cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
EuCo2P2: A Model Molecular-Field Helical Heisenberg Antiferromagnet
Creators: name: Sangeetha, N. S.
name: Cuervo-Reyes, Eduardo
name: Pandey, Abhishek
name: Johnston, D. C.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The metallic compound EuCo2P2 with the body-centered tetragonal ThCr2Si2 structure containing Eu spins 7/2 was previously shown from single-crystal neutron diffraction measurements to exhibit a helical antiferromagnetic (AFM) structure below TN = 66.5 K with the helix axis along the c axis and with the ordered moments aligned within the ab-plane. Here we report crystallography, electrical resistivity, heat capacity, magnetization and magnetic susceptibility measurements on single crystals of this compound. We demonstrate that EuCo2P2 is a model molecular-field helical Heisenberg antiferromagnet from comparisons of the anisotropic magnetic susceptibility chi, high-field magnetization and magnetic heat capacity of EuCo2P2 single crystals at temperature T < TN with the predictions of our recent formulation of molecular field theory. Values of the Heisenberg exchange interactions between the Eu spins are derived from the data. The low-T magnetic heat capacity ~ T^3 arising from spin-wave excitations with no anisotropy gap is calculated and found to be comparable to the lattice heat capacity. The density of states at the Fermi energy of EuCo2P2 and the related compound BaCo2P2 are found from the heat capacity data to be large, 10 and 16 states/eV per formula unit for EuCo2P2 and BaCo2P2, respectively. These values are enhanced by a factor of ~2.5 above those found from DFT electronic structure calculations for the two compounds. The calculations also find ferromagnetic Eu-Eu exchange interactions within the ab-plane and AFM interactions between nearest- and next-nearest planes, in agreement with the MFT analysis of chi{ab}(T < TN).
description: 20 pages, 17 figures, 3 tables, 46 references. This is an extended replacement of arXiv:1512.02958 with an additional coauthor
Homalictus koghiensis Donovan & Pauly 2015, sp. nov.
Creators: name: Pauly, Alain
name: Donovan, Barry
name: Munzinger, Jérôme
Publisher: name: Zenodo
Year: 2015
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Halictidae
Homalictus
Homalictus koghiensis

description: Homalictus koghiensis Donovan & Pauly sp. nov.
(Fig. 9)
Description. Mâle. Longueur 7 mm. Corps complètement vert bronzé métallique, pattes complètement noires. Tête (Fig. 9a). L/l = 0,92. Front avec de fines rides anastomosées. Aires paraoculaires finement tessellées, presque pas ridées. Vertex avec de très fines rides parallèles. Antennes avec les articles 4 et suivants aussi longs que larges. Yeux assez épais. Mesosoma. Scutum complètement tessellé avec une ponctuation dense, les espaces entre les points égaux au diamètre des points (Fig. 9b). Scutellum avec la même texture que le scutum. Propodeum non caréné aux angles.
Aire propodéale en forme de croissant légèrement rebordé sur son bord postérieur, les plis de l'aire très anastomosés et non alignés en rides parallèles (Fig. 9c). Les flancs du propodeum avec des rides et des rugosités anastomosées comme sur l'aire propodéale. Pleures finement rugueuses, sans stries sauf plus ou moins sur la partie ventrale. Metasoma. Couleur. Tergites complètement striés avec une ponctuation fine et indistincte sur la base des tergites 2 et suivants (Fig. 9d). Marge apicale des tergites 1 et suivants bien marquée. Base du tergite 2 légèrement déprimée et striée. Aire pygidiale brun noir, en forme de large trapèze (Fig. 9e). Sternites avec des soies de longueur moyenne et sans oragnisation particulière.
Etymologie. Des Monts Koghis où le holotype a été récolté.
Holotype ♂. Nouvelle-Calédonie, Mts des Koghis, 400-600m, I.1969, leg. N.L.H. Krauss (BBMH).
Paratypes. 2♂, idem holotype.
description: Published as part of Pauly, Alain, Donovan, Barry & Munzinger, Jérôme, 2015, Les abeilles du genre Homalictus Cockerell, 1919 en Nouvelle-Calédonie (Hymenoptera: Apoidea: Halictidae), pp. 1-30 in Belgian Journal of Entomology 34 on pages 16-17, DOI: 10.5281/zenodo.13599345
High-precision broad-band linear polarimetry of early-type binaries I. Discovery of variable, phase-locked polarization in HD 48099
Creators: name: Berdyugin, A.
name: Piirola, V.
name: Sadegi, S.
name: Tsygankov, S.
name: Sakanoi, T.
name: Kagitani, M.
name: Yoneda, M.
name: Okano, S.
name: Poutanen, J.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences
subject: 85-08 (Primary)

description: We investigate the structure of the O-type binary system HD 48099 by measuring linear polarization that arises due to light scattering process. Linear polarization measurements of HD 48099 in the B, V and R passbands with the high-precision Dipol-2 polarimeter have been carried out. The data have been obtained with the 60 cm KVA (Observatory Roque de los Muchachos, La Palma, Spain) and T60 (Haleakala, Hawaii, USA) remotely controlled telescopes during 31 observing nights. Polarimetry in the optical wavelengths has been complemented by observations in the X-rays with the SWIFT space observatory. Optical polarimetry revealed small intrinsic polarization in HD 48099 with 0.1% peak to peak variation over the orbital period of 3.08 days. The variability pattern is typical for binary systems, showing strong second harmonic of the orbital period. We apply our model code for the electron scattering in the circumstellar matter to put constraints on the system geometry. A good model fit is obtained for scattering of light on a cloud produced by the colliding stellar winds. The geometry of the cloud, with a broad distribution of scattering particles away from the orbital plane, helps in constraining the (low) orbital inclination. We derive from the polarization data the inclination i = 17 deg +/- 2deg and the longitude of the ascending node Omega = 82 deg +/- 1 deg of the binary orbit. The available X-ray data provide additional evidence for the existence of the colliding stellar winds in the system. Another possible source of the polarized light could be scattering from the stellar photospheres. The models with circumstellar envelopes, or matter confined to the orbital plane, do not provide good constraints on the low inclination, better than i < 27 deg, as is already suggested by the absence of eclipses.
description: 10 pages, 9 figures to be published in Astronomy & Astrophysics
Synthesis and characterization of a novel Mannich base benzimidazole derivative to explore interaction with human serum albumin and antimicrobial property: experimental and theoretical approach
Creators: name: Ahamed, F. M. Mashood
name: Shakya, Barkha
name: Shakya, Sonam
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Physical Sciences not elsewhere classified
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified

description: The novel Mannich base benzimidazole derivative (CB-1), 1-((1H-benzo[d]imidazol-1-yl)(3-chlorophenyl)methyl)-3-phenylurea) has been designed and synthesized by reacting benzimidazole, 3-chloro benzaldehyde, and N-Phenyl urea. CB-1 has been characterized by UV- Visible, FTIR, and 1H NMR. CB-1 was explored to study the interaction with the most abundant blood protein which involved in the role of transport of molecules (drugs), human serum albumin (HSA). Fluorescence results are evident for the presence of both dynamic and static quenching mechanisms in the binding of CB-1 to HSA. Antimicrobial screening were carried out against three bacteria and three fungi pathogens employing disc diffusion method. Molecular docking using AutoDock Vina tool further confirms the experimental binding interactions obtained from fluorescence. Density functional theory (DFT) with B3LYP/6-311G++ basis set was used for correlating theoretical data and obtaining optimized structures of CB-1 along with reactants with molecular electrostatic potential (MEP) map and HOMO→LUMO energy gap calculation. HIGHLIGHTSThe novel Mannich base benzimidazole derivative (CB-1) has been designed and synthesized by Mannich reaction.CB-1 has been characterized by UV- Visible, FTIR, and 1H NMR.Fluorescence quenching reveals that HSA binds to CB-1 via aromatic residues, which is corroborated by molecular docking.Antifungal and antibacterial activity was evaluated in comparison to Nystatin and Gentamicin standard drugs, respectively.DFT calculations support experimental data and provide HOMO-LUMO energy gap. The novel Mannich base benzimidazole derivative (CB-1) has been designed and synthesized by Mannich reaction. CB-1 has been characterized by UV- Visible, FTIR, and 1H NMR. Fluorescence quenching reveals that HSA binds to CB-1 via aromatic residues, which is corroborated by molecular docking. Antifungal and antibacterial activity was evaluated in comparison to Nystatin and Gentamicin standard drugs, respectively. DFT calculations support experimental data and provide HOMO-LUMO energy gap. Communicated by Ramaswamy H. Sarma
Petroleum Refinery Multi-Antenna Propagation Measurements
Creators: name: Gaafar, Mohamed
name: Messier, Geoffrey G
Publisher: name: arXiv
Year: 2016
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: This paper presents the results of the first multi- antenna propagation measurement campaign to be conducted at an operating petroleum refining facility. The measurement equipment transmits pseudo-random noise test signals from two antennas at a 2.47 GHz carrier with a signal bandwidth of approximately 25 MHz. The measurement data is analyzed to extract path loss exponent, shadowing distribution, fading distribution, coherence bandwidth and antenna correlation. The results reveal an environment where large scale attenuation is relatively mild, fading is severe and good performance is expected from both antenna and frequency diversity.
Supplementary table 1
Creators: name: Kumagai, Hiroshi
Publisher: name: figshare
Year: 2021
Subjects: subject: 110602 Exercise Physiology
subject: FOS: Health sciences

description: Supplementary table for Kumagai et al. (J Appl Physiol. in revision). This table shows serum CK activity and coal time in female subjects by each genetic polymorphism.
Multi-critical absorbing phase transition in a class of exactly solvable models
Creators: name: Chatterjee, Arijit
name: Mohanty, P. K.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study diffusion of hardcore particles on a one dimensional periodic lattice subjected to a constraint that the separation between any two consecutive particles does not increase beyond a fixed value $(n+1);$ initial separation larger than $(n+1)$ can however decrease. These models undergo an absorbing state phase transition when the conserved particle density of the system falls bellow a critical threshold $ρ_c= 1/(n+1).$ We find that $ϕ_k$s, the density of $0$-clusters ($0$ representing vacancies) of size $0\le k
description: 6 pages, 6 eps figures, epl2.cls style
5-State Rotation-Symmetric Number-Conserving Cellular Automata are not Strongly Universal
Creators: name: Imai, Katsunobu
name: Ishizaka, Hisamichi
name: Poupet, Victor
Publisher: name: arXiv
Year: 2016
Subjects: subject: Formal Languages and Automata Theory (cs.FL)
subject: Cellular Automata and Lattice Gases (nlin.CG)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences
subject: F.1.1

description: We study two-dimensional rotation-symmetric number-conserving cellular automata working on the von Neumann neighborhood (RNCA). It is known that such automata with 4 states or less are trivial, so we investigate the possible rules with 5 states. We give a full characterization of these automata and show that they cannot be strongly Turing universal. However, we give example of constructions that allow to embed some boolean circuit elements in a 5-states RNCA.
Comparative homology of Pleurotus ostreatus laccase enzyme: Swiss model or Modeller?
Creators: name: Silva, Marco Antonio
name: do Nascimento Júnior, José Cordeiro
name: Thomaz, Douglas Vieira
name: Maia, Rafael Trindade
name: Amador, Vinícius Costa
name: Tommaso, Giovana
name: Coelho, Glauciane Danusa
Publisher: name: Taylor & Francis
Year: 2022
Subjects: Biophysics
Biochemistry
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer

description: Laccases stand out in the industrial context due to their versatile biotechnological applications. Although these enzymes are frequently investigated, currently, Pleurotus ostreatus laccase structural model is unknown. Therefore, this research aims to predict and validate a P. ostreatus laccase theoretical model by means of comparative homology. The laccase target’s primary structure (AOM73725.1) was obtained from the NCBI database, the model was predicted from homologous structures obtained from the PDB (PDB-ID: 5A7E, 2HRG, 4JHU, 1GYC) using the Swiss-Model and Modeller, and was refined in GalaxyRefine. The models were validated using PROCHECK, VERIFY 3D, ERRAT, PROVE and QMEAN Z-score servers. Moreover, molecular docking between the laccase model (Lacc4MN) and ABTS was performed on AutoDock Vina. The models that were generated by the Modeller showed superior stereochemical and structural characteristics to those predicted by the Swiss Model. The refinement made it difficult to stabilize the copper atoms which are typical of laccases. The Lacc4MN model showed the interactions between the amino acids in the active site of the laccase and the copper atoms, thereby hinting the stabilization of the metal through electrostatic interactions with histidine and cysteine. The molecular docking between Lacc4MN and ABTS showed negative free energy and the formation of two hydrogen bonds involving the amino acids ASP 208 and GLY 268, and a Pi–sulfur bond between residue HIS 458 and ABTS, which demonstrates the typical catalytic functionality of laccases. Furthermore, the theoretical model Lacc4MN presented stereochemical and structural characteristics that allow its use in silico tests. Communicated by Ramaswamy H. Sarma
On an equality for the iterated weighted spherical mean and its applications
Creators: name: Shishkina, E. L.
name: Sitnik, S. M.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: 35C15

description: Spherical means are well-known useful tool in the theory of partial differential equations with applications to solving hyperbolic and ultrahyperbolic equations and problems of integral geometry, tomography and Radon transforms. We generalize iterated spherical means to weighted ones based on generalized translation operators and consider applications to B-hyperbolic equations and transmission tomography problems.
description: 12 pages. In Russian, abstracts in English
The UK Infrared Telescope M33 monitoring project. V. The star formation history across the galactic disc
Creators: name: Javadi, Atefeh
name: van Loon, Jacco Th.
name: Khosroshahi, Habib
name: Tabatabaei, Fatemeh
name: Golshan, Roya Hamedani
name: Rashidi, Maryam
Publisher: name: arXiv
Year: 2016
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We have conducted a near-infrared monitoring campaign at the UK InfraRed Telescope (UKIRT), of the Local Group spiral galaxy M33 (Triangulum). On the basis of their variability, we have identified stars in the very final stage of their evolution, and for which the luminosity is more directly related to the birth mass than the more numerous less-evolved giant stars that continue to increase in luminosity. In this fifth paper of the series, we construct the birth mass function and hence derive the star formation history across the galactic disc of M33. The star formation rate has varied between $\sim0.010\pm0.001$ ($\sim0.012\pm0.007$) and 0.060$\pm0.005$ (0.052$\pm0.009$)M$_\odot$ yr$^{-1}$ kpc$^{-2}$ statistically (systematically) in the central square kiloparsec of M33, comparable with the values derived previously with another camera. The total star formation rate in M33 within a galactocentric radius of 14 kpc has varied between $\sim0.110\pm0.005$ ($\sim0.174\pm0.060$) and $\sim0.560\pm0.028$ ($\sim0.503\pm0.100$) M$_\odot$ yr$^{-1}$ statistically (systematically). We find evidence of two epochs during which the star formation rate was enhanced by a factor of a few -- one that started $\sim6$ Gyr ago and lasted $\sim3$ Gyr and produced $\geq71$% of the total mass in stars, and one $\sim250$ Myr ago that lasted $\sim200$ Myr and formed $\leq13$% of the mass in stars. Radial star formation history profiles suggest that the inner disc of M33 was formed in an inside-out formation scenario. The outskirts of the disc are dominated by the old population, which may be the result of dynamical effects over many Gyr. We find correspondence to spiral structure for all stars, but enhanced only for stars younger than $\sim100$ Myr; this suggests that the spiral arms are transient features and not part of a global density wave potential.
description: Accepted for publication in MNRAS
Synthesis, crystallographic, DNA binding, and molecular docking/dynamic studies of a privileged chalcone-sulfonamide hybrid scaffold as a promising anticancer agent
Creators: name: Shaldam, Moataz
name: Tawfik, Haytham
name: Elmansi, Heba
name: Belal, Fathalla
name: Yamaguchi, Koki
name: Sugiura, Masaharu
name: Magdy, Galal
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Space Science
Physical Sciences not elsewhere classified
Molecular Biology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Cancer
Computational Biology

description: In the present study, a drug-like molecular hybrid structure between chalcone and sulfonamide moieties was synthesized and characterized. The structural peculiarities of the synthesized hybrid were further verified by means of single crystal X-ray crystallography. Furthermore, its biological activity as an anticancer agent was evaluated. The synthesized model of chalcone-sulfonamide hybrid 3 was found to have potent anticancer properties against the studied cancer cell lines. Hence, the in vitro binding interaction of hybrid 3 with Calf thymus DNA (CT-DNA) was studied at a simulated physiological pH to confirm its anticancer activity for the first time. This was investigated by applying different spectroscopic techniques, ionic strength measurements, viscosity measurements, thermodynamics, molecular dynamic simulation and molecular docking studies. The obtained results showed a clear binding interaction between hybrid 3 and CT-DNA with a moderate affinity via a minor groove binding mechanism. The binding constant (Kb) at 298 K calculated from the Benesi-Hildebrand equation was found to be 3.49 × 104 M−1. The entropy and enthalpy changes (ΔS0 and ΔH0) were 204.65 J mol−1 K−1 and 35.08 KJ mol−1, respectively, indicating that hydrophobic interactions constituted the major binding forces. The results obtained from molecular docking and dynamic simulation studies confirmed the minor groove binding interaction and the stability of the formed complex. This study can contribute to further understanding of the molecular mechanism of hybrid 3 as a potential antitumor agent and can also guide future clinical and pharmacological studies for rational drug design with enhanced or more selective activity and greater efficacy. Communicated by Ramaswamy H. Sarma
Homalictus melanasiae Donovan & Pauly 2015, sp. nov.
Creators: name: Pauly, Alain
name: Donovan, Barry
name: Munzinger, Jérôme
Publisher: name: Zenodo
Year: 2015
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Halictidae
Homalictus
Homalictus melanasiae

description: Homalictus melanasiae Donovan & Pauly sp. nov.
(Fig. 11)
 Homalictus sp. 8 in DONOVAN et al., 2013.
Description. Femelle. Longueur 7,5 mm. Corps noir avec de faibles reflets bleuté métallique sur la tête et le mesosoma, pattes noires. Tête (Figs 11a,b). L/l = 0,85. Front et vertex avec de fortes rides parallèles. Aires paraoculaires le long du bord antérieur des yeux déprimées en sillon contrastant avec les stries. Aire supraclypéale et clypeus à texture finement tessellée. Mesosoma. Scutum mat tessellé à ponctuation éparse, avec quelques plis sur la partie antérieure (Fig. 11c). Scutellum tessellé à ponctuation éparse. Propodeum caréné aux angles (Fig. 11d). Pleures complètement sculptées de fortes rides parallèles. Metasoma (Figs 11e,f). Tergites mats finement striés, presque sans ponctuation.
Etymologie. Nommé en référence à la couleur presque noire de cette espèce.
 Holotype ♀. Nouvelle-Calédonie, Thy Valley, 200m, 5.V.1981, Polyscias [Tieghemopanax] sp., leg. G. McPherson (col. B. Donovan).
 Paratypes. Nouvelle-Calédonie. Haute Vallée de la Ni, 750m, 29.IV.2004, Alphitonia neocaledonica, 1♀, leg. J. Munzinger n°395i, 396i, 397i, 398i. – Piste Ni-Dzumacs, 7.V.2004, Myodocarpus sp. nov. (?) (Lowry 6509), 1♀, leg. J. Munzinger n°400i. – Mt Koghi, near Noumea, 500m, 8.X.1969, 4♀, leg. Y. Hirashima (BBMH). – Thi River Valley, 6.XI.1940, Ageratum sp., 1♀, leg. F.X. Williams (IRD). – Mt Koghi, 1.II.1961, 1♀, leg. N.L.H. Krauss (BBMH). – Mts Koghis, Auberge, 23.VII.2003, 1♀, leg. B. Donovan. – Mt Dzumac, 800m, 24.II.1980, Polyscias [Tieghemopanax cf. sessiliflorus], 1♀, leg. G. McPherson. – Thy Valley, 100m, 18.VI.1980, Litchi chinensis, 1♀, 3.VII.1980, Litchi chinensis, 1♀, leg. G. McPherson. – Thy Valley, 200m, 5.V.1981, Polyscias [Tieghemopanax] sp., 5♀, leg. G. McPherson. – Col de Mouirange, 10.X.1980, Guioa villosa, 1♀, leg. B. Donovan. – Houailou, about 20 km S, 30.VII.2003, on yellow-flowered shrub, 1♀, leg. B. Donovan.
description: Published as part of Pauly, Alain, Donovan, Barry & Munzinger, Jérôme, 2015, Les abeilles du genre Homalictus Cockerell, 1919 en Nouvelle-Calédonie (Hymenoptera: Apoidea: Halictidae), pp. 1-30 in Belgian Journal of Entomology 34 on pages 18-20, DOI: 10.5281/zenodo.13599345
3D QSAR pharmacophore based lead identification of G9a lysine methyltransferase towards epigenetic therapeutics
Creators: name: Jana, Abhisek
name: Naga, Rahul
name: Saha, Sougata
name: Banerjee, Deb Ranjan
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: The G9a, Lysine Methyltransferase that methylates the histone 3 lysine 9 (H3K9) of the nucleosome, is an excellent epigenetic target having no clinically passed inhibitor currently owing to adverse in vivo ADMET toxicities. In this work, we have carried out detailed computational investigations to find novel and safer lead against the target using advanced 3 D QSAR pharmacophore screening of databases containing more than 400000 entrees of natural compounds. The screening was conducted at different levels at increasing stringencies by employing pharmacophore mapping, druglikenesses and interaction profiles of the selected to identify potential hit compounds. The potential hits were further screened by advanced flexible docking, ADME and toxicity analysis to eight hit compounds. Based on the comparative analysis of the hits with the reference inhibitor, we identified one lead inhibitor against the G9a, having better binding efficacy and a safer ADMET profile than the reference inhibitor. Finally, the results were further verified using robust molecular dynamics simulation and MM-GBSA binding energy calculation. The natural compounds are generally considered benign due to their long human uses and this is the first attempt of in silico screening of a large natural compound library against G9a to our best knowledge. Therefore, the finding of this study may add value towards the development of epigenetic therapeutics against the G9a. Communicated by Ramaswamy H. Sarma
Coupled orbital and spin evolution of the CoRoT-7 two-planet system using a Maxwell viscoelastic rheology
Creators: name: Colucci, Adrián Rodríguez
name: Callegari, Nelson
name: Correia, Alexandre
Publisher: name: arXiv
Year: 2016
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We investigate the orbital and rotational evolution of the CoRoT-7 two-planet system, assuming that the innermost planet behaves like a Maxwell body. We numerically resolve the coupled differential equations governing the instantaneous deformation of the inner planet together with the orbital motion of the system. We show that, depending on the relaxation time for the deformation of the planet, the orbital evolution has two distinct behaviours: for relaxation times shorter than the orbital period, we reproduce the results from classic tidal theories, for which the eccentricity is always damped. However, for longer relaxation times, the eccentricity of the inner orbit is secularly excited and can grow to high values. This mechanism provides an explanation for the present high eccentricity observed for CoRoT-7 b, as well as for other close-in super-Earths in multiple planetary systems.
description: Accepted for publication in MNRAS
Unravelling hub genes as potential therapeutic targets in lung cancer using integrated transcriptomic meta-analysis and in silico approach
Creators: name: Mushtaq, Aiman
name: Singh, Prithvi
name: Tabassum, Gulnaz
name: Mohammad, Taj
name: Hassan, Md Imtaiyaz
name: Syed, Mansoor Ali
name: Dohare, Ravins
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Lung cancer (LC) is the leading cause of cancer-related deaths worldwide. Smoking has been identified as the main contributing cause of the disease’s development. The study aimed to identify the key genes in small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), the two major types of LC. Meta-analysis was performed with two datasets GSE74706 and GSE149507 obtained from Gene Expression Omnibus (GEO). Both the datasets comprised samples from cancerous and adjacent non-cancerous tissues. Initially, 633 differentially expressed genes (DEGs) were identified. To understand the underlying molecular mechanism of the identified genes, pathway enrichment, gene ontology (GO) and protein–protein interaction (PPI) analyses were done. A total of 9 hub genes were identified which were subjected to mutation study analysis in LC patients using cBioPortal. These 9 genes (i.e. AURKA, AURKB, KIF23, RACGAP1, KIF2C, KIF20A, CENPE, TPX2 and PRC1) have shown overexpression in LC patients and can be explored as potential candidates for prognostic biomarkers. TPX2 reported a maximum mutation of 4%. This was followed with high throughput screening and docking analysis to identify the potential drug candidates following competitive inhibition of the AURKA-TPX2 complex. Four compounds, CHEMBL431482, CHEMBL2263042, CHEMBL2385714, and CHEMBL1206617 were identified. The results signify that the selected 9 genes can be explored as biomarkers in disease prognosis and targeted therapy. Also, the identified 4 compounds can be further analyzed as promising therapeutic candidates. Communicated by Ramaswamy H. Sarma
Ubiquitous diffraction resonances in positronium formation from fullerenes
Creators: name: Hervieux, Paul-Antoine
name: Chakraborty, Anzumaan R.
name: Chakraborty, Himadri S.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Atomic and Molecular Clusters (physics.atm-clus)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Due to the dominant electron capture by positrons from the molecular wall and the spatial dephasing across the wall-width, a powerful diffraction effect universally underlies the positronium (Ps) formation from fullerenes. This results into trains of resonances in the Ps formation cross section as a function of the positron beam energy, producing uniform structures in recoil momenta in analogy with classical single-slit diffraction fringes in the configuration space. The prediction opens a hitherto unknown avenue of Ps spectroscopy with nanomaterials.
description: 6 pages, 3 figures, submitted
Phonon-Plasmon Interaction in Metal-Insulator-Metal Localized Surface Plasmon Systems
Creators: name: Mrabti, Abdelali
name: Lévêque, Gaëtan
name: Nicolas, Rana
name: Maurer, Thomas
name: Adam, Pierre-Michel
name: Akjouj, Abdellatif
name: Pennec, Yan
name: Djafari-Rouhani, Bahram
Publisher: name: arXiv
Year: 2016
Subjects: subject: Optics (physics.optics)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We investigate theoretically and numerically the coupling between elastic and localized surface plasmon modes in a system of gold nanocylinders separated from a thin gold film by a dielectric spacer of few nanometers thickness. That system supports plasmon modes confined in between the bottom of the nanocylinder and the top of the gold film, which arise from the formation of interference patterns by short-wavelength metal-insulator-metal propagating plasmon. First we present the plasmonic properties of the system though computer-simulated extinction spectra and field maps associated to the different optical modes. Next a simple analytical model is introduced, which allows to correctly reproduce the shape and wavelengths of the plasmon modes. This model is used to investigate the efficiency of the coupling between an elastic deformation and the plasmonic modes. In the last part of the paper, we present the full numerical simulations of the phononic properties of the system, and then compute the acousto-plasmonic coupling between the different plasmon modes and five acoustic modes of very different shape. The efficiency of the coupling is assessed first by evaluating the modulation of the resonance wavelength, which allows comparison with the analytical model, and finally in term of time-modulation of the transmission spectra on the full visible range, computed for realistic values of the deformation of the nanoparticle.
description: 12 pages, 9 figures
Orientational dynamics of colloidal ribbons self-assembled from microscopic magnetic ellipsoids
Creators: name: Martinez-Pedrero, Fernando
name: Cebers, Andrejs
name: Tierno, Pietro
Publisher: name: arXiv
Year: 2016
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We combine experiments and theory to investigate the orientational dynamics of dipolar ellipsoids, which self-assemble into elongated ribbon-like structures due to the presence in each particle of a permanent magnetic moment perpendicular to the long axis. Monodisperse hematite ellipsoids are synthesized via sol-gel technique, and arrange into ribbons in presence of static or time-dependent magnetic fields. We find that under an oscillating field, the ribbons reorient perpendicular to the field direction, in contrast with the behaviour observed under a static field. This observation is explained theoretically by treating a chain of interacting ellipsoids as a single particle with an orientational and demagnetizing field energy. The model allows describing the orientational behaviour of the chain and captures well its dynamics at different strengths of the actuating field. The understanding of the complex dynamics and assembly of anisotropic magnetic colloids is a necessary step towards controlling the structure formation which has direct applications in different fluid-based microscale technologies.
Identification of potential mutational hotspots in serratiopeptidase to address its poor pH tolerance issue
Creators: name: Dhiman, Ankita
name: Purohit, Rituraj
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified

description: Serratiopeptidase is the multifunctionality metalloendopeptidase extensively employed in biopharmaceutical and industrial biotechnology. Despite its poor pH tolerance, serratiopeptidase must withstand the highly acidic environment of the gastrointestinal tract to be used as a potent anti-inflammatory and analgesic medication. In earlier studies, post-translational deamination related mutations showed alteration in the net charge of protein’s surface. Therefore, the current study aimed to enhance the acid resistance of serratiopeptidase via implementing computational interventions to screen out the most stable mutational hotspot. The methodology used in this study is as follows: (a) Higher accessibility to surface (b) 4 Å away from active site region to avoid interference with its proteolytic activity, and (c) By converting non-conserved amide residues to acidic residues. A docking study has been conducted to establish the substrate specificity and binding affinity to native and mutant proteins. The docking outcomes were then validated using molecular dynamic simulations to clarify each mutant’s molecular stability and conformation while preserving their activity. The results showed that N412D is the best-screened mutant with negative electrostatic potential that can alter the overall charge on the protein’s surface with increased H+ ions. Alteration in overall charge leads to protein surface more acidic that causes a common ion effect in stomach pH and act as a buffer which could stabilize the serratiopeptidase amid extreme pH. Communicated by Ramaswamy H. Sarma
A Linear Acceleration Theorem for 2D Cellular Automata on all Complete Neighborhoods
Creators: name: Grandjean, Anaël
name: Poupet, Victor
Publisher: name: arXiv
Year: 2016
Subjects: subject: Formal Languages and Automata Theory (cs.FL)
subject: Cellular Automata and Lattice Gases (nlin.CG)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences
subject: F.1.1

description: Linear acceleration theorems are known for most computational models. Although such results have been proved for two-dimensional cellular automata working on specific neighborhoods, no general construction was known. We present here a technique of linear acceleration for all two-dimensional languages recognized by cellular automata working on complete neighborhoods.
Structure and dynamic simulation-based interactions of benzenoids, pyrroles and organooxygen compounds for effective targeting of GPX4 in ischemic stroke
Creators: name: Sangwan, Namrata
name: Singh, Jitender
name: Chauhan, Arushi
name: Prakash, Ajay
name: Khanduja, Krishan L.
name: Medhi, Bikash
name: Avti, Pramod K
Publisher: name: Taylor & Francis
Year: 2022
Subjects: Biophysics
Biochemistry
Neuroscience
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Hematology
Computational Biology

description: The discovery of a novel drug for ischemic stroke is plagued by expensive and unsuccessful outcomes. FDA-approved drugs could be a viable repurposing strategy for stroke therapy. Emerging evidence suggests the regulating role of Glutathione peroxidase (GPX4) in stroke and attracts as a potential target. To overcome limited therapeutic interventions, a drug repurposing in silico investigation of FDA-approved drugs is proposed for the GPX4 receptor in distinctive species (Homo sapiens and Mus musculus). The GPX4 UniProt wild type ids, that is, P36969 (Homo sapiens), P36970 (Rattus norvegicus) and O70325 (Mus musculus) are Swiss modelled, and resultant templates are 2OBI and 6HN3 for Homo sapiens, and 5L71 for Mus musculus with a sequence identity of ∼88%. Enrichment analysis reveals high sensitivity and ranked actives with ROC and AUC values of 0.59 and 0.61, respectively. Virtual screening at extra precision resulted hit Acarbosum, is similar between 2OBI and 6HN3, demonstrating a multiple-target specificity and Iopromide, targeting 2OBI. MD simulation at 100 ns following trajectory analysis provides RMSD (∼1.2–1.8Å), RMSF (∼1.6–2.7Å), Rgyr (∼15–15.6Å) depicting stabilisation of receptor–ligand complexes. Furthermore, average B-factor value of 2OBI, 6HN3 and 5L71 is 25Å, 24Å and 60Å with a defined resolution of 1.55Å, 1.01Å and 1.80Å, respectively, depicting the thermodynamic stability of the protein structures. The dynamic cross-correlation and principal component analysis of residual fluctuations reveal more positive correlation, high atomic displacements and greater residual clustering of residues from atomic coordinates. Therefore, Acarbosum, an FDA-approved drug, could act as a potential repurposing drug with a multi-target approach translating from preclinical to clinical stages. Communicated by Ramaswamy H. Sarma
On Slow-roll Glueball Inflation from Holography
Creators: name: Anguelova, Lilia
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We investigate glueball inflation model-building via the methods of the gauge/gravity duality. For that purpose, we consider a certain 5d consistent truncation of type IIB supergravity. This theory admits a solution, whose metric is of the form of a $dS_4$ fibration over a fifth dimension. We find a new time-dependent deformation around this solution, which allows for a small $η$ parameter of the corresponding inflationary model. This resolves a problem with a previous solution that allowed only $η$ of order one and thus gave only an ultra-slow roll regime, but not regular slow roll.
description: 9 pages, contribution to the proceedings of the 3rd Bulgarian National Congress on Physical Sciences, Sofia, 2016
Size-dependence of nanosecond-scale spin-torque switching in perpendicularly magnetized tunnel junctions
Creators: name: Devolder, T.
name: Goff, A. Le
name: Nikitin, V.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We time-resolve the spin-transfer-torque-induced switching in perpendicularly magnetized tunnel junctions of diameters from 50 to 250 nm in the thermally activated regime. When the field and the spin-torque concur to favor the P to AP transition, the reversal yields monotonic resistance ramps that can be interpreted as a domain wall propagation through the device at velocities of 17 to 30 nm/ns; smaller cells switch hence faster. When the field hinders the P to AP transition, the switching is preceded by repetitive switching attempts, during which the resistance transiently increases until successful reversal occurs. At 50 nm, the P to AP switching proceeds reproducibly in 3 ns, with a monotonic increase of the device resistance. In the reverse transition (AP to P), several reversal paths are possible even in the smallest junctions. Besides, the non uniform nature of the response seems still present at nanoscale, with sometimes electrical signatures of strong disorder during the reversal. The AP to P transition is preceded by a strong instability of the AP state in devices above 100 nm. The resistance becomes extremely agitated before switching to P in a path yielding a slow (20-50 ns) irregular increase of the conductance with variability. Unreversed bubbles of 60 nm can persist a few microseconds in the largest junctions. The complexity of the AP to P switching is reduced but not suppressed when the junctions are downsized below 60 nm. The instability of the initial AP state is no longer detected but the other features remain. In the smallest junctions (50 nm) we occasionally observe much faster (sub-1 ns) switching events. We discuss the origin of the switching asymmetry and its size dependence, with an emphasis on the role of the non uniformities of the stray field emanating from the reference layers, which affects the zones in which nucleation is favored.
Interaction of heavy metals in Drosophila melanogaster larvae: Fourier transform infrared spectroscopy and single-cell electrophoresis study
Creators: name: Saroha, B.
name: Kumar, A.
name: Bhan, V.
name: Singh, S.
name: Tumba, K.
name: Singh, P.
name: Bahadur, I.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Cell Biology
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Computational Biology

description: The present study evaluates the Murraya Koenigii (CuLE) and Tinospora Crispa (TiSE) antimutagenic effect and the impact of industrial soil and solid waste leachate on Drosophila larvae. Larvae were exposed to leachate prepared at different pH (7, 4.93, 2.88) and treated with TiSE and CuLE at different concentration (4 g/L and 6 g/L) mixed with standard Drosophila medium. Emphasis was given to the binding interaction of heavy metals with proteins in Drosophila. The change in structure and molecular composition in Drosophila by leachate containing heavy metals induced toxicity has been studied by using Fourier transform infrared (FTIR) spectroscopy. Results from the study demonstrated that CuLE/TiSE administration restored the level of oxidative stress as evidenced by an enhanced antioxidant system and a decrease in lipid peroxidation and protein oxidation. The amide I and amide II bands spectral shifting revealed the binding interaction. The shift in the peak of PO2− asymmetric stretching might be due to compositional changes in nucleic acids. Single-cell electrophoresis was performed to detect the DNA damage which also proved to be ameliorated by administration of CuLE/TiSE. The result concludes that CuLE/TiSE may have great potential in the protection of Drosophila larvae from leachate induced oxidative stress through antioxidant and antimutagenic mechanisms this might help to cope with environmental toxicants. Communicated by Ramaswamy H. Sarma
Magnetic Exchange Interaction in the Spin Polarized Electron Gas
Creators: name: Valizadeh, Mohammad M.
name: Satpathy, Sashi
Publisher: name: arXiv
Year: 2016
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The exchange interaction between two magnetic moments embedded in a host metal is fundamental to the description of the magnetic behavior of solids. In the standard spin-degenerate electron gas, it leads to the well known Ruderman-Kittel-Kasuya-Yoshida (RKKY) interaction, which is of the Heisenberg form $J\vec S_1\cdot \vec S_2$, where the interaction strength $J$ oscillates and falls off with the distance between the moments in a characteristic way. Here, we study the more general case of the spin-polarized electron gas both in two and three dimensions, by evaluating the interaction strength as an integration over the product of the host Green's functions. We find that in addition to the Heisenberg term, an additional Ising-like term appears in the magnetic interaction, so that the net interaction for the spin-polarized gas is of the form $J_1 \vec S_1\cdot \vec S_2 + J_2 S_{1z} S_{2z}$. The interactions show a beating pattern as a function of distance, caused by the two different Fermi momenta for the two spins.
Real-time calibration and alignment of the LHCb RICH detectors
Creators: name: He, Jibo
Publisher: name: arXiv
Year: 2016
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: In 2015, the LHCb experiment established a new and unique software trigger strategy with the purpose of increasing the purity of the signal events by applying the same algorithms online and offline. To achieve this, real-time calibration and alignment of all LHCb sub-systems is needed to provide vertexing, tracking, and particle identification of the best possible quality. The calibration of the refractive index of the RICH radiators, the calibration of the Hybrid Photon Detector image, and the alignment of the RICH mirror system, are reported in this contribution. The stability of the RICH performance and the particle identification performance are also discussed.
description: Proceeding of RICH 2016
Virtually selected phytochemicals from edible seeds as possible potential medicaments for hypercholesterolemia: an in silico approach
Creators: name: Singh, Shubhi
name: Gaur, Smriti
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: Hypercholesterolemia is one of the major health concerns in today’s time. Bioactive compounds from various sources have been implicated in managing the conditions of Hypercholesterolemia. With advancements in research, several edible seeds have been explored in managing the disease. This study employs in silico approach to gain insights into the binding interactions of the bioactive compounds which are reportedly present in Edible seeds, against the protein HMG-CoA reductase, which plays a crucial role in cholesterol metabolism. The bioactive compounds were virtually screened and selected based on molecular docking studies which revealed the strong binding interactions of HMG-CoA reductase with Acacetin (-7.6 kcal/mol), Irilone (-7.5 kcal/mol), Orobanchol (-7.5 kcal/mol), Diadzein (-7.4 kcal/mol) and Malvidin (-7.4 kcal/mol). These compounds largely conformed to drug likeliness criteria and ADME properties with lesser mutagenic, hepatotoxic effects and higher absorption percentage in human intestine. Moreover, we performed molecular dynamics simulation studies for docked complexes to explore their stability under simulated conditions. Data gathered from this study will support the future in vitro and in vivo research in development of potential medicaments using the bioactive compounds from edible seeds for management of hypercholesterolemia. Communicated by Ramaswamy H. Sarma