Accurate Determination of the Shear Viscosity of the One-Component Plasma

The shear viscosity coefficient of the one-component plasma is calculated with unprecedented accuracy using equilibrium molecular dynamics simulations and the Green-Kubo relation. Numerical and statistical uncertainties and their mitigation for improving accuracy are analyzed. In the weakly coupled regime, our the results agree with the Landau-Spitzer prediction. In the moderately and strongly coupled regimes, our results are found in good agreement with recent results obtained for the Yukawa one-component plasma using non-equilibrium molecular dynamics. A practical formula is provided for evaluating the viscosity coefficient across coupling regimes, from the weakly-coupled regime up to solidification threshold. The results are used to test theoretical predictions of the viscosity coefficients found in the literature.Comment: 13 pages, 10 figure

Effective Potential Theory: A Practical Way to Extend Plasma Transport Theory to Strong Coupling

The effective potential theory is a physically motivated method for extending traditional plasma transport theories to stronger coupling. It is practical in the sense that it is easily incorporated within the framework of the Chapman-Enskog or Grad methods that are commonly applied in plasma physics and it is computationally efficient to evaluate. The extension is to treat binary scatterers as interacting through the potential of mean force, rather than the bare Coulomb or Debye-screened Coulomb potential. This allows for aspects of many-body correlations to be included in the transport coefficients. Recent work has shown that this method accurately extends plasma theory to orders of magnitude stronger coupling when applied to the classical one-component plasma model. The present work shows that similar accuracy is realized for the Yukawa one-component plasma model and it provides a comparison with other approaches.Comment: 6 pages, 3 figures, Proceedings of the Strongly Coupled Coulomb Systems conference 201

Genome-wide inference of ancestral recombination graphs

The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of n chromosomes conditional on an ARG of n-1 chromosomes, an operation we call "threading." Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the true posterior distribution and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. Preliminary results also indicate that our methods can be used to gain insight into complex features of human population structure, even with a noninformative prior distribution.Comment: 88 pages, 7 main figures, 22 supplementary figures. This version contains a substantially expanded genomic data analysi

Leucine supplementation differentially enhances pancreatic cancer growth in lean and overweight mice

Kristyn A Liu1†, Laura M Lashinger1†, Audrey J Rasmussen1† and Stephen D Hursting12* Author Affiliations 1 Department of Nutritional Sciences, University of Texas at Austin, Austin, TX 78723, USA 2 Department of Molecular Carcinogenesis, University of Texas M.D. Anderson Cancer Center, 1808 Park Road 1c, Smithville, TX 78957, USABackground: The risk of pancreatic cancer, the 4th deadliest cancer for both men and women in the United States, is increased by obesity. Calorie restriction (CR) is a well-known dietary regimen that prevents or reverses obesity and suppresses tumorigenesis in a variety of animal models, at least in part via inhibition of mammalian target of rapamycin (mTOR) signaling. Branched-chain amino acids (BCAA), especially leucine, activate mTOR and enhance growth and proliferation of myocytes and epithelial cells, which is why leucine is a popular supplement among athletes. Leucine is also increasingly being used as a treatment for pancreatic cancer cachexia, but the effects of leucine supplementation on pancreatic tumor growth have not been elucidated. Results: Supplementation with leucine increased pancreatic tumor growth in both lean (104 ± 17 mm3 versus 46 ± 13 mm3; P <0.05) and overweight (367 ± 45 mm3 versus 230 ± 39 mm3; P <0.01) mice, but tumor enhancement was associated with different biological outcomes depending on the diet. In the lean mice, leucine increased phosphorylation of mTOR and downstream effector S6 ribosomal protein, but in the overweight mice, leucine reduced glucose clearance and thus increased the amount of circulating glucose available to the tumor. Conclusion: These findings show that leucine supplementation enhances tumor growth in both lean and overweight mice through diet-dependent effects in a murine model of pancreatic cancer, suggesting caution against the clinical use of leucine supplementation for the purposes of skeletal muscle enhancement in cachectic patients.Nutritional Science

On toric geometry, Spin(7) manifolds, and type II superstring compactifications

We consider type II superstring compactifications on the singular Spin(7) manifold constructed as a cone on SU(3)/U(1). Based on a toric realization of the projective space CP^2, we discuss how the manifold can be viewed as three intersecting Calabi-Yau conifolds. The geometric transition of the manifold is then addressed in this setting. The construction is readily extended to higher dimensions where we speculate on possible higher-dimensional geometric transitions. Armed with the toric description of the Spin(7) manifold, we discuss a brane/flux duality in both type II superstring theories compactified on this manifold.Comment: 14 pages, v2: version to be publishe

Properties of the mechanosensitive channel MscS pore revealed by tryptophan scanning mutagenesis

Funding This work was supported by a Wellcome Trust Programme grant [092552/A/10/Z awarded to I.R.B., S.M., J. H. Naismith (University of St Andrews, St Andrews, U.K.), and S. J. Conway (University of Oxford, Oxford, U.K.)] (T.R. and M.D.E.), by a BBSRC grant (A.R.) [BB/H017917/1 awarded to I.R.B., J. H. Naismith, and O. Schiemann (University of St Andrews)], by a Leverhulme Emeritus Fellowship (EM-2012-060\2), and by a CEMI grant to I.R.B. from the California Institute of Technology. The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013 FP7/2007-2011) under Grant PITN-GA-2011-289384 (FP7-PEOPLE-2011-ITN NICHE) (H.G.) (awarded to S.M.).Peer reviewedPublisher PD

Higher su(N) tensor products

We extend our recent results on ordinary su(N) tensor product multiplicities to higher su(N) tensor products. Particular emphasis is put on four-point couplings where the tensor product of four highest weight modules is considered. The number of times the singlet occurs in the decomposition is the associated multiplicity. In this framework, ordinary tensor products correspond to three-point couplings. As in that case, the four-point multiplicity may be expressed explicitly as a multiple sum measuring the discretised volume of a convex polytope. This description extends to higher-point couplings as well. We also address the problem of determining when a higher-point coupling exists, i.e., when the associated multiplicity is non-vanishing. The solution is a set of inequalities in the Dynkin labels.Comment: 17 pages, LaTe