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The physics of diffuse, ionized gases - plasmas - and gravity in deep space are of great interest to researchers investigating how the early universe developed. The use of high-performance computing allows computational astrophysicists to create simulations that extend over cosmic times and distances.
Professor Tom Jones, an MSI Fellow from the Minnesota Institute for Astrophysics in the School of Physics and Astronomy (College of Science and Engineering), has used MSI’s supercomputers to investigate plasmas and gravitational fields in astrophysical environments since the 1980s. The various pioneering projects covered in this research program have formed the basis of a large number of Ph.D. theses and have resulted in many publications. In current projects, the Jones group is using powerful magnetohydrodynamics (MHD) codes on the supercomputers to create simulations that allow them to study the physical processes in diffuse gases in galaxy clusters and to investigate the outflow from massive black holes. The group has developed a high-performance MHD code called “WOMBAT,” which they are continuing to expand in order to create even high-resolution simulations and to include additional physical processes.
A 2014 paper in the Astrophysical Journal discussed a phenomenological model for thermal leakage injection in the diffusive shock acceleration (DSA) process. DSA is the acceleration that ions and electrons undergo when being repeatedly reflected and it plays an important role in astrophysical models, such as solar flares and supernova shock waves. Recently this process has been invoked to explain giant radio structures in galaxy clusters spanning several million light years. Professor Jones and his colleagues Dr. Hyesung Kang (Pusan National University, Korea), Dr. Vahe Petrosian (Stanford University, California), and Dr. Dongsu Ryu (UNIST, Korea) developed a model for injection of particles into the DSA process from kappa-like suprathermal particle populations into diffusive shock acceleration. (Kang, Hyesung, Vahe Petrosian, Dongsu Ryu, and Thomas W. Jones. 2014. Injection of kappa-like suprathermal particles into diffusive shock acceleration. Astrophysical Journal 788 (2) (JUN 20): 142.) The kappa distribution represents “thermal” population modified by resonant interactions between particles and plasma waves generated by the shock that propagate ahead of the shock. In related work, a 2013 Astrophysical Journal paper investigated nonlinear effects of wave-particle interactions on the DSA process in Type-1a-like supernova remnant blast waves. Supernova remnants are strong sources of nonthermal radiation. (Kang, Hyesung, Thomas W. Jones, and Paul P. Edmon. 2013. Nonthermal radiation from supernova remnants: Effects of magnetic field amplification and particle escape. Astrophysical Journal 777 (1) (NOV 1): 25.)
Other publications by Professor Jones during 2014 include:
• Brunetti, Gianfranco, and Thomas W. Jones. 2014. Cosmic rays in galaxy clusters and their nonthermal emission. International Journal of Modern Physics D 23 (4) (JAN 01).
• Wykes, Sarka, Huib T. Intema, Martin J. Hardcastle, Abraham Achterberg, Thomas W. Jones, Helmut Jerjen, Emanuela Orru, et al. 2014. Filaments in the southern giant lobe of Centaurus A: Constraints on nature and origin from modelling and GMRT observations. Monthly Notices of the Royal Astronomical Society 442 (4) (JAN 01): 2867-82.
Some of the largest simulations the Jones group have carried out at MSI follow the full dynamic formation of the galaxy clusters as they fall out of the expansion of the universe because of gravity. One particular study in that effort is shown in the visualizations above. The images show a snapshot in time of one cluster of galaxies formed in a simulation. The focus of this study is development of turbulent plasma flows on large scales during the collisions of clusters. A simple way to measure the strength of turbulence is to calculate the rate at which turbulent eddies spin, a measure called vorticity. In the image above, the left image shows the distribution of vorticity; the right image shows one of the physical processes that drives the generation of turbulence. From analyses like this it is possible to establish, for example, that shock waves are the principle sources for turbulence in the cluster.
posted on October 15, 2014
Epstein-Barr Virus (EBV) is a common virus in the human herpes family. It is well known as the cause of infectious mononucleosis, but it also is associated with some forms of cancer and with autoimmune diseases such as systemic lupus erythematosus and multiple sclerosis. Much of the population is infected with EBV with no symptoms, but we don’t understand why some individuals become sick while others do not. There is no vaccine and no treatment for EBV infection.
MSI Principal Investigator Kristin Hogquist, a professor in the Department of Laboratory Medicine and Pathology and Center for Immunology (Medical School), and her University of Minnesota colleagues recently investigated immune responses to EBV. They used transcriptome analysis to study the immune responses of patients who acquired EBV infections naturally. They found an interesting gene expression profile during acute infection, but no lasting changes during latent infection. They also discovered similarities in responses to EBV and the Dengue fever virus. These results provide important new information relating to natural herpesvirus infections.
The results of this research were published in the journal PLoS One (Dunmire, Samantha K., Oludare A. Odumade, Jean L. Porter, Juan Reyes-Genere, David O. Schmeling, Hatice Bilgic, Danhua Fan, Emily C. Baechler, Henry H. Balfour Jr., and Kristin A. Hogquist. 2014. Primary EBV infection induces an expression profile distinct from other viruses but similar to hemophagocytic syndromes. PLoS One 9 (1) (JAN 17), 10.1371/journal.pone.0085422). Dr. Kevin Silverstein, of MSI’s RISS group, provided assistance to the authors with bioinformatics analysis and software. The paper can be read on the PLoS One website.
Image description: A distinct gene expression profile is apparent during acute EBV infection, but not latent infection. (A) Microarray analysis was performed on pre-infection, acute, and latent timepoints for 10 subjects with primary EBV infection. 464 genes were shown to be significantly changed during the primary response to EBV at a fold change of ≥ 2 and a p-value of ≤ 0.05. No genes were significantly changed during the latent phase of infection using the same criteria. (B) Ingenuity Pathway Analysis of the 464 acute genes revealed 14 pathways that were enriched amongst the genes that changed during primary EBV. These had a significant p-value (the negative log is shown) following evaluation with the Benjamin-Hochberg multiple tests correction. (C) A heatmap representation of the highest (≥ 3 fold) gene changes during the acute and latent stages of EBV infection. (Image and description, S.K. Dunmire, et al., PLoS One 9 (1) (JAN 17), 10.1371/journal.pone.0085422).
posted on October 1, 2014
Among many other disadvantages, being poor often means that people are more likely to live in polluted environments. A recent study by MSI Principal Investigators Julian Marshall (an associate professor in the Department of Civil, Environmental, and Geo- Engineering, College of Science and Engineering, and Fellow of the Institute on the Environment) and Dylan Millet (an associate professor in the Department of Soil, Water, and Climate, College of Food, Agricultural, and Natural Resource Sciences, and Fellow of the Institute on the Environment), published in PLoS One, investigated disparities in health risks in a variety of areas within the US. This included regions, states, and cities. Specifically targeting the air pollutant NO2, one of the US EPA’s criteria pollutants, this research showed that poorer populations are more likely to be exposed to higher levels of NO2, which is related to poorer health. Poorer populations may also be more affected by pollutants because of compounding factors such as more limited access to health-care services.
While other studies about the relationship between pollution and socioeconomic status have been done within some cities, there is little data concerning broader patterns across the entire US. This research covered the contiguous US states, and also included both urban and rural areas. This research used US Census demographic data and a recently published high-resolution dataset of outdoor NO2 concentrations. The authors used MSI computational resources to process the data.
The results of this study showed that, within a given urban area, nonwhites are exposed to more NO2 than whites, and lower-income people are exposed to more NO2 than those with higher incomes. The comparative amount of NO2 that poorer populations and nonwhites are exposed to may have serious health implications. The results for counties and cities may give policy-makers means to determine how pollution-control efforts should be directed. The article can be read on the PLoS One website (Clark, Lara P., Dylan B. Millet, and Julian D. Marshall. 2014. National patterns in environmental injustice and inequality: Outdoor NO2 air pollution in the United States. PLoS One 9 (4) (APR 15): e94431.)
Image description: The left side shows differences in population-weighted mean NO2 concentrations between low-income nonwhites (LIN) and high-income whites (HIW), with large positive differences (red colors) indicating higher injustice (larger concentration difference between LIN and HIW). The right column shows the Atkinson Index (NO2 inequality), with higher values indicating greater inequality. This image shows results for urban areas in the contiguous US. (Image and description, L. Clark, et al., PLoS One 9 (4) (APR 15): e94431.)
posted on September 17, 2014
Anyone who plays video games or who goes to movies that use computer-generated imaging knows that virtual environments are becoming more and more realistic. Also, computers available to consumers continue to get more powerful, with multiple cores. The algorithms that use these computers to create virtual environments need to be structured in such a way that they can create realistic, interactive realms in games and other virtual-reality applications as efficiently as possible.
One way to improve efficiency is to create a parallel program, which is broken into several pieces that are run concurrently, instead of each piece running sequentially. Software developers of video games are working to develop programs that can be parallelized in order to make use of multiple cores or computer clusters. MSI Principal Investigator Stephen Guy, an assistant professor in the Department of Computer Science and Engineering (College of Science and Engineering), and members of his group are working on these kinds of programs. At the 6th International Conference of Motion in Games in Dublin, Ireland, in November 2013, Professor Guy, along with student John Koenig and post-doctoral researcher Dr. Ioannis Karamouzas, presented a paper discussing a new object-centric algorithm for parallel rigid-body simulation. The object-centric method means that each simulated body is modeled independently and is therefore self-contained. Objects that are more isolated from other objects can be modeled with larger time-steps, which improves efficiency and saves computation time for objects that are interacting more closely.
This object-centric method results in interactive, real-time simulations that can scale across many CPU cores. This paper included scenarios that consisted of hundreds of interacting objects. The paper can be found at the Association for Computer Machinery’s Digital Library (Koenig, John, Ioannis Karamouzas, Stephen J. Guy. Object-centric parallel rigid body simulation with timewarp. 2013. Proceedings of MIG ’13, Motion of Games, 203-212. DOI: 10.1145/2522628.2522652).
Image description: A dynamic scene with two hundred spheres falling onto five static cylinders. This simulation approach is object-centric, with each modeled as a soft-thread and simulated independently. This results in scalable performance, achieving a 5-6x simulation speedup on eight cores and a 9-10x speedup on 16 cores. Image and description J. Koenig et al., Proceedings of MIG ’13, Motion of Games, 203-212 (2013). ©2013 Association for Computer Machinery
posted on September 3, 2014
Graphene, a form of pure carbon that exists in one-atom-thick sheets, is of great interest to scientists and engineers because of its strength and other remarkable properties. Graphene sheets can be formed into other structures. The mechanical properties of a graphene nanostructure are different than structures in the macroscale.
A graphene tube with a radius of less than one nanometer is known as a carbon nanotube. MSI Principal Investigator Traian Dumitrica, a professor in the Department of Mechanical Engineering (College of Science and Engineering), has been studying the mechanical properties of carbon nanotubes for several years. In a recent paper that appeared in Physical Review B, Professor Dumitrica and his colleagues modeled bent graphene as a large-radius (> 1nm) carbon nanotube to investigate its bending rigidity. The authors developed a simple analytic formula for the bending energy, which was confirmed by tight-binding objective molecular dynamics calculations. They believe that this simulation approach may also be applicable to understanding bending behavior of other atomic monolayers. The article can be found on the Physical Review B website (I. Nikiforov, E. Dontsova, R.D. James, T. Dumitrica. Tight-binding theory of graphene bending. 2014. Physical Review B. 89, 155437).
Earlier research relating to this work appeared in a 2011 paper in Physical Review Letters (D.-B. Zhang, E. Akatyeva, T. Dumitrica. Bending ultrathin graphene at the margins of continuum mechanics. 2011. Physical Review Letters. 106, 255503). An article also appeared in MSI’s Research Bulletin (Understanding and Predicting Properties of Nanostructures: Insights From Atomic-level Simulations. Supercomputing Institute Research Bulletin, Spring 2010).
Image description: Schematic of the symmetries used in objective molecular dynamics simulations. The model simulated carbon nanotubes (CNTs) of varying diameter; these simulated ideal graphene sheets rolled into constant-curvature cylinders. (a) Pure rotation around the CNT axis of angle ψ. (b) Rotation around the CNT axis of angle γ combined with translation ρ along the CNT axis. Image and description Nikiforov, I., et al., Phys Rev B, 2014, 106:155437. ©2014 American Physical Society
posted on August 20, 2014.