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IMA Newsletter #373

November 2007

2007-2008 Program

Mathematics of Molecular and Cellular Biology

See http://www.ima.umn.edu/2007-2008 for a full description of the 2007-2008 program on Mathematics of Molecular and Cellular Biology.

News and Notes

M.C. Escher film was a success

The U.S. premier of the film ACHIEVING THE UNACHIEVABLE, a documentary relating math and the art of M.C. Escher took place on Thursday, November 1 and it was a tremendous success. Over 700 Escher enthusists including students, faculty, film critics and many other groups gathered in Wiley Hall at the University of Minnesota to view the film. The story of the film began with M.C. Escher's 1956 lithograph The Print Gallery, left uncompleted because the artist found himself trapped by a seemingly insuperable barrier. The puzzling enigma of his uncompleted master-piece was solved half a century later, when mathematician Hendrik Lenstra drew a fantastic bridge between the intuition of the artist and his own, and completed the work mathematically. After the screening, the film's director, Jean Bergeron, who had flown from Montreal for the premier, answered many questions from the audience.

  • IMA program organizer wins Nobel prize. Leonid Hurwicz, who organized the second IMA annual program back in 1983-1984, was named one of three winners of the Nobel prize for economics on October 15.
  • Annual thematic program on Complex Fluids and Complex Flows was approved by IMA Board of Governors for 2009–2010.

    Application deadlines: If you are interested in applying for one of the IMA "New Directions Research Professorship" or "Postdoctoral Fellowship" positions in connection with the 2008-2009 thematic program: Mathematics and Chemistry, the deadline for applying for the postdoc positions is January 5, 2008 and the deadline for the New Directions Research Professorships is January 15, 2008. You can find the applications for these positions at our Applications site.

    IMA Events

    IMA Annual Program Year Workshop

    RNA in Biology, Bioengineering and Nanotechnology

    October 29 - November 2, 2007

    Organizers: Tamar Schlick (New York University), Eric Westhof (Université de Strasbourg I (Louis Pasteur))
    Schedule

    Thursday, November 1

    10:45a-11:45aCoffee and TreatsLind Hall 400 W10.29-11.2.07
    1:00p-1:30pCoffeeEE/CS 3-176 W10.29-11.2.07
    1:30p-2:00pHow RNA tells right from wrong: base pairs, tertiary interactions, and counterions in RNA foldingSarah Woodson (Johns Hopkins University)EE/CS 3-180 W10.29-11.2.07
    2:05p-2:35pStructure, dynamics and catalytic mechanisms of two ribozymesDavid M.J. Lilley (University of Dundee)EE/CS 3-180 W10.29-11.2.07
    2:35p-2:50pDiscussionsEE/CS 3-180 W10.29-11.2.07
    2:50p-3:20pCoffeeEE/CS 3-176 W10.29-11.2.07
    3:20p-3:50pA topological classification of RNA foldsHenri Orland (Commissariat à l'Énergie Atomique Saclay (CEA))EE/CS 3-180 W10.29-11.2.07
    3:55p-4:25pExploring the energy landscape of RNADevarajan Thirumalai (University of Maryland)EE/CS 3-180 W10.29-11.2.07
    4:30p-5:00pRNA / RNP synthetic biology Tan Inoue (Kyoto University)EE/CS 3-180 W10.29-11.2.07
    5:00p-6:30pMath Matters public lecture receptionLind Hall 400 W10.29-11.2.07
    7:00p-8:15pMath Matters public lecture: U.S. premier screening of the film "Achieving the unachievable" with the film's writer/director Jean Bergeron (Alpha-Zoulou Films)Willey Hall 125 (free and open to the public) W10.29-11.2.07

    Friday, November 2

    9:30a-10:00aCoffee W10.29-11.2.07
    10:00a-10:30aComputational approaches to RNA nanodesignBruce A. Shapiro (National Cancer Institute)EE/CS 3-180 W10.29-11.2.07
    10:35a-11:05aRNA tertiary structure as a proto-language for nano-constructionLuc Jaeger (University of California)EE/CS 3-180 W10.29-11.2.07
    11:05a-11:20aDiscussionsEE/CS 3-180 W10.29-11.2.07
    11:20a-11:30aConcluding remarksTamar Schlick (New York University)
    Eric Westhof (Université de Strasbourg I (Louis Pasteur))
    EE/CS 3-180 W10.29-11.2.07

    Tuesday, November 6

    11:15a-12:15pWaiting for k mutations: with applications to DNA regulatory sequence evolution and cancerDeena Schmidt (University of Minnesota)Lind Hall 409 PS

    Wednesday, November 7

    11:15a-12:15pStrong fluctuations and cycling in biological systemsTimothy Newman (Arizona State University)Lind Hall 409 MMCB

    Friday, November 9

    1:25p-2:25pNetworked target tracking architecturesRandy C. Paffenroth (Numerica Corporation)Vincent Hall 570 IPS

    Tuesday, November 13

    11:15a-12:15pModels for mesenchymal motion in tissueZhian Wang (University of Minnesota)Lind Hall 409 PS

    Wednesday, November 14

    11:15a-12:15pGilad Lerman Defining functional distance using manifold embeddings of gene ontology annotationsLind Hall 409 MMCB

    Thursday, November 22

    All DayThanksgiving Day. The IMA is closed.

    Friday, November 23

    All DayFloating holiday. The IMA is closed.

    Tuesday, November 27

    11:15a-12:15pMultiscale mechanical modeling of bioartificial tissuesVictor Barocas (University of Minnesota)Lind Hall 409 PS

    Wednesday, November 28

    11:15a-12:15pGraphical invariants and topological indices as biomolecular descriptorsDebra Knisley (East Tennessee State University)Lind Hall 409 MMCB

    Friday, November 30

    1:25p-2:15pMarketing optimizationBalaji Gopalakrishnan (SAS Institute Inc.)Vincent Hall 570 IPS
    Abstracts
    Gilad Lerman Defining functional distance using manifold embeddings of gene ontology annotations
    Abstract: Although rigorous measures of similarity for sequence and structure are now well established, the problem of defining functional relationships has been particularly daunting. Here, we present several manifold embedding techniques to compute distances between Gene Ontology (GO) functional annotations and consequently estimate functional distances between protein domains. To evaluate accuracy, we correlate the functional distance to the well established measures of sequence, structural, and phylogenetic similarities. Finally, we show that manual classification of structures into folds and superfamilies is mirrored by proximity in the newly defined function space. We show how functional distances place structure-function relationships in biological context resulting in insight into divergent and convergent evolution. Our methods and results can be readily generalized and applied to a wide array of biologically relevant investigations, such as accuracy of annotation transference, the relationship between sequence, structure, and function, or coherence of expression modules. This work is joint work Boris Shakhnovich and described in http://www.pnas.org/cgi/reprint/0702965104v1.
    Victor Barocas (University of Minnesota) Multiscale mechanical modeling of bioartificial tissues
    Abstract: As biopolymer-based tissue engineering matures as a discipline, we are faced with a fundamental challenge: we understand to a degree how changes in fabrication and culture conditions can affect the structure and composition of the final model tissue, but we do not understand how those changes determine the mechanical properties. The problem is further complicated by the fact that the structural scale of the network is in microns (or tens of microns), but the functional scale is millimeters to centimeters. Our group uses volume averaging theory to develop models of bioartificial tissue mechanics based on a microscopic-scale network model coupled to a macroscopic-scale continuum model. The model has been applied to collagen gels, and also to a simplified model of arterial tissue. The talk will present the model as well as some more recent work on a biphasic formulation (accounting for interstitial flow) and on an extension to migrating cells.
    Jean Bergeron (Alpha-Zoulou Films) Math Matters public lecture: U.S. premier screening of the film "Achieving the unachievable" with the film's writer/director
    Abstract: M.C. Escher is among the most mathematical of artists. In 1956 he challenged the laws of perspective with his graphic Print Gallery, and found himself trapped by an impossible barrier. His uncompleted master-piece quickly became the most puzzling enigma of modern art, for both artists and scientists. Half a century later, mathematician Hendrik Lenstra took everyone by surprise by drawing a fantastic bridge between the intuition of the artist and his own, and completed Escher's work mathematically. This story is presented in the 52 minute film Achieving the Unachievable by documentary filmmaker Jean Bergeron. After the screening, the film's U.S. premier, Bergeron will be available to answer questions.
    Balaji Gopalakrishnan (SAS Institute Inc.) Marketing optimization
    Abstract: All marketing organizations — including the successful ones — are under increased pressure to do more with less. Throughout the marketing and fulfillment delivery chain marketers face competing business goals, multiple marketing programs and constraints like channel capacity, budget and customer contact policies. Typically it is required to maximize/minimize an objective such as the return on investment while satisfying these marketing goals/constraints. In this talk we will discuss the formulation of this problem as a binary integer programming model and outline the computational challenges involved in solving the model to optimality. We will also present an overview of the methodology used by the SAS Marketing Optimization software followed by some computational results.
    Tan Inoue (Kyoto University) RNA / RNP synthetic biology
    Abstract: In general, molecular design of RNA is difficult at the 3D level because of its highly complicated folding process. In the 1990s, biochemical and structural analyses revealed that many functional noncoding natural RNAs are organized into modules and fold into defined 3D structures. Moreover, several commonly used RNA–RNA binding motifs in these RNAs were identified by phylogenetic comparison and high-resolution structural analyses. Consequently, it has become possible to design self-folding RNAs precisely by employing such motifs and mimicking the modular organization of natural RNAs. As one such example, we have investigated the design and construction of a self-folding RNA scaffold consisting of standard doublestranded helices connected by the two RNA–RNA binding motifs. Results indicated that the constructed RNA folds compactly into the designed 3D structure. We have also reported the synthesis and development of an artificial RNA enzyme by installing a reaction site and a catalytic site into the designed RNA scaffold. For medical and biological applications, the goals of our current project are 1) to establish multifunctional RNP molecules with tumor seeking sensors, imaging agents and toxins that kill target cells, and 2) to establish artificial signal transduction systems for regulating function of a cell by employing designed RNA and RNP molecules. The strategy may be applicable to the synthesis and development of a variety of nonnatural functional RNAs with defined 3D structures.
    Luc Jaeger (University of California) RNA tertiary structure as a proto-language for nano-construction
    Abstract: Common occurrence of many small structural motifs in natural RNA molecules suggests that nature utilize s a vocabulary of sequence patterns to compose structural molecules with sophisticated topologies such as the ribosome and large ribozymes. By careful analysis of sequences and tertiary structures of natural RNAs, 3D RNA modules and their folding and assembly principles are presently gathered for generating the syntax of a proto-language for rational design and prediction of RNA 3D shapes. RNA architectonics refers to the creation of this proto-language and to its use to build new RNAs with self-assembly properties. Recently, RNA architectonics led to the reliable prediction and design of the tertiary structure of several artificial RNA building blocks able to form programmable filaments and 2D RNA arrays at the nano-scale level. As a proof of concept, we also demonstrated that structurally complex RNAs based on a syntax involving a repertoire of several different RNA motifs can self-assemble into complex supra-molecular 3D nano-particles. This studies show that RNA architectonics can be used as a tool to explore and compare the biophysical properties of various RNA tertiary structure motifs that would be otherwise more difficult to investigate in isolation or within their natural context. It also demonstrates that RNA is an ideal medium for sculpting addressable and responsive self-assembling architectures of any desired shapes in the 20 to 50 nm scale. Moreover, it suggests that RNA supra-molecular assembly can potentially lead to the development of highly sophisticated therapeutic nano-devices for biological and medical applications. References 1. Jaeger, L. & Chworos, A. (2006) The Architectonics of Programmable RNA and DNA Nanostructures. Current Opinion in Structural Biology, 16, 531-543. 2. Chworos, A, Severcan, I., Koyfman, A. Y., Wienkam, P., Oroudjev, E., Hansma, H. G. & Jaeger, L. (2004). Building programmable jigsaw puzzles with RNA. Science 306, 2068-2072. 3. Nasalean, L., Baudrey, S., Leontis, N.B. & Jaeger, L. (2006) Controlling RNA self-assembly to form filaments. Nucleic Acids Res. 34, 1381-1392 4. Bates, A.D., Callen B.P., Cooper J.M., Cosstick, R., Geary, C., Glidle, A., Jaeger, L., Pearson, J.L., Proupín-Pérez, M., Xu, C., & Cumming, D.R. S. (2006) Construction and characterization of a gold nanoparticle wire assembled using Mg2+-dependent RNA-RNA interactions. Nanoletters 6, 445-448.
    Debra Knisley (East Tennessee State University) Graphical invariants and topological indices as biomolecular descriptors
    Abstract: A number of molecular descriptors of small molecules are derived from graphical representations of the molecule. These descriptors, sometimes called topological indices, are used to identify or relate the structure of a molecular with expected bioactivity and they are an essential tool in the drug design industry. It is generally accepted that these molecular descriptors are not applicable to macromolecules. However, topological indices are equivalent to graphical invariants in graph theory. Graph theory offers a wealth of graphical invariants annotated with structural implications, primarily for large graphs. Thus we consider applying known graphical measures to quantify macromolecules, including secondary RNA structures, amino acids and several families of proteins.
    David M.J. Lilley (University of Dundee) Structure, dynamics and catalytic mechanisms of two ribozymes
    Abstract: CR-UK Nucleic Acid Structure Group, MSI/WTB complex, University of Dundee, Dundee DD1 5EH, UK d.m.j.lilley@dundee.ac.uk The nucleolytic ribozymes are catalytic RNA molecules that generate site-specific cleavage by means of a transesterification reaction involving the 2’ and 5’ O atoms. We have made a study of two of these, the hairpin and VS ribozymes. The hairpin ribozyme folds to generate an intimate loop-loop interaction to create the local environment in which catalysis can proceed. By means of FRET we can observe individual hairpin ribozyme molecules as they undergo multiple cycles of cleavage and ligation, and measure the rates of the internal reactions. On average, the cleaved ribozyme undergoes several docking-undocking events before a ligation reaction occurs. On the basis of these experiments, we have explored the role of the nucleobases G8 and A38 in the catalysis. Both cleavage and ligation reactions are pH dependent, corresponding to the titration of a group with pKA = 6.2. We have used a novel ribonucleoside in which these bases are replaced by imidazole to investigate the role of acid-base catalysis in this ribozyme. We observe significant rates of cleavage and ligation, and a bell-shaped pH dependence for both. The VS ribozyme is the largest of the nucleolytic ribozymes, and the only one for which there is no crystal structure. The ribozyme consists of five helical sections organised by two three-way junctions, each of which undergo metal ion-induced folding. Using a ‘divide and conquer’ approach based principally on the analysis of component junctions by FRET, we deduced the global structure of the ribozyme. We have now solved the structure of the complete ribozyme at low resolution using small-angle X-ray scattering in solution. The binding of the substrate stem-loop generates a catalytically-productive interaction with the A730 loop active site. We have identified two critical nucleotides in the catalytic process; A756 within the A730 loop, and G638 in the substrate internal loop. Mutation or functional group substitution of either nucleobase leads to > 1,000-fold impairment of catalytic activity, while leaving the structure and binding to the ribozyme unaltered. The pH dependencies of the rate of cleavage of substrate with guanine, adenine, 2,6-diaminopurine or inosine at position 638 are fully consistent with a mechanism in which G638 and A756 act in concert in general acid-base catalysis. The proposed mechanism of the VS and hairpin ribozymes, together with the manner of the generation of the active sitea and their topology, are strikingly similar each other. This has probably arisen by convergent evolution. M.K. Nahas, T.J. Wilson, S. Hohng, K. Jarvie, D.M.J. Lilley and T. Ha Observation of internal cleavage and ligation reactions of a ribozyme Nature Struct. Molec. Biol. 11, 1107-1113 (2004). Z. Zhao, A. McLeod, S. Harusawa, L. Araki, M. Yamaguchi, T. Kurihara and D. M. J. Lilley Nucleobase participation in ribozyme catalysis. J. Amer. Chem. Soc. 127, 5026-5027 (2005). T. J. Wilson, J. Ouellet, Z. Zhao, S. Harusawa, L. Araki, T. Kurihara and D. M. J. Lilley Nucleobase catalysis in the hairpin ribozyme. RNA 12, 980-987 (2006). T. J. Wilson, A. C. McLeod and D. M. J. Lilley A guanine nucleobase important for catalysis by the VS ribozyme EMBO J. 26, 2489-2500 (2007).
    Timothy Newman (Arizona State University) Strong fluctuations and cycling in biological systems
    Abstract: In this talk I describe a mechanism for generating cycles in a large class of "mesoscale" biological populations (meaning populations composed of thousands to tens of thousands of units). Cycles are caused by a resonant amplification of the system dynamics triggered by internal noise. I will discuss this mechanism in the context of two classes of simple systems: ecological (e.g. predator-prey, host- pathogen) and biochemical (e.g. small gene regulation networks, modules of metabolic processes)
    Henri Orland (Commissariat à l'Énergie Atomique Saclay (CEA)) A topological classification of RNA folds
    Abstract: After reviewing some elementary properties of RNA, we show how the RNA folding problem can be formulated exactly in terms of an NxN matrix field theory. This formulation introduces a classification of RNA structures according to their topological genus. The large N limit of this theory generates the secondary structures of RNA (planar graphs), whereas 1/N corrections are identified as pseudo-knots. We show how the RNA structures can be analyzed in terms of primitive pseudo knots of low genus and how this concept can be included in Monte Carlo calculations to actually predict RNA folds.
    Randy C. Paffenroth (Numerica Corporation) Networked target tracking architectures
    Abstract: The coordinated use of multiple distributed sensors by network communication has the potential to substantially improve estimates of target positions, features, and attributes. This improvement is primarily due to geometric diversity, complementary sensor information, and different coverage areas. Unfortunately, sensor networks are not without their challenges. In particular, there is a balance between network bandwidth constraints and the maintenance of a consistent picture of the scenario across the network participants. In this talk we will discuss pertinent issues including network communication schemes, track initiation and maintenance, and bias mitigation.
    Deena Schmidt (University of Minnesota) Waiting for k mutations: with applications to DNA regulatory sequence evolution and cancer
    Abstract: We consider the population genetics problem: How long does it take before some member of the population has k specified mutations? The case k=2 is relevant to the onset of cancer due to the inactivation of both copies of a tumor suppresor gene. Results of Nowak and collaborators give the waiting time distribution in this case and the time until the mutant phenotype becomes fixed in the population. Here we apply these results to obtain insights into regulatory sequence evolution in Drosophila and humans. In particular, we examine the waiting time for a pair of mutations, the first of which inactivates an existing transcription factor binding site and the second which creates a new one. Consistent with recent experimental observations for Drosophila, we find that a few million years is sufficient, but for humans with a much smaller effective population size, this type of change would take more than 100 million years. In addition, we'll discuss models for larger k, which are needed for colon cancer and other diseases where a sequence of mutations leads to cells with uncontrolled growth.
    Bruce A. Shapiro (National Cancer Institute) Computational approaches to RNA nanodesign
    Abstract: We have developed a number of computational tools that permit a user to design RNA based nano-particles with various functionalities. One of these tools is a newly developed relational database, RNAJunction, which contains structural and sequence information for all known RNA n-way junctions and kissing loop interactions. The database also contains the results from applying molecular mechanics and structural clustering techniques to the motifs. The database of motifs can be searched in a variety of ways and provide a source for further analysis and RNA nano building blocks. Another computational tool, NanoTiler, permits a user to interactively and automatically construct user specified RNA-based nano-scale shapes. The combination of the RNAJunction database, NanoTiler and other computational tools allows the rapid prototyping of designed RNA shapes. We discuss some of the principles involved in these design tools and show how the RNA nanodesign process can be accomplished with the use of these methodologies.
    Devarajan Thirumalai (University of Maryland) Exploring the energy landscape of RNA
    Abstract: Recent single molecule experiments and high-resolution temperature jump experiments show that the energy landscape of RNA is rugged. As a result, even the formation of a hairpin, exhibits all the signatures of folding (multiple pathways and complex kinetics) usually associated with self-assembly of ribozymes. I will describe the kinetics of hairpin formation, initiated by both temperature and force quench, using computations. The profound differences between the two methods will be illustrated in terms of the pathways to the native state. Analogies to folding of ribozymes will also be given.
    Zhian Wang (University of Minnesota) Models for mesenchymal motion in tissue
    Abstract: The interaction between cells and extracelluar matrix (ECM) is highly complex and many biological mechanisms have been identified, which provides significant insights of understanding cell invasion such as wound healing, cancer progression and so on. The cell migration using the two strategies, i.e., contact guidance and remodeling of matrix, is termed mesenchymal motion. The mathematical models of mesenchymal motion were developed by Thomas Hillen (2006) and numerical scheme was investigated by Painter (2007). In my talk, I will present the analytic results in addition to their works and explain the findings in the context of biological applications of cell movement in tissues.
    Sarah Woodson (Johns Hopkins University) How RNA tells right from wrong: base pairs, tertiary interactions, and counterions in RNA folding
    Abstract: RNAs must self-assemble into unique three-dimensional structures in the cell, yet how RNA molecules find their native structure in a short time is not well understood. This is a challenging problem, because RNA secondary structures are thermodynamically stable but not uniquely specified by the sequence, while tertiary interactions are specific but not very stable. Consequently, many RNAs become trapped in metastable, non-native intermediates. Recent footprinting and SAXS experiments on a bacterial ribozyme show that tertiary interactions make helix assembly more specific during the initial collapse transition. Specific collapse increases the flux through folding pathways that lead directly to the native structure. The stability of the folded RNA also depends on the charge density of the counterions; small multivalent counterions stabilize the RNA more than large monovalent ions. In low charge density counterions, the transition state ensemble becomes broader, accelerating the search for the native structure.
    Visitors in Residence
    Mirela Andronescu University of British Columbia 10/28/2007 - 11/2/2007
    Douglas N. Arnold University of Minnesota 7/15/2001 - 6/30/2008
    F. Javier Arsuaga San Francisco State University 9/3/2007 - 12/21/2007
    Rolf Backofen Albert-Ludwigs-Universität Freiburg 10/27/2007 - 11/4/2007
    Nina Barnett University of Minnesota 10/29/2007 - 11/2/2007
    Victor Barocas University of Minnesota 11/27/2007 - 11/27/2007
    Alex Bateman Wellcome Trust Sanger Institute 10/28/2007 - 11/3/2007
    Daniel J. Bates University of Minnesota 9/1/2006 - 8/31/2008
    Peter W. Bates Michigan State University 9/1/2007 - 12/31/2007
    John Baxter University of Minnesota 8/1/2007 - 7/30/2009
    Jean Bergeron Alpha-Zoulou Films 10/31/2007 - 11/2/2007
    Yermal Sujeet Bhat University of Minnesota 9/1/2006 - 8/31/2008
    Eckart Bindewald SAIC-Frederick, Inc. 10/28/2007 - 11/2/2007
    Michael Bon Commissariat à l'Énergie Atomique (CEA)-Centre d'Études Nucléaires de Saclay (CENS) 10/28/2007 - 11/2/2007
    Kevin G. Bowcutt Boeing 11/14/2007 - 11/16/2007
    Anke Busch Albert-Ludwigs-Universität Freiburg 10/26/2007 - 11/4/2007
    Maria-Carme T. Calderer University of Minnesota 10/29/2007 - 11/2/2007
    Hannah Callender University of Minnesota 9/1/2007 - 8/31/2009
    Graham Candler University of Minnesota 11/14/2007 - 11/16/2007
    David Case Scripps Research Institute 10/28/2007 - 11/2/2007
    Shi-Jie Chen University of Missouri 9/3/2007 - 11/3/2007
    Arkadiusz Chworos University of California 10/28/2007 - 11/2/2007
    Peter Clote Boston College 10/28/2007 - 11/2/2007
    Anne E. Condon University of Wisconsin 10/28/2007 - 11/2/2007
    Ludovica Cecilia Cotta-Ramusino University of Minnesota 10/1/2007 - 8/30/2009
    Irma Cruz-White Chipola College 10/28/2007 - 11/2/2007
    Isabel K. Darcy University of Iowa 9/1/2007 - 1/19/2008
    Kaushik Dayal University of Minnesota 10/29/2007 - 11/2/2007
    Maciej Dlugosz University of Warsaw 10/27/2007 - 11/3/2007
    Olivier Dubois University of Minnesota 9/3/2007 - 8/31/2009
    Mauricio Esguerra Rutgers University 10/28/2007 - 11/2/2007
    Marcia O. Fenley Florida State University 10/23/2007 - 11/2/2007
    Jes Frellsen University of Copenhagen 10/27/2007 - 11/3/2007
    Hin Hark Gan New York University 10/28/2007 - 11/2/2007
    Paul Gardner Wellcome Trust Sanger Institute 10/28/2007 - 11/3/2007
    Daniel Gautheret Université de Paris XI (Paris-Sud) 10/29/2007 - 11/2/2007
    Zhumur Ghosh Indian Association for the Cultivation of Science (IACS) 10/28/2007 - 11/3/2007
    George Madalin Giambasu University of Minnesota 10/29/2007 - 11/2/2007
    Haipeng Gong University of Chicago 10/29/2007 - 11/2/2007
    Balaji Gopalakrishnan SAS Institute Inc. 11/29/2007 - 12/1/2007
    Jan Gorodkin University of Copenhagen 10/28/2007 - 11/2/2007
    Jason E. Gower University of Minnesota 9/1/2006 - 8/31/2008
    Thomas Grandine Boeing 11/14/2007 - 11/16/2007
    Christine E. Heitsch Georgia Institute of Technology 9/4/2007 - 11/3/2007
    Hugh Heldenbrand University of Minnesota 10/29/2007 - 11/2/2007
    Milena Hering University of Minnesota 9/1/2006 - 8/31/2008
    Peter Hinow University of Minnesota 9/1/2007 - 8/31/2009
    Ivo L. Hofacker Universität Wien 10/28/2007 - 11/2/2007
    Mihaela Iftime Boston University 10/28/2007 - 11/1/2007
    Tan Inoue Kyoto University 10/28/2007 - 11/3/2007
    Kai Ishihara Saitama University 11/18/2007 - 11/24/2007
    Hosna Jabbari University of British Columbia 10/28/2007 - 11/2/2007
    Luc Jaeger University of California 10/28/2007 - 11/2/2007
    Richard D. James University of Minnesota 9/4/2007 - 6/30/2008
    Tiefeng Jiang University of Minnesota 9/1/2007 - 6/30/2008
    Wojciech (Voytek) Kasprzak National Cancer Institute 10/28/2007 - 11/2/2007
    Abdelouahab Kenoufi Universität Basel 10/29/2007 - 11/2/2007
    Namhee Kim New York University 10/27/2007 - 11/2/2007
    Soojeong Kim University of Iowa 8/30/2007 - 1/20/2008
    Rob Knight University of Colorado 10/28/2007 - 11/2/2007
    Debra Knisley East Tennessee State University 8/17/2007 - 6/1/2008
    Erick kuechler University of Minnesota 10/29/2007 - 11/2/2007
    Christian Laing New York University 10/28/2007 - 11/2/2007
    Chang Hyeong Lee Worcester Polytechnic Institute 10/14/2007 - 1/4/2008
    Hyunju Lee University of Minnesota 10/29/2007 - 11/2/2007
    Tai-Sing Lee Carnegie Mellon University 10/29/2007 - 11/2/2007
    Neocles B. Leontis Bowling Green State University 10/28/2007 - 11/2/2007
    Anton Leykin University of Minnesota 8/16/2006 - 8/15/2008
    David M.J. Lilley University of Dundee 10/28/2007 - 11/2/2007
    Stinus Lindgreen University of Copenhagen 10/27/2007 - 11/4/2007
    Carlos Siva Lopez University of Minnesota 10/29/2007 - 11/2/2007
    Andy Lorenz Boston College 10/28/2007 - 11/2/2007
    Roger Lui Worcester Polytechnic Institute 9/1/2007 - 6/30/2008
    Laura Lurati University of Minnesota 9/1/2006 - 8/31/2008
    Maciej Maciejczyk Cornell University 10/28/2007 - 11/4/2007
    Francois Major University of Montreal 10/28/2007 - 11/2/2007
    Bibekanand Mallick Indian Association for the Cultivation of Science (IACS) 10/28/2007 - 11/2/2007
    David H. Mathews University of Rochester 10/27/2007 - 11/2/2007
    Roderick Melnik Wilfrid Laurier University 10/28/2007 - 11/2/2007
    Ezra Miller University of Minnesota 9/1/2007 - 6/30/2008
    Maria Giovanna Mora International School for Advanced Studies (SISSA/ISAS) 9/1/2007 - 12/31/2007
    Alejandro Morales Valencia University of Guadalajara 10/27/2007 - 11/4/2007
    Ethan K. Murphy Colorado State University 11/14/2007 - 11/17/2007
    Junalyn Navarra-Madsen Texas Woman's University 10/27/2007 - 11/3/2007
    Timothy Newman Arizona State University 9/1/2007 - 6/30/2008
    Olalla Nieto Faza University of Minnesota 10/29/2007 - 11/2/2007
    Asamoah Nkwanta Morgan State University 10/28/2007 - 11/2/2007
    Duane Nykamp University of Minnesota 9/1/2007 - 6/30/2008
    Wilma K. Olson Rutgers University 10/29/2007 - 11/2/2007
    Una-May O'Reilly Massachusetts Institute of Technology 11/13/2007 - 11/15/2007
    Henri Orland Commissariat à l'Énergie Atomique Saclay (CEA) 10/28/2007 - 11/2/2007
    Hans G. Othmer University of Minnesota 9/1/2007 - 6/30/2008
    Randy C. Paffenroth Numerica Corporation 11/8/2007 - 11/10/2007
    Tao Pan University of Chicago 10/28/2007 - 11/2/2007
    Jakob Skou Pedersen University of Copenhagen 10/28/2007 - 11/2/2007
    Yann Ponty Boston College 10/28/2007 - 11/2/2007
    Eric Rawdon University of St. Thomas 10/29/2007 - 11/2/2007
    Jens Reeder Universität Bielefeld 10/28/2007 - 11/2/2007
    Yongwu Rong George Washington University 10/30/2007 - 11/2/2007
    Ioulia Rouzina University of Minnesota 10/29/2007 - 11/2/2007
    Walter Larry Ruzzo University of Washington 10/28/2007 - 11/2/2007
    Tamar Schlick New York University 10/25/2007 - 11/2/2007
    Deena Schmidt University of Minnesota 9/1/2007 - 8/31/2009
    Hullas Sehcal University of Minnesota 10/29/2007 - 11/2/2007
    Chehrzad Shakiban University of Minnesota 9/1/2006 - 8/31/2008
    Bruce A. Shapiro National Cancer Institute 10/28/2007 - 11/2/2007
    Koya Shimokawa Saitama University 11/18/2007 - 11/24/2007
    Tobin R. Sosnick University of Chicago 10/28/2007 - 11/2/2007
    Andrew Stein University of Minnesota 9/1/2007 - 8/31/2009
    Michael Stich Instituto Nacional de Tecnica Aeroespacial 10/27/2007 - 11/4/2007
    Andrew M. Stuart University of Warwick 10/29/2007 - 11/2/2007
    De Witt L. Sumners Florida State University 10/24/2007 - 11/8/2007
    Vladimir Sverak University of Minnesota 9/1/2007 - 6/30/2008
    David Swigon University of Pittsburgh 9/4/2007 - 12/14/2007
    Berhanu Tameru Tuskegee University 10/28/2007 - 11/2/2007
    Chris Thachuk University of British Columbia 10/28/2007 - 11/2/2007
    Devarajan Thirumalai University of Maryland 10/28/2007 - 11/2/2007
    Madhan Tirumalai University of Houston 10/28/2007 - 11/2/2007
    Elfar Torarinsson University of Copenhagen 10/28/2007 - 11/4/2007
    Erkan Tüzel University of Minnesota 9/1/2007 - 8/31/2009
    Jan Vandenbrande Boeing 11/13/2007 - 11/26/2007
    Tanya Vassilevska Lawrence Livermore National Laboratory 10/28/2007 - 11/2/2007
    Sébastien Vaucher Empa 11/14/2007 - 11/17/2007
    Mariel Vazquez San Francisco State University 9/3/2007 - 12/21/2007
    Jérôme Waldispühl Massachusetts Institute of Technology 10/28/2007 - 11/3/2007
    Haiyan Wang Arizona State University 10/28/2007 - 11/1/2007
    Zhian Wang University of Minnesota 9/1/2007 - 8/31/2009
    Stefan Washietl Universität Wien 10/28/2007 - 11/2/2007
    Eric Westhof Université de Strasbourg I (Louis Pasteur) 10/28/2007 - 11/2/2007
    Sebastian Will Albert-Ludwigs-Universität Freiburg 10/26/2007 - 11/4/2007
    Sarah Woodson Johns Hopkins University 10/31/2007 - 11/2/2007
    Zhijun Wu Iowa State University 9/4/2007 - 6/1/2008
    Yurong Xin New York University 10/27/2007 - 11/2/2007
    Yi Xing University of Iowa 10/28/2007 - 11/2/2007
    Yanji Xu Minnesota Supercomputing Institute 10/29/2007 - 11/2/2007
    Chuan Xue University of Minnesota 10/29/2007 - 11/2/2007
    Vadim V. Yakovlev Worcester Polytechnic Institute 11/13/2007 - 11/17/2007
    Masoud Yari Indiana University 10/29/2007 - 11/2/2007
    Darrin M. York University of Minnesota 10/28/2007 - 11/2/2007
    Giovanni Zanzotto Università di Padova 11/15/2007 - 11/30/2007
    Arghir Dani Zarnescu University of Oxford 11/12/2007 - 12/11/2007
    Hongchao Zhang University of Minnesota 9/1/2006 - 8/31/2008
    Zhichuan Zhang University of British Columbia 10/28/2007 - 11/2/2007
    Likun Zheng University of Minnesota 10/29/2007 - 11/2/2007
    Craig L. Zirbel Bowling Green State University 10/28/2007 - 11/2/2007
    Michael Zuker Rensselaer Polytechnic Institute 10/27/2007 - 11/2/2007
    Legend: Postdoc or Industrial Postdoc Long-term Visitor

    IMA Affiliates:
    3M, Arizona State University, Boeing, Carnegie Mellon University, Corning, ExxonMobil, Ford, General Electric, General Motors, Georgia Institute of Technology, Honeywell, IBM, Indiana University, Iowa State University, Johnson & Johnson, Kent State University, Lawrence Livermore National Laboratory, Lockheed Martin, Los Alamos National Laboratory, Medtronic, Michigan State University, Michigan Technological University, Microsoft Research, Mississippi State University, Motorola, Northern Illinois University, Ohio State University, Pennsylvania State University, Purdue University, Rice University, Rutgers University, Sandia National Laboratories, Schlumberger-Doll, Schlumberger-Doll Research, Seoul National University, Siemens, Telcordia, Texas A & M University, University of Central Florida, University of Chicago, University of Cincinnati, University of Delaware, University of Houston, University of Illinois at Urbana-Champaign, University of Iowa, University of Kentucky, University of Maryland, University of Michigan, University of Minnesota, University of Notre Dame, University of Pittsburgh, University of Tennessee, University of Texas, University of Wisconsin, University of Wyoming, US Air Force Research Laboratory, Wayne State University, Worcester Polytechnic Institute