Design of Force Fields from Data at Finite Temperature

We investigate the problem of how to obtain the force field between atoms of an experimentally determined structure. We show how this problem can be efficiently solved, even at finite temperature, where the position of the atoms differs substantially from the ground state. We apply our method to systems modeling proteins and demonstrate that the correct potentials can be recovered even in the presence of thermal noise.Comment: 10 pages, 1 postcript figure, Late

Steric constraints in model proteins

A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable. Furthermore, several of the encodable structures are highly designable and are the non-degenerate ground state of several sequences. Even though the native state conformations are typically compact, not all compact conformations are encodable. The incorporation of the hydrophobic and polar nature of amino acids further enhances the attractive features of the model.Comment: RevTex, 5 pages, 3 postscript figure

Technical and economic feasibility of centralized facilities for solar hydrogen production via photocatalysis and photoelectrochemistry

Photoelectrochemical water splitting is a promising route for the renewable production of hydrogen fuel. This work presents the results of a technical and economic feasibility analysis conducted for four hypothetical, centralized, large-scale hydrogen production plants based on this technology. The four reactor types considered were a single bed particle suspension system, a dual bed particle suspension system, a fixed panel array, and a tracking concentrator array. The current performance of semiconductor absorbers and electrocatalysts were considered to compute reasonable solar-to-hydrogen conversion efficiencies for each of the four systems. The U.S. Department of Energy H2A model was employed to calculate the levelized cost of hydrogen output at the plant gate at 300 psi for a 10 tonne per day production scale. All capital expenditures and operating costs for the reactors and auxiliaries (compressors, control systems, etc.) were considered. The final cost varied from $1.60–$10.40 per kg H2 with the particle bed systems having lower costs than the panel-based systems. However, safety concerns due to the cogeneration of O_2 and H_2 in a single bed system and long molecular transport lengths in the dual bed system lead to greater uncertainty in their operation. A sensitivity analysis revealed that improvement in the solar-to-hydrogen efficiency of the panel-based systems could substantially drive down their costs. A key finding is that the production costs are consistent with the Department of Energy's targeted threshold cost of $2.00–$4.00 per kg H_2 for dispensed hydrogen, demonstrating that photoelectrochemical water splitting could be a viable route for hydrogen production in the future if material performance targets can be met

Surface layering of liquids: The role of surface tension

Recent measurements show that the free surfaces of liquid metals and alloys are always layered, regardless of composition and surface tension; a result supported by three decades of simulations and theory. Recent theoretical work claims, however, that at low enough temperatures the free surfaces of all liquids should become layered, unless preempted by bulk freezing. Using x-ray reflectivity and diffuse scattering measurements we show that there is no observable surface-induced layering in water at T=298 K, thus highlighting a fundamental difference between dielectric and metallic liquids. The implications of this result for the question in the title are discussed.Comment: 5 pages, 4 figures, to appear in Phys. Rev. B. 69 (2004

Predicting the Impact of Climate Change on Threatened Species in UK Waters

Global climate change is affecting the distribution of marine species and is thought to represent a threat to biodiversity. Previous studies project expansion of species range for some species and local extinction elsewhere under climate change. Such range shifts raise concern for species whose long-term persistence is already threatened by other human disturbances such as fishing. However, few studies have attempted to assess the effects of future climate change on threatened vertebrate marine species using a multi-model approach. There has also been a recent surge of interest in climate change impacts on protected areas. This study applies three species distribution models and two sets of climate model projections to explore the potential impacts of climate change on marine species by 2050. A set of species in the North Sea, including seven threatened and ten major commercial species were used as a case study. Changes in habitat suitability in selected candidate protected areas around the UK under future climatic scenarios were assessed for these species. Moreover, change in the degree of overlap between commercial and threatened species ranges was calculated as a proxy of the potential threat posed by overfishing through bycatch. The ensemble projections suggest northward shifts in species at an average rate of 27 km per decade, resulting in small average changes in range overlap between threatened and commercially exploited species. Furthermore, the adverse consequences of climate change on the habitat suitability of protected areas were projected to be small. Although the models show large variation in the predicted consequences of climate change, the multi-model approach helps identify the potential risk of increased exposure to human stressors of critically endangered species such as common skate (Dipturus batis) and angelshark (Squatina squatina)

PROTEINCHALLENGE: Crowd sourcing in proteomics analysis and software development

AbstractIn large-scale proteomics studies there is a temptation, after months of experimental work, to plug resulting data into a convenient—if poorly implemented—set of tools, which may neither do the data justice nor help answer the scientific question. In this paper we have captured key concerns, including arguments for community-wide open source software development and “big data” compatible solutions for the future. For the meantime, we have laid out ten top tips for data processing. With these at hand, a first large-scale proteomics analysis hopefully becomes less daunting to navigate.However there is clearly a real need for robust tools, standard operating procedures and general acceptance of best practises. Thus we submit to the proteomics community a call for a community-wide open set of proteomics analysis challenges—PROTEINCHALLENGE—that directly target and compare data analysis workflows, with the aim of setting a community-driven gold standard for data handling, reporting and sharing. This article is part of a Special Issue entitled: New Horizons and Applications for Proteomics [EuPA 2012]

Quantum Cryptography

Quantum cryptography could well be the first application of quantum mechanics at the individual quanta level. The very fast progress in both theory and experiments over the recent years are reviewed, with emphasis on open questions and technological issues.Comment: 55 pages, 32 figures; to appear in Reviews of Modern Physic

Pericyte Migration: A Novel Mechanism of Pericyte Loss in Experimental Diabetic Retinopathy

OBJECTIVE— The mechanism underlying pericyte loss during incipient diabetic retinopathy remains controversial. Hyperglycemia induces angiopoietin-2 (Ang-2) transcription, which modulates capillary pericyte coverage. In this study, we assessed loss of pericyte subgroups and the contribution of Ang-2 to pericyte migration

Beliefs and practices of patients with advanced cancer: implications for communication

The aim of this study was to investigate the beliefs that patients with advanced cancer held about the curability of their cancer, their use of alternatives to conventional medical treatment, and their need to have control over decisions about treatment. Of 149 patients who fulfilled the criteria for participation and completed a self-administered questionnaire, 45 patients (31%) believed their cancer was incurable, 61 (42%) were uncertain and 39 (27%) believed their cancer was curable. The index of need for control over treatment decisions was low in 53 patients (35.6%) and high in only 17 patients (11.4%). Committed users of alternatives to conventional medical treatments were more likely to believe that their cancer was curable (

Plasma Dynamics

Contains reports on seventeen research projects split into two sections.National Science Foundation (Grant ENG77-00340)U. S. Energy Research and Development Administration (Contract E(11-1)-2766)U. S. Energy Research and Development Administration (Contract EY-76-S-02-2766)U. S. Air Force - Office of Scientific Research (Grant AFOSR-77-3143)U. S. Department of Energy (Grant EG-77-G-01-4107