Strong scaling of general-purpose molecular dynamics simulations on GPUs

We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based code, LAMMPS (Plimpton, J. Comp. Phys. 117, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., J. Comp. Phys. 227, 2008). The software supports short-ranged pair force and bond force fields and achieves optimal GPU performance using an autotuning algorithm. We are able to demonstrate equivalent or superior scaling on up to 3,375 GPUs in Lennard-Jones and dissipative particle dynamics (DPD) simulations of up to 108 million particles. GPUDirect RDMA capabilities in recent GPU generations provide better performance in full double precision calculations. For a representative polymer physics application, HOOMD-blue 1.0 provides an effective GPU vs. CPU node speed-up of 12.5x.Comment: 30 pages, 14 figure

The HOSTS Survey—Exozodiacal Dust Measurements for 30 Stars

The Hunt for Observable Signatures of Terrestrial Systems survey searches for dust near the habitable zones (HZs) around nearby, bright main-sequence stars. We use nulling interferometry in the N band to suppress the bright stellar light and to probe for low levels of HZ dust around the 30 stars observed so far. Our overall detection rate is 18%, including four new detections, among which are the first three around Sun-like stars and the first two around stars without any previously known circumstellar dust. The inferred occurrence rates are comparable for early-type and Sun-like stars, but decrease from 60^(+16)_(-21)% for stars with previously detected cold dust to 8^(+10)_(-3)% for stars without such excess, confirming earlier results at higher sensitivity. For completed observations on individual stars, our sensitivity is five to ten times better than previous results. Assuming a lognormal excess luminosity function, we put upper limits on the median HZ dust level of 13 zodis (95% confidence) for a sample of stars without cold dust and of 26 zodis when focusing on Sun-like stars without cold dust. However, our data suggest that a more complex luminosity function may be more appropriate. For stars without detectable Large Binocular Telescope Interferometer (LBTI) excess, our upper limits are almost reduced by a factor of two, demonstrating the strength of LBTI target vetting for future exo-Earth imaging missions. Our statistics are limited so far, and extending the survey is critical to informing the design of future exo-Earth imaging surveys

The effect of prolonged simulated non- gravitational environment on mineral balance in the adult male, volume 1 Final report

Effect of prolonged bed rest with simulated weightlessness on mineral balance in male adult - Vol.

Combining brain-computer interfaces and assistive technologies: state-of-the-art and challenges

In recent years, new research has brought the field of EEG-based Brain-Computer Interfacing (BCI) out of its infancy and into a phase of relative maturity through many demonstrated prototypes such as brain-controlled wheelchairs, keyboards, and computer games. With this proof-of-concept phase in the past, the time is now ripe to focus on the development of practical BCI technologies that can be brought out of the lab and into real-world applications. In particular, we focus on the prospect of improving the lives of countless disabled individuals through a combination of BCI technology with existing assistive technologies (AT). In pursuit of more practical BCIs for use outside of the lab, in this paper, we identify four application areas where disabled individuals could greatly benefit from advancements in BCI technology, namely,“Communication and Control”, “Motor Substitution”, “Entertainment”, and “Motor Recovery”. We review the current state of the art and possible future developments, while discussing the main research issues in these four areas. In particular, we expect the most progress in the development of technologies such as hybrid BCI architectures, user-machine adaptation algorithms, the exploitation of users’ mental states for BCI reliability and confidence measures, the incorporation of principles in human-computer interaction (HCI) to improve BCI usability, and the development of novel BCI technology including better EEG devices

Shape and symmetry determine two-dimensional melting transitions of hard regular polygons

The melting transition of two-dimensional (2D) systems is a fundamental problem in condensed matter and statistical physics that has advanced significantly through the application of computational resources and algorithms. 2D systems present the opportunity for novel phases and phase transition scenarios not observed in 3D systems, but these phases depend sensitively on the system and thus predicting how any given 2D system will behave remains a challenge. Here we report a comprehensive simulation study of the phase behavior near the melting transition of all hard regular polygons with $3\leq n\leq 14$ vertices using massively parallel Monte Carlo simulations of up to one million particles. By investigating this family of shapes, we show that the melting transition depends upon both particle shape and symmetry considerations, which together can predict which of three different melting scenarios will occur for a given $n$. We show that systems of polygons with as few as seven edges behave like hard disks; they melt continuously from a solid to a hexatic fluid and then undergo a first-order transition from the hexatic phase to the fluid phase. We show that this behavior, which holds for all $7\leq n\leq 14$, arises from weak entropic forces among the particles. Strong directional entropic forces align polygons with fewer than seven edges and impose local order in the fluid. These forces can enhance or suppress the discontinuous character of the transition depending on whether the local order in the fluid is compatible with the local order in the solid. As a result, systems of triangles, squares, and hexagons exhibit a KTHNY-type continuous transition between fluid and hexatic, tetratic, and hexatic phases, respectively, and a continuous transition from the appropriate "x"-atic to the solid. [abstract truncated due to arxiv length limitations]

Non-linear response of single-molecule magnets: field-tuned quantum-to-classical crossovers

Quantum nanomagnets can show a field dependence of the relaxation time very different from their classical counterparts, due to resonant tunneling via excited states (near the anisotropy barrier top). The relaxation time then shows minima at the resonant fields H_{n}=n D at which the levels at both sides of the barrier become degenerate (D is the anisotropy constant). We showed that in Mn12, near zero field, this yields a contribution to the nonlinear susceptibility that makes it qualitatively different from the classical curves [Phys. Rev. B 72, 224433 (2005)]. Here we extend the experimental study to finite dc fields showing how the bias can trigger the system to display those quantum nonlinear responses, near the resonant fields, while recovering an classical-like behaviour for fields between them. The analysis of the experiments is done with heuristic expressions derived from simple balance equations and calculations with a Pauli-type quantum master equation.Comment: 4 pages, 3 figures. Submitted to Phys. Rev. B, brief report

The HOSTS survey for exo-zodiacal dust: preliminary results and future prospects

The presence of large amounts of dust in the habitable zones of nearby stars is a significant obstacle for future exo-Earth imaging missions. We executed the HOSTS (Hunt for Observable Signatures of Terrestrial Systems) survey to determine the typical amount of such exozodiacal dust around a sample of nearby main sequence stars. The majority of the data have been analyzed and we present here an update of our ongoing work. Nulling interferometry in N band was used to suppress the bright stellar light and to detect faint, extended circumstellar dust emission. We present an overview of the latest results from our ongoing work. We find seven new N band excesses in addition to the high confidence confirmation of three that were previously known. We find the first detections around Sun-like stars and around stars without previously known circumstellar dust. Our overall detection rate is 23%. The inferred occurrence rate is comparable for early type and Sun-like stars, but decreases from 71^(+11)_(-20)% for stars with previously detected mid- to far-infrared excess to 11^(+9)_(-4)% for stars without such excess, confirming earlier results at high confidence. For completed observations on individual stars, our sensitivity is five to ten times better than previous results. Assuming a lognormal luminosity function of the dust, we find upper limits on the median dust level around all stars without previously known mid to far infrared excess of 11.5 zodis at 95% confidence level. The corresponding upper limit for Sun-like stars is 16 zodis. An LBTI vetted target list of Sun-like stars for exo-Earth imaging would have a corresponding limit of 7.5 zodis. We provide important new insights into the occurrence rate and typical levels of habitable zone dust around main sequence stars. Exploiting the full range of capabilities of the LBTI provides a critical opportunity for the detailed characterization of a sample of exozodiacal dust disks to understand the origin, distribution, and properties of the dust

First Keck Nulling Observations of a Young Stellar Object: Probing the Circumstellar Environment of the Herbig Ae star MWC 325

We present the first N-band nulling plus K- and L-band V2 observations of a young stellar object, MWC325, taken with the 85 m baseline Keck Interferometer. The Keck nuller was designed for the study of faint dust signatures associated with debris disks, but it also has a unique capability for studying the temperature and density distribution of denser disks found around young stellar objects. Interferometric observations of MWC 325 at K, L and N encompass a factor of five in spectral range and thus, especially when spectrally dispersed within each band, enable characterization of the structure of the inner disk regions where planets form. Fitting our observations with geometric models such as a uniform disk or a Gaussian disk show that the apparent size increases monotonically with wavelength in the 2-12 um wavelength region, confirming the widely held assumption based on radiative transfer models, now with spatially resolved measurements over broad wavelength range, that disks are extended with a temperature gradient. The effective size is a factor of about 1.3 and 2 larger in the L-band and N-band, respectively, compared to that in the K-band. The existing interferometric measurements and the spectral energy distribution can be reproduced by a flat disk or a weakly-shadowed nearly flat-disk model, with only slight flaring in the outer regions of the disk, consisting of representative "sub-micron" (0.1 um) and "micron" (2 um) grains of a 50:50 ratio of silicate and graphite. This is marked contrast with the disks previously found in other Herbig Ae/Be stars suggesting a wide variety in the disk properties among Herbig Ae/Be stars.Comment: Accepted for publication in the Ap

Phospho1 deficiency transiently modifies bone architecture yet produces consistent modification in osteocyte differentiation and vascular porosity with ageing

PHOSPHO1 is one of principal proteins involved in initiating bone matrix mineralisation. Recent studies have found that Phospho1 KO mice (Phospho1-R74X) display multiple skeletal abnormalities with spontaneous fractures, bowed long bones, osteomalacia and scoliosis. These analyses have however been limited to young mice and it remains unclear whether the role of PHOSPHO1 is conserved in the mature murine skeleton where bone turnover is limited. In this study, we have used ex-vivo computerised tomography to examine the effect of Phospho1 deletion on tibial bone architecture in mice at a range of ages (5, 7, 16 and 34 weeks of age) to establish whether its role is conserved during skeletal growth and maturation. Matrix mineralisation has also been reported to influence terminal osteoblast differentiation into osteocytes and we have also explored whether hypomineralised bones in Phospho1 KO mice exhibit modified osteocyte lacunar and vascular porosity. Our data reveal that Phospho1 deficiency generates age-related defects in trabecular architecture and compromised cortical microarchitecture with greater porosity accompanied by marked alterations in osteocyte shape, significant increases in osteocytic lacuna and vessel number. Our in vitro studies examining the behaviour of osteoblast derived from Phospho1 KO and wild-type mice reveal reduced levels of matrix mineralisation and modified osteocytogenic programming in cells deficient in PHOSPHO1. Together our data suggest that deficiency in PHOSPHO1 exerts modifications in bone architecture that are transient and depend upon age, yet produces consistent modification in lacunar and vascular porosity. It is possible that the inhibitory role of PHOSPHO1 on osteocyte differentiation leads to these age-related changes in bone architecture. It is also intriguing to note that this apparent acceleration in osteocyte differentiation evident in the hypomineralised bones of Phospho1 KO mice suggests an uncoupling of the interplay between osteocytogenesis and biomineralisation. Further studies are required to dissect the molecular processes underlying the regulatory influences exerted by PHOSPHO1 on the skeleton with ageing

First L-band Interferometric Observations of a Young Stellar Object: Probing the Circumstellar Environment of MWC 419

We present spatially-resolved K- and L-band spectra (at spectral resolution R = 230 and R = 60, respectively) of MWC 419, a Herbig Ae/Be star. The data were obtained simultaneously with a new configuration of the 85-m baseline Keck Interferometer. Our observations are sensitive to the radial distribution of temperature in the inner region of the disk of MWC 419. We fit the visibility data with both simple geometric and more physical disk models. The geometric models (uniform disk and Gaussian) show that the apparent size increases linearly with wavelength in the 2-4 microns wavelength region, suggesting that the disk is extended with a temperature gradient. A model having a power-law temperature gradient with radius simultaneously fits our interferometric measurements and the spectral energy distribution data from the literature. The slope of the power-law is close to that expected from an optically thick disk. Our spectrally dispersed interferometric measurements include the Br gamma emission line. The measured disk size at and around Br gamma suggests that emitting hydrogen gas is located inside (or within the inner regions) of the dust disk.Comment: Accepted for publication in Ap