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

Islands of conformational stability for Filopodia

Filopodia are long, thin protrusions formed when bundles of fibers grow outwardly from a cell surface while remaining closed in a membrane tube. We study the subtle issue of the mechanical stability of such filopodia and how this depends on the deformation of the membrane that arises when the fiber bundle adopts a helical configuration. We calculate the ground state conformation of such filopodia, taking into account the steric interaction between the membrane and the enclosed semiflexible fiber bundle. For typical filopodia we find that a minimum number of fibers is required for filopodium stability. Our calculation elucidates how experimentally observed filopodia can obviate the classical Euler buckling condition and remain stable up to several tens of . We briefly discuss how experimental observation of the results obtained in this work for the helical-like deformations of enclosing membrane tubes in filopodia could possibly be observed in the acrosomal reactions of the sea cucumber Thyone, and the horseshoe crab Limulus. Any realistic future theories for filopodium stability are likely to rely on an accurate treatment of such steric effects, as analysed in this work

Lattice-switch Monte Carlo

We present a Monte Carlo method for the direct evaluation of the difference between the free energies of two crystal structures. The method is built on a lattice-switch transformation that maps a configuration of one structure onto a candidate configuration of the other by `switching' one set of lattice vectors for the other, while keeping the displacements with respect to the lattice sites constant. The sampling of the displacement configurations is biased, multicanonically, to favor paths leading to `gateway' arrangements for which the Monte Carlo switch to the candidate configuration will be accepted. The configurations of both structures can then be efficiently sampled in a single process, and the difference between their free energies evaluated from their measured probabilities. We explore and exploit the method in the context of extensive studies of systems of hard spheres. We show that the efficiency of the method is controlled by the extent to which the switch conserves correlated microstructure. We also show how, microscopically, the procedure works: the system finds gateway arrangements which fulfill the sampling bias intelligently. We establish, with high precision, the differences between the free energies of the two close packed structures (fcc and hcp) in both the constant density and the constant pressure ensembles.Comment: 34 pages, 9 figures, RevTeX. To appear in Phys. Rev.

Zero-point vacancies in quantum solids

A Jastrow wave function (JWF) and a shadow wave function (SWF) describe a quantum solid with Bose--Einstein condensate; i.e. a supersolid. It is known that both JWF and SWF describe a quantum solid with also a finite equilibrium concentration of vacancies x_v. We outline a route for estimating x_v by exploiting the existing formal equivalence between the absolute square of the ground state wave function and the Boltzmann weight of a classical solid. We compute x_v for the quantum solids described by JWF and SWF employing very accurate numerical techniques. For JWF we find a very small value for the zero point vacancy concentration, x_v=(1.4\pm0.1) x 10^-6. For SWF, which presently gives the best variational description of solid 4He, we find the significantly larger value x_v=(1.4\pm0.1) x 10^-3 at a density close to melting. We also study two and three vacancies. We find that there is a strong short range attraction but the vacancies do not form a bound state.Comment: 19 pages, submitted to J. Low Temp. Phy

Coevolved mutations reveal distinct architectures for two core proteins in the bacterial flagellar motor

Switching of bacterial flagellar rotation is caused by large domain movements of the FliG protein triggered by binding of the signal protein CheY to FliM. FliG and FliM form adjacent multi-subunit arrays within the basal body C-ring. The movements alter the interaction of the FliG C-terminal (FliGC) "torque" helix with the stator complexes. Atomic models based on the Salmonella entrovar C-ring electron microscopy reconstruction have implications for switching, but lack consensus on the relative locations of the FliG armadillo (ARM) domains (amino-terminal (FliGN), middle (FliGM) and FliGC) as well as changes during chemotaxis. The generality of the Salmonella model is challenged by the variation in motor morphology and response between species. We studied coevolved residue mutations to determine the unifying elements of switch architecture. Residue interactions, measured by their coevolution, were formalized as a network, guided by structural data. Our measurements reveal a common design with dedicated switch and motor modules. The FliM middle domain (FliMM) has extensive connectivity most simply explained by conserved intra and inter-subunit contacts. In contrast, FliG has patchy, complex architecture. Conserved structural motifs form interacting nodes in the coevolution network that wire FliMM to the FliGC C-terminal, four-helix motor module (C3-6). FliG C3-6 coevolution is organized around the torque helix, differently from other ARM domains. The nodes form separated, surface-proximal patches that are targeted by deleterious mutations as in other allosteric systems. The dominant node is formed by the EHPQ motif at the FliMMFliGM contact interface and adjacent helix residues at a central location within FliGM. The node interacts with nodes in the N-terminal FliGc α-helix triad (ARM-C) and FliGN. ARM-C, separated from C3-6 by the MFVF motif, has poor intra-network connectivity consistent with its variable orientation revealed by structural data. ARM-C could be the convertor element that provides mechanistic and species diversity.JK was supported by Medical Research Council grant U117581331. SK was supported by seed funds from Lahore University of Managment Sciences (LUMS) and the Molecular Biology Consortium

Behavioural syndrome in a solitary predator is independent of body size and growth rate.

Models explaining behavioural syndromes often focus on state-dependency, linking behavioural variation to individual differences in other phenotypic features. Empirical studies are, however, rare. Here, we tested for a size and growth-dependent stable behavioural syndrome in the juvenile-stages of a solitary apex predator (pike, Esox lucius), shown as repeatable foraging behaviour across risk. Pike swimming activity, latency to prey attack, number of successful and unsuccessful prey attacks was measured during the presence/absence of visual contact with a competitor or predator. Foraging behaviour across risks was considered an appropriate indicator of boldness in this solitary predator where a trade-off between foraging behaviour and threat avoidance has been reported. Support was found for a behavioural syndrome, where the rank order differences in the foraging behaviour between individuals were maintained across time and risk situation. However, individual behaviour was independent of body size and growth in conditions of high food availability, showing no evidence to support the state-dependent personality hypothesis. The importance of a combination of spatial and temporal environmental variation for generating growth differences is highlighted

Utjecaj izloženosti 1,6-heksametilen diizocijanatu (HDI) na vršni ekspiratorni protok u autolakirera u Iranu

The aim of this study was to investigate the effects of occupational exposure to 1,6-hexamethylene diisocyanate (HDI) on peak flowmetry in automobile body paint shop workers in Iran. We studied a population of 43 car painters exposed to HDI at their workplaces. Peak expiratory fl ow was tested for one working week, from the start to the end of each shift. Air was sampled and HDI analysed in parallel, according to the OSHA 42 method. Daily and weekly HDI exposure averages were (0.42±0.1) mg m-3 and (0.13±0.05) mg m-3, respectively. On painting days, 72 % of workers showed more than a 10 % variation in peak expiratory fl ow. Inhalation exposure exceeded the threshold limit value (TLV) ten times over. This strongly suggests that HDI affected the peak fl owmetry in the studied workers.Cilj je ovog ispitivanja bio utvrditi vršni protok u 43 iranska autolakirera profesionalno izložena 1,6-heksametilen diizocijanatu (HDI). Vršni ekspiratorni protok testiran je tjedan dana na početku i kraju svake smjene. Uzorkovanje i mjerenje HDI-ja u zraku radilo se istodobno s testiranjem vršnoga protoka, prema metodi OSHA 42. Prosječna dnevna izloženost radnika HDI-ju iznosila je (0.42±0.1) mg m-3, a tjedna (0.13±0.05) mg m-3. U 72 % radnika vršni ekspiratorni protok tijekom dana varirao je više od 10 %. Radnici su udisali deset puta više razine HDI-ja od graničnih te je moguće da je HDI utjecao na mjerenja plućne funkcije

Morphological evaluation of experimental autologous rectus fascia sheath vascular grafts used for arterial replacement in a dog model

Although experimental autologous patch or tubular conduit vascular grafts made from the internal rectus fascia sheath (IRFS) have been reported in the literature, thorough morphological evaluation and verification of the histological arterialisation of such grafts are lacking. Four purpose-bred Beagle dogs were utilised to create eight arterial internal rectus fascia sheath (ARFS) grafts implanted between bisected ends of the external iliac arteries. Four out of the eight ARFS grafts were patent after three months. Haematoxylin-eosin and Azan staining verified that the grafts gained a vessel-like layered structure with the presence of large amounts of collagen fibres. Although the inner surface of the intact IRFS was originally covered with claudin-5-negative and pancytokeratin-positive mesothelial cells in control samples, the internal cells of the ARFS grafts became claudin-5 positive and pancytokeratin negative like in intact arteries. Spindle-shaped cells of the wall of ARFS grafts were α-smooth muscle actin (α-SMA) positive just like the smooth muscle cells of intact arteries, but α-SMA immunoreactivity was negative in the intact IRFS. According to these findings, the fibroblast cells of the ARFS graft have changed into myofibroblast cells. The study has proved that ARFS grafts may be used as an alternative in arterial replacement, since the graft becomes morphologically and functionally similar to the host vessel via arterialisation

Phase equilibria and glass transition in colloidal systems with short-ranged attractive interactions. Application to protein crystallization

We have studied a model of a complex fluid consisting of particles interacting through a hard core and a short range attractive potential of both Yukawa and square-well form. Using a hybrid method, including a self-consistent and quite accurate approximation for the liquid integral equation in the case of the Yukawa fluid, perturbation theory to evaluate the crystal free energies, and mode-coupling theory of the glass transition, we determine both the equilibrium phase diagram of the system and the lines of equilibrium between the supercooled fluid and the glass phases. For these potentials, we study the phase diagrams for different values of the potential range, the ratio of the range of the interaction to the diameter of the repulsive core being the main control parameter. Our arguments are relevant to a variety of systems, from dense colloidal systems with depletion forces, through particle gels, nano-particle aggregation, and globular protein crystallization.Comment: 20 pages, 10 figure

The influence of preoperative determinants on quality of life, functioning and pain after total knee and hip replacement:A pooled analysis of Dutch cohorts

Background: Previous research has identified preoperative determinants that predict health related quality of life (HRQoL), functioning and pain after total knee or hip arthroplasty (TKA/THA), but these differed between studies and had opposite directions. This may be due to lack of power and not adjusting for confounders. The present study aims to identify the preoperative determinants that influence health related quality of life (HRQoL), functioning and pain after total knee or hip arthroplasty (TKA/THA). Methods: We pooled individual patient from 20 cohorts with OA patients data (n = 1783 TKA and n = 2400 THA) in the Netherlands. We examined the influence of age, gender, BMI and preoperative values of HRQoL, functioning and pain on postoperative status and total improvement. Linear mixed models were used to estimate the effect of each preoperative variable on a particular outcome for each cohort separately. These effects were pooled across cohorts using a random effects model. Results: For each increase in preoperative point in HRQoL, the postoperative HRQoL increased by 0.51 points in TKA and 0.37 points in THA (SF-36 scale). Similarly, each point increase in preoperative functioning, resulted in a higher postoperative functioning of 0.31 (TKA) and 0.21 (THA) points (KOOS/HOOS-ADL scale). For pain this was 0.18 (TKA) and 0.15 (THA) points higher (KOOS/HOOS-pain scale) (higher means less pain). Even though patients with better preoperative values achieved better postoperative outcomes, their improvement was smaller. Women and patients with a higher BMI had more pain after a TKA and THA. Higher age and higher BMI was associated with lower postoperative HRQoL and functioning and more pain after a THA.Conclusions: Patients with a better preoperative health status have better outcomes, but less improvement. Even though the independent effects may seem small, combined results of preoperative variables may result in larger effects on postoperative outcomes.</p