Simulating Solidification in Metals at High Pressure: The Drive to Petascale Computing

We investigate solidification in metal systems ranging in size from 64,000 to 524,288,000 atoms on the IBM BlueGene/L computer at LLNL. Using the newly developed ddcMD code, we achieve performance rates as high as 103 TFlops, with a performance of 101.7 TFlop sustained over a 7 hour run on 131,072 cpus. We demonstrate superb strong and weak scaling. Our calculations are significant as they represent the first atomic-scale model of metal solidification to proceed, without finite size effects, from spontaneous nucleation and growth of solid out of the liquid, through the coalescence phase, and into the onset of coarsening. Thus, our simulations represent the first step towards an atomistic model of nucleation and growth that can directly link atomistic to mesoscopic length scales

Beyond Finite Size Scaling in Solidification Simulations

Although computer simulation has played a central role in the study of nucleation and growth since the earliest molecular dynamics simulations almost 50 years ago, confusion surrounding the effect of finite size on such simulations have limited their applicability. Modeling solidification in molten tantalum on the BlueGene/L computer, we report here on the first atomistic simulation of solidification that verifies independence from finite size effects during the entire nucleation and growth process, up to the onset of coarsening. We show that finite size scaling theory explains the observed maximal grain sizes for systems up to about 8,000,000 atoms. For larger simulations, a cross-over from finite size scaling to more physical size-independent behavior is observed

Atoms in the Surf: Molecular Dynamics Simulation of the Kelvin-Helmholtz Instability using 9 Billion Atoms

We present a fluid dynamics video showing the results of a 9-billion atom molecular dynamics simulation of complex fluid flow in molten copper and aluminum. Starting with an atomically flat interface, a shear is imposed along the copper-aluminum interface and random atomic fluctuations seed the formation of vortices. These vortices grow due to the Kelvin-Helmholtz instability. The resulting vortical structures are beautifully intricate, decorated with secondary instabilities and complex mixing phenomena. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.Comment: Description of video submitted to APS DFD Gallery of Fluid Motion 200

High-Pressure Tailored Compression: Controlled Thermodynamic Paths

We have recently carried out novel and exploratory dynamic experiments where the sample follows a prescribed thermodynamic path. In typical dynamic compression experiments, the samples are thermodynamically limited to the principal Hugoniot or quasi-isentrope. With recent developments in the functionally graded material impactor, we can prescribe and shape the applied pressure profile with similarly-shaped, non-monotonic impedance profile in the impactor. Previously inaccessible thermodynamic states beyond the quasi-isentropes and Hugoniot can now be reached in dynamic experiments with these impactors. In the light gas-gun experiments on copper reported here, we recorded the particle velocities of the Cu-LiF interfaces and employed hydrodynamic simulations to relate them to the thermodynamic phase diagram. Peak pressures for these experiments were on the order of megabars, and the time-scales ranged from nanoseconds to several microseconds. The strain rates of the quasi-isentropic experiments are approximately 10{sup 4} s{sup -1} to 10{sup 6} s{sup -1} in samples with thicknesses up to 5 mm. Though developed at a light-gas gun facility, such shaped pressure-profiles are also feasible in principle with laser ablation or magnetic driven compression techniques allowing for new directions to be taken in high pressure physics

Non-magnetic impurities in two dimensional superconductors

A numerical approach to disordered 2D superconductors described by BCS mean field theory is outlined. The energy gap and the superfluid density at zero temperature and the quasiparticle density of states are studied. The method involves approximate self-consistent solutions of the Bogolubov-de$\,$Gennes equations on finite square lattices. Where comparison is possible, the results of standard analytic approaches to this problem are reproduced. Detailed modeling of impurity effects is practical using this approach. The {\it range} of the impurity potential is shown to be of {\it quantitative importance} in the case of strong potential scatterers. We discuss the implications for experiments, such as the rapid suppression of superconductivity by Zn doping in Copper-Oxide superconductors.Comment: 16 pages, latex, 8 figures( available upon request

NS1 Specific CD8(+) T-Cells with Effector Function and TRBV11 Dominance in a Patient with Parvovirus B19 Associated Inflammatory Cardiomyopathy

Background: Parvovirus B19 (B19V) is the most commonly detected virus in endomyocardial biopsies (EMBs) from patients with inflammatory cardiomyopathy (DCMi). Despite the importance of T-cells in antiviral defense, little is known about the role of B19V specific T-cells in this entity. Methodology and Principal Findings: An exceptionally high B19V viral load in EMBs (115,091 viral copies/mg nucleic acids), peripheral blood mononuclear cells (PBMCs) and serum was measured in a DCMi patient at initial presentation, suggesting B19V viremia. The B19V viral load in EMBs had decreased substantially 6 and 12 months afterwards, and was not traceable in PBMCs and the serum at these times. Using pools of overlapping peptides spanning the whole B19V proteome, strong CD8(+) T-cell responses were elicited to the 10-amico-acid peptides SALKLAIYKA (19.7% of all CD8(+) cells) and QSALKLAIYK (10%) and additional weaker responses to GLCPHCINVG (0.71%) and LLHTDFEQVM (0.06%). Real-time RT-PCR of IFN gamma secretion-assay-enriched T-cells responding to the peptides, SALKLAIYKA and GLCPHCINVG, revealed a disproportionately high T-cell receptor Vbeta (TRBV) 11 expression in this population. Furthermore, dominant expression of type-1 (IFN gamma, IL2, IL27 and Tbet) and of cytotoxic T-cell markers (Perforin and Granzyme B) was found, whereas gene expression indicating type-2 (IL4, GATA3) and regulatory T-cells (FoxP3) was low. Conclusions: Our results indicate that B19V Ag-specific CD8(+) T-cells with effector function are involved in B19V associated DCMi. In particular, a dominant role of TRBV11 and type-1/CTL effector cells in the T-cell mediated antiviral immune response is suggested. The persistence of B19V in the endomyocardium is a likely antigen source for the maintenance of CD8(+) T-cell responses to the identified epitopes

Patenting and licensing of university research: promoting innovation or undermining academic values?

Since the 1980s in the US and the 1990s in Europe, patenting and licensing activities by universities have massively increased. This is strongly encouraged by governments throughout the Western world. Many regard academic patenting as essential to achieve 'knowledge transfer' from academia to industry. This trend has far-reaching consequences for access to the fruits of academic research and so the question arises whether the current policies are indeed promoting innovation or whether they are instead a symptom of a pro-intellectual property (IP) culture which is blind to adverse effects. Addressing this question requires both empirical analysis (how real is the link between academic patenting and licensing and 'development' of academic research by industry?) and normative assessment (which justifications are given for the current policies and to what extent do they threaten important academic values?). After illustrating the major rise of academic patenting and licensing in the US and Europe and commenting on the increasing trend of 'upstream' patenting and the focus on exclusive as opposed to non-exclusive licences, this paper will discuss five negative effects of these trends. Subsequently, the question as to why policymakers seem to ignore these adverse effects will be addressed. Finally, a number of proposals for improving university policies will be made

Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen

The temperature equilibration rate in dense hydrogen (for both T_{i}>T_{e} and T_i<T_e) has been calculated with molecular dynamics simulations for temperatures between 10 and 600 eV and densities between 10^{20}/cc to 10^{24}/cc. Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L>1, a model by Gericke-Murillo-Schlanges (GMS) [Gericke et al., PRE 65, 036418 (2002)] based on a T-matrix method and the approach by Brown-Preston-Singleton [Brown et al., Phys. Rep. 410, 237 (2005)] agrees with the simulation data to within the error bars of the simulation. For smaller Coulomb logarithms, the GMS model is consistent with the simulation results. Landau-Spitzer models are consistent with the simulation data for L>4

Automating unobtrusive personalized services in ambient media environments

The final publication is available at Springer via http://dx.doi.org/10.1007/s11042-013-1634-2In the age of ambient media, people are surrounded by lots of physical objects (media objects) for rendering the digital world in the natural environment. These media objects should interact with users in a way that is not disturbing for them. To address this issue, this work presents a design and automation strategy for augmenting the world around us with personalized ambient media services that behave in a considerate manner. That is, ambient services are capable of adjusting its obtrusiveness level (i.e., the extent to which each service intrudes the user¿s mind) by using the appropriate media objects for each user¿s situation.This work has been developed with the support of MICINN, under the project EVERYWARE TIN2010-18011, and the support of the Christian Doppler Forschungsgesellschaft and the BMWFJ, Austria.Serral Asensio, E.; Gil Pascual, M.; Valderas Aranda, PJ.; Pelechano Ferragud, V. (2014). Automating unobtrusive personalized services in ambient media environments. Multimedia Tools and Applications. 71(1):159-178. https://doi.org/10.1007/s11042-013-1634-2S159178711Bencomo N, Grace P, Flores-Cortés CA, Hughes D, Blair GS (2008) Genie: supporting the model driven development of reflective, component-based adaptive systems. In: ICSE, pp 811–814Blumendorf M, Lehmann G, Albayrak S (2010) Bridging models and systems at runtime to build adaptive user interfaces. In: Proc. of EICS 2010. 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Risk of Malignant Progression in Barrett’s Esophagus Patients: Results from a Large Population-Based Study

BACKGROUND: Barrett’s esophagus (BE) is a premalignant lesion that predisposes to esophageal adenocarcinoma. However, the reported incidence of esophageal adenocarcinoma in patients with BE varies widely. We examined the risk of malignant progression in patients with BE using data from the Northern Ireland Barrett’s esophagus Register (NIBR), one of the largest population-based registries of BE worldwide, which includes every adult diagnosed with BE in Northern Ireland between 1993 and 2005. SUBJECTS AND METHODS: We followed 8522 patients with BE, defined as columnar lined epithelium of the esophagus with or without specialized intestinal metaplasia (SIM), until the end of 2008. Patients with incident adenocarcinomas of the esophagus or gastric cardia or with high-grade dysplasia of the esophagus were identified by matching the NIBR with the Northern Ireland Cancer Registry, and deaths were identified by matching with records from the Registrar General’s Office. Incidence of cancer outcomes or high-grade dysplasia was calculated as events per 100 person-years (% per year) of follow-up, and Cox proportional hazard models were used to determine incidence by age, sex, length of BE segment, presence of SIM, macroscopic BE, or low-grade dysplasia. All P values were from two-sided tests. RESULTS: After a mean of 7.0 years of follow-up, 79 patients were diagnosed with esophageal cancer, 16 with cancer of the gastric cardia, and 36 with high-grade dysplasia. In the entire cohort, incidence of esophageal or gastric cardia cancer or high-grade dysplasia combined was 0.22% per year (95% confidence interval [CI] = 0.19% to 0.26%). SIM was found in 46.0% of patients. In patients with SIM, the combined incidence was 0.38% per year (95% CI = 0.31 to 0.46%). The risk of cancer was statistically significantly elevated in patients with vs without SIM at index biopsy (0.38% per year vs 0.07% per year; hazard ratio [HR] = 3.54, 95% CI = 2.09 to 6.00, P < .001), in men compared with women (0.28% per year vs 0.13% per year; HR = 2.11, 95% CI = 1.41 to 3.16, P < .001), and in patients with low-grade dysplasia compared with no dysplasia (1.40% per year vs 0.17% per year; HR = 5.67, 95% CI = 3.77 to 8.53, P < .001). CONCLUSION: We found the risk of malignant progression among patients with BE to be lower than previously reported, suggesting that currently recommended surveillance strategies may not be cost-effective