Institute for Mathematics and its Applications University of Minnesota 114 Lind Hall 207 Church Street SE Minneapolis, MN 55455 
20072008 Program
See http://www.ima.umn.edu/20072008 for a full description of the 20072008 program on Mathematics of Molecular and Cellular Biology.
Doug Arnold, the director of IMA, has been elected as the new president of SIAM. His 2year term will begin in January, 2009.
Möbius Transformations Revealed, a short video by IMA director Douglas Arnold and colleague Jonathan Rogness, which depicts the beauty of Möbius transformations and shows how moving to a higher dimension reveals their essential unity, is currently the top featured video on www.youtube.com and has been watched by almost 1000,000 viewers.  so for a brief shining moment, at least, stereographic projection and Möbius Transformations are getting top billing over talking cats and charging an iPod with gatorade. It can be found at www.ima.umn.edu/~arnold/moebius/ .
The IMA is looking for a new associate director to begin September 1, 2008.
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 20082009 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.11:15a12:15p  Using mathematical modeling to make testable predictions of cellular signaling pathways  Hannah Callender (University of Minnesota)  Lind Hall 409  PS 
11:15a12:15p  The solution of the boundaryvalue problems for the simulation of transitions of protein conformations  Zhijun Wu (Iowa State University)  Lind Hall 409  MMCB 
1:00p3:00p  IMA Holiday Potluck Luncheon  Lind Hall 400 
10:00a11:00a  Panel discussion on how to write a grant  Isabel K. Darcy (University of Iowa)  Lind Hall 409  
11:15a12:15p  Models for mitosis: microtubules and motors  David Odde (University of Minnesota)  Lind Hall 409  PS 
11:15a12:15p  Topological analysis of DNAprotein complexes  Soojeong Kim (University of Iowa)  Lind Hall 409  MMCB 
11:15a12:15p  Mesoscopic model for the fluctuating hydrodynamics of binary and ternary mixtures  Erkan Tüzel (University of Minnesota)  Lind Hall 409  PS 
All Day  Floating holiday. The IMA is closed. 
All Day  Christmas Day. The IMA is closed. 
All Day  The IMA is closed. 
Event Legend: 

MMCB  Mathematics of Molecular and Cellular Biology Seminar 
PS  IMA Postdoc Seminar 
Hannah Callender (University of Minnesota)  Using mathematical modeling to make testable predictions of cellular signaling pathways 
Abstract: We propose a mathematical model of the Gprotein signaling pathway in RAW 264.7 macrophages downstream of P2Y6 activation by the ubiquitous signaling nucleotide uridine 5diphosphate. The model is based on timecourse measurements of P2Y6 surface receptors, inositol trisphosphate, cytosolic calcium, and with a particular focus on differential dynamics of multiple species of diacylglycerol. When using the canonical representation, the model predicted that key interactions were missing from the current pathway structure. Indeed, the model suggested that to accurately depict experimental observations, an additional branch to the signaling pathway was needed, whereby an intracellular pool of diacylglycerol is immediately phosphorylated upon stimulation of an extracellular receptor for uridine 5diphosphate and subsequently used to aid replenishment of phosphatidylinositol. As a result of sensitivity analysis of the model parameters, key predictions can be made regarding which of these parameters are the most sensitive to perturbations and are therefore most responsible for output uncertainty.  
Soojeong Kim (University of Iowa)  Topological analysis of DNAprotein complexes 
Abstract: Difference topology is a methodology to derive the number of DNA crossings trapped in an unknown protein complex. By this method, Pathania, Jayaram, and Harshey revealed the topological structure within the Mu protein complex which consisted of three DNA segments containing five nodes [1]. In their experiments, they used a member of the sitespecific recombinases which is known as Cre. Cre mediates DNA exchange by rearranging target sites of the DNA segments. During this DNA recombination, there are no extra DNA crossings introduced. The initial DNA conformation is unknotted. After Cre recombination, the products are knots or catenanes. Recently, Darcy, Luecke, and Vazquez analyzed these experimental results and proved that the fivenoded conformation is the only biologically reasonable structure of the Mu protein DNA complex [2]. We address the possibility of protein complexes that binds four DNA segments. By the useful property of Cre, we can make the assumption that after Cre recombination, the topology of a DNAprotein complex would be a knot or catenane. The latest results of the topological tangle model for this case and very basic biological and mathematical backgrounds will be discussed.
Reference: [1] S. Pathania, M. Jayaram, and R. Harshey, Path of DNA within the Mu transpososome: Transposase interaction bridging two Mu ends and the enhancer trap five DNA supercoils, Cell 109 (2002), 425436. [2] I. K. Darcy, J. Luecke, and M. Vazquez, A tangle analysis of the Mu transpososome protein complex which binds three DNA segments, Preprint. 

David Odde (University of Minnesota)  Models for mitosis: microtubules and motors 
Abstract: After a genome is replicated, it must be properly segregated into the two daughter cells. A segregation machine, known as the mitotic spindle, moves sister chromosomes into proper position for their eventual parting. This machine is composed of linear polymers known as microtubules, which dynamically selfassemble via an energydissipating process known as "dynamic instability". I will discuss our Monte Carlo modeling of microtubule dynamics during mitosis as it occurs in the budding yeast. Through experimental testing of our models we found that molecular motors play a key role in regulating microtubule dynamics to properly sort chromosomes during yeast mitosis.  
Erkan Tüzel (University of Minnesota)  Mesoscopic model for the fluctuating hydrodynamics of binary and ternary mixtures 
Abstract: Recent improvements in fluorescence microscopy and digital image processing enable direct observations of thermal fluctuations in phase separating binary mixtures. For example, the analysis of capillary wave statics and dynamics in suspended mixed lipid monolayer membranes is being used to gain insight into the nature of the intermolecular interactions. Due to the level of complexity in these systems, mesoscale simulations which incorporate thermal fluctuations can significantly improve our understanding of these systems. Here we describe a recently introduced particlebased model for the fluid dynamics of immiscible binary mixtures. Excluded volume interactions between the two components are modeled by stochastic multiparticle collisions which depend on the local velocities and densities. Momentum and energy are conserved locally, and entropically driven phase separation occurs for high collision rates. An explicit expression for the equation of state is derived. Analytic results for the phase diagram are in excellent agreement with simulation data. Results for the line tension obtained from the analysis of the capillary wave spectrum of a droplet agree with measurements based on the Laplace's equation. The dispersion relation for the capillary waves is derived and compared with the numerical measurements of the time correlations of the radial fluctuations in the damped and overdamped limits. The introduction of ``amphiphilic'' dimers makes it possible to model the phase behavior of ternary surfactant mixtures.  
Zhijun Wu (Iowa State University)  The solution of the boundaryvalue problems for the simulation of transitions of protein conformations 
Abstract: Under certain kinetic or thermodynamic conditions, proteins make conformational transitions, resulting in significant functional variations. Such dynamic properties can be studied through molecular dynamics simulation. However, in contrast to conventional dynamics simulation protocols where an initialvalue problem is solved, the simulation of transitions of protein conformations can be done by solving a boundaryvalue problem, with the beginning and ending states of the protein as the boundary conditions. While a boundaryvalue problem is more difficult to solve in general, it provides a more realistic model for the study of protein conformational transitions and has certain computational advantages as well, especially for large scale simulations. Here we study the solution of the boundaryvalue problems for the simulation of transitions of protein conformations using a standard class of numerical methods called the multiple shooting methods. We describe the methods and discuss the issues related to their implementations for our specific applications, including the definition of the boundary conditions, the formation of the initial trajectories, and the convergence of the solutions. We present the results from using the multiple shooting methods for the study of conformational transitions of a small molecular cluster and an alanine dipeptide, and show the potential extension of the methods to larger biomolecular systems. 
Douglas N. Arnold  University of Minnesota  7/15/2001  6/30/2008 
Donald G. Aronson  University of Minnesota  9/1/2007  8/31/2009 
F. Javier Arsuaga  San Francisco State University  9/3/2007  12/31/2007 
Daniel J. Bates  University of Minnesota  9/1/2006  8/31/2008 
Peter W. Bates  Michigan State University  9/1/2007  12/22/2007 
John Baxter  University of Minnesota  8/1/2007  7/30/2009 
Yermal Sujeet Bhat  University of Minnesota  9/1/2006  8/31/2008 
Hannah Callender  University of Minnesota  9/1/2007  8/31/2009 
Ludovica Cecilia CottaRamusino  University of Minnesota  10/1/2007  8/30/2009 
Isabel K. Darcy  University of Iowa  9/1/2007  1/19/2008 
Olivier Dubois  University of Minnesota  9/3/2007  8/31/2009 
Jason E. Gower  University of Minnesota  9/1/2006  8/31/2008 
Milena Hering  University of Minnesota  9/1/2006  8/31/2008 
Peter Hinow  University of Minnesota  9/1/2007  8/31/2009 
Richard D. James  University of Minnesota  9/4/2007  6/30/2008 
Tiefeng Jiang  University of Minnesota  9/1/2007  6/30/2008 
Markus Keel  University of Minnesota  12/7/2007  12/7/2007 
Soojeong Kim  University of Iowa  8/30/2007  1/20/2008 
Debra Knisley  East Tennessee State University  8/17/2007  6/1/2008 
Attila Gyula Kocsis  Budapest University of Technology and Economics  12/1/2007  12/31/2007 
Chang Hyeong Lee  Worcester Polytechnic Institute  10/14/2007  1/4/2008 
Anton Leykin  University of Minnesota  8/16/2006  8/15/2008 
Roger Lui  Worcester Polytechnic Institute  9/1/2007  6/30/2008 
Laura Lurati  University of Minnesota  9/1/2006  8/31/2008 
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 
Timothy Newman  Arizona State University  9/1/2007  6/30/2008 
Duane Nykamp  University of Minnesota  9/1/2007  6/30/2008 
David Odde  University of Minnesota  12/11/2007  12/11/2007 
Hans G. Othmer  University of Minnesota  9/1/2007  6/30/2008 
Deena Schmidt  University of Minnesota  9/1/2007  8/31/2009 
Chehrzad Shakiban  University of Minnesota  9/1/2006  8/31/2008 
Andrew Stein  University of Minnesota  9/1/2007  8/31/2009 
Vladimir Sverak  University of Minnesota  9/1/2007  6/30/2008 
David Swigon  University of Pittsburgh  9/4/2007  12/14/2007 
Erkan Tüzel  University of Minnesota  9/1/2007  8/31/2009 
Mariel Vazquez  San Francisco State University  9/3/2007  12/31/2007 
Zhian Wang  University of Minnesota  9/1/2007  8/31/2009 
Zhijun Wu  Iowa State University  9/4/2007  6/1/2008 
Arghir Dani Zarnescu  University of Oxford  11/12/2007  12/9/2007 
Hongchao Zhang  University of Minnesota  9/1/2006  8/31/2008 