ReaDDyMM: fast interacting-particle reaction-diffusion simulations using graphical processing units

AbstractReaDDy is a modular particle simulation package combining off-lattice reaction kinetics with arbitrary particle interaction forces. Here we present a graphical processing unit implementation of ReaDDy that employs the fast multiplatform molecular dynamics package OpenMM. A speedup of up to two orders of magnitude is demonstrated, giving us access to timescales of multiple seconds on single graphical processing units. This opens up the possibility of simulating cellular signal transduction events while resolving all protein copies

Simulation of a finishing operation : milling of a turbine blade and influence of damping

Milling is used to create very complex geometries and thin parts, such as turbine blades. Irreversible geometric defects may appear during finishing operations when a high surface quality is expected. Relative vibrations between the tool and the workpiece must be as small as possible, while tool/workpiece interactions can be highly non-linear. A general virtual machining approach is presented and illustrated. It takes into account the relative motion and vibrations of the tool and the workpiece. Both deformations of the tool and the workpiece are taken into account. This allows predictive simulations in the time domain. As an example the effect of damping on the behavior during machining of one of the 56 blades of a turbine disk is analysed in order to illustrate the approach potential

Parallel Selection on TRPV6 in Human Populations

We identified and examined a candidate gene for local directional selection in Europeans, TRPV6, and conclude that selection has acted on standing genetic variation at this locus, creating parallel soft sweep events in humans. A novel modification of the extended haplotype homozygosity (EHH) test was utilized, which compares EHH for a single allele across populations, to investigate the signature of selection at TRPV6 and neighboring linked loci in published data sets for Europeans, Asians and African-Americans, as well as in newly-obtained sequence data for additional populations. We find that all non-African populations carry a signature of selection on the same haplotype at the TRPV6 locus. The selective footprints, however, are significantly differentiated between non-African populations and estimated to be younger than an ancestral population of non-Africans. The possibility of a single selection event occurring in an ancestral population of non-Africans was tested by simulations and rejected. The putatively-selected TRPV6 haplotype contains three candidate sites for functional differences, namely derived non-synonymous substitutions C157R, M378V and M681T. Potential functional differences between the ancestral and derived TRPV6 proteins were investigated by cloning the ancestral and derived forms, transfecting cell lines, and carrying out electrophysiology experiments via patch clamp analysis. No statistically-significant differences in biophysical channel function were found, although one property of the protein, namely Ca2+ dependent inactivation, may show functionally relevant differences between the ancestral and derived forms. Although the reason for selection on this locus remains elusive, this is the first demonstration of a widespread parallel selection event acting on standing genetic variation in humans, and highlights the utility of between population EHH statistics

Runaway dilaton models: improved constraints from the full cosmological evolution

One of the few firm predictions of string theory is the existence of a massless scalar field coupled to gravity, the dilaton. In its presence, the value of the fundamental constants of the universe, such as the fine-structure constant, will vary with the time-dependent vacuum expectation value of this field, in direct violation of the Einstein Equivalence Principle. The \emph{runaway dilaton} proposed by Damour, Piazza, and Veneziano provides a physically motivated cosmological scenario which reconciles the existence of a massless dilaton with observations, while still providing non-standard and testable predictions. Furthermore, the field can provide a natural candidate for dynamical dark energy. While this model has been previously constrained from local laboratory experiments and low-redshift observations, we provide here the first full self-consistent constraints, also including high redshift data, in particular from the cosmic microwave background. We consider various possible scenarios in which the field could act as quintessence. Despite the wider parameter space, we make use of recent observational progress to significantly improve constraints on the model's coupling parameters, showing that order unity couplings (which would be natural in string theory) are ruled out.Comment: Published in Phys. Rev.

News from the Swampland -- Constraining string theory with astrophysics and cosmology

Our current best guess for a unified theory of gravitation and quantum field theory (string theory) generically predicts a set of requirements for a consistently quantized theory, the Swampland criteria. Refined versions of these criteria have recently been shown to be in mild tension with cosmological observations. We summarize the status of the current impact of and constraints on the Swampland conjectures from cosmology, and subject a variety of dark energy quintessence models to recently released cosmological datasets. We find that instead of tightening the tension, the new data allows for slightly more freedom in the Swampland criteria. We further demonstrate that if there is no theoretical argument made to prevent interactions of the moduli fields with the electromagnetic sector, a novel fine-tuning argument arises from the extremely tight current constraints on such interactions. Finally, we conclude with a cautionary tale on model-independent reconstructions of the Swampland criteria from expansion rate data.Comment: 35 pages, 20 figures, 4 tables. All comments are welcome! [v2: Added citations, corrected eq. 2.6

Genomic basis for skin phenotype and cold adaptation in the extinct Steller’s sea cow

Steller’s sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller’s descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller’s sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold aquatic (or marine) environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse models cause ichthyosis, a skin disease characterized by a thick, hyperkeratotic epidermis that recapitulates Steller’s sea cows’ reportedly bark-like skin. We also found that Steller’s sea cows’ abundance was continuously declining for tens of thousands of years before their description, implying that environmental changes also contributed to their extinction

Search for non-relativistic Magnetic Monopoles with IceCube

The IceCube Neutrino Observatory is a large Cherenkov detector instrumenting $1\,\mathrm{km}^3$ of Antarctic ice. The detector can be used to search for signatures of particle physics beyond the Standard Model. Here, we describe the search for non-relativistic, magnetic monopoles as remnants of the GUT (Grand Unified Theory) era shortly after the Big Bang. These monopoles may catalyze the decay of nucleons via the Rubakov-Callan effect with a cross section suggested to be in the range of $10^{-27}\,\mathrm{cm^2}$ to $10^{-21}\,\mathrm{cm^2}$. In IceCube, the Cherenkov light from nucleon decays along the monopole trajectory would produce a characteristic hit pattern. This paper presents the results of an analysis of first data taken from May 2011 until May 2012 with a dedicated slow-particle trigger for DeepCore, a subdetector of IceCube. A second analysis provides better sensitivity for the brightest non-relativistic monopoles using data taken from May 2009 until May 2010. In both analyses no monopole signal was observed. For catalysis cross sections of $10^{-22}\,(10^{-24})\,\mathrm{cm^2}$ the flux of non-relativistic GUT monopoles is constrained up to a level of $\Phi_{90} \le 10^{-18}\,(10^{-17})\,\mathrm{cm^{-2}s^{-1}sr^{-1}}$ at a 90% confidence level, which is three orders of magnitude below the Parker bound. The limits assume a dominant decay of the proton into a positron and a neutral pion. These results improve the current best experimental limits by one to two orders of magnitude, for a wide range of assumed speeds and catalysis cross sections.Comment: 20 pages, 20 figure

Determining neutrino oscillation parameters from atmospheric muon neutrino disappearance with three years of IceCube DeepCore data

We present a measurement of neutrino oscillations via atmospheric muon neutrino disappearance with three years of data of the completed IceCube neutrino detector. DeepCore, a region of denser instrumentation, enables the detection and reconstruction of atmospheric muon neutrinos between 10 GeV and 100 GeV, where a strong disappearance signal is expected. The detector volume surrounding DeepCore is used as a veto region to suppress the atmospheric muon background. Neutrino events are selected where the detected Cherenkov photons of the secondary particles minimally scatter, and the neutrino energy and arrival direction are reconstructed. Both variables are used to obtain the neutrino oscillation parameters from the data, with the best fit given by $\Delta m^2_{32}=2.72^{+0.19}_{-0.20}\times 10^{-3}\,\mathrm{eV}^2$ and $\sin^2\theta_{23} = 0.53^{+0.09}_{-0.12}$ (normal mass hierarchy assumed). The results are compatible and comparable in precision to those of dedicated oscillation experiments.Comment: 10 pages, 7 figure

Determining neutrino oscillation parameters from atmospheric muon neutrino disappearance with three years of IceCube DeepCore data

We present a measurement of neutrino oscillations via atmospheric muon neutrino disappearance with three years of data of the completed IceCube neutrino detector. DeepCore, a region of denser instrumentation, enables the detection and reconstruction of atmospheric muon neutrinos between 10 GeV and 100 GeV, where a strong disappearance signal is expected. The detector volume surrounding DeepCore is used as a veto region to suppress the atmospheric muon background. Neutrino events are selected where the detected Cherenkov photons of the secondary particles minimally scatter, and the neutrino energy and arrival direction are reconstructed. Both variables are used to obtain the neutrino oscillation parameters from the data, with the best fit given by $\Delta m^2_{32}=2.72^{+0.19}_{-0.20}\times 10^{-3}\,\mathrm{eV}^2$ and $\sin^2\theta_{23} = 0.53^{+0.09}_{-0.12}$ (normal mass hierarchy assumed). The results are compatible and comparable in precision to those of dedicated oscillation experiments.Comment: 10 pages, 7 figure