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IMA Newsletter #374

December 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

Doug Arnold -- President-elect of SIAM

Doug Arnold, the director of IMA, has been elected as the new president of SIAM. His 2-year term will begin in January, 2009.

Math video -- the top featured video on youtube

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/ .

IMA is seeking a new associate director:

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 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.

Schedule

Tuesday, December 4

11:15a-12:15pUsing mathematical modeling to make testable predictions of cellular signaling pathwaysHannah Callender (University of Minnesota)Lind Hall 409 PS

Wednesday, December 5

Monday, December 10

1:00p-3:00pIMA Holiday Potluck LuncheonLind Hall 400

Tuesday, December 11

10:00a-11:00aPanel discussion on how to write a grantIsabel K. Darcy (University of Iowa)Lind Hall 409
11:15a-12:15pModels for mitosis: microtubules and motorsDavid Odde (University of Minnesota)Lind Hall 409 PS

Wednesday, December 12

11:15a-12:15pTopological analysis of DNA-protein complexesSoojeong Kim (University of Iowa)Lind Hall 409 MMCB

Tuesday, December 18

11:15a-12:15pMesoscopic model for the fluctuating hydrodynamics of binary and ternary mixturesErkan Tüzel (University of Minnesota)Lind Hall 409 PS

Monday, December 24

All DayFloating holiday. The IMA is closed.

Tuesday, December 25

All DayChristmas Day. The IMA is closed.

Monday, December 31

All DayThe IMA is closed.
Abstracts
Hannah Callender (University of Minnesota) Using mathematical modeling to make testable predictions of cellular signaling pathways
Abstract: We propose a mathematical model of the G-protein signaling pathway in RAW 264.7 macrophages downstream of P2Y6 activation by the ubiquitous signaling nucleotide uridine 5-diphosphate. The model is based on time-course 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 5-diphosphate 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 DNA-protein 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 site-specific 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 five-noded 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 DNA-protein 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), 425-436.

[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 self-assemble via an energy-dissipating 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 particle-based 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 over-damped 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 boundary-value 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 initial-value problem is solved, the simulation of transitions of protein conformations can be done by solving a boundary-value problem, with the beginning and ending states of the protein as the boundary conditions. While a boundary-value 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 boundary-value 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.
Visitors in Residence
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 Cotta-Ramusino 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
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