Three-dimensional molecular dynamics simulations of void coalescence during dynamic fracture of ductile metals

Void coalescence and interaction in dynamic fracture of ductile metals have been investigated using three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. The interaction of the voids is not reflected in the volumetric asymptotic growth rate of the voids, as demonstrated here. Finally, the practice of using a single void and periodic boundary conditions to study coalescence is examined critically and shown to produce results markedly different than the coalescence of a pair of isolated voids.Comment: Accepted for publication in Physical Review

Genetic Improvement of computational biology software

There is a cultural divide between computer scientists and biologists that needs to be addressed. The two disciplines used to be quite unrelated but many new research areas have arisen from their synergy. We selectively review two multi-disciplinary problems: dealing with contamination in sequencing data repositories and improving software using biology inspired evolutionary computing. Through several examples, we show that ideas from biology may result in optimised code and provide surprising improvements that overcome challenges in speed and quality trade-offs. On the other hand, development of computational methods is essential for maintaining contamination free databases. Computer scientists and biologists must always be sceptical of each others data, just as they would be of their own

Distinct encounter complexes of PAI-1 with plasminogen activators and vitronectin revealed by changes in the conformation and dynamics of the reactive center loop

© 2015 The Protein Society Plasminogen activator inhibitor-1 (PAI-1) is a biologically important serine protease inhibitor (serpin) that, when overexpressed, is associated with a high risk for cardiovascular disease and cancer metastasis. Several of its ligands, including vitronectin, tissue-type and urokinase-type plasminogen activator (tPA, uPA), affect the fate of PAI-1. Here, we measured changes in the solvent accessibility and dynamics of an important unresolved functional region, the reactive center loop (RCL), upon binding of these ligands. Binding of the catalytically inactive S195A variant of tPA to the RCL causes an increase in fluorescence, indicating greater solvent protection, at its C-terminus, while mobility along the loop remains relatively unchanged. In contrast, a fluorescence increase and large decrease in mobility at the N-terminal RCL is observed upon binding of S195A-uPA to PAI-1. At a site distant from the RCL, binding of vitronectin results in a modest decrease in fluorescence at its proximal end without restricting overall loop dynamics. These results provide the new evidence for ligand effects on RCL conformation and dynamics and differences in the Michaelis complex with plasminogen activators that can be used for the development of more specific inhibitors to PAI-1. This study is also the first to use electron paramagnetic resonance (EPR) spectroscopy to investigate PAI-1 dynamics. Significance: Balanced blood homeostasis and controlled cell migration requires coordination between serine proteases, serpins, and cofactors. These ligands form noncovalent complexes, which influence the outcome of protease inhibition and associated physiological processes. This study reveals differences in binding via changes in solvent accessibility and dynamics within these complexes that can be exploited to develop more specific drugs in the treatment of diseases associated with unbalanced serpin activity

Fast Monte Carlo simulations and singularities in the probability distributions of non-equilibrium systems

A numerical technique is introduced that reduces exponentially the time required for Monte Carlo simulations of non-equilibrium systems. Results for the quasi-stationary probability distribution in two model systems are compared with the asymptotically exact theory in the limit of extremely small noise intensity. Singularities of the non-equilibrium distributions are revealed by the simulations.Comment: 4 pages, 4 figure

Dynamic ductile to brittle transition in a one-dimensional model of viscoplasticity

We study two closely related, nonlinear models of a viscoplastic solid. These models capture essential features of plasticity over a wide range of strain rates and applied stresses. They exhibit inelastic strain relaxation and steady flow above a well defined yield stress. In this paper, we describe a first step in exploring the implications of these models for theories of fracture and related phenomena. We consider a one dimensional problem of decohesion from a substrate of a membrane that obeys the viscoplastic constitutive equations that we have constructed. We find that, quite generally, when the yield stress becomes smaller than some threshold value, the energy required for steady decohesion becomes a non-monotonic function of the decohesion speed. As a consequence, steady state decohesion at certain speeds becomes unstable. We believe that these results are relevant to understanding the ductile to brittle transition as well as fracture stability.Comment: 10 pages, REVTeX, 12 postscript figure

Neutron reflection from the liquid helium surface.

The reflection of neutrons from a helium surface has been observed for the first time. The 4He surface is smoother in the superfluid state at 1.54 K than in the case of the normal liquid at 2.3 K. In the superfluid state we also observe a surface layer ~200 Å thick which has a subtly different neutron scattering cross-section, which may be explained by an enhanced Bose-Einstein condensate fraction close to the helium surface. The application of neutron reflectometry described in this paper creates new and exciting opportunities for the surface and interfacial study of quantum fluids

When to be discrete: the importance of time formulation in understanding animal movement

Animal movement is essential to our understanding of population dynamics, animal behavior, and the impacts of global change. Coupled with high-resolution biotelemetry data, exciting new inferences about animal movement have been facilitated by various specifications of contemporary models. These approaches differ, but most share common themes. One key distinction is whether the underlying movement process is conceptualized in discrete or continuous time. This is perhaps the greatest source of confusion among practitioners, both in terms of implementation and biological interpretation. In general, animal movement occurs in continuous time but we observe it at fixed discrete-time intervals. Thus, continuous time is conceptually and theoretically appealing, but in practice it is perhaps more intuitive to interpret movement in discrete intervals. With an emphasis on state-space models, we explore the differences and similarities between continuous and discrete versions of mechanistic movement models, establish some common terminology, and indicate under which circumstances one form might be preferred over another. Counter to the overly simplistic view that discrete- and continuous-time conceptualizations are merely different means to the same end, we present novel mathematical results revealing hitherto unappreciated consequences of model formulation on inferences about animal movement. Notably, the speed and direction of movement are intrinsically linked in current continuous-time random walk formulations, and this can have important implications when interpreting animal behavior. We illustrate these concepts in the context of state-space models with multiple movement behavior states using northern fur seal (Callorhinus ursinus) biotelemetry data.Fil: McClintock, Brett T.. National Marine Mammal Laboratory; Estados UnidosFil: Johnson, Devin S.. National Marine Mammal Laboratory; Estados UnidosFil: Hooten, Mevin B.. State University Of Colorado - Fort Collins; Estados UnidosFil: Ver Hoef, Jay M.. National Marine Mammal Laboratory; Estados UnidosFil: Morales, Juan Manuel. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche. Laboratorio de Ecotono; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación en Biodiversidad y Medioambiente; Argentin

From pup to predator; generalized hidden Markov models reveal rapid development of movement strategies in a naïve long‐lived vertebrate

Rapid development of a successful foraging strategy is critical for juvenile survival, especially for naïve animals that receive no parental guidance. However, this process is poorly understood for many species. Although observation of early‐life movements is increasingly possible with miniaturisation of animal‐borne telemetry devices, analytical limitations remain. Here, we tracked 29 recently‐weaned, grey seal Halichoerus grypus pups from colonies in two geographically distinct regions of the United Kingdom. We analysed at‐sea movements of pups throughout their initial months of nutritional independence to investigate the ontogeny of behaviour‐specific (foraging and travelling) movement patterns. Using generalized hidden Markov models (HMMs), we extended the conventional HMM framework to account for temporal changes in putative foraging and travelling movement characteristics, and investigate the effects of intrinsic (sex) and extrinsic (environment) factors on this process. Putative foraging behaviour became more tortuous with time, and travelling became faster and more directed, suggesting a reduction in search scale and an increase in travel efficiency as pups shifted from exploration to an adult‐like repeatable foraging strategy. Sex differences in movement characteristics were evident from colony departure, but sex‐specific activity budgets were only detected in one region. We show that sex‐specific behavioural strategies emerge before sexual size dimorphism in grey seals, and suggest that this phenomenon may occur in other long‐lived species. Our results also indicate that environmental variation may affect the emergence of sex‐specific foraging behaviour, highlighting the need to consider interacting intrinsic and extrinsic factors in shaping movement strategies of long‐lived vertebrates. Moreover, comparing the behavioural state estimations to those of a conventional HMM (no variation in state‐specific movement parameters) revealed differences in the amount and location of foraging activity, with implications for spatial conservation management. Overlooking intrinsic and extrinsic variation in movement processes could distort our understanding of foraging ecology, population dynamics, and conservation requirements

The Discovery of a Neutron Star with a Spin Frequency of 530 Hz in A1744-361

We report the detection with the Rossi X-ray Timing Explorer (RXTE) Proportional Counter Array (PCA) of 530 Hz burst oscillations in a thermonuclear (type I) burst from the transient X-ray source A1744-361. This is only the second burst ever observed from this source, and the first to be seen in any detail. Our results confirm that A1744-361 is a low mass X-ray binary (LMXB) system harboring a rapidly rotating neutron star. The oscillations are first detected along the rising edge of the burst, and they show evidence for frequency evolution of a magnitude similar to that seen in other burst sources. The modulation amplitude and its increase with photon energy are also typical of burst oscillations. The lack of any strong indication of photospheric radius expansion during the burst suggests a 9 kpc upper limit of the source distance. We also find energy dependent dips, establishing A1744-361 as a high inclination, dipping LMXB. The timescale between the two episodes of observed dips suggests an orbital period of ~ 97 minutes. We have also detected a 2 - 4 Hz quasi-periodic-oscillation (QPO) for the first time from this source. This QPO appears consistent with ~ 1 Hz QPOs seen from other high-inclination systems. We searched for kilohertz QPOs, and found a suggestive 2.3 sigma feature at 800 Hz in one observation. The frequency, strength, and quality factor are consistent with that of a lower frequency kilohertz QPO, but the relatively low significance argues for caution, so we consider this a tentative detection requiring confirmation.Comment: 8 pages, 4 figures, published in ApJ Letter