Efficient multiple time scale molecular dynamics: using colored noise thermostats to stabilize resonances

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple colored noise thermostatting scheme which selectively targets the high frequency modes in the system. For two sample problems, flexible water and solvated alanine dipeptide, we demonstrate that this allows the use of large outer time steps while still obtaining accurate sampling and minimizing the perturbation of the dynamics. Furthermore, this approach is shown to be comparable to constraining fast motions, thus providing an alternative to molecular dynamics with constraints.Comment: accepted for publication by the Journal of Chemical Physic

Host-parasite fluctuating selection in the absence of specificity

Fluctuating selection driven by coevolution between hosts and parasites is important for the generation of host and parasite diversity across space and time. Theory has focused primarily on infection genetics, with highly specific ‘matching allele’ frameworks more likely to generate fluctuating selection dynamics (FSD) than ‘gene-for-gene’ (generalist-specialist) frameworks. However, the environment, ecological feedbacks, and life-history characteristics may all play a role in determining when FSD occurs. Here, we develop eco- evolutionary models with explicit ecological dynamics to explore the ecological, epidemiological and host life-history drivers of FSD. Our key result is to demonstrate for the first time that specificity between hosts and parasites is not required to generate FSD. Furthermore, highly specific host-parasite interactions produce unstable, less robust stochastic fluctuations in contrast to interactions that lack specificity altogether or those that vary from generalist to specialist, which produce predictable limit cycles. Given the ubiquity of ecological feedbacks and the variation in the nature of specificity in host parasite interactions, our work emphasizes the underestimated potential for host- parasite coevolution to generate fluctuating selection

The Lemaitre-Schwarzschild Problem Revisited

The Lemaitre and Schwarzschild analytical solutions for a relativistic spherical body of constant density are linked together through the use of the Weyl quadratic invariant. The critical radius for gravitational collapse of an incompressible fluid is shown to vary continuously from 9/8 of the Schwarzschild radius to the Schwarzschild radius itself while the internal pressures become locally anisotropic.Comment: Final version as accepted by GR&G (to appear in vol. 34, september 2002

Late Light Curves of Normal Type Ia Supernovae

We present late-epoch optical photometry (BVRI) of seven normal/super-luminous Type Ia supernovae: SN 2000E, SN 2000ce, SN 2000cx, SN 2001C, SN 2001V, SN 2001bg, SN 2001dp. The photometry of these objects was obtained using a template subtraction method to eliminate galaxy light contamination during aperture photometry. We show the optical light curves of these supernovae out to epochs of up to ~640 days after the explosion of the supernova. We show a linear decline in these data during the epoch of 200-500 days after explosion with the decline rate in the B,V,& R bands equal to about 1.4 mag/100 days, but the decline rate of the I-band is much shallower at 0.94 mag/100 days.Comment: 33 pages, 11 figures, Accepted for publication in The Astronomical Journa

Casimir Energy of a Spherical Shell

The Casimir energy for a conducting spherical shell of radius $a$ is computed using a direct mode summation approach. An essential ingredient is the implementation of a recently proposed method based on Cauchy's theorem for an evaluation of the eigenfrequencies of the system. It is shown, however, that this earlier calculation uses an improper set of modes to describe the waves exterior to the sphere. Upon making the necessary corrections and taking care to ensure that no mathematically ill-defined expressions occur, the technique is shown to leave numerical results unaltered while avoiding a longstanding criticism raised against earlier calculations of the Casimir energy.Comment: LaTeX, 14 pages, 1 figur

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

The D/H Ratio in Interstellar Gas Towards G191-B2B

We reinvestigate the question of spatial variation of the local D/H abundance, using both archival GHRS spectra, and new echelle spectra of G191-B2B obtained with the Space Telescope Imaging Spectrograph (STIS) aboard HST. Our analysis uses stratified line-blanketed non-LTE model atmosphere calculations to determine the shape of the intrinsic WD Lyman-alpha profile and estimate the WD photospheric contamination of the interstellar lines. Although three velocity components were reported previously towards G191-B2B, we detect only two velocity components. The first component is at V(hel) ~ 8.6 km/s and the second at V(hel) ~ 19.3 km/s, which we identify with the Local Interstellar Cloud (LIC). From the STIS data we derive D/H = 1.60(+0.39,-0.27)X10^-5 for the LIC component, and D/H > 1.26X10^-5 for the 8.6 km/s component (uncertainties denote 2-sigma or 95% confidence limits). The STIS data provide no evidence for local or component-to-component variation in the D/H ratio. Despite using two velocity components for the profile fitting and using a more physically realistic WD Lyman-alpha profile for G191-B2B, our re-analysis of the GHRS data indicates a component-to-component variation as well as a variation of the D/H ratio in the LISM, neither of which are supported by the newer STIS data. We believe the most probable cause for this difference is the characterization of the background due to scattered light in the GHRS and STIS spectrographs. The two-dimensional MAMA detectors of STIS measure both the spatial and wavelength dependences of scattered light, allowing more accurate scattered light corrections than was possible with GHRS.Comment: Accepted for publication in Astrophysical Journal Letters. 10 pages + 3 figures. (Abstract is abridged.

The relationship between leadership, teamworking, structure, burnout and attitude to patients on acute psychiatric wards

Contains fulltext : 99818.pdf (publisher's version ) (Open Access)Background: Conflict (aggression, substance use, absconding, etc.) and containment (coerced medication, manual restraint, etc.) threaten the safety of patients and staff on psychiatric wards. Previous work has suggested that staff variables may be significant in explaining differences between wards in their rates of these behaviours, and that structure (ward organisation, rules and daily routines) might be the most critical of these. This paper describes the exploration of a large dataset to assess the relationship between structure and other staff variables. Methods: A multivariate cross-sectional design was utilised. Data were collected from staff on 136 acute psychiatric wards in 26 NHS Trusts in England, measuring leadership, teamwork, structure, burnout and attitudes towards difficult patients. Relationships between these variables were explored through principal components analysis (PCA), structural equation modelling and cluster analysis. Results: Principal components analysis resulted in the identification of each questionnaire as a separate factor, indicating that the selected instruments assessed a number of non-overlapping items relevant for ward functioning. Structural equation modelling suggested a linear model in which leadership influenced teamwork, teamwork structure; structure burnout; and burnout feelings about difficult patients. Finally, cluster analysis identified two significantly distinct groups of wards: the larger of which had particularly good leadership, teamwork, structure, attitudes towards patients and low burnout; and the second smaller proportion which was poor on all variables and high on burnout. The better functioning cluster of wards had significantly lower rates of containment events. Conclusion: The overall performance of staff teams is associated with differing rates of containment on wards. Interventions to reduce rates of containment on wards may need to address staff issues at every level, from leadership through to staff attitudes

Surface-sensitive NMR in optically pumped semiconductors

We present a scheme of surface-sensitive nuclear magnetic resonance in optically pumped semiconductors, where an NMR signal from a part of the surface of a bulk compound semiconductor is detected apart from the bulk signal. It utilizes optically oriented nuclei with a long spin-lattice relaxation time as a polarization reservoir for the second (target) nuclei to be detected. It provides a basis for the nuclear spin polarizer [IEEE Trans. Appl. Supercond. 14, 1635 (2004)], which is a polarization reservoir at a surface of the optically pumped semiconductor that polarizes nuclear spins in a target material in contact through the nanostructured interfaces.Comment: 4 pages, 5 figure