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In the ongoing study of viruses, researchers are using powerful computer resources to create visualizations of virus structures. MSI Principal Investigator Wei Zhang, a research assistant professor in the Department of Diagnostic and Biological Sciences (School of Dentistry), is investigating several viruses by using cryoelectron microscopy and creating three-dimensional reconstructions of their structures using advanced software.
In a recent paper that appeared in the Proceedings of the National Academy of Sciences of the USA, Professor Zhang and Research Associate Dr. Sheng Cao described how they were able to create visualizations of an intermediate step in membrane fusion, using the Sindbis virus, a prototypical alphavirus. (Sheng Cao and Wei Zhang. 2013. Characterization of an early-stage fusion intermediate of Sindbis virus using cryoelectron microscopy. Proceedings of the National Academy of Sciences of the United States of America 110 (33) (AUG 13): 13362-7.) The authors created an environment where the virus could bind with liposomes, took electron micrographs of the virus-liposome complex, and generated three-dimensional reconstructions. These 3D images show the structure of an early-stage fusion intermediate of an enveloped virus and may be beneficial in determining target locations for antiviral drugs. The authors have placed the reconstructions in the EMDataBank (www.emdatabank.org), an online resource for storing and sharing electron microscopy images.
Professor Zhang also uses MSI resources to study the human T-lymphotropic virus type 1 (HTLV-1), which is responsible for a number of disorders including adult T cell leukemia/lymphoma and HTLV-1 associated myelopathy/tropical paraperesis. As they did with the Sindbis virus, the Zhang group uses cryoelectron microscopy and three-dimensional reconstruction to study the structure of HTLV-1. This work may provide insights that will help in drug design.
Image description: Cryo-EM image and reconstruction of Sindbis viruses (SINV). (A-B) 3D reconstruction and cross-section of SINV (Zhang, W., S. Mukhopadhyay, S. V. Pletnev, T. S. Baker, R. J. Kuhn, M. G. Rossmann. 2002. Placement of the structural proteins in Sindbis virus. J. Virol. 76:11645-11658). (C) Image of the SINV viral particles (arrows) attached to a liposome (L) at acidic pH (Sheng Cao and Wei Zhang. 2013. Characterization of an Early-Stage Fusion Intermediate of Sindbis Virus using Cryo-electron Microscopy. PNAS 110: 13362-13367).
posted July 9, 2014
People have always talked about the weather, but these days weather and climate have become a major topic for discussion. Extreme weather events throughout the country and the world lead news stories and many people are concerned with what is causing these events and how the climate may be changing.
Assistant Professor Peter Snyder (Soil, Water, and Climate) is using MSI to support his work examining how climate change will affect extreme precipitation and severe weather in the central U.S. over the next century. The group uses the Weather Research and Forecasting (WRF) model, which is ideal for examining future changes in drought both because simulations with extremely high spatial and temporal resolution can effectively resolve the physical processes that drive precipitation processes and the model can efficiently represent synoptic-scale dynamical motion (e.g., blocking highs) that contribute to initiation and persistence of drought. This model is especially valuable for simulating events in the central region of the U.S., where severe weather and extremes in precipitation happen often. This region is the home of major agricultural production, so changes in climate and increases in drought may have significant effects on food security.
In a recent paper, Professor Snyder and members of his research group investigated whether dynamical downscaling could improve the WRF’s simulation capabilities for precipitation extremes. Their results showed a positive affect on the model’s results, which could mean that it would be easier to make predictions about rainfall. The researchers were able to use models that performed well to predict how rainfall might change over the Midwest in different climate-change scenarios. This work also provided some indications about the mechanisms that contribute to the intensification of heavy precipitation events. The paper appeared in November 2013 in the Journal of Geophysical Research - Atmospheres (Harding, Keith J., Peter K. Snyder, and Stefan Liess. 2013. Use of dynamical downscaling to improve the simulation of central US warm season precipitation in CMIP5 models. Journal of Geophysical Research: Atmospheres 118 (22) (NOV 27): 12522-36). Professor Snyder and his research group are continuing their research at MSI, performing additional simulations using different datasets. These simulations will provide insights into how droughts in the Midwest might change in the future and how they might impact water resources and food security.
The Snyder group is also participating in a study of the phenomenon of “urban heat islands,” which is a situation where cities have higher temperatures that the surrounding areas. The study, called Islands in the Sun, is a four-year project funded by the University of Minnesota Institute on the Environment and the College of Food, Agricultural, and Natural Resource Sciences. An article about this study recently appeared in the Minnesota Daily (Kristopher Teague, “Can’t take the heat? Get out of the city,” Minnesota Daily, May 6, 2014, online, downloaded May 7, 2014.)
Image description: The 1979–2005 June-July-August (a and b) precipitation (mm), (c and d) 850 hPa wind speed (m s−1). Figures a and c show the average of all observational (or reanalysis) datasets for each variable. Figure b shows the multimodel ensemble (MME) mean minus observations, while Figure d shows the MME mean. Image and description adapted from Harding, KJ, et al., Journal of Geophysical Research: Atmospheres, 118(22):12522-12636 (2013). © American Geophysical Union.
posted on June 18, 2014
Associate Professor Jeff Schwinefus, who is a faculty member at St. Olaf College in Northfield, Minnesota, is a physical chemist investigating the role of naturally occurring organic molecules in the hydration and stability of nucleic acids. He and his students perform experiments in the lab and also use molecule dynamics (MD) simulation techniques. This is interdisciplinary research that involves chemistry, biology, and physics.
The Schwinefus group’s research at MSI studies the cosolutes glycine betaine, proline, and urea, which all destabilize DNA and RNA secondary structures. The cosolutes interact with the nucleic acid surface area exposed during unfolding. The group is using lab work and MD simulations to understand this process.
Professor Schwinefus, members of his research group, and colleagues at the University of Wisconsin-Madison, published a recent paper about their work in the Journal of the American Chemical Society (Guinn, Emily J., Jeffrey J. Schwinefus, Hyo Keun Cha, Joseph L. McDevitt, Wolf E. Merker, Ryan Ritzer, Gregory W. Muth, Samuel W. Engelsgjerd, Kathryn E. Mangold, Perry J. Thompson, Michael J. Kerins, and M. Thomas Record. 2013. Quantifying functional group interactions that determine urea effects on nucleic acid helix formation. Journal of the American Chemical Society 135 (15) (APR 17): 5828-38). This paper investigated urea as a destabilizing agent of the helical and folded conformations of nucleic acids and proteins as well as protein-nucleic acid complexes. Their results demonstrated that urea can be used as a quantitative probe of conformational changes in nucleic acid processes.
Image description: Interaction potentials quantifying interactions of urea with unit surface areas of nucleic acid functional groups (heterocyclic aromatic ring, ring methyl, carbonyl and phosphate O, amino N, sugar (C and O)); urea interacts favorably with all these groups. Image and description taken from Guinn, EJ, et al., 2013. JACS 135(15): 5828-38. © American Chemical Society
Posted on June 4, 2014.
Electronic and magnetic materials are enormously valuable in a number of technologies. Professor Chris Leighton (Chemical Engineering and Materials Science) and his research group and collaborators are at the forefront of research into these materials. They are especially interested in research that furthers fundamental knowledge about these materials, but which also may have implications for important industrial applications, such as in information storage and microelectronics. Professor Leighton and his research group use scientific software available through MSI to analyze large datasets containing magnetization, electrical transport, and X-ray diffraction information for magnetic materials. They also generate data by using neutron scattering facilities, which allows study of crystalline structure and magnetic properties.
One class of materials currently under study by the Leighton group is perovskite oxides, materials that have interesting features that correlate with important properties like high-temperature superconductivity and colossal magnetoresistance, which are of great interest to researchers and have practical applications in industry. In a recent paper appearing in Physical Review B, the Leighton group, collaborating with Oak Ridge National Laboratory, published new results on a set of oxides known as perovskite cobaltites. Specifically, they reported comparisons of the properties of the Pr-based cobalt perovskite Pr1-xCaxCoO3-delta (PCCO) with Nd1-xCaxCoO3-delta (NCCO). PCCO has been studied quite heavily recently, and researchers believe that its unique physical properties, in particular a massive change in electrical resistance at a specific temperature, relate to an unusual situation with the material’s Pr-O bond. The authors compared PCCO’s properties to those of NCCO and determined the latter’s phase diagram. This research not only expanded knowledge about the basic physics of narrow bandwidth perovskite cobaltites, but added critical confirmation to the importance of the Pr-O bond in PCCO. It is hoped that future work can build on this to understand the origin of the unusual, and potentially useful, properties of this material. (D. Phelan, Y. Suzuki, S. Wang, A. Huq, C. Leighton. 2013. Structural, transport, and magnetic properties of narrow bandwidth Nd1-xCaxCoO3-delta and comparisons to Pr1-xCaxCoO3-delta. Physical Review B 88 (7) (AUG 9): 075119.)
Professor Leighton was recently named a McKnight Distinguished University Professor by the University of Minnesota.
Image description: Magnetic and electronic phase diagram of NCCO. Temperature axis is on a logarithmic scale. D Phelan, et al., Phys Rev B, 88, 075119 (2013) ©American Physical Society.
posted on May 21, 2014
The challenge of finding “green” energy resources to replace non-renewable fossil fuels is a topic of great interest for researchers. Chris Cramer (Distinguished McKnight Professor of Chemistry; MSI Fellow) and his research group and collaborators are among those who are using high-performance computational methods for their research in this area.
Plants have been using solar power to generate energy for millions of years. In photosynthesis, plants transform the sun’s rays into chemical energy that they can use. This process involves the oxidation of water in the plant. Researchers are interesting in creating artificial systems that can mimic this process. The method is known as water-oxidation catalysis, and, while it has been receiving a great deal of attention in recent years, a great deal of work still needs to be done to create a system that is economically practical for large-scale use.
Professor Cramer and a former student and MSI researcher, Dr. Mehmed Ertem, in collaboration with other investigators at Brookhaven National Laboratory, the Catalonian Institute for Chemical Research, Berlin Technical University, and Yale University, recently published a paper in Angewandte Chemie that discusses a new water-oxidation catalyst (Lopez, Isidoro, Mehmed Z. Ertem, Somnath Maji, Jordi Benet-Buchholz, Anke Keidel, Uwe Kuhlmann, Peter Hildebrandt, Christopher J. Cramer, Victor S. Batista, and Antoni Llobet. 2014. A self-improved water-oxidation catalyst: Is one site really enough? Angewandte Chemie-International Edition 53 (1) (JAN 3): 205-9). The authors have demonstrated a dinuclear ruthenium (Ru) water-oxidation catalyst that is created from a mononuclear catalyst during the catalytic process. The dinuclear catalyst is rugged and powerful and does not decompose over time. The researchers used kinetic analysis and density functional theory computational studies to characterize this reaction.
Green energy is just one of the many topics under investigation by the Cramer group. They are developing computer models to study many areas of chemical, biological, and environmental interest and have a large number of publications. A sample is shown below:
• Angeles-Boza, Alfredo M., Mehmed Z. Ertem, Rupam Sarma, Christian H. Ibanez, Somnath Maji, Antoni Llobet, Christopher J. Cramer, and Justine P. Roth. 2014. Competitive oxygen-18 kinetic isotope effects expose O-O bond formation in water oxidation catalysis by monomeric and dimeric ruthenium complexes.Chemical Science 5 (3) (MAR): 1141-52.
• Gao, Jiali, B.J. Jankiewicz, J. Reece, H. Sheng, Christopher J. Cramer, J.J. Nash, H.I. Kenttämaa. 2014. On the factors that control the reactivity of meta-benzynes. Chemical Science. In press.
• Isley, William C., III, S. Zarra, R.K. Carlso, R.A. Bilbeisi, T.K. Ronson, J.R. Nitschke, Laura Gagliardi, Christopher J. Cramer. 2014. Predicting paramagnetic 1H NMR chemical shifts and state-energy separations in spin-crossover host-guest systems. Physical Chemistry Chemical Physics. In press.
• Lee, Kyuho, William C. Isley, III, Allison L. Dzubak, Pragya Verma, Samuel J. Stoneburner, Li-Chiang Lin, Joshua D. Howe, et al. [Christopher Cramer; Donald Truhlar; Laura Gagliardi] 2014. Design of a metal-organic framework with enhanced back bonding for separation of N2 and CH4. Journal of the American Chemical Society 136 (2) (JAN 15): 698-704.
• Meng, W., A.B. League, T.K. Ronson, J.K. Clegg, William C. Isley, D. Semrouni, Laura Gagliardi, Christopher J. Cramer, J.R. Nitschke. 2014. Empirical and theoretical insights into the structural features and host-guest chemistry of M8L4 tube architectures. Journal of the American Chemical Society 136, 3972.
• Hirahara, Masanari, Mehmed Z. Ertem, Manabu Komi, Hirosato Yamazaki, Christopher J. Cramer, and Masayuki Yagi. 2013. Mechanisms of photoisomerization and water-oxidation catalysis of mononuclear ruthenium(II) monoaquo complexes. Inorganic Chemistry 52 (11) (JUN 3): 6354-64.
• Marenich, Aleksandr V., Christopher J. Cramer, and Donald G. Truhlar. 2013. Generalized born solvation model SM12. Journal of Chemical Theory and Computation 9 (1) (JAN): 609-20.
• Marenich, Aleksandr V., Christopher J. Cramer, and Donald G. Truhlar. 2013. Reduced and quenched polarizabilities of interior atoms in molecules. Chemical Science 4 (6): 2349-56.
• Marenich, Aleksandr V., Christopher J. Cramer, and Donald G. Truhlar. 2013. Uniform treatment of solute-solvent dispersion in the ground and excited electronic states of the solute based on a solvation model with state-specific polarizability. Journal of Chemical Theory and Computation 9 (8) (AUG): 3649-59.
• McGrath, Matthew J., I-F Will Kuo, Brice F. W. Ngouana, Julius N. Ghogomu, Christopher J. Mundy, Aleksandr V. Marenich, Christopher J. Cramer, Donald G. Truhlar, and J. Ilja Siepmann. 2013. Calculation of the Gibbs free energy of solvation and dissociation of HCl in water via Monte Carlo simulations and continuum solvation models. Physical Chemistry Chemical Physics 15 (32): 13578-85.
• Miro, Pere, and Christopher J. Cramer. 2013. Water clusters to nanodrops: A tight-binding density functional study. Physical Chemistry Chemical Physics 15 (6): 1837-43.
• Semrouni, David, Isley,William C.,,III, Carine Clavaguera, Jean-Pierre Dognon, Christopher J. Cramer, and Laura Gagliardi. 2013. Ab initio extension of the AMOEBA polarizable force field to Fe2+. Journal of Chemical Theory and Computation 9 (7) (JUL): 3062-71.
• Suess, Alison M., Mehmed Z. Ertem, Christopher J. Cramer, and Shannon S. Stahl. 2013. Divergence between organometallic and single-electron-transfer mechanisms in copper(II)-mediated aerobic C-H oxidation. Journal of the American Chemical Society 135 (26) (JUL 3): 9797-804.
Professor Cramer is a long-time MSI Principal Investigator and Fellow of the Institute. He is also a member of the Chemical Theory Center, whose other members include several MSI Principal Investigators: Regents Professor Donald Truhlar, Professor Laura Gagliardi, Professor J. Ilja Siepmann, and Professor Jiali Gao. MSI interviewed Professor Cramer about his research in September 2012.
Image Description: Ball-and-stick representation of the optimized transition-state structures for O–O bond-formation (left) and O2-evolution steps (right) for the Ru catalyst. H atoms are shown only for the aqua and hydroxy ligands. Figure and description © Angewandte Chemie; Lopez, I., et al., Angewandte Chemie-International Edition 53(1):205-9 (2014)
posted on May 7, 2014