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

Being Healthy: a Grounded Theory Study of Help Seeking Behaviour among Chinese Elders living in the UK

The health of older people is a priority in many countries as the world’s population ages. Attitudes towards help seeking behaviours in older people remain a largely unexplored field of research. This is particularly true for older minority groups where the place that they have migrated to presents both cultural and structural challenges. The UK, like other countries,has an increasingly aging Chinese population about who relatively little is known. This study used a qualitative grounded theory design following the approach of Glaser (1978). Qualitative data were collected using semi-structured interviews with 33 Chinese elders who were aged between 60 and 84, using purposive and theoretical sampling approaches. Data were analysed using the constant comparative method until data saturation occurred and a substantive theory was generated. ‘Being healthy’ (the core category) with four interrelated categories: self-management, normalizing/minimizing, access to health services, and being cured form the theory. The theory was generated around the core explanations provided by participants and Chinese elders’ concerns about health issues they face in their daily life. We also present data about how they direct their health-related activities towards meeting their physical and psychological goals of being healthy. Their differential understanding of diseases and a lack of information about health services were potent predictors of non�help seeking and ‘self’ rather than medical management of their illnesses. This study highlights the need for intervention and health support for Chinese elders

Static and Dynamic Phases for Vortex Matter with Attractive Interactions

Exotic vortex states with long range attraction and short range repulsion have recently been proposed to arise in superconducting hybrid structures and multi-band superconductors. Using large scale simulations we examine the static and dynamic properties of such vortex states interacting with random and periodic pinning. In the absence of pinning this system does not form patterns but instead completely phase separates. When pinning is present there is a transition from inhomogeneous to homogeneous vortex configurations similar to a wetting phenomenon. Under an applied drive, a dynamical dewetting process can occur from a strongly pinned homogeneous state into pattern forming states. We show that a signature of the exotic vortex interactions under transport measurements is a robust double peak feature in the differential conductivity curves.Comment: 5 pages, 4 postscript figure

Broadband Relaxation-Optimized Polarization Transfer in Magnetic Resonance

Many applications of magnetic resonance are limited by rapid loss of spin coherence caused by large transverse relaxation rates. In nuclear magnetic resonance (NMR) of large proteins, increased relaxation losses lead to poor sensitivity of experiments and increased measurement time. In this paper we develop broadband relaxation optimized pulse sequences (BB-CROP) which approach fundamental limits of coherence transfer efficiency in the presence of very general relaxation mechanisms that include cross-correlated relaxation. These broadband transfer schemes use new techniques of chemical shift refocusing (STAR echoes) that are tailored to specific trajectories of coupled spin evolution. We present simulations and experimental data indicating significant enhancement in the sensitivity of multi-dimensional NMR experiments of large molecules by use of these methods

Geodesics for Efficient Creation and Propagation of Order along Ising Spin Chains

Experiments in coherent nuclear and electron magnetic resonance, and optical spectroscopy correspond to control of quantum mechanical ensembles, guiding them from initial to final target states by unitary transformations. The control inputs (pulse sequences) that accomplish these unitary transformations should take as little time as possible so as to minimize the effects of relaxation and decoherence and to optimize the sensitivity of the experiments. Here we give efficient syntheses of various unitary transformations on Ising spin chains of arbitrary length. The efficient realization of the unitary transformations presented here is obtained by computing geodesics on a sphere under a special metric. We show that contrary to the conventional belief, it is possible to propagate a spin order along an Ising spin chain with coupling strength J (in units of Hz), significantly faster than 1/(2J) per step. The methods presented here are expected to be useful for immediate and future applications involving control of spin dynamics in coherent spectroscopy and quantum information processing

Bereavement and marriage are associated with antibody response to influenza vaccination in the elderly

Stressful life events exposure including bereavement, an event commonly experienced by elderly people, social support, marital status and satisfaction were examined in relation to antibody response to the annual trivalent influenza vaccination in an elderly community sample (N = 184). Antibody response was assessed at baseline, and at one and 12 months following vaccination. Taking into account baseline antibody titer, overall life events exposure and social support were not associated with response to any of the influenza strains. However, bereavement in the year prior to vaccination was negatively associated with the one-month response to the A/Panama and B/Shangdong strains. Being married and having higher marital satisfaction was also associated with higher peak responses to the A/Panama influenza strain at one month. The positive association between marital satisfaction and A/Panama response was particularly evident in the younger half of the married sample. These associations largely withstood adjustment for potential confounders. Thus, in the elderly, peak antibody response was associated with bereavement and marriage, and not the more general factors, life events and social support, related to antibody response in student samples. This suggests the importance of taking a life course approach to examining relationships between psychosocial factors and immunity, and that interventions to modify the impact of these factors should address those most salient for each age group