Dipolar ordering in Fe8?

We show that the low-temperature physics of molecular nanomagnets, contrary to the prevailing one-molecule picture, must be determined by the long-range magnetic ordering due to many-body dipolar interactions. The calculations here performed, using Ewald's summation, suggest a ferromagnetic ground state with a Curie temperature of about 130 mK. The energy of this state is quite close to those of an antiferromagnetic state and to a glass of frozen spin chains. The latter may be realized at finite temperature due to its high entropy.Comment: 7 pages, no figures, submitted to EP

Analysis of the atmospheric distribution, sources, and sinks of oxygenated volatile organic chemicals based on measurements over the Pacific during TRACE-P

Airborne measurements of a large number of oxygenated volatile organic chemicals (OVOC) were carried out in the Pacific troposphere (0.1 - 12 km) in winter/spring of 2001 (24 February to 10 April). Specifically, these measurements included acetone (CH3COCHA3), methylethyl ketone (CH3COC2H5, MEK), methanol (CH3OH), ethanol (C2H5OH), acetaldehyde (CH3CHO), propionaldehyde C2H 5CHO), peroxyacylnitrates (PANs) (CnH 2n+1COO2NO2), and organic nitrates (CnH2n+1ONO2). Complementary measurements of formaldehyde (HCHO), methyl hydroperoxide (CH 3OOH), and selected tracers were also available. OVOC were abundant in the clean troposphere and were greatly enhanced in the outflow regions from Asia. Background mixing ratios were typically highest in the lower troposphere and declined toward the upper troposphere and the lowermost stratosphere. Their total abundance (ΣOVOC) was nearly twice that of nonmethane hydrocarbons (Σ C2-C8 NMHC. Throughout the troposphere, the OH reactivity of OVOC is comparable to that of methane and far exceeds that of NMHC. A comparison of these data with western Pacific observations collected some 7 years earlier (February-March 1994) did not reveal significant differences. Mixing ratios of OVOC were strongly correlated with each other as well as with tracers of fossil and biomass/biofuel combustion. Analysis of the relative enhancement of selected OVOC with respect to CH 3Cl and CO in 12 plumes originating from fires and sampled in the free troposphere (3-11 km) is used to assess their primary and secondary emissions from biomass combustion. The composition of these plumes also indicates a large shift of reactive nitrogen into the PAN reservoir thereby limiting ozone formation. A three-dimensional global model that uses state of the art chemistry and source information is used to compare measured and simulated mixing ratios of selected OVOC. While there is reasonable agreement in many cases, measured aldehyde concentrations are significantly larger than predicted. At their observed levels, acetaldehyde mixing ratios are shown to be an important source of HCHO (and HOx) and PAN in the troposphere. On the basis of presently known chemistry, measured mixing ratios of aldehydes and PANs are mutually incompatible. We provide rough estimates of the global sources of several OVOC and conclude that collectively these are extremely large (150-500 Tg C yr-1) but remain poorly quantified. Copyright 2004 by the American Geophysical Union

An integral equation approach to effective interactions between polymers in solution

We use the thread model for linear chains of interacting monomers, and the ``polymer reference interaction site model'' (PRISM) formalism to determine the monomer-monomer pair correlation function $h_{mm}(r)$ for dilute and semi-dilute polymer solutions, over a range of temperatures from very high (where the chains behave as self-avoiding walks) to below the $\theta$ temperature, where phase separation sets in. An inversion procedure, based on the HNC integral equation, is used to extract the effective pair potential between ``average'' monomers on different chains. An accurate relation between $h_{mm}(r)$, $h_{cc}(r)$ [the pair correlation function between the polymer centers of mass (c.m.)], and the intramolecular form factors is then used to determine $h_{cc}(r)$, and subsequently extract the effective c.m.-c.m. pair potential $v_{cc}(r)$ by a similar inversion procedure. $v_{cc}(r)$ depends on temperature and polymer concentration, and the predicted variations are in reasonable agreement with recent simulation data, except at very high temperatures, and below the $\theta$ temperature.Comment: 13 pages, 13 figures, revtex ; revised versio

Bubble collisions and measures of the multiverse

To compute the spectrum of bubble collisions seen by an observer in an eternally-inflating multiverse, one must choose a measure over the diverging spacetime volume, including choosing an "initial" hypersurface below which there are no bubble nucleations. Previous calculations focused on the case where the initial hypersurface is pushed arbitrarily deep into the past. Interestingly, the observed spectrum depends on the orientation of the initial hypersurface, however one's ability observe the effect rapidly decreases with the ratio of inflationary Hubble rates inside and outside one's bubble. We investigate whether this conclusion might be avoided under more general circumstances, in particular placing the observer's bubble near the initial hypersurface. We find that it is not. As a point of reference, a substantial appendix reviews relevant aspects of the measure problem of eternal inflation.Comment: 24 pages, two figures, plus 16-page appendix with one figure; v2: minor improvements and clarifications, conclusions unchanged (version to appear in JCAP

Thiosquaramides: pH switchable anion transporters

The transport of anions across cellular membranes is an important biological function governed by specialised proteins. In recent years, many small molecules have emerged that mimick the anion transport behaviour of these proteins, but only a few of these synthetic molecules also display the gating/switching behaviour seen in biological systems. A small series of thiosquar-amides was synthesised and their pH-dependent chloride binding and anion transport behaviour was investigated using 1H NMR titrations, single crystal X-ray diffraction and a variety of vesicle-based techniques. Spectrophotometric titrations and DFT calculations revealed that the thiosquaramides are significantly more acidic than their oxosquaramide analogues, with pKa values between 4.0 and 9.0. This led to the observation that at pH 7.2 the anion transport ability of the thiosquaramides is fully switched OFF due to deprotonation of the receptor, but is completely switched ON at lower pH

GraphCombEx: A Software Tool for Exploration of Combinatorial Optimisation Properties of Large Graphs

We present a prototype of a software tool for exploration of multiple combinatorial optimisation problems in large real-world and synthetic complex networks. Our tool, called GraphCombEx (an acronym of Graph Combinatorial Explorer), provides a unified framework for scalable computation and presentation of high-quality suboptimal solutions and bounds for a number of widely studied combinatorial optimisation problems. Efficient representation and applicability to large-scale graphs and complex networks are particularly considered in its design. The problems currently supported include maximum clique, graph colouring, maximum independent set, minimum vertex clique covering, minimum dominating set, as well as the longest simple cycle problem. Suboptimal solutions and intervals for optimal objective values are estimated using scalable heuristics. The tool is designed with extensibility in mind, with the view of further problems and both new fast and high-performance heuristics to be added in the future. GraphCombEx has already been successfully used as a support tool in a number of recent research studies using combinatorial optimisation to analyse complex networks, indicating its promise as a research software tool

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Next generation sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the evolutionary placement algorithm (EPA) included in RAxML, or PPLACER, are being increasingly used for this purpose. However, due to the steady progress in NGS technologies, the current implementations face substantial scalability limitations. Herein, we present EPA-NG, a complete reimplementation of the EPA that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA and PPLACER. EPA-NG can be executed on standard shared memory, as well as on distributed memory systems (e.g., computing clusters). To demonstrate the scalability of EPA-NG, we placed 1 billion metagenetic reads from the Tara Oceans Project onto a reference tree with 3748 taxa in just under 7 h, using 2048 cores. Our performance assessment shows that EPA-NG outperforms RAxML-EPA and PPLACER by up to a factor of 30 in sequential execution mode, while attaining comparable parallel efficiency on shared memory systems. We further show that the distributed memory parallelization of EPA-NG scales well up to 2048 cores. EPA-NG is available under the AGPLv3 license

HMGA1 is a novel downstream nuclear target of the insulin receptor signaling pathway

High-mobility group AT-hook 1 (HMGA1) protein is an important nuclear factor that activates gene transcription by binding to AT-rich sequences in the promoter region of DNA. We previously demonstrated that HMGA1 is a key regulator of the insulin receptor (INSR) gene and individuals with defects in HMGA1 have decreased INSR expression and increased susceptibility to type 2 diabetes mellitus. In addition, there is evidence that intracellular regulatory molecules that are employed by the INSR signaling system are involved in post-translational modifications of HMGA1, including protein phosphorylation. It is known that phosphorylation of HMGA1 reduces DNA-binding affinity and transcriptional activation. In the present study, we investigated whether activation of the INSR by insulin affected HMGA1 protein phosphorylation and its regulation of gene transcription. Collectively, our findings indicate that HMGA1 is a novel downstream target of the INSR signaling pathway, thus representing a new critical nuclear mediator of insulin action and function