81 research outputs found
Langevin dynamics in constant pressure extended systems
No full textThe advantages of performing Langevin dynamics in extended systems are discussed. A simple Langevin dynamics scheme for producing the canonical ensemble is reviewed, and is then extended to the Hoover ensemble. We show that the resulting equations of motion generate the isobaric–isothermal ensemble. The Parrinello–Rahman ensemble is then discussed and we show that despite the presence of intrinsic probability gradients in this system, a Langevin dynamics approach samples the extended phase space in the correct fashion. The implementation of these methods in the ab initio plane wave density functional theory code CASTEP [M. D. Segall, P. L. D. Lindan, M. J. Probert, C. J. Pickard, P. J. Hasnip, S. J. Clarke, and M. C. Payne, J. Phys.: Condens. Matter 14, 2717 (2003)] is demonstrated
Defamation, A Camouflage of Psychic Interests: The Beginning of a Behavioral Analysis
No full textDoes the law of defamation need to be reformed? The author thinks so. Professor Probert rejects the doctrine of libel per se and questions the courts\u27 understanding and use of the term reputation. It is his belief that plaintiffs on an individual basis should have increased benefit of the knowledge accumulated by the various social sciences in proving the harm done by the alleged defamation, with more liberalization in the requirements of pleading and proof than is now generally countenanced by the courts
A periodic genetic algorithm with real-space representation for crystal structure and polymorph prediction
No full textA genetic algorithm is described that is suitable for determining the global minimum energy configurations of crystal structures and which can also be used as a polymorph search technique. This algorithm requires no prior assumptions about unit cell size, shape, or symmetry, nor about the ionic configuration within the unit cell. This therefore enables true ab initio crystal structure and polymorph prediction. Our algorithm uses a real-space representation of the population members, and makes use of a periodic cut for the crossover operation. Results on large Lennard-Jones systems with fcc- and hcp-commensurate cells show robust convergence to the bulk structure from a random initial assignment and an ability to successfully discriminate between competing low enthalpy configurations. Results from an ab initio carbon polymorph search show the spontaneous emergence of both Lonsdaleite and graphite-like structures
Improving the convergence of defect calculations in supercells: An ab initio study of the neutral silicon vacancy
No full textWe present a systematic methodology for the accurate calculation of defect structures in supercells, which we illustrate with a study of the neutral vacancy in silicon. This is a prototypical defect which has been studied extensively using ab initio methods, yet remarkably there is still no consensus about the energy or structure of this defect, or even whether the nearest-neighbor atoms relax inwards or outwards. In this paper, we show that the differences between previous calculations can be attributed to supercell convergence errors, and we demonstrate how to systematically reduce each such source of error. The various sources of scatter in previous theoretical studies are discussed and a different effect, that of supercell symmetry, is identified. It is shown that a consistent treatment of this effect is crucial in understanding the systematic effects of increasing the supercell size. This work therefore also presents the best converged ab initio study of the neutral silicon vacancy to date
Environmentally induced transgenerational changes in seed longevity: Maternal and genetic influence
No full textBackground and Aims: Seed longevity, a fundamental plant trait for ex situ conservation and persistence in the soil of many species, varies across populations and generations that experience different climates. This study investigates the extent to which differences in seed longevity are due to genetic differences and/or modified by adaptive responses to environmental changes. Methods: Seeds of two wild populations of Silene vulgaris from alpine (wA) and lowland (wL) locations and seeds originating from their cultivation in a lowland common garden for two generations (cA1, cL1, cA2 and cL2) were exposed to controlled ageing at 45 °C, 60 % relative humidity and regularly sampled for germination and relative mRNA quantification (SvHSP17.4 and SvNRPD12). Key Results: The parental plant growth environment affected the longevity of seeds with high plasticity. Seeds of wL were significantly longer lived than those of wA. However, when alpine plants were grown in the common garden, longevity doubled for the first generation of seeds produced (cA1). Conversely, longevity was similar in all lowland seed lots and did not increase in the second generation of seeds produced from alpine plants grown in the common garden (cA2). Analysis of parental effects on mRNA seed provisioning indicated that the accumulation of gene transcripts involved in tolerance to heat stress was highest in wL, cL1 and cL2, followed by cA1, cA2 and wA. Conclusions: Seed longevity has a genetic basis, but may show strong adaptive responses, which are associated with differential accumulation of mRNA via parental effects. Adaptive adjustments of seed longevity due to transgenerational plasticity may play a fundamental role in the survival and persistence of the species in the face of future environmental challenges. The results suggest that regeneration location may have important implications for the conservation of alpine plants held in seed banks. © 2014 The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: [email protected]
State and Law
No full textThis is the author accepted manuscript. The final version is available in print format only from Bloombsbury
TNF and its receptors in the CNS: The essential, the desirable and the deleterious effects
No full textAbstractTumor necrosis factor (TNF) is the prototypic pro-inflammatory cytokine. It is central to host defense and inflammatory responses but under certain circumstances also triggers cell death and tissue degeneration. Its pleiotropic effects often lead to opposing outcomes during the development of immune-mediated diseases, particularly those affecting the central nervous system (CNS). The reported contradictions may result from lack of precision in discussing TNF. TNF signaling comprises at minimum a two-ligand (soluble and transmembrane TNF) and two-receptor (TNFR1 and TNFR2) system, with ligands and receptors both differentially expressed and regulated on different cell types. The “functional multiplicity” this engenders is the focus of much research, but there is still no general consensus on functional outcomes of TNF signaling in general, let alone in the CNS. In this review, evidence showing the effects of TNF in the CNS under physiological and pathophysiological conditions is placed in the context of major advances in understanding of the cellular and molecular mechanisms that govern TNF function in general. Thus the roles of TNF signaling in the CNS shift from the conventional dichotomy of beneficial and deleterious, that mainly explain effects under pathological conditions, to incorporate a growing number of “essential” and “desirable” roles for TNF and its main cellular source in the CNS, microglia, under physiological conditions including regulation of neuronal activity and maintenance of myelin. An improved holistic view of TNF function in the CNS might better reconcile the expansive experimental data with stark clinical evidence that reduced functioning of TNF and its dominant pro-inflammatory receptor, TNFR1, are risk factors for the development of multiple sclerosis. It will also facilitate the safe translation of basic research findings from animal models to humans and propel the development of more selective anti-TNF therapies aimed at selectively inhibiting deleterious effects of this cytokine while maintaining its essential and desirable ones, in the periphery and the CNS
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