Ab initio Molecular Dynamical Investigation of the Finite Temperature Behavior of the Tetrahedral Au19_{19} and Au20_{20} Clusters

Density functional molecular dynamics simulations have been carried out to understand the finite temperature behavior of Au$_{19}$ and Au$_{20}$ clusters. Au$_{20}$ has been reported to be a unique molecule having tetrahedral geometry, a large HOMO-LUMO energy gap and an atomic packing similar to that of the bulk gold (J. Li et al., Science, {\bf 299} 864, 2003). Our results show that the geometry of Au$_{19}$ is exactly identical to that of Au$_{20}$ with one missing corner atom (called as vacancy). Surprisingly, our calculated heat capacities for this nearly identical pair of gold cluster exhibit dramatic differences. Au$_{20}$ undergoes a clear and distinct solid like to liquid like transition with a sharp peak in the heat capacity curve around 770 K. On the other hand, Au$_{19}$ has a broad and flat heat capacity curve with continuous melting transition. This continuous melting transition turns out to be a consequence of a process involving series of atomic rearrangements along the surface to fill in the missing corner atom. This results in a restricted diffusive motion of atoms along the surface of Au$_{19}$ between 650 K to 900 K during which the shape of the ground state geometry is retained. In contrast, the tetrahedral structure of Au$_{20}$ is destroyed around 800 K, and the cluster is clearly in a liquid like state above 1000 K. Thus, this work clearly demonstrates that (i) the gold clusters exhibit size sensitive variations in the heat capacity curves and (ii) the broad and continuous melting transition in a cluster, a feature which has so far been attributed to the disorder or absence of symmetry in the system, can also be a consequence of a defect (absence of a cap atom) in the structure.Comment: 7 figure

CAPSULE: Language and system support for efficient state sharing in distributed stream processing systems

Data stream processing applications are often expressed as data flow graphs, composed of operators connected via streams. This structured representation provides a simple yet powerful paradigm for building large-scale, distributed, high-performance applications. However, there are many tasks that require sharing data across operators, and across operators and the runtime using a less structured mechanism than point-to-point data flows. Examples include updating control variables, sending notifications, collecting metrics, building collective models, etc. In this paper we describe CAPSULE, which fills this gap. CAPSULE is a code generation and runtime framework that offers an easy to use and highly flexible framework for developers to realize shared variables (CAPSULE term for shared state) by specifying a data structure (at the programming-language level), and a few associated configuration parameters that qualify the expected usage scenario. Besides the easy of use and flexibility, CAPSULE offers the following important benefits: (1) Custom Code Generation - CAPSULE makes use of user-specified configuration parameters and information from the runtime to generate shared variable servers that are tailored for the specific usage scenario, (2) Composability - CAPSULE supports deployment time composition of the shared variable servers to achieve desired levels of scalability, performance and fault-tolerance, and (3) Extensibility - CAPSULE provides simple interfaces for extending the CAPSULE framework with more protocols, transports, caching mechanisms, etc. We describe the motivation for CAPSULE and its design, report on its implementation status, and then present experimental results. Copyright © 2012 ACM

Non-isothermal model for the direct isotropic/smectic-A liquid crystalline transition

An extension to a high-order model for the direct isotropic/smectic-A liquid crystalline phase transition was derived to take into account thermal effects including anisotropic thermal diffusion and latent heat of phase-ordering. Multi-scale multi-transport simulations of the non-isothermal model were compared to isothermal simulation, showing that the presented model extension corrects the standard Landau-de Gennes prediction from constant growth to diffusion-limited growth, under shallow quench/undercooling conditions. Non-isothermal simulations, where meta-stable nematic pre-ordering precedes smectic-A growth, were also conducted and novel non-monotonic phase-transformation kinetics observed.Comment: First revision: 20 pages, 7 figure

Majorations explicites de fonctions de Hilbert-Samuel géométrique et arithmétique

International audienceBy using the $\mathbb R$-filtration approach of Arakelov geometry, one establishes explicit upper bounds for geometric and arithmetic Hilbert-Samuel function for line bundles on projective varieties and hermitian line bundles on arithmetic projective varieties

Moving towards public policy-ready science: philosophical insights on the social-ecological systems perspective for conservation science

The social-ecological systems (SES) perspective stems from the need to rethink the ways humans relate to the environment, given the evidence that conventional conservation and management approaches are often ineffective in dealing with complex socio-environmental problems. The SES approach conceives non-scientific and scientific knowledge as equally necessary in the process of management and public policy formation. Thus, the adoption of the SES approach must also serve to make better decisions about what kind of science and technology would be ‘public policy-ready’ (as well as also ‘policy-relevant’); that is, a science oriented and conceived to provide concrete solutions to societal needs and demands. Here we review and reinterpret the SES perspective as a real paradigm change for conservation science. Under the lenses of philosophy, we try to untangle some weak points of the SES approach in order to advance to a conservation science closer to the process of science-based public policy creation and to enhance the intertwining with other types of knowledge. In this sense, we discuss how co-production of knowledge and decision-making process under the SES perspective are a huge step forward towards fulfilling the need to bring increasingly closer the spheres of science and policy, narrowing its interface.Fil: Sala, Juan Emilio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Biología de Organismos Marinos; Argentina. Universidad Nacional de la Patagonia "San Juan Bosco"; ArgentinaFil: Torchio, Gabriela María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Biología de Organismos Marinos; Argentin

Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks

<p>Abstract</p> <p>Background</p> <p>For large-scale biological networks represented as signed graphs, the index of frustration measures how far a network is from a monotone system, i.e., how incoherently the system responds to perturbations.</p> <p>Results</p> <p>In this paper we find that the frustration is systematically lower in transcriptional networks (modeled at functional level) than in signaling and metabolic networks (modeled at stoichiometric level). A possible interpretation of this result is in terms of energetic cost of an interaction: an erroneous or contradictory transcriptional action costs much more than a signaling/metabolic error, and therefore must be avoided as much as possible. Averaging over all possible perturbations, however, we also find that unlike for transcriptional networks, in the signaling/metabolic networks the probability of finding the system in its least frustrated configuration tends to be high also in correspondence of a moderate energetic regime, meaning that, in spite of the higher frustration, these networks can achieve a globally ordered response to perturbations even for moderate values of the strength of the interactions. Furthermore, an analysis of the energy landscape shows that signaling and metabolic networks lack energetic barriers around their global optima, a property also favouring global order.</p> <p>Conclusion</p> <p>In conclusion, transcriptional and signaling/metabolic networks appear to have systematic differences in both the index of frustration and the transition to global order. These differences are interpretable in terms of the different functions of the various classes of networks.</p

In silico evolution of signaling networks using rule-based models: bistable response dynamics

One of the ultimate goals in biology is to understand the design principles of biological systems. Such principles, if they exist, can help us better understand complex, natural biological systems and guide the engineering of de novo ones. Towards deciphering design principles, in silico evolution of biological systems with proper abstraction is a promising approach. Here, we demonstrate the application of in silico evolution combined with rule-based modelling for exploring design principles of cellular signaling networks. This application is based on a computational platform, called BioJazz, which allows in silico evolution of signaling networks with unbounded complexity. We provide a detailed introduction to BioJazz architecture and implementation and describe how it can be used to evolve and/or design signaling networks with defined dynamics. For the latter, we evolve signaling networks with switch-like response dynamics and demonstrate how BioJazz can result in new biological insights on network structures that can endow bistable response dynamics. This example also demonstrated both the power of BioJazz in evolving and designing signaling networks and its limitations at the current stage of development.Comment: 24 pages, 7 figure

Development of methods for the preparation of radiopure ⁸²Se sources for the SuperNEMO neutrinoless double-beta decay experiment

A radiochemical method for producing 82Se sources with an ultra-low level of contamination of natural radionuclides (40K, decay products of 232Th and 238U) has been developed based on cation-exchange chromatographic purification with reverse removal of impurities. It includes chromatographic separation (purification), reduction, conditioning (which includes decantation, centrifugation, washing, grinding, and drying), and 82Se foil production. The conditioning stage, during which highly dispersed elemental selenium is obtained by the reduction of purified selenious acid (H2SeO3) with sulfur dioxide (SO2) represents the crucial step in the preparation of radiopure 82Se samples. The natural selenium (600 g) was first produced in this procedure in order to refine the method. The technique developed was then used to produce 2.5 kg of radiopure enriched selenium (82Se). The produced 82Se samples were wrapped in polyethylene (12 μm thick) and radionuclides present in the sample were analyzed with the BiPo-3 detector. The radiopurity of the plastic materials (chromatographic column material and polypropylene chemical vessels), which were used at all stages, was determined by instrumental neutron activation analysis. The radiopurity of the 82Se foils was checked by measurements with the BiPo-3 spectrometer, which confirmed the high purity of the final product. The measured contamination level for 208Tl was 8-54 μBq/kg, and for 214Bi the detection limit of 600 μBq/kg has been reached.</p