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In the past few decades, researchers specializing in condensed matter physics have been intensely interested in studying the properties of strongly correlated quantum many-body systems, which are systems on the microscopic scale that include more than two particles that interact with each other. Researchers especially want to be able to explain how the macroscopic behavior of materials can be explained by the fundamental interactions of the material’s microscopic constituents.
Particular interest has focused on quantum spin-lattice systems, where the interactions can be simply described, but where different types of interaction can compete with one another. (The “spin” of an elementary particle is an inherent property it possesses in quantum mechanics that has no classical counterpart, although it can loosely be thought of as a form of internal angular momentum. In a standard computational model in condensed matter physics, these spins are arranged on a lattice and coupled through magnetic interactions.) The system can then find itself in a frustrated state in which different forms of ordering are trying to emerge in competition with one another. The often subtle interplay between this frustration and quantum fluctuations can lead to quantum spin-lattice models exhibiting ground-state (i.e., at zero temperature) phase diagrams that are very different from their classical counterparts. Of greatest theoretical interest are the so-called quantum critical points where phase transitions occur.
Computer models for quantum-mechanical wave functions of strongly interacting many-spin systems are extremely complex. This is especially so near the quantum critical points, where the ground-state phase has special properties and involves a very large set of fluctuating configurations. Methods for modeling these systems have included techniques from quantum field theory or large-scale numerical simulations such as Monte Carlo methods. Since the effects of quantum fluctuations, and hence the complexity of the wave functions, increase the closer one approaches the quantum critical points, very accurate quantum many-body techniques are necessary.
Professor Charles Campbell (Physics and Astronomy) and his colleagues Professor Raymond Bishop and Dr. Peggy Li at the University of Manchester (UK), and their collaborators elsewhere, have developed and adapted one such many-body method, the so-called coupled cluster method (CCM), to study a large and diverse array of two-dimensional (2D) quantum spin systems of theoretical and experimental interest. The CCM is now widely accepted as being one of the most successful and most widely applicable of all modern methods of microscopic quantum many-body theory. The CCM techniques pioneered by Professor Bishop and his collaborators are probably now the best available for these strongly frustrated 2D quantum spin-lattice systems, and their results are now setting benchmarks in the field. The group runs their CCM codes on MSI’s supercomputers. The interesting magnetic phenomena displayed by such systems make them suitable candidates for a large number of technological applications, many of which are already in widespread use. This research is also providing insights into exciting new systems, such as exotic superconducting systems and non-superconducting systems that have unusual magnetic properties.
Professor Bishop’s contributions to the development and applications of the CCM resulted in his sharing the Eugene Feenberg Memorial Medal in 2005. (The Feenberg Medal is awarded for work that significantly advances the field of many-body physics.) His co-recipient, the late Hermann Kuemmel, is generally acknowledged as the inventor of the CCM. Among other contributions, Professor Bishop has adapted the CCM to several important quantum many-body systems, including the quantum magnetism problems described above. Professor Campbell, who is a long-time researcher at MSI in the field of quantum fluid research, has been working with Professor Bishop and his former student and now post-doctoral associate Dr. Li, adding his own area of expertise to the CCM. Bishop, Li, and Campbell have used MSI resources for several years in their work to advance this technique.
Approximately 10 papers describing this research using MSI have been published since the start of 2012. These have appeared in the journals Physical Review B, Journal of Physics: Condensed Matter, and the European Physical Journal B. Two of the articles were chosen by the editors for special highlighting. The group has especially concentrated on the spin-1/2 J1-J2-J3 model on the honeycomb lattice and the spin-1/2 J1-J2 model on the checkerboard lattice (otherwise known as the anisotropic planar pyrochlore), which have recently become very hot topics in the field.
Image Description: Phase diagram of the spin-1/2 J1−J2 model on the honeycomb lattice (with J1 > 0 and x ≡ J2/J1 > 0), as obtained by a CCM analysis. The four phases shown are Néel, plaquette valence-bond crystalline (PVBC), staggered dimer valence-bond crystalline (SDVBC), and Néel-II. The quantum critical points (phase transitions) are at xc1 ≈ 0.207(3), xc2 ≈ 0.385(10), and xc3 ≈ 0.65(5), as shown in the diagram. From “Valence-bond crystalline order in the s = 1/2 J1−J2 model on the honeycomb lattice,” R.F. Bishop, P.H.Y. Li and C.E. Campbell, Journal of Physics: Condensed Matter 25:306002, DOI=10.1088/0953-8984/25/30/306002 (2013) ©2013 IOP Publishing Ltd.
Posted on October 30, 2013.
As the earth’s climate changes, scientists are concerned about the effects these changes will have on the earth’s ecosystems. Regents Professor Peter B. Reich (Forest Resources, Institute on the Environment) and post-doctoral researcher Emily Peters (Institute on the Environment) specialize in discovering the impacts of these changes. The Reich group’s main area of focus is the part of central North America that includes Minnesota. In this part of the continent, several types of ecosystems converge, including boreal forests (forest consisting mostly of coniferous trees), temperate hardwood forests, oak woodlands/savannas, and grasslands.
MSI has been working with Professor Reich and Dr. Peters to develop a distributed computing framework for the parallel photosynthesis and evapotranspiration model (PPnET). PPnET allows researchers to efficiently use PnET-CN (a widely used and well-tested ecosystem model) to simulate the effects of many simultaneously changing environmental factors on forests over large geographic areas. MSI is providing hardware, software, and consulting support to this project. Dr. Shuxia Zhang, in the HPC Operations group, developed an MPI-based program that allowed parallel jobs to start and restart flexibly. This made allowances for the availability of software licenses at any given time, as well as the availability of compute nodes on the supercomputers. Dr. Zhang also developed script tools that verified data integrity and the success of hundreds of thousands of inputs.
The Reich group used PPnET to simulate ecosystem responses to changes in climate and atmospheric CO2 concentrations in the Great Lakes region of North America. This simulation had 1 km spatial resolution, consisting of 200,000 forest grid cells. The computing time, which would take 25 days for serial runs – and would therefore be impractical – was reduced to six hours using 96 cores on a Linux cluster. This research has been published in the Canadian Journal of Forest Research (“Potential Climate Change Impacts on Temperature Forest Ecosystem Processes,” EB Peters, K Wythers, S Zhang, JB Bradford, PB Reich, Canadian Journal of Forest Research, DOI:10.1139/cjfr-2013-0013, published online July 17, 2013.)
(Left) Forest types with a 1-km grid resolution over the northern Great Lakes region of the United States, also known as the Laurentian Mixed Forest Province. This region includes six major forest types.
(Right) Map of changes in above-ground net primary production predicted from 1970 to 2100, under a high-emissions climate change scenario.
©Canadian Journal of Forest Research, NRC Research Press (2013)
posted on October 9, 2013.
Update, October 28, 2013: The Minneapolis Star-Tribune published an article about climate change's effects on the north woods of Minnesota. Professor Reich and his project, B4WARMED, are discussed at the end of the article.
In 2004, the U.S. Department of Homeland Security established the National Center for Food Protection and Defense (NCFPD), headquartered at the University of Minnesota. This research consortium, which includes researchers from over 30 other universities, addresses the vulnerability of the nation’s food supply to attack. The NCFPD’s research and education mission is to reduce the potential for contamination of the food supply and to mitigate the potentially catastrophic public-health and economic effects of such an event. Dr. Amy Kircher, who has been working with MSI on the projects described below, was recently appointed Director of the NCFPD.
One threat to the food supply is called “economically motivated adulteration” or EMA. This type of food adulteration, in which less-expensive products are added to or substituted for higher-priced food in order to increase profits, has occurred for centuries. Recent examples from the news include the selling of horsemeat as beef in Europe, and, in China, adding melamine as an extender to milk and wheat gluten. The NCFPD is working to better understand the food supply, identify high-risk supplies, and do real-time analysis using a variety of data.
One of the agencies with which NCFDP works is U.S. Customs and Border Patrol, which monitors shipments of food into the U.S. MSI was contacted by NCFPD to develop tools that they could use to store and analyze this data. This project, which was completed earlier this year, included:
A database to store the CBP data and a tool to automatically import new data.
A private web interface that allows NCFPD researchers to select and perform statistical analyses on selected datasets using their own algorithms. The interface generates plots and other summaries.
Visualizations of imported food using the Google Maps API. Researchers can select countries and food products to see what is entering the country. They can view entry to specific ports or the view can show a single connection to the country exporting the food with a line thickness proportional to the weight of the imported food. The graphic above shows importation information for apples.
MSI is also providing hosting services for the application. MSI is also currently working with the NCFPD on a further project to extend these tools and capabilities.
These projects are part of an MSI program that provides long-term, at-cost, individualized support for projects meeting certain criteria. Information can be found on the MSI website.
Posted on September 25, 2013.
Polymers, which many people think refer only to plastic, are actually a large group of natural and man-made materials. They have many uses in industry and as consumer products. Some of these include the super-absorbant polymers used in disposable diapers, the heat-stable materials used for non-stick cookware, and the fiber spandex, used for stretchy clothing like athletic wear and foundation garments. The research group of Associate Professor Kevin Dorfman (Chemical Engineering and Materials Science) is using MSI for research into the structures and dynamics of polymers, especially DNA. On the engineering side, understanding the dynamics of DNA has many important applications in genomics. On the scientific side, DNA is a model system for investigating the basic physical properties of semiflexible polymers. The Dorfman group is using several computer-simulation techniques, including Metropolis and chain growth Monte Carlo methods.
Professor Dorfman and graduate student Douglas Tree, along with their colleague Yanwei Wang (Soochow University, China), recently published research in Physical Review Letters concerning DNA confinement in nanochannels. DNA confinement is becoming an important tool for genomics research. It also provides researchers a platform for testing theories concerning confined wormlike polymers. The classical theories for polymer chains in confinement only work in cases where the nanochannels are very small or very large compared to the polymer. The Dorfman group has investigated an intermediate case between the two models. In the graphic above, the Odijk theory applies to DNA in small channels and the Flory-de Gennes theory works for large channels. The newly proposed regime of behavior, called the “Gauss-de Gennes” regime by the researchers, works for the intermediate channel sizes that have been typically used in genomic devices. The researchers propose that this regime applies to the general class of semiflexible polymers, which includes DNA as a special case.
The article can be read on the American Physical Society website: “Extension of DNA in a Nanochannel as a Rod-to-Coil Transition,” DR Tree, Y Wang, DK Dorfman, Physical Review Letters, 110:208103, DOI:10.1103/PhysRevLett.110.208103 (2013).
Image description: Illustration of the analogy between free solution and confined configurations of a wormlike chain. The classical theories renormalize the chain into a series of subchains, where these subchains are either rodlike (Odijk) or excluded-volume blobs (de Gennes). (For clarity, the authors refer to the classic de Gennes regime as the “Flory-de Gennes” regime.) The middle drawing illustrates a universal Gauss-de Gennes regime in confinement that is an intermediate step between the two classical ones. © 2013 American Physical Society
Posted on September 11, 2013.
In the course of the history of agriculture, humans have tried to change the properties of the crops they raise. Maize (corn) is a very valuable and widely grown crop, and researchers are able to trace how modern maize has been developed from its wild ancestor, a plant called teosinte (Zea mays ssp. parviglumis).
Three MSI Principal Investigators – Assistant Professor Chad Myers (Computer Science and Engineering), Associate Professor Peter Tiffin (Plant Biology), and Professor Nathan Springer (Plant Biology) - were co-authors on a paper published last year in the Proceedings of the National Academy of Sciences (“Reshaping of the Maize Transcriptome by Domestication,” R Swanson-Wagner, R Briskine, R Schaefer, MH Hufford, J Ross-Ibarra, C Myers, P Tiffin, NM Springer, PNAS, 109(29):11878, DOI: 10.1073/pnas.1201961109 (2012)), that reveals changes in the maize transcriptome after it was domesticated. The transcriptome is the set of all RNA molecules in a set of cells. For this paper, the researchers used expression profiling to determine that over 600 genes have altered expression levels in maize compared with teosinte. They studied over 18,000 genes for 38 maize genotypes and 24 teosinte genotypes. The domestication process from teosinte to modern maize is a model for studying how complex traits in plants can be changed over time. The researchers used software and user support available at MSI to help with the data analysis.
Professor Myers uses MSI resources to analyze large-scale genetic interaction networks. Professor Tiffin is involved in several projects related to the evolutionary history of species and connecting genotype (genetic makeup) to phenotype (composite of observable traits or characteristics). Professor Springer uses MSI to study epigenetic variation in maize. (Epigenetics is the study of heritable variation that is not solely attributable to genetic changes.)
Image Description: The scatterplot in the left image shows the correlation between all gene pairs in maize (x axis) relative to the correlation for the same gene pair in teosinte (y axis). The relative density of data points in the left image was compared with the average for 1,000 bootstrap coexpression networks in the image at right. Blue regions indicate fewer observed correlations relative to the bootstrap networks, whereas red coloration indicates an excess of actual observations, providing evidence for an enrichment of gene pairs with varying correlations in maize and teosinte. Image and description © 2012 by National Academy of Sciences.
Posted on August 28, 2013.