Thermodynamic interpretation of the scaling of the dynamics of supercooled liquids

The recently discovered scaling law for the relaxation times, tau=f(T,V^g), where T is temperature and V the specific volume, is derived by a revision of the entropy model of the glass transition dynamics originally proposed by Avramov [I. Avramov, J. Non-Cryst. Solids 262, 258 (2000).]. In this modification the entropy is calculated by an alternative route, while retaining the approximation that the heat capacity is constant with T and P. The resulting expression for the variation of the relaxation time with T and V is shown to accurately fit experimental data for several glass-forming liquids and polymers over an extended range encompassing the dynamic crossover. From this analysis, which is valid for any model in which the relaxation time is a function of the entropy. we find that the scaling exponent g can be identified with the Gruneisen constant.Comment: 24 pages, 7 figure

Stationary probability density of stochastic search processes in global optimization

A method for the construction of approximate analytical expressions for the stationary marginal densities of general stochastic search processes is proposed. By the marginal densities, regions of the search space that with high probability contain the global optima can be readily defined. The density estimation procedure involves a controlled number of linear operations, with a computational cost per iteration that grows linearly with problem size

Constant-time solution to the Global Optimization Problem using Bruschweiler's ensemble search algorithm

A constant-time solution of the continuous Global Optimization Problem (GOP) is obtained by using an ensemble algorithm. We show that under certain assumptions, the solution can be guaranteed by mapping the GOP onto a discrete unsorted search problem, whereupon Bruschweiler's ensemble search algorithm is applied. For adequate sensitivities of the measurement technique, the query complexity of the ensemble search algorithm depends linearly on the size of the function's domain. Advantages and limitations of an eventual NMR implementation are discussed.Comment: 14 pages, 0 figure

Density scaling and quasiuniversality of flow-event statistics for athermal plastic flows

Athermal plastic flows were simulated for the Kob-Andersen binary Lennard-Jones system and its repulsive version in which the sign of the attractive terms is changed to a plus. Properties evaluated from simulations at different densities include the distributions of energy drops, stress drops, and strain intervals between the flow events. By reference to hidden scale invariance we show that simulations at a single density in conjunction with an equilibrium-liquid simulation at the same density allows one to predict the plastic flow-event properties at other densities. We furthermore demonstrate quasiuniversality of the flow-event statistics

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost andduringmushroomformation.The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation aremore highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics

Discovery of functionally selective C5aR2 ligands: novel modulators of C5a signalling.

The complement cascade is comprised of a highly sophisticated network of innate immune proteins that are activated in response to invading pathogens or tissue injury. The complement activation peptide, C5a, binds two seven transmembrane receptors, namely the C5a receptor 1 (C5aR1) and C5a receptor 2 (C5aR2, or C5L2). C5aR2 is a non-G-protein-signalling receptor whose biological role remains controversial. Some of this controversy arises owing to the lack of selective ligands for C5aR2. In this study, a library of 61 peptides based on the C-terminus of C5a was assayed for the ability to selectively modulate C5aR2 function. Two ligands (P32 and P59) were identified as functionally selective C5aR2 ligands, exhibiting selective recruitment of β-arrestin 2 via C5aR2, partial inhibition of C5a-induced ERK1/2 activation and lipopolysaccharide-stimulated interleukin-6 release from human monocyte-derived macrophages. Importantly, neither ligand could induce ERK1/2 activation or inhibit C5a-induced ERK1/2 activation via C5aR1 directly. Finally, P32 inhibited C5a-mediated neutrophil mobilisation in wild-type, but not C5aR2(-/-) mice. These functionally selective ligands for C5aR2 are novel tools that can selectively modulate C5a activity in vitro and in vivo, and thus will be valuable tools to interrogate C5aR2 function.Immunology and Cell Biology advance online publication, 17 May 2016; doi:10.1038/icb.2016.43

Positive Semidefiniteness and Positive Definiteness of a Linear Parametric Interval Matrix

We consider a symmetric matrix, the entries of which depend linearly on some parameters. The domains of the parameters are compact real intervals. We investigate the problem of checking whether for each (or some) setting of the parameters, the matrix is positive definite (or positive semidefinite). We state a characterization in the form of equivalent conditions, and also propose some computationally cheap sufficient\,/\,necessary conditions. Our results extend the classical results on positive (semi-)definiteness of interval matrices. They may be useful for checking convexity or non-convexity in global optimization methods based on branch and bound framework and using interval techniques

Implementing Parallel Differential Evolution on Spark

[Abstract] Metaheuristics are gaining increased attention as an efficient way of solving hard global optimization problems. Differential Evolution (DE) is one of the most popular algorithms in that class. However, its application to realistic problems results in excessive computation times. Therefore, several parallel DE schemes have been proposed, most of them focused on traditional parallel programming interfaces and infrastruc- tures. However, with the emergence of Cloud Computing, new program- ming models, like Spark, have appeared to suit with large-scale data processing on clouds. In this paper we investigate the applicability of Spark to develop parallel DE schemes to be executed in a distributed environment. Both the master-slave and the island-based DE schemes usually found in the literature have been implemented using Spark. The speedup and efficiency of all the implementations were evaluated on the Amazon Web Services (AWS) public cloud, concluding that the island- based solution is the best suited to the distributed nature of Spark. It achieves a good speedup versus the serial implementation, and shows a decent scalability when the number of nodes grows.[Resumen] Las metaheurísticas están recibiendo una atención creciente como técnica eficiente en la resolución de problemas difíciles de optimización global. Differential Evolution (DE) es una de las metaheurísticas más populares, sin embargo su aplicación en problemas reales deriva en tiempos de cómputo excesivos. Por ello se han realizado diferentes propuestas para la paralelización del DE, en su mayoría utilizando infraestructuras e interfaces de programación paralela tradicionales. Con la aparición de la computación en la nube también se han propuesto nuevos modelos de programación, como Spark, que permiten manejar el procesamiento de datos a gran escala en la nube. En este artículo investigamos la aplicabilidad de Spark en el desarrollo de implementaciones paralelas del DE para su ejecución en entornos distribuidos. Se han implementado tanto la aproximación master-slave como la basada en islas, que son las más comunes. También se han evaluado la aceleración y la eficiencia de todas las implementaciones usando el cloud público de Amazon (AWS, Amazon Web Services), concluyéndose que la implementación basada en islas es la más adecuada para el esquema de distribución usado por Spark. Esta implementación obtiene una buena aceleración en relación a la implementación serie y muestra una escalabilidad bastante buena cuando el número de nodos aumenta.[Resume] As metaheurísticas están recibindo unha atención a cada vez maior como técnica eficiente na resolución de problemas difíciles de optimización global. Differential Evolution (DE) é unha das metaheurísticas mais populares, ainda que a sua aplicación a problemas reais deriva en tempos de cómputo excesivos. É por iso que se propuxeron diferentes esquemas para a paralelización do DE, na sua maioría utilizando infraestruturas e interfaces de programación paralela tradicionais. Coa aparición da computación na nube tamén se propuxeron novos modelos de programación, como Spark, que permiten manexar o procesamento de datos a grande escala na nube. Neste artigo investigamos a aplicabilidade de Spark no desenvolvimento de implementacións paralelas do DE para a sua execución en contornas distribuidas. Implementáronse tanto a aproximación master-slave como a baseada en illas, que son as mais comúns. Tamén se avaliaron a aceleración e a eficiencia de todas as implementacións usando o cloud público de Amazon (AWS, Amazon Web Services), tirando como conclusión que a implementación baseada en illas é a mais acaida para o esquema de distribución usado por Spark. Esta implementación obtén unha boa aceleración en relación á implementación serie e amosa unha escalabilidade bastante boa cando o número de nos aumenta.Ministerio de Economía y Competitividad; DPI2014-55276-C5-2-RXunta de Galicia; GRC2013/055Xunta de Galicia; R2014/04

Mechanical Relaxation in Glasses and at the Glass Transition

The Gilroy-Phillips model of relaxational jumps in asymmetric double-well potentials, developed for the Arrhenius-type secondary relaxations of the glass phase, is extended to a formal description of the breakdown of the shear modulus at the glass transition, the flow process.Comment: 13 pages, 11 figures, 49 ref