Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Stabilization of monodomain polarization in ultrathin PbTiO3 films

Using in situ high-resolution synchrotron x-ray scattering, the Curie temperature T-C has been determined for ultrathin c-axis epitaxial PbTiO3 films on conducting substrates (SrRuO3 on SrTiO3), with surfaces exposed to a controlled vapor environment. The suppression of T-C was relatively small, even for the thinnest film (1.2 nm). We observe that 180 degrees stripe domains do not form, indicating that the depolarizing field is compensated by free charge at both interfaces. This is confirmed by ab initio calculations that find polar ground states in the presence of ionic adsorbates.open15511

Efficient molecular dynamics using geodesic integration and solvent-solute splitting

We present an approach to Langevin dynamics in the presence of holonomic constraints based on decomposition of the system into components representing geodesic flow, constrained impulse and constrained diffusion. We show that a particular ordering of the components results in an integrator that is an order of magnitude more accurate for configurational averages than existing alternatives. Moreover, by combining the geodesic integration method with a solvent–solute force splitting, we demonstrate that stepsizes of at least 8 fs can be used for solvated biomolecules with high sampling accuracy and without substantially altering diffusion rates, approximately increasing by a factor of two the efficiency of molecular dynamics sampling for such systems. The methods described in this article are easily implemented using the standard apparatus of modern simulation codes

Ecological and Behavioural Correlates of Intracellular Buffering Capacity in the Muscles of Antarctic Fishes

Five species of antarctic fishes can be arranged in order of increasing anaerobic capacity of the white muscles for burst swimming: Rhigophila dearborni (Zoarcidae), icefish (Channichthyidae), Dissostichus mawsoni, Trematomus centronotus, and Pagothenia borchgrevinki (Nototheniidae). This order reflects in-creasing dependence on anaerobic work done during short bursts of speed during prey capture or predator avoidance. Buffer capacity (beta) for white muscle was lower than that of behaviourally equivalent fish from lower latitudes and beta is itself temperature-dependent

Principles of meiotic chromosome assembly revealed in S. cerevisiae

During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we use Saccharomyces cerevisiae to explore how this elaborate three-dimensional chromosome organisation is linked to genomic sequence. As cells enter meiosis, we observe that strong cohesin-dependent grid-like Hi-C interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extrusion with growth limited by barriers, in which a heterogeneous population of expanding loops develop along the chromosome. Importantly, CTCF, the factor that imposes similar features in mammalian interphase, is absent in S. cerevisiae, suggesting alternative mechanisms of barrier formation. While grid-like interactions emerge independently of meiotic chromosome synapsis, synapsis itself generates additional compaction that matures differentially according to telomere proximity and chromosome size. Collectively, our results elucidate fundamental principles of chromosome assembly and demonstrate the essential role of cohesin within this evolutionarily conserved process

Global data for ecology and epidemiology: a novel algorithm for temporal Fourier processing MODIS data

Background. Remotely-sensed environmental data from earth-orbiting satellites are increasingly used to model the distribution and abundance of both plant and animal species, especially those of economic or conservation importance. Time series of data from the MODerate-resolution Imaging Spectroradiometer (MODIS) sensors on-board NASA's Terra and Aqua satellites offer the potential to capture environmental thermal and vegetation seasonality, through temporal Fourier analysis, more accurately than was previously possible using the NOAA Advanced Very High Resolution Radiometer (AVHRR) sensor data. MODIS data are composited over 8- or 16-day time intervals that pose unique problems for temporal Fourier analysis. Applying standard techniques to MODIS data can introduce errors of up to 30% in the estimation of the amplitudes and phases of the Fourier harmonics. Methodology/Principal Findings. We present a novel spline-based algorithm that overcomes the processing problems of composited MODIS data. The algorithm is tested on artificial data generated using randomly selected values of both amplitudes and phases, and provides an accurate estimate of the input variables under all conditions. The algorithm was then applied to produce layers that capture the seasonality in MODIS data for the period from 2001 to 2005. Conclusions/Significance. Global temporal Fourier processed images of 1 km MODIS data for Middle Infrared Reflectance, day- and night-time Land Surface Temperature (LST), Normalised Difference Vegetation Index (NDVI), and Enhanced Vegetation Index (EVI) are presented for ecological and epidemiological applications. The finer spatial and temporal resolution, combined with the greater geolocational and spectral accuracy of the MODIS instruments, compared with previous multi-temporal data sets, mean that these data may be used with greater confidence in species' distribution modelling

Transit Timing and Duration Variations for the Discovery and Characterization of Exoplanets

Transiting exoplanets in multi-planet systems have non-Keplerian orbits which can cause the times and durations of transits to vary. The theory and observations of transit timing variations (TTV) and transit duration variations (TDV) are reviewed. Since the last review, the Kepler spacecraft has detected several hundred perturbed planets. In a few cases, these data have been used to discover additional planets, similar to the historical discovery of Neptune in our own Solar System. However, the more impactful aspect of TTV and TDV studies has been characterization of planetary systems in which multiple planets transit. After addressing the equations of motion and parameter scalings, the main dynamical mechanisms for TTV and TDV are described, with citations to the observational literature for real examples. We describe parameter constraints, particularly the origin of the mass/eccentricity degeneracy and how it is overcome by the high-frequency component of the signal. On the observational side, derivation of timing precision and introduction to the timing diagram are given. Science results are reviewed, with an emphasis on mass measurements of transiting sub-Neptunes and super-Earths, from which bulk compositions may be inferred.Comment: Revised version. Invited review submitted to 'Handbook of Exoplanets,' Exoplanet Discovery Methods section, Springer Reference Works, Juan Antonio Belmonte and Hans Deeg, Eds. TeX and figures may be found at https://github.com/ericagol/TTV_revie

Environmental Costs of Government-Sponsored Agrarian Settlements in Brazilian Amazonia

Brazil has presided over the most comprehensive agrarian reform frontier colonization program on Earth, in which ~1.2 million settlers have been translocated by successive governments since the 1970's, mostly into forested hinterlands of Brazilian Amazonia. These settlements encompass 5.3% of this ~5 million km2 region, but have contributed with 13.5% of all land conversion into agropastoral land uses. The Brazilian Federal Agrarian Agency (INCRA) has repeatedly claimed that deforestation in these areas largely predates the sanctioned arrival of new settlers. Here, we quantify rates of natural vegetation conversion across 1911 agrarian settlements allocated to 568 Amazonian counties and compare fire incidence and deforestation rates before and after the official occupation of settlements by migrant farmers. The timing and spatial distribution of deforestation and fires in our analysis provides irrefutable chronological and spatially explicit evidence of agropastoral conversion both inside and immediately outside agrarian settlements over the last decade. Deforestation rates are strongly related to local human population density and road access to regional markets. Agrarian settlements consistently accelerated rates of deforestation and fires, compared to neighboring areas outside settlements, but within the same counties. Relocated smallholders allocated to forest areas undoubtedly operate as pivotal agents of deforestation, and most of the forest clearance occurs in the aftermath of government-induced migration

Preparation and properties of copper-oil-based nanofluids

In this study, the lipophilic Cu nanoparticles were synthesized by surface modification method to improve their dispersion stability in hydrophobic organic media. The oil-based nanofluids were prepared with the lipophilic Cu nanoparticles. The transport properties, viscosity, and thermal conductivity of the nanofluids have been measured. The viscosities and thermal conductivities of the nanofluids with the surface-modified nanoparticles have higher values than the base fluids do. The composition has more significant effects on the thermal conductivity than on the viscosity. It is valuable to prepare an appropriate oil-based nanofluid for enhancing the heat-transfer capacity of a hydrophobic system. The effects of adding Cu nanoparticles on the thermal oxidation stability of the fluids were investigated by measuring the hydroperoxide concentration in the Cu/kerosene nanofluids. The hydroperoxide concentrations are observed to be clearly lower in the Cu nanofluids than in their base fluids. Appropriate amounts of metal nanoparticles added in a hydrocarbon fuel can enhance the thermal oxidation stability

What is an "adult protection" issue? Victims, perpetrators and the professional construction of adult protection issues

Drawing on data from a Scottish research study, this paper explores the relationship of professionals’ perceptions about specific perpetrators and victims to their constructions of ‘adult protection’ issues in practice. It finds that professionals’ perceptions of victim distress did not consistently coincide with the construction of adult protection issues, whilst the connection to any assessment of victims’ heightened vulnerability in specific cases was not clear. With respect to perpetrators, implicit practice rules were evidenced which differed from explicit policy criteria. In particular, there were different rules for relatives, staff and service user perpetrators, whilst harms attributed to institutions were de-emphasized. Explanations of the findings are advanced based on the complex power relations underpinning practice but unacknowledged in policies. More research is recommended to deepen this analysis in a changing policy context, to foreground service user perspectives, and to contextualize harms potentially resolvable through adult support and protection/safeguarding routes with respect to harms better addressed in other ways