Computer simulations of cosmic-ray diffusion near supernova remnant shock waves

A plasma simulation model was used to study the resonant interactions between streaming cosmic-ray ions and a self-consistent spectrum of Alfven waves, such as might exist in the interstellar medium upstream of a supernova remnant shock wave. The computational model is a hybrid one, in which the background interstellar medium is an MHD fluid and the cosmic-rays are discrete kinetic particles. The particle sources for the electromagnetic fields are obtained by averaging over the fast cyclotron motions. When the perturbed magnetic field is larger than 10 percent of the background field, the macro- and microphysics are no longer correctly predicted by quasi-linear theory. The particles are trapped by the waves and show sharp jumps in their pitch-angles relative to the background magnetic field, and the effective ninety-degree scattering time for diffusion parallel to the background magnetic field is reduced to between 5 and 30 cyclotron periods. Simulation results suggest that Type 1 supernova remnants may be the principal sites of cosmic ray acceleration

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.

Knowing the catalytic turnover numbers of enzymes is essential for understanding the growth rate, proteome composition, and physiology of organisms, but experimental data on enzyme turnover numbers is sparse and noisy. Here, we demonstrate that machine learning can successfully predict catalytic turnover numbers in Escherichia coli based on integrated data on enzyme biochemistry, protein structure, and network context. We identify a diverse set of features that are consistently predictive for both in vivo and in vitro enzyme turnover rates, revealing novel protein structural correlates of catalytic turnover. We use our predictions to parameterize two mechanistic genome-scale modelling frameworks for proteome-limited metabolism, leading to significantly higher accuracy in the prediction of quantitative proteome data than previous approaches. The presented machine learning models thus provide a valuable tool for understanding metabolism and the proteome at the genome scale, and elucidate structural, biochemical, and network properties that underlie enzyme kinetics

Community Detection as an Inference Problem

We express community detection as an inference problem of determining the most likely arrangement of communities. We then apply belief propagation and mean-field theory to this problem, and show that this leads to fast, accurate algorithms for community detection.Comment: 4 pages, 2 figure

Neuropilins 1 and 2 mediate neointimal hyperplasia and re-endothelialization following arterial injury

AIMS: Neuropilins 1 and 2 (NRP1 and NRP2) play crucial roles in endothelial cell migration contributing to angiogenesis and vascular development. Both NRPs are also expressed by cultured vascular smooth muscle cells (VSMCs) and are implicated in VSMC migration stimulated by PDGF-BB, but it is unknown whether NRPs are relevant for VSMC function in vivo. We investigated the role of NRPs in the rat carotid balloon injury model, in which endothelial denudation and arterial stretch induce neointimal hyperplasia involving VSMC migration and proliferation. METHODS AND RESULTS: NRP1 and NRP2 mRNAs and proteins increased significantly following arterial injury, and immunofluorescent staining revealed neointimal NRP expression. Down-regulation of NRP1 and NRP2 using shRNA significantly reduced neointimal hyperplasia following injury. Furthermore, inhibition of NRP1 by adenovirally overexpressing a loss-of-function NRP1 mutant lacking the cytoplasmic domain (ΔC) reduced neointimal hyperplasia, whereas wild-type (WT) NRP1 had no effect. NRP-targeted shRNAs impaired, while overexpression of NRP1 WT and NRP1 ΔC enhanced, arterial re-endothelialization 14 days after injury. Knockdown of either NRP1 or NRP2 inhibited PDGF-BB-induced rat VSMC migration, whereas knockdown of NRP2, but not NRP1, reduced proliferation of cultured rat VSMC and neointimal VSMC in vivo. NRP knockdown also reduced the phosphorylation of PDGFα and PDGFβ receptors in rat VSMC, which mediate VSMC migration and proliferation. CONCLUSION: NRP1 and NRP2 play important roles in the regulation of neointimal hyperplasia in vivo by modulating VSMC migration (via NRP1 and NRP2) and proliferation (via NRP2), independently of the role of NRPs in re-endothelialization

Digital Hydrography Underestimates Stream Length and Leads to Underestimates of Trout Population Size

Stream length is measured for many fisheries management applications. Characteristics of populations and habitats measured at field sites are commonly generalized to unsampled areas using estimates of stream length or stream network length. There are many ways to measure stream length, but map-based stream length measurements are commonly used in fisheries applications even though they are known to be biased. We evaluated how length of headwater streams in Arizona may be underestimated by the National Hydrography Dataset and how that bias influences streamwide abundance estimates for adult Apache Trout Oncorhynchus apache. As expected, stream lengths measured using National Hydrography Dataset flowlines underestimated true length revealed by National Agricultural Imagery Program imagery on average 11.1% (SD = 4.1%), and this bias was higher in meadow versus forested habitats. The observed bias led to streamwide estimates of adult Apache Trout abundance that were only 88% on average (SD = 5%) of those made with more realistic imagery-based stream measurements. As we have shown, high-resolution imagery, now widely available, can be used to assess and quantify stream length bias, and we conclude that it is important to assess whether this bias has the potential to negatively impact important fishery management decisions

Transport in Floquet-Bloch bands

We report Floquet band engineering of long-range transport and direct imaging of Floquet-Bloch bands in an amplitude-modulated optical lattice. In one variety of Floquet-Bloch band we observe tunable rapid long-range high-fidelity transport of a Bose condensate across thousands of lattice sites. Quenching into an opposite-parity Floquet-hybridized band allows Wannier-Stark localization to be controllably turned on and off using modulation. A central result of this work is the use of transport dynamics to demonstrate direct imaging of a Floquet-Bloch band structure. These results demonstrate that transport in dynamical Floquet-Bloch bands can be mapped to transport in quasi-static effective bands, opening a path to cold atom quantum emulation of ultrafast multi-band electronic dynamics.Comment: 5 pages, 4 figure

High Harmonic Generation in SF6_{6}: Raman-excited Vibrational Quantum Beats

In a recent experiment (N. Wagner et al., PNAS v103, p13279) on SF$_{6}$, a high-harmonic generating laser pulse is preceded by a pump pulse which stimulates Raman-active modes in the molecule. Varying the time delay between the two pulses modulates high harmonic intensity, with frequencies equal to the vibration frequencies of the Raman-active modes. We propose an explanation of this modulation as a quantum interference between competing pathways that occur via adjacent vibrational states of the molecule. The Raman and high harmonic processes act as beamsplitters, producing vibrational quantum beats among the Raman-active vibrational modes that are excited by the first pulse. We introduce a rigorous treatment of the electron-ion recombination process and the effect of the ionic Coulomb field in the electron propagation outside the molecule, improving over the widely-used three-step model.Comment: submitted to PR

Magnetically-controlled velocity selection in a cold atom sample using stimulated Raman transitions

We observe velocity-selective two-photon resonances in a cold atom cloud in the presence of a magnetic field. We use these resonances to demonstrate a simple magnetometer with sub-mG resolution. The technique is particularly useful for zeroing the magnetic field and does not require any additional laser frequencies than are already used for standard magneto-optical traps. We verify the effects using Faraday rotation spectroscopy.Comment: 5 pages, 6 figure