An SOA-based model for the integrated provisioning of cloud and grid resources

In the last years, the availability and models of use of networked computing resources within reach of e-Science are rapidly changing and see the coexistence of many disparate paradigms: high-performance computing, grid, and recently cloud. Unfortunately, none of these paradigms is recognized as the ultimate solution, and a convergence of them all should be pursued. At the same time, recent works have proposed a number of models and tools to address the growing needs and expectations in the field of e-Science. In particular, they have shown the advantages and the feasibility of modeling e-Science environments and infrastructures according to the service-oriented architecture. In this paper, we suggest a model to promote the convergence and the integration of the different computing paradigms and infrastructures for the dynamic on-demand provisioning of resources from multiple providers as a cohesive aggregate, leveraging the service-oriented architecture. In addition, we propose a design aimed at endorsing a flexible, modular, workflow-based computing model for e-Science. The model is supplemented by a working prototype implementation together with a case study in the applicative domain of bioinformatics, which is used to validate the presented approach and to carry out some performance and scalability measurements

Theoretical evidence for efficient p-type doping of GaN using beryllium

Ab initio calculations predict that Be is a shallow acceptor in GaN. Its thermal ionization energy is 0.06 eV in wurtzite GaN; the level is valence resonant in the zincblende phase. Be incorporation is severely limited by the formation of Be_3N_2. We show however that co-incorporation with reactive species can enhance the solubility. H-assisted incorporation should lead to high doping levels in MOCVD growth after post-growth annealing at about 850 K. Be-O co-incorporation produces high Be and O concentrations at MBE growth temperatures.Comment: revised Feb 24 199

Geometric effects in the infinite-layer nickelates

Geometric effects in the infinite-layer nickelates $R$NiO$_2$ associated with the relative size of the $R$-site atom are investigated via first-principles calculations. We consider, in particular, the prospective YNiO$_2$ material to illustrate the impact of these effects. Compared to LaNiO$_2$, we find that the La $\to$ Y substitution is equivalent to a pressure of 19 GPa and that the presence of topotactic hydrogen can be precluded. However, the electronic structure of YNiO$_2$ departs from the cuprate-like picture due to an increase in both self-doping effect and $e_g$ hybridization. Furthermore, we find that geometric effects introduce a quantum critical point in the $R$NiO$_2$ series. This implies a $P4/mmm \leftrightarrow I4/mcm$ structural transformation associated to a $A_3^+$ normal mode, according to which the oxygen squares undergo an in-plane rotation around Ni that alternates along $c$. We find that such a $A_3^+$-mode instability has a generic character in the infinite-layer nickelates and can be tuned via either the effective $R$-site atom size or epitaxial strain.Comment: 6 pages, 4 figures, 4 table

Die "Erfindung" von Saatgut in Österreich

Die "Erfindung" von Saatgut in Österreich und die Entstehung des ersten Saatgutgesetzes 1934 waren Entwicklungsprozesse, die von komplexen Netzwerken bestimmt wurden. Viele verschiedene Akteure suchten in Diskussions- und Verhandlungsprozessen gemeinschaftlich eine neue Definition von Saatgut, weshalb von der "Erfindung" von Saatgut gesprochen wird. In dieser Arbeit wird die Ko-Produktion des Begriffes "Saatgut" durch die Ansprüche und Möglichkeiten der beteiligten Personen aus Wissenschaft und Gesellschaft verdeutlicht. Es wird gezeigt das die vereinbarte Definition durch ein Gesetz praktisch Umsetzung erfährt und die Ko-Produktion eines Begriffes so in den Alltag vieler Menschen getragen wird. Die konstruierte Definition von Saatgut beinhaltet auch die Vermischung von Kultur und Natur, nach der die Akteur - Netzwerk - Theorie aus den Science- und Technology Studies sucht. Mit verschiedenen Annahmen der Actor - Network - Theory wird ein differenzierter Blick auf die Verflechtungen und Mechanismen geworfen, die zur Formulierung des Gesetzes führten. Der Fokus hierbei liegt auf der Untersuchung der Methoden und Materialien, die dazu beitrugen, Wissen und Macht zu generieren, um die jeweiligen Interessen im Gesetz durchzusetzen. Die Rolle "der Wissenschaft" als Vermittlerin zwischen der Welt der Menschen und der Natur des Saatgutes sowie die Verwissenschaftlichung der Landwirtschaft in der ersten Hälfte des 20. Jahrhunderts in Österreich sind Schwerpunkte dieser Diplomarbeit

Time-Dependent Density Functional Theory Investigation on the Electronic and Optical Properties of Poly-C,Si,Ge-acenes

We report a comparative computational investigation on the first six members of linear poly-C,Si,Ge-acenes (X4n+2H2n+4, X = C,Si,Ge; n = 1, 2, 3, 4, 5, 6). We performed density functional theory (DFT) and time-dependent DFT calculations to compare morphological, electronic, and optical properties. While C-acenes are planar, Si-and Ge-acenes assume a buckled configuration. Electronic properties show similar trends as a function of size for all families. In particular, differently from C-based compounds, in the case of both Si-and Ge-acenes, the excitation energies of the strongest low-lying electronic transition (β peaks) span the visible region of the spectrum, demonstrating their size tunability. For all families, we assessed the plasmonic character of this transition and found a linear relationship for the wavelength-dependence of the β peaks as a function of the number of rings. A similar slope of about 56 nm is observed for Si-and Ge-acenes, although the peak positions of the former are located at lower wavelengths. Outcomes of this study are compared with existing theoretical results for 2D lattices and nanoribbons, and experiments where available

Impact of synthetic conditions on the anisotropic thermal conductivity of poly(3,4-ethylenedioxythiophene) (PEDOT) : a molecular dynamics investigation

In this work we study the effect of different synthetic conditions on thermal transport properties of poly(3,4-ethylenedioxythiophene) (PEDOT) by focusing in particular on the role of proton scavengers. To this aim, different PEDOT samples were generated in silico using a novel computational algorithm based on a combination of first-principles density functional theory and classical molecular dynamics simulations. The corresponding thermal conductivities were then estimated using the approach to equilibrium molecular dynamics methodology. The results show that the initial synthetic conditions strongly affect the corresponding thermal conductivities, which display variations up to a factor of ∼2 depending on the proton scavenger. By decomposing the thermal conductivity tensor along the direction of maximum chain alignment and the corresponding perpendicular directions, we attribute the thermal conductivity differences to the variations in the average polymer chain length λave. A dependence of the thermal conductivity with the polydispersity index was finally observed, suggesting a possible role of intercrystallite chains in enhancing thermal transport properties. By means of the Green-Kubo modal analysis, we eventually characterize the vibrational modes involved in PEDOT thermal transport and investigate how they are related to the thermal conductivity values of the samples

Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations

The development of drugs targeting somatostatin receptor 2 (SSTR2), generally overexpressed in neuroendocrine tumors, is focus of intense research. A few molecules in conjugation with radionuclides are in clinical use for both diagnostic and therapeutic purposes. These radiopharmaceuticals are composed of a somatostatin analogue biovector conjugated to a chelator moiety bearing the radionuclide. To date, despite valuable efforts, a detailed molecular-level description of the interaction of radiopharmaceuticals in complex with SSTR2 has not yet been accomplished. Therefore, in this work, we carefully analyzed the key dynamical features and detailed molecular interactions of SSTR2 in complex with six radiopharmaceutical compounds selected among the few already in use (64Cu/68Ga-DOTATATE, 68Ga-DOTATOC, 64Cu-SARTATE) and some in clinical development (68Ga-DOTANOC, 64Cu-TETATATE). Through molecular dynamics simulations and exploiting recently available structures of SSTR2, we explored the influence of the different portions of the compounds (peptide, radionuclide, and chelator) in the interaction with the receptor. We identified the most stable binding modes and found distinct interaction patterns characterizing the six compounds. We thus unveiled detailed molecular interactions crucial for the recognition of this class of radiopharmaceuticals. The microscopically well-founded analysis presented in this study provides guidelines for the design of new potent ligands targeting SSTR2

Molecular interactions of carbapenem antibiotics with the multidrug efflux transporter acrb of escherichia coli

The drug/proton antiporter AcrB, engine of the major efflux pump AcrAB(Z)-TolC of Escherichia coli and other bacteria, is characterized by its impressive ability to transport chemically diverse compounds, conferring a multi-drug resistance (MDR) phenotype. Although hundreds of small molecules are known to be AcrB substrates, only a few co-crystal structures are available to date. Computational methods have been therefore intensively employed to provide structural and dynamical fingerprints related to transport and inhibition of AcrB. In this work, we performed a systematic computational investigation to study the interaction between representative carbapenem antibiotics and AcrB. We focused on the interaction of carbapenems with the so-called distal pocket, a region known for its importance in binding inhibitors and substrates of AcrB. Our findings reveal how the different physico-chemical nature of these antibiotics is reflected on their binding preference for AcrB. The molecular-level information provided here could help design new antibiotics less susceptible to the efflux mechanism

Recognition of quinolone antibiotics by the multidrug efflux transporter MexB of Pseudomonas aeruginosa

The drug/proton antiporter MexB is the engine of the major efflux pump MexAB-OprM in Pseudomonas aeruginosa. This protein is known to transport a large variety of compounds, including antibiotics, thus conferring a multi-drug resistance phenotype. Due to the difficulty of producing co-crystals, only two X-ray structures of MexB in a complex with ligands are available to date, and mechanistic aspects are largely hypothesized based on the body of data collected for the homologous protein AcrB of Escherichia coli. In particular, a recent study (Ornik-Cha, Wilhelm, Kobylka et al., Nat. Commun., 2021, 12, 6919) reported a co-crystal structure of AcrB in a complex with levofloxacin, an antibiotic belonging to the important class of (fluoro)-quinolones. In this work, we performed a systematic ensemble docking campaign coupled to the cluster analysis and molecular-mechanics optimization of docking poses to study the interaction between 36 quinolone antibiotics and MexB. We additionally investigated surface complementarity between each molecule and the transporter and thoroughly assessed the computational protocol adopted against the known experimental data. Our study reveals different binding preferences of the investigated compounds towards the sub-sites of the large deep binding pocket of MexB, supporting the hypothesis that MexB substrates oscillate between different binding modes with similar affinity. Interestingly, small changes in the molecular structure translate into significant differences in MexB-quinolone interactions. All the predicted binding modes are available for download and visualization at the following link: https://www.dsf.unica.it/dock/mexb/quinolones