Enabling Detailed, Biophysics-Based Skeletal Muscle Models on HPC Systems

Realistic simulations of detailed, biophysics-based, multi-scale models often require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are typically designed to allow for high flexibility and generality in model development. Flexibility and model development, however, are often a limiting factor for large-scale simulations. Therefore, new models are typically tested and run on small-scale compute facilities. By using a detailed biophysics-based, chemo-electromechanical skeletal muscle model and the international open-source software library OpenCMISS as an example, we present an approach to upgrade an existing muscle simulation framework from a moderately parallel version toward a massively parallel one that scales both in terms of problem size and in terms of the number of parallel processes. For this purpose, we investigate different modeling, algorithmic and implementational aspects. We present improvements addressing both numerical and parallel scalability. In addition, our approach includes a novel visualization environment which is based on the MegaMol framework and is capable of handling large amounts of simulated data. We present the results of a number of scaling studies at the Tier-1 supercomputer HazelHen at the High Performance Computing Center Stuttgart (HLRS). We improve the overall runtime by a factor of up to 2.6 and achieve good scalability on up to 768 cores

Quasi-spherical ice in convective clouds

Homogeneous freezing of supercooled droplets occurs in convective systems in low and midlatitudes. This droplet-freezing process leads to the formation of a large amount of small ice particles, so-called frozen droplets, that are transported to the upper parts of anvil outflows, where they can influence the cloud radiative properties. However, the detailed microphysics and, thus, the scattering properties of these small ice particles are highly uncertain. Here, the link between the microphysical and optical properties of frozen droplets is investigated in cloud chamber experiments, where the frozen droplets were formed, grown, and sublimated under controlled conditions. It was found that frozen droplets developed a high degree of small-scale complexity after their initial formation and subsequent growth. During sublimation, the small-scale complexity disappeared, releasing a smooth and near-spherical ice particle. Angular light scattering and depolarization measurements confirmed that these sublimating frozen droplets scattered light similar to spherical particles: that is, they had angular light-scattering properties similar to water droplets. The knowledge gained from this laboratory study was applied to two case studies of aircraft measurements in midlatitude and tropical convective systems. The in situ aircraft measurements confirmed that the microphysics of frozen droplets is dependent on the humidity conditions they are exposed to (growth or sublimation). The existence of optically spherical frozen droplets can be important for the radiative properties of detraining convective outflows.Peer reviewe

Exclusive rho^0 muoproduction on transversely polarised protons and deuterons

The transverse target spin azimuthal asymmetry A_UT in hard exclusive production of rho^0 mesons was measured at COMPASS by scattering 160 GeV/c muons off transversely polarised protons and deuterons. The measured asymmetry is sensitive to the nucleon helicity-flip generalised parton distributions E^q, which are related to the orbital angular momentum of quarks in the nucleon. The Q^2, x_B and p_t^2 dependence of A_UT is presented in a wide kinematic range. Results for deuterons are obtained for the first time. The measured asymmetry is small in the whole kinematic range for both protons and deuterons, which is consistent with the theoretical interpretation that contributions from GPDs E^u and E^d approximately cancel.Comment: 20 pages, 9 figures and 4 tables, updated author lis

Bourdieusian Reflections on Language: Unavoidable Conditions of the Real Speech Situation

The main purpose of this paper is to shed light on Pierre Bourdieu’s conception of language. Although he has dedicated a significant part of his work to the study of language and even though his analysis of language has been extensively discussed in the literature, almost no attention has been paid to the factthat Bourdieu’s account of language is based on a number of ontological presuppositions, that is, on a set of universal assumptions about the very nature of language. This article aims to fill this gap in the literature by offering a detailed overview of 10 key features which, from a Bourdieusian point of view, can be regarded as inherent in language. On the basis of this enquiry,the study seeks todemonstrate that——contraryto commonbelief——there is not only a Bourdieusian sociology of language but also a Bourdieusian philosophy of language, which provides a useful theoretical framework for examining the unavoidable conditions of the real speech situation. The paper draws to a close by reflecting on the flaws and limitations of Bourdieu’s approach to language

The high energy neutrino cross-section in the Standard Model and its uncertainty

Updated predictions are presented for high energy neutrino and antineutrino charged and neutral current cross-sections within the conventional DGLAP formalism of NLO QCD using modern PDF fits. PDF uncertainties from model assumptions and parametrization bias are considered in addition to the experimental uncertainties. Particular attention is paid to assumptions and biases which could signal the need for extension of the conventional formalism to include effects such as ln(1/x) resummation or non-linear effects of high gluon density.Comment: 15 pages, 13 figures, 2 tables (REVTeX4); clarifying comments and link to tabulated cross sections at http://www-pnp.physics.ox.ac.uk/~cooper/neutrino/ added; to appear in JHE

Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function

In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10−9) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10−4-2.2 × 10−7. Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in genera