use during malware analysis. The tools included with Kaiju give malware analysts many advantages as they are faced with increasingly diverse and complex malware threats.
Reconstructing the shock history in the CMZ of NGC 253 with ALCHEMI
Creators: name: Huang, K. -Y.
name: Viti, S.
name: Holdship, J.
name: Mangum, J. G.
name: Martín, S.
name: Harada, N.
name: Muller, S.
name: Sakamoto, K.
name: Tanaka, K.
name: Yoshimura, Y.
name: Herrero-Illana, R.
name: Meier, D. S.
name: Behrens, E.
name: van der Werf, P. P.
name: Henkel, C.
name: García-Burillo, S.
name: Rivilla, V. M.
name: Emig, K. L.
name: Colzi, L.
name: Humire, P. K.
name: Aladro, R.
name: Bouvier, M.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: HNCO and SiO are well known shock tracers and have been observed in nearby galaxies, including the nearby (D=3.5 Mpc) starburst galaxy NGC 253. The simultaneous detection of these two species in regions where the star formation rate is high may be used to study the shock history of the gas. We perform a multi-line molecular study using these two shock tracers (SiO and HNCO) with the aim of characterizing the gas properties. We also explore the possibility of reconstructing the shock history in NGC 253's Central Molecular Zone (CMZ). Six SiO transitions and eleven HNCO transitions were imaged at high resolution $1''.6$ (28 pc) with the Atacama Large Millimeter/submillimeter Array (ALMA) as part of the ALCHEMI Large Programme. Both non-LTE radiative transfer analysis and chemical modelling were performed in order to characterize the gas properties, and to investigate the chemical origin of the emission. The non-LTE radiative transfer analysis coupled with Bayesian inference shows clear evidence that the gas traced by SiO has different densities and temperatures than that traced by HNCO, with an indication that shocks are needed to produce both species. Chemical modelling further confirms such a scenario and suggests that fast and slow shocks are responsible for SiO and HNCO production, respectively, in most GMCs. We are also able to infer the physical characteristics of the shocks traced by SiO and HNCO for each GMC. Radiative transfer and chemical analysis of the SiO and HNCO in the CMZ of NGC 253 reveal a complex picture whereby most of the GMCs are subjected to shocks. We speculate on the possible shock scenarios responsible for the observed emission and provide potential history and timescales for each shock scenario. Higher spatial resolution observations of these two species are required in order to quantitatively differentiate between scenarios.
Accurate simulation of direct laser acceleration in a laser wakefield accelerator
Creators: name: Miller, Kyle G.
name: Palastro, John P.
name: Shaw, Jessica L.
name: Li, Fei
name: Tsung, Frank S.
name: Decyk, Viktor K.
name: Mori, Warren B.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: In a laser wakefield accelerator (LWFA), an intense laser pulse excites a plasma wave that traps and accelerates electrons to relativistic energies. When the pulse overlaps the accelerated electrons, it can enhance the energy gain through direct laser acceleration (DLA) by resonantly driving the betatron oscillations of the electrons in the plasma wave. The particle-in-cell (PIC) algorithm, although often the tool of choice to study DLA, contains inherent errors due to numerical dispersion and the time staggering of the electric and magnetic fields. Further, conventional PIC implementations cannot reliably disentangle the fields of the plasma wave and laser pulse, which obscures interpretation of the dominant acceleration mechanism. Here, a customized field solver that reduces errors from both numerical dispersion and time staggering is used in conjunction with a field decomposition into azimuthal modes to perform PIC simulations of DLA in an LWFA. Comparisons with traditional PIC methods, model equations, and experimental data show improved accuracy with the customized solver and convergence with an order-of-magnitude fewer cells. The azimuthal-mode decomposition reveals that the most energetic electrons receive comparable energy from DLA and LWFA.
description: 10 pages, 5 figures, to submit to Physics of Plasmas
Extragalactic magnetism with SOFIA (SALSA Legacy Program) -- V: First results on the magnetic field orientation of galaxies
Creators: name: Borlaff, Alejandro S.
name: Lopez-Rodriguez, Enrique
name: Beck, Rainer
name: Clark, Susan E.
name: Ntormousi, Evangelia
name: Tassis, Konstantinos
name: Martin-Alvarez, Sergio
name: Tahani, Mehrnoosh
name: Dale, Daniel A.
name: Castro, Ignacio del Moral
name: Roman-Duval, Julia
name: Marcum, Pamela M.
name: Beckman, John E.
name: Subramanian, Kandaswamy
name: Eftekharzadeh, Sarah
name: Proudfit, Leslie
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We present the analysis of the magnetic field ($B$-field) structure of galaxies measured with far-infrared (FIR) and radio (3 and 6 cm) polarimetric observations. We use the first data release of the Survey on extragALactic magnetiSm with SOFIA (SALSA) of 14 nearby ($<20$ Mpc) galaxies with resolved (5 arcsec-18 arcsec; $90$ pc--$1$ kpc) imaging polarimetric observations using HAWC+/SOFIA from $53$ to $214$ \um. We compute the magnetic pitch angle ($Ψ_{B}$) profiles as a function of the galactrocentric radius. We introduce a new magnetic alignment parameter ($ζ$) to estimate the disordered-to-ordered $B$-field ratio in spiral $B$-fields. We find FIR and radio wavelengths to not generally trace the same $B$-field morphology in galaxies. The $Ψ_{B}$ profiles tend to be more ordered with galactocentric radius in radio ($ζ_{\rm{6cm}} = 0.93\pm0.03$) than in FIR ($ζ_{\rm{154μm}} = 0.84\pm0.14$). For spiral galaxies, FIR $B$-fields are $2-75$\% more turbulent than the radio $B$-fields. For starburst galaxies, we find that FIR polarization is a better tracer of the $B$-fields along the galactic outflows than radio polarization. Our results suggest that the $B$-fields associated with dense, dusty, turbulent star-forming regions, those traced at FIR, are less ordered than warmer, less-dense regions, those traced at radio, of the interstellar medium. The FIR $B$-fields seem to be more sensitive to the activity of the star-forming regions and the morphology of the molecular clouds within a vertical height of few hundred pc in the disk of spiral galaxies than the radio $B$-fields.
description: 28 pages, 14 figures. Accepted for publication in The Astrophysical Journal
Implications of evaporative cooling by H$_2$ for 1I/`Oumuamua
Creators: name: Hoang, Thiem
name: Loeb, Abraham
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The first interstellar object observed in our solar system, 1I/`Oumuamua, exhibited several peculiar properties, including extreme elongation and non-gravitational acceleration. Bergner and Seligman (hereafter BS23) proposed that evaporation of trapped H$_2$ created by cosmic rays (CRs) can explain the non-gravitational acceleration. However, their modeling of the thermal structure of 1I/`Oumuamua ignored the crucial cooling effect of evaporating H$_2$. By taking into account the cooling by H$_2$ evaporation, we show that the surface temperature of H$_2$-water ice is a factor of 9 lower than the case without evaporative cooling. As a result, the thermal speed of outgassing H$_2$ is decreased by a factor of 3. Our one-dimensional thermal modeling that takes into account evaporative cooling for two chosen values of thermal conductivity of $κ=0.01$ and $0.1$ WK$^{-1}$m$^{-1}$ shows that the water ice volume available for H$_2$ sublimation at $T>30$ K would be reduced by a factor of 9 and 5 compared to the results of BS23, not enabling enough hydrogen to propel 1I/`Oumuamua.
description: 6 pages, 2 figure; Accepted for publication, Astrophysical Journal Letters
Introducing CERT Kaiju: Malware Analysis Tools for Ghidra
Creators: name: Wassermann, Garret
name: Gennari, Jeffrey
Publisher: name: Carnegie Mellon University
Year: 2021
Subjects: subject: 80303 Computer System Security
subject: FOS: Computer and information sciences

description: Since the National Security Agency publicly released the software reverse engineering (SRE) tool suite, we have been working to integrate Ghidra into our Pharos malware analysis tool. Ghidra provides many useful reverse engineering services including disassembly, function partitioning, decompilation, and various other types of program analyses. As this post details, we have been developing a new suite of tools, known as Kaiju, for malware analysis and reverse engineering to take advantage of Ghidra’s capabilities and interface. Ghidra provides a compelling environment for reverse engineering tools that are relatively easy to use during malware analysis. The tools included with Kaiju give malware analysts many advantages as they are faced with increasingly diverse and complex malware threats.