cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Sharpe portfolio using a cross-efficiency evaluation
Creators: name: Monge, Juan F.
name: Landete, Mercedes
name: Ruiz, José L.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Portfolio Management (q-fin.PM)
subject: FOS: Economics and business
subject: 91Bxx

description: The Sharpe ratio is a way to compare the excess returns (over the risk free asset) of portfolios for each unit of volatility that is generated by a portfolio. In this paper we introduce a robust Sharpe ratio portfolio under the assumption that the risk free asset is unknown. We propose a robust portfolio that maximizes the Sharpe ratio when the risk free asset is unknown, but is within a given interval. To compute the best Sharpe ratio portfolio all the Sharpe ratios for any risk free asset are considered and compared by using the so-called cross-efficiency evaluation. An explicit expression of the Cross-Eficiency Sharpe ratio portfolio is presented when short selling is allowed.
Micelle structure of nonionic surfactants containing carbon dioxide moieties in protic ionic liquids
Creators: name: Miao, Shurui
name: Gradzielski, Michael
name: Warr, Gregory
Publisher: name: Technische Universität Berlin
Year: 2023
Subjects: subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften
subject: self-assembly
subject: ionic liquids
subject: carbon dioxide
subject: neutron scattering

description: Partial substitution of ethylene oxide with carbon dioxide moieties can yield greener nonionic surfactants with comparable functionalities. In water, studies showed that the incorporation of CO2 moieties suppresses the formation of liquid crystalline phases at high concentrations. A similar reduction in solvation and suppression of liquid crystal formation is observed here in the ionic liquids ethylammonium nitrate and propylammonium nitrate. Small-angle neutron scattering is used to study the solvation and packing of micelles in ionic liquids as functions of temperature, concentration, and content of CO2 moieties. By comparing with aqueous solutions, this work shows that while the nature of surfactant-solvent interaction is comparable among water and alkylammonium nitrate ILs, their behaviours in the solvated micelle shell are different. The lack of liquid crystalline phases should be attributed to the small excluded volume of micelles, which can be fine-tuned via ion design and choice of solvent.
Spin Hall conductance in a Y-shaped junction device in presence of tunable spin-orbit coupling
Creators: name: Ganguly, Sudin
name: Basu, Saurabh
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study spin Hall effect in a three terminal Y-shaped device in presence of tunable spin-orbit (SO) interactions via Landauer-Büttiker formalism. We have evolved a fabrication technique for creating different angular separation between the two arms of the Y-shaped device so as to investigate the effect of angular width on the spin Hall conductance (SHC). A smaller angular separation yields a larger conductance. Also arbitrary orientation of the spin quantization axes yields interesting three dimensional contour maps for the SHC corresponding to different angular separation of the Y-shaped device. The results explicitly show breaking of the spin rotational symmetry. Further a systematic study is carried out to compare and contrast between the different SO terms, such as Rashba and Dresselhaus SO interactions and the interplay of the angular separation therein.
Gamma-ray opacity of the anisotropic stratified broad-line regions in blazars
Creators: name: Abolmasov, Pavel
name: Poutanen, Juri
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The GeV-range spectra of blazars are shaped not only by non-thermal emission processes internal to the relativistic jet but also by external pair-production absorption on the thermal emission of the accretion disc and the broad-line region (BLR). For the first time, we compute here the pair-production opacities in the GeV range produced by a realistic BLR accounting for the radial stratification and radiation anisotropy. Using photoionization modelling with the CLOUDY code, we calculate a series of BLR models of different sizes, geometries, cloud densities, column densities and metallicities. The strongest emission features in the model BLR are Ly$α$ and HeII Ly$α$. Contribution of recombination continua is smaller, especially for hydrogen, because Ly continuum is efficiently trapped inside the large optical depth BLR clouds and converted to Lyman emission lines and higher-order recombination continua. The largest effects on the gamma-ray opacity are produced by the BLR geometry and localization of the gamma-ray source. We show that when the gamma-ray source moves further from the central source, all the absorption details move to higher energies and the overall level of absorption drops because of decreasing incidence angles between the gamma-rays and BLR photons. The observed positions of the spectral breaks can be used to measure the geometry and the location of the gamma-ray emitting region relative to the BLR. Strong dependence on geometry means that the soft photons dominating the pair-production opacity may be actually produced by a different population of BLR clouds than the bulk of the observed broad line emission.
description: 18 pages, 19 figures, accepted by MNRAS
Tannakian reconstruction of reductive group schemes
Creators: name: Zhao, Yifei
Publisher: name: arXiv
Year: 2021
Subjects: subject: Algebraic Geometry (math.AG)
subject: Category Theory (math.CT)
subject: FOS: Mathematics
subject: 14L15, 18M25

description: We give sharp criteria for when a reductive group scheme satisfies Tannakian reconstruction. When the base scheme is Noetherian, we explicitly identify its Tannaka group scheme.
description: 9 pages
Oblique spatial dispersive shock waves in nonlinear Schrödinger flows
Creators: name: Hoefer, M. A.
name: El, G. A.
name: Kamchatnov, A. M.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: In dispersive media, hydrodynamic singularities are resolved by coherent wavetrains known as dispersive shock waves (DSWs). Only dynamically expanding, temporal DSWs are possible in one-dimensional media. The additional degree of freedom inherent in two-dimensional media allows for the generation of time-independent DSWs that exhibit spatial expansion. Spatial oblique DSWs, dispersive analogs of oblique shocks in classical media, are constructed utilizing Whitham modulation theory for a class of nonlinear Schrödinger boundary value problems. Self-similar, simple wave solutions of the modulation equations yield relations between the DSW's orientation and the upstream/downstream flow fields. Time dependent numerical simulations demonstrate a convective or absolute instability of oblique DSWs in supersonic flow over obstacles. The convective instability results in an effective stabilization of the DSW.
description: 23 pages, 7 figures
Comparison of different eigensolvers for calculating vibrational spectra using low-rank, sum-of-product basis functions
Creators: name: Leclerc, Arnaud
name: Thomas, Phillip S.
name: Carrington, Tucker
Publisher: name: arXiv
Year: 2016
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Computational Physics (physics.comp-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Vibrational spectra and wavefunctions of polyatomic molecules can be calculated at low memory cost using low-rank sum-of-product (SOP) decompositions to represent basis functions generated using an iterative eigensolver. Using a SOP tensor format does not determine the iterative eigensolver. The choice of the interative eigensolver is limited by the need to restrict the rank of the SOP basis functions at every stage of the calculation. We have adapted, implemented and compared different reduced-rank algorithms based on standard iterative methods (block-Davidson algorithm, Chebyshev iteration) to calculate vibrational energy levels and wavefunctions of the 12-dimensional acetonitrile molecule. The effect of using low-rank SOP basis functions on the different methods is analyzed and the numerical results are compared with those obtained with the reduced rank block power method introduced in J. Chem. Phys. 140, 174111 (2014). Relative merits of the different algorithms are presented, showing that the advantage of using a more sophisticated method, although mitigated by the use of reduced-rank sum-of-product functions, is noticeable in terms of CPU time.
description: 18 pages, 1 figure
Novel insights into the structural changes induced by disease-associated mutations in TDP-43: a computational approach
Creators: name: Sharma, Abhibhav
name: Dey, Pinki
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
classificationCode: 29999
subject: Physical Sciences not elsewhere classified
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
classificationCode: 80699
subject: Information Systems not elsewhere classified
subject: Cancer

description: Over the last two decades, the pathogenic aggregation of TAR DNA-binding protein 43 (TDP-43) is found to be strongly associated with several fatal neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTD), etc. While the mutations and truncation in TDP-43 protein have been suggested to be responsible for TDP-43 pathogenesis by accelerating the aggregation process, the effects of these mutations on the bio-mechanism of pathological TDP-43 protein remained poorly understood. Investigating this at the molecular level, we formulized an integrated workflow of molecular dynamic simulation and machine learning models (MD-ML). By performing an extensive structural analysis of three disease-related mutations (i.e., I168A, D169G, and I168A-D169G) in the conserved RNA recognition motifs (RRM1) of TDP-43, we observed that the I168A-D169G double mutant delineates the highest packing of the protein inner core as compared to the other mutations, which may indicate more stability and higher chances of pathogenesis. Moreover, through our MD-ML workflow, we identified the biological descriptors of TDP-43 which includes the interacting residue pairs and individual protein residues that influence the stability of the protein and could be experimentally evaluated to develop potential therapeutic strategies. Communicated by Ramaswamy H. Sarma
Magnetic field structure of IC 63 and IC 59 associated to H II region - Sh 185
Creators: name: Soam, A.
name: Maheswar, G.
name: Lee, Chang Won
name: Neha, S.
name: Andersson, B-G
Publisher: name: arXiv
Year: 2016
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Bright-rimmed clouds (BRCs) are formed at the periphery of H$~$II regions as the radiation from the central star interacts with dense gas. The ionization and resulting compression of the clouds may lead to cloud disruption causing secondary star formation depending on the stellar and gas parameters. Here we use R-band polarimetry to probe the plane-of-the sky magnetic field in the two near-by BRCs IC\,59 and IC\,63. Both nebulae are illuminated by $γ$ Cas with the direction of ionizing radiation being orientated parallel or perpendicular to the local magnetic field, allowing us to probe the importance of magnetic field pressure in the evolution of BRCs. Because of the proximity of the system ($\sim$200pc) we have acquired a substantial sample of over 500 polarization measurements for stars background to the nebulae. On large scales, the magnetic field geometries of both clouds are anchored to the ambient magnetic field. For IC 63, the magnetic field is aligned parallel to the head-tail morphology of the main condensation, with convex morphology relative to the direction of the ionizing radiation. We estimate the plane of the sky magnetic field strength in IC\,63 to be $\sim90μ$G. In IC\,59, the projected magnetic field follows the M shape morphology of the cloud. Here, field lines present a concave shape with respect to the direction of the ionizing radiation from $γ$ Cas. Comparing our observations to published theoretical models we find good general agreement, supporting the importance of magnetic fields in BRC evolution.
description: 11 pages, 6 figures, Accepted for publication in MNRAS
Tree-Level Color-Kinematics Duality Implies Loop-Level Color-Kinematics Duality up to Counterterms
Creators: name: Borsten, Leron
name: Jurco, Branislav
name: Kim, Hyungrok
name: Macrelli, Tommaso
name: Saemann, Christian
name: Wolf, Martin
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Color-kinematics (CK) duality is a remarkable symmetry of gluon amplitudes that is the key to the double copy which links gauge theory and gravity amplitudes. Here we show that the complete Yang-Mills action itself, including its gauge-fixing and ghost sectors required for quantization, can be recast to manifest CK duality using a series of field redefinitions and gauge choices. Crucially, the resulting loop-level integrands are automatically CK-dual, up to potential Jacobian counterterms required for unitarity. While these counterterms may break CK duality, they exist, are unique and, since the tree-level is unaffected, may be deduced from the action or the integrands. Consequently, CK duality is a symmetry of the action like any other symmetry, and it is anomalous in a controlled and mostly harmless sense. Our results apply to any theory with CK-dual tree-level amplitudes. We also show that two CK duality-manifesting parent actions may be factorized and fused into a consistent quantizable offspring, with the double copy as the prime example. This provides a direct proof of the double copy to all loop orders.
description: v3: 71 pages; arguments, statements, and presentation extended and improved; clarifications added; typos fixed; published version
Numerical modelling of the lobes of radio galaxies in cluster environments - III. Powerful relativistic and nonrelativistic jets
Creators: name: English, William
name: Hardcastle, Martin J.
name: Krause, Martin G. H.
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present results from two suites of simulations of powerful radio galaxies in poor cluster environments, with a focus on the formation and evolution of the radio lobes. One suite of models uses relativistic hydrodynamics and the other relativistic magnetohydrodynamics; both are set up to cover a range of jet powers and velocities. The dynamics of the lobes are shown to be in good agreement with analytical models and with previous numerical models, confirming in the relativistic regime that the observed widths of radio lobes may be explained if they are driven by very light jets. The ratio of energy stored in the radio lobes to that put into the intracluster gas is seen to be the same regardless of jet power, jet velocity or simulation type, suggesting that we have a robust understanding of the work done on the ambient gas by this type of radio source. For the most powerful jets we at times find magnetic field amplification by up to a factor of two in energy, but mostly the magnetic energy in the lobes is consistent with the magnetic energy injected. We confirm our earlier result that for jets with a toroidally injected magnetic field, the field in the lobes is predominantly aligned with the jet axis once the lobes are well developed, and that this leads to radio flux anisotropies of up to a factor of about two for mature sources. We reproduce the relationship between 151-MHz luminosity and jet power determined analytically in the literature.
description: 19 pages, 20 figures, 2 tables. Accepted for publication in MNRAS
Global Crustal Dynamics of Magnetars in Relation to their Bright X-ray Outbursts
Creators: name: Thompson, Christopher
name: Yang, Huan
name: Ortiz, Néstor
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: This paper considers the yielding response of a neutron star crust to smooth, unbalanced Maxwell stresses imposed at the core-crust boundary, and the coupling of the dynamic crust to the external magnetic field. Stress buildup and yielding in a magnetar crust is a global phenomenon: an elastic distortion radiating from one plastically deforming zone is shown to dramatically increase the creep rate in distant zones. Runaway creep to dynamical rates is shown to be possible, being enhanced by in situ heating and suppressed by thermal conduction and shearing of an embedded magnetic field. A global and time-dependent model of elastic, plastic, magnetic, and thermal evolution is developed. Fault-like structures develop naturally, and a range of outburst timescales is observed. Transient events with time profiles similar to giant magnetar flares (millisecond rise, $\sim$ 0.1 s duration, and decaying power-law tails) result from runaway creep that starts in localized sub-km-sized patches and spreads across the crust. A one-dimensional model of stress relaxation in the vertically stratified crust shows that a modest increase in applied stress allows embedded magnetic shear to escape the star over $\sim$ 3-10 ms, dissipating greater energy if the exterior field is already sheared. Several such zones coupled to each other naturally yield a burst of duration $\sim$ 0.1 s, as is observed over a wide range of burst energies. The collective interaction of many plastic zones forces an overstability of global elastic modes of the crust, consistent with QPO activity extending over $\gtrsim$ 100 s. Giant flares probably involve sudden meltdown in localized zones, with high-frequency ($\gg$ 100 Hz) QPOs corresponding to standing Alfvén waves within these zones.
description: 25 pages, 20 figures, submitted to the Astrophysical Journal
Instantaneous charge state of Uranium projectiles in fully ionized plasmas from energy loss experiments
Creators: name: Morales, Roberto
name: Barriga-Carrasco, Manuel D.
name: Casas, David
Publisher: name: arXiv
Year: 2016
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: The instantaneous charge state of uranium ions traveling through a fully ionized hydrogen plasma has been theoretically studied and compared with one of the first energy loss experiments in plasmas, carried out at GSI-Darmstadt by Hoffmann \textit{et al.} in the 90's. For this purpose, two different methods to estimate the instantaneous charge state of the projectile have been employed: (1) rate equations using ionization and recombination cross sections, and (2) equilibrium charge state formulas for plasmas. Also, the equilibrium charge state has been obtained using these ionization and recombination cross sections, and compared with the former equilibrium formulas. The equilibrium charge state of projectiles in plasmas is not always reached, it depends mainly on the projectile velocity and the plasma density. Therefore, a non-equilibrium or an instantaneous description of the projectile charge is necessary. The charge state of projectile ions cannot be measured, except after exiting the target, and experimental data remain very scarce. Thus, the validity of our charge state model is checked by comparing the theoretical predictions with an energy loss experiment, as the energy loss has a generally quadratic dependence on the projectile charge state. The dielectric formalism has been used to calculate the plasma stopping power including the Brandt-Kitagawa (BK) model to describe the charge distribution of the projectile. In this charge distribution, the instantaneous number of bound electrons instead of the equilibrium number has been taken into account. Comparing our theoretical predictions with experiments, it is shown the necessity of including the instantaneous charge state and the BK charge distribution for a correct energy loss estimation. The results also show that the initial charge state has a strong influence in order to estimate the energy loss of the uranium ions.
description: 27 pages, 8 figures
Reform of Australian general practice : a budget-holding model?
Creators: name: Wilton, Paula.
Publisher: name: Monash University
Year: 2022

description: This thesis was scanned from the print manuscript for digital preservation and is copyright the author.
 Researchers can access this thesis by asking their local university, institution or public library to
 make a request on their behalf. Monash staff and postgraduate students can use the link in the References field.
Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies
Creators: name: Giron, Carolina Corrêa
name: Laaksonen, Aatto
name: da Silva, Fernando Luís Barroso
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Cancer
classificationCode: 110309
subject: Infectious Diseases
subject: FOS: Health sciences
classificationCode: 60506
subject: Virology

description: SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus. Communicated by Ramaswamy H. Sarma
Unique Minimizers and the Representation of Convex Envelopes in Locally Convex Vector Spaces
Creators: name: Ruf, Thomas
name: Schmidt, Bernd
Publisher: name: arXiv
Year: 2021
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: It is well known that a strictly convex minimand admits at most one minimizer. We prove a partial converse: Let $X$ be a locally convex Hausdorff space and $f \colon X \mapsto \left( - \infty , \infty \right]$ a function with compact sublevel sets and exhibiting some mildly superlinear growth. Then each tilted minimization problem \begin{equation} \label{eq. minimization problem} \min_{x \in X} f(x) - \langle x' , x \rangle_X \end{equation} admits at most one minimizer as $x'$ ranges over $\text{dom} \left( \partial f^* \right)$ if and only if the biconjugate $f^{**}$ is essentially strictly convex and agrees with $f$ at all points where $f^{**}$ is subdifferentiable. We prove this via a representation formula for $f^{**}$ that might be of independent interest.
Extended Graded Modalities in Strategy Logic
Creators: name: Aminof, Benjamin
name: Malvone, Vadim
name: Murano, Aniello
name: Rubin, Sasha
Publisher: name: arXiv
Year: 2016
Subjects: subject: Computer Science and Game Theory (cs.GT)
subject: Artificial Intelligence (cs.AI)
subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences
subject: I.2.11

description: Strategy Logic (SL) is a logical formalism for strategic reasoning in multi-agent systems. Its main feature is that it has variables for strategies that are associated to specific agents with a binding operator. We introduce Graded Strategy Logic (GradedSL), an extension of SL by graded quantifiers over tuples of strategy variables, i.e., "there exist at least g different tuples (x_1,...,x_n) of strategies" where g is a cardinal from the set N union {aleph_0, aleph_1, 2^aleph_0}. We prove that the model-checking problem of GradedSL is decidable. We then turn to the complexity of fragments of GradedSL. When the g's are restricted to finite cardinals, written GradedNSL, the complexity of model-checking is no harder than for SL, i.e., it is non-elementary in the quantifier rank. We illustrate our formalism by showing how to count the number of different strategy profiles that are Nash equilibria (NE), or subgame-perfect equilibria (SPE). By analyzing the structure of the specific formulas involved, we conclude that the important problems of checking for the existence of a unique NE or SPE can both be solved in 2ExpTime, which is not harder than merely checking for the existence of such equilibria.
description: In Proceedings SR 2016, arXiv:1607.02694
Valley splitting of single-electron Si MOS quantum dots
Creators: name: Gamble, John King
name: Harvey-Collard, Patrick
name: Jacobson, N. Tobias
name: Baczewski, Andrew D.
name: Nielsen, Erik
name: Maurer, Leon
name: Montaño, Inès
name: Rudolph, Martin
name: Carroll, M. S.
name: Yang, C. H.
name: Rossi, A.
name: Dzurak, A. S.
name: Muller, Richard P.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Silicon-based metal-oxide-semiconductor quantum dots are prominent candidates for high-fidelity, manufacturable qubits. Due to silicon's band structure, additional low-energy states persist in these devices, presenting both challenges and opportunities. Although the physics governing these valley states has been the subject of intense study, quantitative agreement between experiment and theory remains elusive. Here, we present data from a new experiment probing the valley states of quantum dot devices and develop a theory that is in quantitative agreement with both the new experiment and a recently reported one. Through sampling millions of realistic cases of interface roughness, our method provides evidence that, despite radically different processing, the valley physics between the two samples is essentially the same. This work provides the first evidence that valley splitting can be deterministically predicted and controlled in metal oxide semiconductor quantum dots, a critical requirement for such systems to realize a reliable qubit platform.
description: 7 pages, 4 figures
Synergistic combination of ritonavir and cisplatin as an efficacious therapy in human cervical cancer cells: a computational drug discovery and in vitro insight
Creators: name: Swami, Dayanand
name: Mudaliar, Priyanka
name: Bichu, Yash Shrinivas
name: Sahu, Vishal Kumar
name: Devarajan, Shine
name: Basu, Soumya
name: Aich, Jyotirmoi
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Pharmacology
subject: Biotechnology
classificationCode: 39999
subject: Chemical Sciences not elsewhere classified
subject: Cancer
classificationCode: 60506
subject: Virology
subject: Computational Biology

description: HIV-protease inhibitor Ritonavir (RTV) is a clinical-stage drug. We exhibit here the synergistic effect of RTV coupled with cisplatin as potential combination therapy for treatment of cervical cancer. Knowledge about the interaction of RTV with the high-expression signatures in cancer is limited. Therefore, we utilized computational techniques to understand and assess the drug-binding affinity and drug-target interaction of RTV with these altered protein signatures. Computational studies revealed the potential interaction ability of RTV along with few other HIV protease inhibitors against these altered cancer targets. All targets exhibited good affinity towards RTV and the highest affinity was exhibited by CYP450 3A4, PDGFR and ALK. RTV established stable interaction with PDGFR and molecular dynamics simulation confirms their frequent interaction for 300 ns. Control docking of PDGFR with standard PDGFR inhibitor exhibited lower binding affinity when compared with RTV-PDGFR complex. In search of drugs as a part of combination therapy to reduce side effects of Cisplatin, this paper further evaluated the effect of combination of RTV and Cisplatin in cervical cancer cells. We propose several combination models that combines anti-viral drug RTV and standard chemotherapeutic agent, Cisplatin to be synergistic with CI value ranging from of 0.01 to 1.14. These observations suggest that anti-viral compound (RTV) could act synergistically with Cisplatin for cervical cancer therapy. However, further studies are warranted to investigate the combinatorial mode of action of RTV and Cisplatin on different molecular pathways to have a translational outcome in cervical cancer. Communicated by Ramaswamy H. Sarma
Representing Strategies
Creators: name: Duijf, Hein
name: Broersen, Jan
Publisher: name: arXiv
Year: 2016
Subjects: subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: Quite some work in the ATL-tradition uses the differences between various types of strategies (positional, uniform, perfect recall) to give alternative semantics to the same logical language. This paper contributes to another perspective on strategy types, one where we characterise the differences between them on the syntactic (object language) level. This is important for a more traditional knowledge representation view on strategic content. Leaving differences between strategy types implicit in the semantics is a sensible idea if the goal is to use the strategic formalism for model checking. But, for traditional knowledge representation in terms of object language level formulas, we need to extent the language. This paper introduces a strategic STIT syntax with explicit operators for knowledge that allows us to charaterise strategy types. This more expressive strategic language is interpreted on standard ATL-type concurrent epistemic game structures. We introduce rule-based strategies in our language and fruitfully apply them to the representation and characterisation of positional and uniform strategies. Our representations highlight crucial conditions to be met for strategy types. We demonstrate the usefulness of our work by showing that it leads to a critical reexamination of coalitional uniform strategies.
description: In Proceedings SR 2016, arXiv:1607.02694
Modelling the welfare implications of protectionist trade policy using computable general equilibrium models
Creators: name: Winston, Ashley R. P. .
Publisher: name: Monash University
Year: 2022

description: This thesis was scanned from the print manuscript for digital preservation and is copyright the author.
 Researchers can access this thesis by asking their local university, institution or public library to
 make a request on their behalf. Monash staff and postgraduate students can use the link in the References field.
In-silico discovery of inhibitors against human papillomavirus E1 protein
Creators: name: Gunasinghe, Juliyan
name: San Hwang, Siaw
name: Yam, Wai Keat
name: Rahman, Taufiq
name: Wezen, Xavier Chee
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
classificationCode: 39999
subject: Chemical Sciences not elsewhere classified
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Cancer
classificationCode: 110309
subject: Infectious Diseases
subject: FOS: Health sciences

description: High-risk (HR) Human papillomavirus (e.g. HPV16 and HPV18) causes approximately two-thirds of all cervical cancers in women. Although the first and second-generation vaccines confer some protection against individuals, there are no approved drugs to treat HR-HPV infections to-date. The HPV E1 protein is an attractive drug target because the protein is highly conserved across all HPV types and is crucial for the regulation of viral DNA replication. Hence, we used the Random Forest algorithm to construct a Quantitative-Structure Activity Relationship (QSAR) model to predict the potential inhibitors against the HPV E1 protein. Our QSAR classification model achieved an accuracy of 87.5%, area under the receiver operating characteristic curve of 1.00, and F-measure of 0.87 when evaluated using an external test set. We conducted a drug repurposing campaign by deploying the model to screen the Drugbank database. The top three compounds, namely Cinalukast, Lobeglitazone, and Efatutazone were analyzed for their cell membrane permeability, toxicity, and carcinogenicity. Finally, these three compounds were subjected to molecular docking and 200 ns-long Molecular Dynamics (MD) simulations. The predicted binding free energies for the candidates were calculated using the MM-GBSA method. The binding free energies for Cinalukast, Lobeglitazone, and Efatutazone were −37.84 kcal/mol, −25.30 kcal/mol, and −29.89 kcal/mol respectively. Therefore, we propose their chemical scaffolds for future rational design of E1 inhibitors. Communicated by Ramaswamy H. Sarma
Spectral and norm estimates for matrix sequences arising from a finite difference approximation of elliptic operators
Creators: name: Coco, Armando
name: Ekström, Sven-Erik
name: Russo, Giovanni
name: Serra-Capizzano, Stefano
name: Stissi, Santina Chiara
Publisher: name: arXiv
Year: 2021
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics
subject: G.1.8; G.1.3
subject: 65M12, 65M06, 65F35

description: When approximating elliptic problems by using specialized approximation techniques, we obtain large structured matrices whose analysis provides information on the stability of the method. Here we provide spectral and norm estimates for matrix sequences arising from the approximation of the Laplacian via ad hoc finite differences. The analysis involves several tools from matrix theory and in particular from the setting of Toeplitz operators and Generalized Locally Toeplitz matrix sequences. Several numerical experiments are conducted, which confirm the correctness of the theoretical findings.
description: 24 pages
A combined in vitro–in silico approach for the discovery of novel endogenous enzymatic and ctDNA sequence of bioactive molecules from aerial and root parts of Centaurea sulphurea as antioxidant’s agents
Creators: name: Lyna, Benhamidat
name: Fouzia, Mesli
name: Okkacha, Bensaid
name: Dib, Mohammed El Amine
name: Muselli, Alain
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Molecular Biology
classificationCode: 39999
subject: Chemical Sciences not elsewhere classified
classificationCode: 69999
subject: Biological Sciences not elsewhere classified

description: The excess free radicals not neutralized by the antioxidant defenses damage the essential macromolecules of our cells, causing abnormalities in the expression of genes and membrane receptors, cell proliferation or death, immune disorders, mutagenesis, deposits of proteins or lipofuschin in tissues. The first objective of this study was to elucidate the composition of the essential oil of the aerial and root part of Centaurea sulphurea during beginning of the vegetative cycle (March), beginning of the flowering stage (April) and full bloom (May/June) using GC/FID and GC/MS. The second aim was to describe the antioxidant activity using three methods (2,2-diphenyl-1-picrylhydrazyl (DPPH), ferric-reducing antioxidant power (FRAP), β-carotene bleaching assay) and bioinformatical study of ctDNA sequence and three endogenous enzymes inhibition. The essential oils obtained from the root during the full bloom period consisted mainly of caryophyllene oxide, aplotaxene and (Z)-phytol. While, the aerial parts were dominated by caryophyllene oxide, verridiflorol and humulene epoxide II. The results showed that essential oil presented an excellent antioxidant activity with IC50 values of 2.06 g/L and 1.29 g/L, for aerial and root parts, compared to butylated hydroxyltoluene (BHT) and Ethylenediaminetetraacetic acid (EDTA) controls and the nicotinamide adenine dinucleotide phosphate (NADPH) co-crystallized inhibitor. The results of the molecular docking revealed that (Z)-phytol (Ligand 39) has an affinity to interact with ctDNA sequence, and three targets Endogenous enzymes. The molecular dynamics study was conducted for the best inhibitors (Z)-phytol. A few key residues were identified at the binding site of receptors. The in-silico assessment of the ADME properties and BOILED-Egg plot reveals that compound (Z)-phytol (L39) is permeable to the blood brain barrier and have high lipophilicity and high coefficient of skin permeability in the intestines with good bioavailability. The ADMET analysis also showed that this oxygenated diterpene is safer to replace the synthetic drugs with side effects. Further testing is needed to assess its effectiveness in reducing oxidative stress for use in the pharmaceutical industry. Communicated by Ramaswamy H. Sarma
Moduli Space of Factorized Ramified Connections and Generalized Isomonodromic Deformation
Creators: name: Inaba, Michi-aki
Publisher: name: arXiv
Year: 2021
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14D20, 34M40, 34M56, 53D30

description: We introduce the notion of factorized ramified structure on a generic ramified irregular singular connection on a smooth projective curve. By using the deformation theory of connections with factorized ramified structure, we construct a canonical 2-form on the moduli space of ramified connections. Since the factorized ramified structure provides a duality on the tangent space of the moduli space, the 2-form becomes nondegenerate. We prove that the 2-form on the moduli space of ramified connections is d-closed via constructing an unfolding of the moduli space. Based on the Stokes data, we introduce the notion of local generalized isomonodromic deformation for generic unramified irregular singular connections on a unit disk. Applying the Jimbo-Miwa-Ueno theory to generic unramified connections, the local generalized isomonodromic deformationis equivalent to the extendability of the family of connections to an integrable connection. We give the same statement for ramified connections. Based on this principle of Jimbo-Miwa-Ueno theory, we construct a global generalized isomonodromic deformation on the moduli space of generic ramified connections by constructing a horizontal lift of a universal family of connections. As a consequence of the global generalized isomonodromic deformation, we can lift the relative symplectic form on the moduli space to a total closed form, which is called a generalized isomonodromic 2-form.
In silico based multi-epitope vaccine design against norovirus
Creators: name: Shanthappa, Pallavi M.
name: Suravajhala, Renuka
name: Suravajhala, Prashanth
name: Kumar, Geetha
name: Melethadathil, Nidheesh
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
classificationCode: 39999
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Cancer
classificationCode: 110309
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Norovirus (NoV) belongs to the Calciviridae family that causes diarrhoea, vomiting, and stomach pain in people who have acute gastroenteritis (AGE). Identifying multi-epitope dependent vaccines for single stranded positive sense viruses such as NoV has been a long due. Although efforts have been in place to look into the candidate epitopes, understanding molecular mimicry and finding new epitopes for inducing immune responses against the T/B-cells which play an important role for the cell-mediated and humoral immunity was not dealt with in great detail. The current study focuses on identifying new epitopes from various databases that were filtered for antigenicity, allergenicity, and toxicity. The adjuvant β-defensin along with different linkers were used for vaccine construction. Further, the binding relationship between the vaccine construct and toll-like immune receptor (TLR3) complex was determined using a molecular docking analysis, followed by molecular dynamics simulation of 100 ns. The vaccine candidate developed expresses good solubility with a score of 0.530, Z-score of –4.39 and molecular docking score of –140.4 ± 12.1. The MD trajectories reveal that there is a stability between TLR3 and the developed vaccine candidate with an average of 0.91 nm RMSD value and also the system highest occupancy H-bond formed between GLU127 of TLR3 and TYR10 of vaccine candidate (61.55%). Four more H-bonds exist with an occupancy of more than 32% between TLR3 and the vaccine candidates which makes it stable. Thus, the multi-epitope based vaccine developed in the present study forms the basis for further experimental investigations to develop a potentially good vaccine against NoV. Communicated by Ramaswamy H. Sarma
Analysis of Pleurotin binding to human thioredoxin reductase using docking and molecular dynamics simulation
Creators: name: Quintanilha, Daniel B.
name: Dos Santos, Hélio F.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
classificationCode: 29999
subject: Physical Sciences not elsewhere classified
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
classificationCode: 39999
subject: Chemical Sciences not elsewhere classified
subject: Computational Biology

description: Thioredoxin reductase (TrxR) has been considered a potential target for cancer chemotherapy. It acts by controlling the redox homeostasis of human cells and, therefore, interfering in its function may trigger apoptosis, which is a crucial tumor suppression mechanism. Despite the great effort in the search for TrxR inhibitors, none was approved for human therapy. In the present study a virtual screening for natural organic compounds is discussed for a set of 72 compounds with known IC-50 for TrxR inhibition. The results suggest the Pleurotin, a naphthoquinone obtained from Hohenbuehelia grisea fungus, as a potential TrxR inhibitor, which acts by binding to the active site of the enzyme, between the N- and C-terminal domains. The presence of the ligand blocks the approximation of the C-terminal arm to the N-terminal, which is an essential step of the enzyme function. Besides, the two equivalent binding sites of TrxR were explored, by docking two ligands simultaneously. The results indicate that both sites have an allosteric correlation and, the presence of the ligand in one site may interfere, or even prevent, the binding of the second ligand at the other site. All these findings are quantitatively discussed based on the analysis of long molecular dynamics trajectories, which provides a full description of the ligand-receptor binding modes, average binding energies and conformational changes. Communicated by Ramaswamy H. Sarma
Biopolymerization chain reactions in protein synthesis
Creators: name: J. Savkovic Stevanovic
Publisher: name: gjrpublication
Year: 2024

description: In this paper biopolymerization reaction of DNA molecules was studied. Chemical and mathematical models were considered. A complex mathematical model of biopolymerization generating microscopic and macroscopic balances of probability distribution function was derived. The three stages initiation, elongation and termination reactions were examined. The distribution function of the oligomers specifies concentration, and temperatures in the spatial coordinates and time and length of the oligonucleotide’s chains. The algorithm for oligomers concentration distribution and temperature distribution functions simulation was derived.
Extending Finite Memory Determinacy to Multiplayer Games
Creators: name: Roux, Stéphane Le
name: Pauly, Arno
Publisher: name: arXiv
Year: 2016
Subjects: subject: Computer Science and Game Theory (cs.GT)
subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences
subject: I.2.2

description: We show that under some general conditions the finite memory determinacy of a class of two-player win/lose games played on finite graphs implies the existence of a Nash equilibrium built from finite memory strategies for the corresponding class of multi-player multi-outcome games. This generalizes a previous result by Brihaye, De Pril and Schewe. For most of our conditions we provide counterexamples showing that they cannot be dispensed with. Our proofs are generally constructive, that is, provide upper bounds for the memory required, as well as algorithms to compute the relevant winning strategies.
description: In Proceedings SR 2016, arXiv:1607.02694
Isolated and dynamical black hole mergers with \texttt{B-POP}: the role of star formation and dynamics, star cluster evolution, natal kicks, mass and spins, and hierarchical mergers
Creators: name: Sedda, Manuel Arca
name: Mapelli, Michela
name: Benacquista, Matthew
name: Spera, Mario
Publisher: name: arXiv
Year: 2021
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The current interpretation of LIGO--Virgo--KAGRA data suggests that the primary mass function of merging binary black holes (BBHs) at redshift $z\lesssim 1$ contains multiple structures, while spins are relatively low. Theoretical models of BBH formation in different environments can provide a key to interpreting the population of observed mergers, but they require the simultaneous treatment of stellar evolution and dynamics, galaxy evolution, and general relativity. We present \texttt{B-POP}, a population synthesis tool to model BBH mergers formed in the field or via dynamical interactions in young, globular, and nuclear clusters. Using \texttt{B-POP}, we explore how BH formation channels, star cluster evolution, hierarchical mergers, and natal BH properties affect the population of BBH mergers. We find that the primary mass distribution of BBH mergers extends beyond $M_1 \simeq 200\,{}$ M$_\odot$, and the effective spin parameter distribution hints at different natal spins for single and binary BHs. Observed BBHs can be interpreted as members of a mixed population comprised of $\sim 34\% \,{}(66\%)$ isolated (dynamical) BBHs, with the latter likely dominating at redshift $z>1$. Hierarchical mergers constitute the $4.6-7.9\%$ of all mergers in the reference model, dominating the primary mass distribution beyond $M_1 > 65\,{}$ M$_\odot$. The inclusion of cluster mass-loss and expansion causes an abrupt decrease in the probability for mergers beyond the third generation to occur. Considering observational biases, we find that $2.7-7.5\%$ of mock mergers involve intermediate-mass black hole (IMBH) seeds formed via stellar collisions. Comparing this percentage to observed values will possibly help us to constrain IMBH formation mechanisms.
description: 26 Pages, 20 Figures, 1 Table. We significantly improved B-POP since the first submission, this led to a major restructuring of the previous version of the manuscript. Accepted for publication in MNRAS