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Current astrophysical research indicates that most of the mass of the Universe is made up of a substance called “dark matter,” so called because it cannot be seen. Its presence is inferred by its gravitational effects. Astrophysicists believe that the gravitational pull of dark matter causes galaxies to hold together and also to form into giant clusters. Little is known about this enigmatic material and a great deal of research is ongoing.
MSI PI Liliya Williams, a professor at the Minnesota Institute for Astrophysics (College of Science and Engineering), was part of a team that discovered indications that dark matter may not only be acted upon by gravity. The team was led by researchers at Durham University in the UK. They studied the galaxy cluster Abell 3827, which is interesting because it contains the remnant stellar nuclei of four bright elliptical galaxies. It also has a strong gravitational lens system that allows the distribution of dark matter to be mapped.
Using Hubble Space Telescope imaging and Very Large Telescope/Multi-Unit Spectroscopic Explorer integral field spectroscopy were used to create the map of dark matter surrounding the four stellar nuclei. One of the two software programs used to create the model of the dark matter is GRALE, which Professor Williams ran on MSI’s supercomputers. (Results from the computer modeling, both in GRALE and LENSTOOL, are shown in the image above.) For one of the stellar nuclei, the mass distribution of the dark matter is offset, which is possible if the dark matter is interacting with a force other than gravity. This is an exciting finding and an area for future research.
The paper was published in April in the journal Monthly Notices of the Royal Astronomical Society: R Massey, L Williams, R Smit, M Swinbank, TD Kitching, et al. 2015 The behaviour of dark matter associated with four bright cluster galaxies in the 10 kpc core of Abell 3827. Monthly Notices of the Royal Astronomical Society 449(4):3393-3406. 10.1093/mnras/stv467.
The article received a great deal of media attention when it was published. A sample of articles that include quotations from Professor Williams are linked below:
Image description: Left panel: map of total mass in the cluster core, reconstructed using GRALE. Green contours show the projected mass density, spaced logarithmically by a factor of 1.15; the thick contour shows convergence κ = 1 for zcℓ = 0.099 and zA = 1.24 (Σcrit = 1.03 g cm−2). Red dots show local maxima in individual realizations of the mass map. Black dots show cluster ellipticals N.1–N.4. Blue circles show the lensed images. Middle panel: mass after subtracting a smooth cluster-scale halo to highlight substructure. The thick contour is at Δκ = 0. The green (positive) and yellow (negative) contours are at Δκ = ±0.025, ±0.05, ±0.1, ±0.2,.... Right panel: total mass, as in the top panel but reconstructed via LENSTOOL. The red dashes show the zA = 1.24 critical curve.
Image and description adapted from R Massey et al., MNRAS 2015;449:3393-3406 © 2015 the authors published by Oxford University Press on behalf of the Royal Astronomical Society.
published on July 27, 2015
Camera traps, which are motion- or heat-activated automatic cameras, are revolutionizing how researchers can study ecosystems, since they are noninvasive, relatively inexpensive, and are capable of monitoring large areas and diverse species. A few years ago, members of the research group of MSI Principal Investigator Craig Packer, a Distinguished McKnight University Professor in the Department of Ecology, Evolution, and Behavior (College of Biological Sciences), set up a camera-trap survey in Africa to study the way predators and their prey co-existed. The study area included 225 camera traps in a 1,100 km2 region in Serengeti National Park in Tanzania.
The world’s largest camera-trap survey, this project generated far more images than the research team was able to identify on their own. Then-grad students Alexandra Swanson (now a post-doc at the University of Oxford) and Margaret Kosmala (now a post-doc at Harvard University) decided to partner with the citizen-science web platform Zooniverse.org to create Snapshot Serengeti, a project that allowed members of the general public to look at the images and classify them. Over 28,000 volunteers participated in the project. Participants were able to identify what species they thought was in the photo, what the animal was doing, whether there was a young animal present, and several other data points. Each image was classified by multiple participants, and an algorithm created by the researchers collected the responses and identified a consensus description for each image. The group has published their research in Scientific Data, which is an online publication of the prestigious journal Nature (Alexandra Swanson, Margaret Kosmala, Chris Lintott, Robert Simpson, Arfon Smith, and Craig Packer. 2015. Snapshot Serengeti, high-frequency annotated camera trap images of 40 mammalian species in an African savanna. Scientific Data 2:150026. 10.1038/sdata.2015.26). The research group hopes that the dataset they’ve collected will be useful for future research and education.
This paper received a huge amount of media attention when it was published in June. Media outlets that have published the stories include the New York Times, the Washington Post, the Los Angeles Times, PBS Newshour, BBC News, the Daily Mail, Scientific American, Discover Magazine, Wired, the New Yorker, major newspapers in Brazil and India, and many others. A story also appeared in the University of Minnesota Discover blog.
From 2010 through 2013, the project generated 1.2 million image sets (each set consisted of 1-3 photos), which comprised 4.5 TB of data. This huge amount of data necessitated a large storage capability that MSI has been able to provide. In February 2015, at the suggestion of the UM Informatics Institute, the research team decided to transfer the images to MSI’s new Ceph object storage system. This system has proven to be an excellent resource for the researchers, particularly since the images can be shared with colleagues outside the University of Minnesota and it has a built-in web serving capability that makes creating sites quick and easy.
MSI has also assisted with another Zooniverse project, Ancient Lives. A Research Spotlight about this project appeared on the MSI website in December 2014.
Image description: The Snapshot Serengeti website interface. This is the primary interface with all available species options (left) and filter that help narrow users’ choices when classifying species (right). Image and description from Swanson et al., Sci. Data 2:150026 DOI:10.1038/sdata.2015.26 (2105).
posted on July 8, 2015
One of the most promising methods of treating cancer is called “tumor-homing” or “targeted drug” therapy. In this method, a cancer drug is linked to a kind of peptide called a “tumor-homing” peptide – the tumor-homing peptide recognizes a specific receptor that appears on tumors, thereby guiding the drug directly to the tumor. One such receptor that has shown promise for targeted drug therapy is called aminopeptidase N (APN).
MSI PI Fang Li, an associate professor in the Department of Pharmacology (Medical School), and his group recently published a paper in the Journal of Biological Chemistry in which they investigated APN-based targeted drug therapy. APN has two unusual functions: it is a receptor for tumor-homing peptides and also mediates cancer cell motility. Using crystallographic and biochemical methods, the authors studied both these functions and found that the same mechanism drives both of them. This research has implications for the development of cancer therapies that target APN.
The Li group uses MSI for studies of the structural and molecular basis of human diseases. The project described in this paper used computer resources available through MSI’s Basic Sciences Computing Laboratory. You can read the entire paper on the Journal of Biological Chemistry website (Chang Liu, Yang Yang, Lang Chen, Yi-Lun Lin, and Fang Li. A unified mechanism for aminopeptidase N-based tumor cell motility and tumor-homing therapy. The Journal of Biological Chemistry 289, (50) (DEC 12), 10.1074/jbc.M114.566802.
Image Description: Crystal structure of porcine APN in complex with a tumor-homing peptide CNGRCG A, overall structure of the pAPN-CNGRCG complex. pAPN contains an ectodomain, a stalk, a transmembrane anchor (TM), and an intracellular tail (IC). The ectodomain contains four domains: head (cyan), side (brown), body (magenta), and tail (yellow). CNGRCG is shown in green as balls and sticks. Zinc is shown as a blue ball. Only one monomer of the dimeric pAPN is shown. B, electron density map of CNGRCG. The electron density map corresponds to Fo − Fc omit map calculated in the absence of CNGRCG and contoured at 2.2 σ. C, another view of the pAPN-CNGRCG complex. The view of the complex is obtained by rotating the view in A first by 90° along a vertical axis and then by 45° along a horizontal axis, in such a way that the active site cavity of pAPN is facing the reader. D, enlarged view of CNGRCG in the active site of pAPN. Image and description from Chang Liu et al., J. Biol. Chem. 2014. 289:34520-34529. © 2014 American Society for Biochemistry and Molecular Biology.
posted on June 10, 2015
Image description: Left: Top and side views of a section of a two-dimensional Cu2Si monolayer. Cu atoms copper colored, Si atoms grey. Right: Bonding structure of the Cu2Si monolayer. (a-c) Individual 4c-2e σ bonds. (d) Superimposition of 4c-2e σ bonds. Copper is orange, silicon is blue. LM Yang, et al., JACS 2015, 137, 2757. © 2015 American Chemical Society.
Two-dimensional materials have become a subject of great interest to researchers during the past decade. These materials, one of the most well-known of which is the carbon monolayer (one atom thick) graphene, have interesting properties that might make them useful for various applications, such as semiconductors, electronics, and composite materials.
Associate Professor Eric Ganz (Physics and Astronomy, College of Science and Engineering) and his collaborators recently published a paper in the Journal of the American Chemical Society about one of these materials. Two-dimensional materials with planar hypercoordinate motifs are extremely rare due to the difficulty in stabilizing the planar hypercoordinate configurations in extended systems. Hypercoordinate means more bonds than normal for a particular atom. The paper describes a two-dimensional monolayer that features planar hexacoordinate copper and planar hexacoordinate silicon. (Hexacoordinate means six atomic bonds.) The researchers used density function theory calculations to study and evaluate this material, Cu2Si. A section of the periodic infinite sheet is shown in the image.
The researchers’ computations showed that the Cu2Si monolayer is very stable, and the framework survives brief molecular dynamics annealing up to 900 K. Bond order analysis and partitioning reveals unusual four center 4c-2e σ bonds that stabilize the two-dimensional structure. (σ bonds are the strongest type of covalent chemical bond.)
The paper can be read on the JACS website (Yang, Li-Ming, Vladimir Bacic, Ivan A. Popov, Alexander I. Boldyrev, Thomas Heine, Thomas Frauenheim, and Eric Ganz. 2015. Two-dimensional Cu2Si monolayer with planar hexacoordinate copper and silicon bonding. Journal of the American Chemical Society 137 (7) (FEB 25): 2757-62.)
posted on May 27, 2015
Mesabi, the Minnesota Supercomputing Institute’s newest supercomputer, was formally dedicated on April 23, 2015. Mesabi is the latest in a long line of supercomputers that have been serving the University of Minnesota research community for 30 years.
Mesabi is a heterogeneous compute system built by HP. Heterogeneous systems incorporate more than one type of processor. This increases performance by allowing specialized processors to handle specific tasks. Mesabi features an HP Apollo 6000 system with Intel Haswell processors and solid-state drives (SSDs), Mellanox Extended Data Rate (EDR) switching, and NVIDIA Graphics Processing Units (GPUs). MSI has also purchased 1 PB of Panasas storage for the system.
Mesabi by the numbers:
• Rated at 352 kW of power (enough to power 270 houses).
• 1.2 million BTUs required for cooling.
• Seven times as powerful as MSI’s Itasca supercomputer.
• More than 62 TB of memory.
• 480 Gbits/second connectivity to Panasas storage.
During the recent MSI Research Exhibition, several MSI users from diverse fields presented work that they will be transferring to Mesabi. Some examples are below:
Benjamin Brummel is a graduate student in the research group of Jonathan Sachs (Biomedical Engineering). Among other projects, the Sachs group is studying α-Synuclein, a protein found in the human brain that is associated with Parkinson’s disease. Mr. Brummel presented a poster titled “Lipids with one saturated and one polyunsaturated DHA chain homogenize lipid rafts and affect the membrane environment of α-Synuclein” (Benjamin E. Brummel, Anthony R. Braun, Jonathan N. Sachs).
Christine Dunbar is a post-doc in MSI Fellow Christopher Cramer’s research group. Professor Cramer is in the Department of Chemistry and is also a member of the Center for Sustainable Polymers and the Chemical Theory Center. Dr. Dunbar presented a poster describing research into sustainable alternatives to petroleum-based polymers (Christine R. Dunbar and Christopher J. Cramer. “Quantum chemical analysis of the mechanisms of epoxide/anhydride copolymerization using metal catalysts.”) The Cramer group develops and applies computational models to study chemical structures, properties, and reactivities in areas of chemical, biological, and environmental interest.
Chris Tessum is a post-doc in the group of Julian Marshall (Civil, Environmental, and Geo- Engineering; Fellow, Institute on the Environment) and Jason Hill (Bioproducts and Biosystems Engineering; Fellow, Institute on the Environment). This group uses models on the supercomputers to study the impacts on air pollution of different types of alternative fuels. They correlate changes made in the transport sector to air quality and public health. Dr. Tessum presented a poster describing how future use of conventional and alternative fuels may impact inequality and injustice in health effects related to air pollution (Christopher Tessum, Jason Hill, Julian Marshall. “Environmental justice and equality aspects of conventional and alternative light-duty transportation in the United States.”).
The name Mesabi was selected by MSI staff from over 140 suggestions from MSI users and others at the U. The Mesabi Range is the largest of the four major iron deposits in northern Minnesota that collectively make up the area known as the Iron Range. It is the chief deposit of iron ore in the U.S. The name comes from an Ojibwe word meaning “immense mountain.” The name reflects Minnesota’s cultural heritage and natural resources and ties in to an informal term for supercomputers, “Big Iron.”
posted on May 13, 2015