Crystal structure prediction using the Minima Hopping method

A structure prediction method is presented based on the Minima Hopping method. Optimized moves on the configurational enthalpy surface are performed to escape local minima using variable cell shape molecular dynamics by aligning the initial atomic and cell velocities to low curvature directions of the current minimum. The method is applied to both silicon crystals and binary Lennard-Jones mixtures and the results are compared to previous investigations. It is shown that a high success rate is achieved and a reliable prediction of unknown ground state structures is possible.Comment: 9 pages, 6 figures, novel approach in structure prediction, submitted to the Journal of Chemical Physic

Electrical anisotropy due to gas hydrate-filled fractures

In 2006, the Indian National Gas Hydrate Program Expedition 01, or NGHP-01, discovered gas hydrate as fill in near-vertical fractures in unconsolidated sediments at several drilling sites on the Indian continental margins. These gas hydrate-filled fractures were identified on logging-while-drilling resistivity images. The gas hydrate-filled fracture intervals coincide with high measured resistivity at the NGHP-01 sites. High measured resistivity translates into high hydrate saturations via Archie's equation; however, these high saturations contradict lower gas hydrate saturations determined from pressure core and chlorinity measurements. Also, in intervals with near-vertical gas hydrate-filled fractures, there is considerable separation between phase shift and attenuation resistivity logs, with 2-MHz resistivity measurements being significantly higher than 400-kHz resistivity measurements. We modeled the sensitivity of the propagation resistivity measurements in the gas hydrate-filled fracture intervals at NGHP-01 Sites 5 and 10. Near-vertical hydrate-filled fractures can cause the abnormally high resistivity measurements in vertical holes due to electrical anisotropy. The model suggests the gas hydrate saturations in situ are usually significantly lower than those calculated from Archie's equation. In addition, these modeled gas hydrate saturations generally agree with the lower gas hydrate saturations obtained from pressure core and chlorinity measurements at NGHP-01 Sites 5 and 10

The Peculiar Phase Structure of Random Graph Bisection

The mincut graph bisection problem involves partitioning the n vertices of a graph into disjoint subsets, each containing exactly n/2 vertices, while minimizing the number of "cut" edges with an endpoint in each subset. When considered over sparse random graphs, the phase structure of the graph bisection problem displays certain familiar properties, but also some surprises. It is known that when the mean degree is below the critical value of 2 log 2, the cutsize is zero with high probability. We study how the minimum cutsize increases with mean degree above this critical threshold, finding a new analytical upper bound that improves considerably upon previous bounds. Combined with recent results on expander graphs, our bound suggests the unusual scenario that random graph bisection is replica symmetric up to and beyond the critical threshold, with a replica symmetry breaking transition possibly taking place above the threshold. An intriguing algorithmic consequence is that although the problem is NP-hard, we can find near-optimal cutsizes (whose ratio to the optimal value approaches 1 asymptotically) in polynomial time for typical instances near the phase transition.Comment: substantially revised section 2, changed figures 3, 4 and 6, made minor stylistic changes and added reference

The performance of Minima Hopping and Evolutionary Algorithms for cluster structure prediction

We compare Evolutionary Algorithms with Minima Hopping for global optimization in the field of cluster structure prediction. We introduce a new {\em average offspring} recombination operator and compare it with previously used operators. Minima Hopping is improved with a {\em softening} method and a stronger feedback mechanism. Test systems are atomic clusters with Lennard-Jones interaction as well as silicon and gold clusters described by force fields. The improved Minima Hopping is found to be well-suited to all these homoatomic problems. The evolutionary algorithm is more efficient for systems with compact and symmetric ground states, including LJ$_{150}$, but it fails for systems with very complex energy landscapes and asymmetric ground states, such as LJ$_{75}$ and silicon clusters with more than 30 atoms. Both successes and failures of the evolutionary algorithm suggest ways for its improvement

Ultrahigh-Energy Neutrino-Nucleon Cross Sections and Perturbative Unitarity

Unitarity relates the total cross section for neutrino-nucleon scattering to the neutrino-nucleon forward scattering amplitude. Assuming the validity of the perturbative expansion of the forward amplitude in the {\em weak} coupling constant, we derive a unitarity bound on the inelastic cross section. The inelastic cross section saturates this bound at a typical neutrino energy $E_\nu \simeq 10^8 {\rm GeV}$. This implies that calculations of the inelastic cross section that use current parton distribution functions and lowest order weak perturbation theory are unreliable above this energy.Comment: 11 pages, 3 figures, RevTeX, additional reference

Geographic Differences in Time to Culture Conversion in Liquid Media: Tuberculosis Trials Consortium Study 28. Culture Conversion Is Delayed in Africa

Tuberculosis Trials Consortium Study 28, was a double blind, randomized, placebo-controlled, phase 2 clinical trial examining smear positive pulmonary Mycobacterium tuberculosis. Over the course of intensive phase therapy, patients from African sites had substantially delayed and lower rates of culture conversion to negative in liquid media compared to non-African patients. We explored potential explanations of this finding.In TBTC Study 28, protocol-correct patients (n = 328) provided spot sputum specimens for M. tuberculosis culture in liquid media, at baseline and weeks 2, 4, 6 and 8 of study therapy. We compared sputum culture conversion for African and non-African patients stratified by four baseline measures of disease severity: AFB smear quantification, extent of disease on chest radiograph, cavity size and the number of days to detection of M. tuberculosis in liquid media using the Kaplan-Meier product-limit method. We evaluated specimen processing and culture procedures used at 29 study laboratories serving 27 sites.African TB patients had more extensive disease at enrollment than non-African patients. However, African patients with the least disease by the 4 measures of disease severity had conversion rates on liquid media that were substantially lower than conversion rates in non-African patients with the greatest extent of disease. HIV infection, smoking and diabetes did not explain delayed conversion in Africa. Some inter-site variation in laboratory processing and culture procedures within accepted practice for clinical diagnostic laboratories was found.Compared with patients from non-African sites, African patients being treated for TB had delayed sputum culture conversion and lower sputum conversion rates in liquid media that were not explained by baseline severity of disease, HIV status, age, smoking, diabetes or race. Further investigation is warranted into whether modest variation in laboratory processes substantially influences the efficacy outcomes of phase 2 TB treatment trials or if other factors (e.g., nutrition, host response) are involved.ClinicalTrials.gov NCT00144417

A Systematic Review of Music Therapy Practice and Outcomes with Acute Adult Psychiatric In-Patients

PMCID: PMC3732280This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited