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This month's talks available at http://www.ima.umn.edu/newsletters

IMA Newsletter #343

May 2005

2004-2005 Program

Mathematics of Materials and Macromolecules

See http://www.ima.umn.edu/matter for a full description of the 2004-2005 program on
Mathematics of Materials and Macromolecules: Multiple Scales, Disorder, and Singularities
and http://www.ima.umn.edu/schedule for schedule updates.

IMA Events

This month the IMA focuses on mathematical biology, offering a series of events bringing mathematicians together with leading biologists:

IMA Annual Program Year Workshop

Experiments in Physical Biology

Part I: May 2-6, 2005       Part II: May 16-20, 2005

Organizers: John Maddocks (Swiss Federal Institute of Technology Lausanne) and Rob Phillips (California Institute of Technology)

http://www.ima.umn.edu/matter/spring/biology.html

The analysis of biological systems is becoming increasingly quantitative. The emergence of quantitative biology is due in no small part to significant advances in structural biology and single molecule biophysics. The advent of these various techniques has led to a situation in which experimental data has advanced at a much more rapid pace than the models aiming to respond to that data. The workshops Experiments in Physical Biology will feature leaders in experimental quantitative biology, presenting the basis of these quantitative insights in a tutorial fashion, and arguing for the types of mathematical models needed to respond to these experiments. Part I focuses on DNA; part II will focus on proteins. An introductory tutorial on proteins, intended for mathematicians with no background in biochemistry, will be given by Julie Mitchell on May 10.

IMA Workshop

Modeling Sequence-Dependent DNA Dynamics: The Third ABC Debriefing

May 7-8, 2005

Organizers: Richard Lavery (CNRS), John H. Maddocks (Swiss Federal Institute of Technology Lausanne), Roman Osman (Mount Sinai School of Medicine)

http://www.ima.umn.edu/matter/SW5.7-8.05/index.html

The Ascona B-DNA Consortium (ABC) was established in 2001 with the aim of creating a database describing the dynamics of DNA as a function of its base sequence. The method chosen was Molecular Dynamics carried out on a series of DNA fragments containing multiple copies of the 136 unique tetranucleotide sequences. The calculations were carried out by a consortium of nine laboratories, four European and five in the USA. The day long meeting on May 7 will have a number of talks describing results arising from, and pertinent to, the ongoing ABC project. On May 8 members of the consortium will meet in closed session.

IMA Workshop

Modeling the Dynamics of Shape Change in Liquid Crystal Elastomers

May 24-25, 2005

Organizers: Peter Palffy-Muhoray (Kent State University), Michael J. Shelley (New York University)

http://www.ima.umn.edu/matter/SW5.24-25.05/index.html

Liquid crystal elastomers are exceptionally responsive materials due to the coupling of mechanical strain and orientational order. The aim of this workshop is to bring together researchers interested in the understanding, modeling and utilizing of dynamic shape changes in liquid crystal elastomers which occur in response to external excitations. Topics of interest are materials structure and interactions at the molecular level, routes to the macroscopic equations of motion, soft active body hydrodynamics, numerical approaches to related moving boundary problems, and the exploration of applications such as actuation and locomotion.
Schedule

Monday, May 2

9:00a-10:15aCoffee and RegistrationEE/CS 3-176 W5.2-6.05
10:15a-10:30aWelcome and IntroductionDouglas N. Arnold
University of Minnesota
EE/CS 3-180 W5.2-6.05
10:30a-12:30pMolecular probes for DNA structure and dynamicsNikolaus Ernsting
Humboldt University of Berlin
EE/CS 3-180 W5.2-6.05
12:30p-2:30pLunch Break W5.2-6.05
2:30p-4:30pDNA condensationNicholas Hud
Georgia Institute of Technology
EE/CS 3-180 W5.2-6.05
3:35p-4:35pLong time averaging for molecular dynamics simulations Frederic Legoll
University of Minnesota
Vincent Hall 570 SMS

Tuesday, May 3

9:00a-9:30aCoffeeEE/CS 3-176 W5.2-6.05
9:30a-10:30aMolecular probes for DNA structure and dynamicsNikolaus Ernsting
Humboldt University of Berlin
EE/CS 3-180 W5.2-6.05
10:30a-11:00aCoffee BreakEE/CS 3-176 W5.2-6.05
11:00a-1:00pDNA bending, twisting, and looping in the control of transcriptionJason Kahn
University of Maryland
EE/CS 3-180 W5.2-6.05
1:00p-2:30pLunch Break W5.2-6.05
2:30p-4:30pSequence-dependent DNA mechanics in very small DNA circles and nucleosomesJonathan Widom
Northwestern University
EE/CS 3-180 W5.2-6.05
4:30p-6:00pReceptionLind Hall 400 W5.2-6.05

Wednesday, May 4

9:00a-9:30aCoffeeEE/CS 3-176 W5.2-6.05
9:30a-10:30aDNA condensationNicholas Hud
Georgia Institute of Technology
EE/CS 3-180 W5.2-6.05
10:30a-11:00aCoffee BreakEE/CS 3-176 W5.2-6.05
11:00a-12:00pDNA bending, twisting, and looping in the control of transcriptionJason Kahn
University of Maryland
EE/CS 3-180 W5.2-6.05
12:00p-1:00pSequence-dependent DNA mechanics in very small DNA circles and nucleosomesJonathan Widom
Northwestern University
EE/CS 3-180 W5.2-6.05
1:00p-2:30pLunch Break W5.2-6.05
1:15p-2:15pRefined Jacobian estimates and vortex dynamics for the Gross-Pitaevsky equationRobert L. Jerrard
University of Toronto
Lind Hall 409 MS
2:30p-4:30pSingle molecule mechanics of DNAZev Bryant
Stanford University
EE/CS 3-180 W5.2-6.05

Thursday, May 5

9:00a-9:30aCoffeeEE/CS 3-176 W5.2-6.05
9:30a-10:30aSingle molecule mechanics of DNAZev Bryant
Stanford University
EE/CS 3-180 W5.2-6.05
10:30a-11:00aCoffee BreakEE/CS 3-176 W5.2-6.05
11:00a-1:00pDNA looping: biology and mechanismsRobert Schleif
Johns Hopkins University
EE/CS 3-180 W5.2-6.05
12:20p-1:20p Variational curve design on surfacesMichael Hofer
University of Minnesota
Lind Hall 409 iPAWS
1:00p-2:30pLunch Break W5.2-6.05
2:30p-4:30pWrapping of DNA on protein surfacesM. Thomas Record
University of Wisconsin
EE/CS 3-180 W5.2-6.05

Friday, May 6

9:00a-9:30aCoffeeEE/CS 3-176 W5.2-6.05
9:30a-10:30aDNA looping: biology and mechanismsRobert Schleif
Johns Hopkins University
EE/CS 3-180 W5.2-6.05
10:30a-11:00aCoffee BreakEE/CS 3-176 W5.2-6.05
11:00a-12:00pLarge-scale conformational changes in RNA polymerase and promoter DNA in transcription initiationM. Thomas Record
University of Wisconsin
EE/CS 3-180 W5.2-6.05
1:25p-2:25pFinite-difference simulation of nanoscopic devicesGeoffrey Burr
IBM Corporation
Vincent Hall 570 IPS
2:00p-3:00pOptimal sampling of a reaction coordinate in molecular dynamicsAndrew Pohorille
NASA Ames Research Center
Lind Hall 409 MS

Saturday, May 7

9:00a-9:45aMolecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. Sequence context effects on the dynamical structures of the 10 unique dinucleotide stepsDavid L. Beveridge
Wesleyan University
EE/CS 3-180 SW5.7-8.05
9:45a-10:15aQuantum chemistry and energetics in Pu-p-Pu Roman Osman
Mount Sinai School of Medicine
EE/CS 3-180 SW5.7-8.05
10:15a-11:00aMolecular dynamics simulations of RNA and noncanonical DNA molecules. Successes and troublesJiri Sponer
Czechoslovakian Academy of Sciences
EE/CS 3-180 SW5.7-8.05
11:00a-11:45aDo longer or bigger simulations of DNA actually teach us anything new?Thomas Cheatham
University of Utah
EE/CS 3-180 SW5.7-8.05
12:00p-1:30pLunch SW5.7-8.05
1:30p-2:15pGeneralized Born studies of ABC DNA sequencesDavid Case
The Scripps Research Institute
EE/CS 3-180 SW5.7-8.05
2:15p-3:00pCURVES+Richard Lavery
CNRS
EE/CS 3-180 SW5.7-8.05
3:00p-3:45pExploring the flexibility of nucleic acids Modesto Orozco
University of Barcelona
EE/CS 3-180SW5.7-8.05
3:45p-4:30pTBAEE/CS 3-180 SW5.7-8.05

Sunday, May 8

All DayModeling Sequence-Dependent DNA Dynamics: The Third ABC Debriefing
(Closed session)
Lind Hall 409 SW5.7-8.05

Monday, May 9

11:15a-12:15pA mathematical description of the invasion of Bacteriophage T4 Richard D. James
University of Minnesota
Lind Hall 409 MS

Tuesday, May 10

10:10a-12:00pTutorial on basics of proteinsJulie C. Mitchell
University of Wisconsin
Lind Hall 409

Wednesday, May 11

11:15a-12:15pVortex patterns in Bose Einstein condensatesAmandine Aftalion
Universite Pierre et Maris Curie (Paris VI)
Lind Hall 409 MS

Friday, May 13

11:15a-12:15pRhythmic hormone delivery based on a gel/enzyme chemomechanical oscillatorsRonald Siegel
University of Minnesota
Lind Hall 409 MS

Monday, May 16

8:30a-9:00aCoffee and RegistrationEE/CS 3-176 W5.16-20.05
9:00a-9:30aIntroduction and overviewRobert Phillips
California Institute of Technology
EE/CS 3-180 W5.16-20.05
9:30a-11:00aBiological adhesion: molecules to tissuesDeborah Leckband
University of Illinois - Urbana-Champaign
EE/CS 3-180 W5.16-20.05
11:00a-11:30acoffee EE/CS 3-176 W5.16-20.05
11:30a-12:00pquestions/discussionEE/CS 3-180 W5.16-20.05
12:00p-1:30plunch W5.16-20.05
1:30p-3:00pBiological adhesion: dynamics, organization, and functionDeborah Leckband
University of Illinois - Urbana-Champaign
EE/CS 3-180 W5.16-20.05
3:00p-3:30pcoffee EE/CS 3-176 W5.16-20.05
3:30p-4:00pquestions/discussionEE/CS 3-180 W5.16-20.05

Tuesday, May 17

9:00a-9:30acoffeeEE/CS 3-176 W5.16-20.05
9:30a-11:00aMolecular motors IPaul Selvin
University of Illinois - Urbana-Champaign
EE/CS 3-180 W5.16-20.05
11:00a-11:30acoffee EE/CS 3-176 W5.16-20.05
11:30a-12:00pquestions/discussionEE/CS 3-180 W5.16-20.05
12:00p-1:30plunch W5.16-20.05
1:30p-3:00pMolecular motors II, DNA haplotyping, and ion channelsPaul Selvin
University of Illinois - Urbana-Champaign
EE/CS 3-180 W5.16-20.05
3:00p-3:30pcoffee EE/CS 3-176 W5.16-20.05
3:30p-4:00pquestions/discussionEE/CS 3-180 W5.16-20.05

Wednesday, May 18

9:00a-9:30acoffeeEE/CS 3-176 W5.16-20.05
9:30a-11:00aA gentle introduction to lipid membranes and resulting miscibility phase diagramsSarah L. Keller
University of Washington
EE/CS 3-180 W5.16-20.05
11:00a-11:30acoffeeEE/CS 3-176 W5.16-20.05
11:30a-12:00pquestions/discussionEE/CS 3-180 W5.16-20.05
12:00p-1:30plunch W5.16-20.05
1:30p-3:00pSeeing spots: Experimentally determining lipid miscibility phase diagrams in free-floating vesicles, supported membranes, and monolayers at an air-water interfaceSarah L. Keller
University of Washington
EE/CS 3-180 W5.16-20.05
3:00p-3:30pcoffeeEE/CS 3-176 W5.16-20.05
3:30p-4:00pquestions/discussionEE/CS 3-180 W5.16-20.05

Thursday, May 19

9:00a-9:30acoffeeEE/CS 3-176 W5.16-20.05
9:30a-11:00aIntroduction to the cytoskeleton and cellular motilityThomas D. Pollard
Yale University
EE/CS 3-180 W5.16-20.05
11:00a-11:30acoffeeEE/CS 3-176 W5.16-20.05
11:30a-12:00pquestions/discussionEE/CS 3-180 W5.16-20.05
12:00p-1:30plunch W5.16-20.05
1:30p-3:00pResearch frontiers and opportunitiesThomas D. Pollard
Yale University
EE/CS 3-180 W5.16-20.05
3:00p-3:30pcoffee EE/CS 3-176 W5.16-20.05
3:30p-4:00pquestions/discussionEE/CS 3-180 W5.16-20.05

Friday, May 20

9:00a-9:30acoffeeEE/CS 3-176 W5.16-20.05
9:30a-11:30aRetrospective and summaryEE/CS 3-180 W5.16-20.05
2:30p-3:30pMolecular dynamics simulations: stability, multiscale approaches and the art of trajectory analysisMarc Q. Ma
New Jersey Institute of Technology
305 Lind Hall MS

Monday, May 23

11:15a-12:15pTBAQiang Du
Pennsylvania State University
Lind Hall 305 MS

Tuesday, May 24

All DayIMA Workshop: Modeling the Dynamics of Liquid Crystal ElastomersEE/CS 3-180 SW5.24-25.05

Wednesday, May 25

All DayIMA Workshop: Modeling the Dynamics of Liquid Crystal ElastomersEE/CS 3-180 SW5.24-25.05

Thursday, May 26

11:15a-12:15pTBATim P. Schulze
University of Tennessee
305 Lind Hall MS

Monday, May 30

11:15a-12:15pTBAFlorian Theil
University of Warwick
Lind Hall 305 MS
Abstracts
David L. Beveridge (Wesleyan University) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
Abstract: Molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide base pair steps are reported. The objective is to obtain the calculated dynamical structure for at least two copies of each case, and use the results to examine outstanding issues with regard to methods and protocols in MD on DNA, convergence and dynamical stability, and to determine the significance of sequence context effects on all unique dinucleotide steps. This information is essential to understanding sequence effects on DNA structure and has implications on diverse problems in the structural biology of DNA. Calculations were carried out on the 136 cases imbedded in 39 DNA oligomers with repeating tetranucleotide sequences, capped on both ends by GC pairs and each having a total length of 15 nucleotide pairs. All simulations were carried out using a well-defined state-of-the-art MD protocol, the AMBER suite of programs, and the parm94 force field. In a previous article (Biophysical Journal 87, 3799-3813), the research design, details of the simulation protocol, and informatics issues were described. Preliminary results from 15 ns MD trajectories were presented for the d(CpG) step in all ten unique sequence contexts. The results indicated the sequence context effects to be small for this step, but revealed that MD on DNA at this length of trajectory is subject to surprisingly persistent cooperative transitions of the sugar-phosphate backbone torsion angles a and g. Here, we report detailed analysis of the entire trajectory database. In particular, we present results on the occurrence of various conformational substates in the light of related experimental observation and discuss their impact on studies of context effects in DNA. At the tetranucleotide level, we observe that in many cases the difference in mean of the individual base pair step helicoidal parameter distributions with different flanking sequence differs by as much as 1 standard deviation, implying that the sequence effects could be significant. We present a novel analysis based on 2D-RMS data for studying the differences in structure and flexibility and employ it to analyze the flexibility of the dinucleotide steps and the effect of the base pair flanking the dinucleotide in the tetra-nucleotide sequences. We observe that the presence of pyrimidine-purine (YpR) steps, esp. the CpG and CpA steps greatly increases the flexibility of DNA while the purine-purine step (YpY/RpR) has a rigidifying effect. The neighboring base pair steps act cooperatively in such a way that the flexible steps tend to dominate the nature of the DNA sequence, there by leading to greater flexibility of the YpY steps in the neighborhood of YpR steps. Further, we observe that the effect of flexible YpR steps extends beyond its place as the first neighbor.
Zev Bryant (Stanford University) Single molecule mechanics of DNA
Abstract: I will begin with a review of single molecule manipulation techniques applied to DNA and what they have taught us about DNA physics and enzymology. I will then concentrate on direct measurements of torque and twist in single stretched DNA molecules. Torque and twist measurements have provided insights into the mechanical properties of DNA and laid the experimental and conceptual groundwork for a new class of mechanistic studies of DNA-associated enzymes. I will conclude with an example of an enzymogical application: a mechanochemical dissection of E. Coli DNA gyrase.
Geoffrey Burr (IBM Corporation) Finite-difference simulation of nanoscopic devices
Abstract: In its simplest manifestation, a finite-difference scheme discretizes a system of partial differential equations directly onto a regular, Cartesian mesh. Since such finite-difference schemes can readily scale to simulations with millions of elements, they have become popular for addressing complex physical simulations. Here we discuss two applications of finite-difference techniques. The first is the use of the Finite-Difference Time-Domain (FDTD) algorithm for simulating Maxwell's Equations in nanophotonic devices such as photonic crystals; the second is a customized multi-physics simulator for non-volatile electronic phase-change memory. The latter solves the diffusion equation by finite-difference techniques in order to simulate heat diffusion as well as to compute the steady-state potentials satisfying Laplace's equation. The tight relationship between the choices of spatial and temporal steps ("Courant stability"), and the resulting impact on the two different finite-difference schemes, will be discussed.
David Case (The Scripps Research Institute) Generalized Born studies of ABC DNA sequences
Abstract: It is often useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. The generalized Born model is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. I will describe two applications of this methodology to the study of DNA duplex oligomers taken from the ABC sequence set. The first uses molecular dynamics simulations to look at mean structures, fluctuations and conformational transitions, with an eye towards explicit solvent simulations already carried out. The second application uses normal mode analysis (as a function of sequence length) to analyze low frequency distortion modes, and to prepare for a parameterization of a low-resolution model that could be used for much large pieces of DNA.
Thomas Cheatham (University of Utah) Do longer or bigger simulations of DNA actually teach us anything new?
Abstract: This past decade may rightly be called the "10 nanosecond era" (hopefully not "error") in relation to molecular dynamic simulation applied to nucleic acids. Computational power (and time) previously limited calculations to small solvated systems (< 25 base pairs) in single sets of simulation on a 1-10ns time scale. Over this time, little advance in the force fields has emerged (with many of the "good" force fields now ~10 years old!). So far, only anecdotal evidence of "failure" has been forthcoming. Usually this is manifest as a structural bias (such as towards A-form structures with the 2005 Gromos force field, low twist with Cornell et al. or wide minor grooves with the CHARMM a27 force field) with sampled structures. It has also become rather clear that there are significant sampling limitations across multiple time and size scales. Examples include the long times needed to relax the counterion atmosphere (~500 ns) and the backbone substates. A concern is that as we push into larger size and longer time scales, previously hidden (and perhaps unrealistic) conformational substates may emerge. We have seen this in simulation of the hairpin loops bridging strands in G-DNA quadruplexes; we are starting to see this, randomly, in simulations pushing 25-50 ns of DNA duplexes. One way to investigate this is to take a set of simulations that appears to be stable on a 5-10 ns time scale and run then for ~500 ns. This has been performed with the d(CGCGAATTCGCG)2 sequence with DAPI bound in two different binding modes in a set of four distinct simulations. What we find is that anomalous backbone states tend to emerge (outside the drug binding region). Another serious concern, often raised by reviewers (and structural biologists), is end-effects (due to finite sequence) in simulations of small DNA helices. To address this question, we have performed a series of simulations of d(GG)n and d(GC)n from n=1 to 18 (i.e. up to 36 base pairs). For some of the small duplexes, such as d(GCGC)2 we see clear biases emerging in the backbone conformational substates. For even smaller duplexes, dissociation (as is expected) is observed. There is good news and bad news: Yes, sometimes there are artifacts (which we hope to find and overcome), however in a large series of simulations of phased A-tracts, nucleosome pro- and anti-positioning sequences and a variety of RNA structures on a 25-75 ns time scale, these artifacts appear minimal (or at haven't been exposed yet). The same is true for even larger DNA and RNA structures including a series of DNA minicircles of 94-106 base pairs and of RNA tRNAlys anticodon stem loop - Aloop interactions on a 25-75 ns time scale. After my first DNA grant submission to NIH in 2000, I received the comment: "One has to wonder how many relatively short MD simulations have to be performend on short DNA fragments before what can be learned will have been learned". My answer, one that is likely shared by the ABC colleagues, is a lot more. Hence my title: "Do longer or bigger simulations of DNA actually teach us anything new?" I think the answer is "yes", but it isn't always good news... [The material discussed in the abstract involves collaborative efforts with a number of different groups and people including: Jiri Sponer, Eva Fadrna, Richard Stefl and Nada Spackova (Czech Acad Sci & Masayrk U), Tom Bishop (Tulane), and Ty Curtis (Utah)].
Nikolaus Ernsting (Humboldt University of Berlin) Molecular probes for DNA structure and dynamics
Abstract: Charge separation and subsequent transport along the pi-stack is one of the mechanisms of radiative damage in double-stranded DNA. Charge transfer (CT) is controlled by electronic interaction between nearby nucleobases, and these interactions in turn depend on the local structure and its fluctuation on a picosecond time scale. The approach up to now has been to measure the charge transfer rate for well-devised systems. In the first lecture I will introduce the basic concepts and outline the most influential experiments to date. Here we aim for an elementary understanding of the distance or sequence dependence of CT. Recent experiments which demonstrate gating of charge transfer by the motion of nucleobases or solvent will also be discussed. The second lecture focuses on structure fluctuations, local (1-3 basepairs) and fast (100 fs- 10 ps), but addresses them separate from a CT process. For this purpose one needs suitable molecular probes. Their excitation with femtosecond light pulses perturbs the structure, and their fluorescence evolution reports the response. The status, scope, and analysis needs of femtosecond bandshape measurements will be discussed. (1) Charge Transfer in ds DNA Energetics and Electronics of Charge Transfer Charge injection: photochemical approach Charge injection: photophysical approach Reason for distance dependence Conformational dynamics influencing Charge Transfer Motions and distributions of nucleobases Solvation dynamics (2) Molecular probing of conformational dynamics Model for the dye in its environment Spectral evolution Example using broadband transient absorption: local charge fluctuations Example using broadband fluorescence upconversion: free volume
Nicholas Hud (Georgia Institute of Technology) DNA condensation
Abstract: Free DNA in solution exists in a quasi-extended state that is often modeled as a worm-like chain. However, in living cells DNA exists in much more compact and ordered states. The most highly compact forms of DNA are those found in viruses and sperm cells, where compaction is of paramount importance and immediate access to the genetic code is not required. In the laboratory, multivalent cations can be used to condense DNA from solution into nanometer-scale particles with morphologies that resemble DNA packaged in viruses and sperm cells. Experimental investigations of DNA condensation in vitro have already revealed much about the physical properties of DNA. Continuing studies of DNA condensation by proteins isolated from different cell types are providing new insights into how high-density packing of DNA is achieved by living organisms.
Richard D. James (University of Minnesota) A mathematical description of the invasion of Bacteriophage T4
Abstract: Bacteriophage T4 is a virus that attacks bacteria by a unique mechanism. It lands on the surface of the bacterium and attaches its baseplate to the cell wall. Aided by Brownian motion and chemical bonding, its tail fibers stick to the cell wall, producing a large moment on the baseplate. This triggers an amazing phase transformation in the tail sheath, of martensitic type, that causes it to shorten and fatten. The transformation strain is about 50%. With a thrusting and twisting motion, this transformation drives the stiff inner tail core through the cell wall of the bacterium. The DNA of the virus then enters the cell through the hollow tail core, leading to the invasion of the host.

This is a natural machine. As we ponder the possibility of making man-made machines that can have intimate interactions with natural ones, on the scale of biochemical processes, it is an interesting prototype. We present a mathematical theory of the martensitic transformation that occurs in T4 tail sheath. Following a suggestion of Pauling, we propose a theory of an active protein sheet with certain local interactions between molecules. The free energy is found to have a double-well structure. Using the explicit geometry of T4 tail sheath we introduce constraints to simplify the theory. Configurations corresponding to the two phases are found and a formula for the force generated by contraction is given. The predicted behavior of the sheet is completely unlike macroscopic sheets. To understand the position of this bioactuator relative to nonbiological actuators, the forces and energies are compared with those generated by inorganic actuators, including nonbiological martensitic transformations. Joint work with Wayne Falk, WF@ddt.biochem.umn.edu

Wayne Falk and R. D. James, An elasticity theory for self-assembled protein lattices with application to the martensitic transformation in Bacteriophage T4 tail sheath, preprint.

K. Bhattacharya and R. D. James, The material is the machine, Science 307 (2005), pp. 53-54.

Robert L. Jerrard (University of Toronto) Refined Jacobian estimates and vortex dynamics for the Gross-Pitaevsky equation
Abstract: We study dynamics of vortices in solutions of the Gross-Pitaevsky equations on 2-dimensional domains. These equations model certain superfluids, and they contain a dimensionless parameter epsilon. Results characterizing vortex dynamics in the limit as epsilon goes to 0 have been known since the 90s; these theorems can be interpreted as asserting that in quantized vortices in certain superfluids evolve (in the "incompressible limit") by the same system of ordinary differential equations satisfied by classical point vortices in an inviscid, incompresible fluid. Our results improve on earlier work in several ways: they are valid for fixed small epsilon rather than only for a sequence of solutions with epsilon tending to zero; and they are valid for larger numbers of vortices and for longer time scales than previous work. The refined Jacobian estimates mentioned in the title play a crucial technical role in the proof and are possibly of independent interest. This is joint work with D. Spirn.
Jason Kahn (University of Maryland) DNA bending, twisting, and looping in the control of transcription
Abstract: Proteins that activate or repress gene expression often bring about DNA deformation, and consequently they respond to DNA shape and flexibility. Examples include the TATA box binding protein (TBP) central to eukaryotic transcription, the lactose repressor (LacI), and the NtrC transcriptional activator . DNA cyclization kinetics applied to the TBP-DNA complex demonstrates unusual anisotropic flexibility of the unbound TATA box DNA sequence and also confirms the general DNA bend observed in crystal structures. The surprising appearance of negatively supercoiled products upon ring closure of short bound DNA suggests that the TBP-DNA complex is capable of flattening in response to external stress, which may be relevant to the recruitment of TBP to remodeled chromatin. Electrophoretic mobility shift, cyclization, Monte Carlo simulation, and bulk and single-molecule FRET experiments applied to DNA constructs designed to stabilize different LacI-DNA loop geometries demonstrate that the protein can adopt both the V-shaped form seen in crystal structures and also a more open conformation. The choice between geometries is dictated by both protein and DNA shape and deformability. Finally, In vivo results on transcriptional activation of E. coli sigma-54 RNA polymerase by NtrC suggest that protein multivalency and flexibility abrogate the expected influence of DNA shape, but suggest that dynamic DNA wrapping within an NtrC enhanceosome may be essential to its function.
Richard Lavery (CNRS) CURVES+
Abstract: A pared-down, souped-up, groovy, outward-looking, new millennium tool for analyzing nucleic acid conformations.
Frederic Legoll (University of Minnesota) Long time averaging for molecular dynamics simulations
Abstract: Many properties of chemical systems (such as the pressure inside a liquid, or radial distributions) are defined as phase space averages of functions depending on the state of the system. A common way to compute these averages is to use Molecular Dynamics and to compute time averages on long trajectories. We will first briefly recall Molecular Dynamics framework. We will then discuss simulations of systems at constant energy, and introduce high-order averaging formulae to compute time averages, in order to improve the convergence rate with respect to the simulation time. Under some assumptions, rigorous error bounds will be derived and illustrated by several numerical examples. The last part of the talk will discuss simulations of systems at constant temperature. This work is joint with Eric Cances, Claude Le Bris, Gabriel Turinici (CERMICS and INRIA Rocquencourt), Francois Castella, Philippe Chartier and Erwan Faou (INRIA Rennes), and ongoing work with Mitchell Luskin and Richard Moeckel.
Marc Q. Ma (New Jersey Institute of Technology) Molecular dynamics simulations: stability, multiscale approaches and the art of trajectory analysis
Abstract: Molecular dynamics (MD) is a venerable computer simulation technique in biomolecular modeling. MD is also known to be very compute-intensive. Using multiple time stepping (MTS) (quasi-)multiscale integrators is one of the key methods for speeding up MD simulations. In this talk, I will revisit the stability issues of MTS MD simulations and show that MTS integrators are really limited by nonlinear instabilities. Then I will present a family of MTS quasi-mutiscale integrators based on targeted Langevin stabilization of stiff modes. Such schemes would become more powerful when they are developed under a general mathematical framework termed as Projective Thermostatting Dynamics. Ideas of new development will be presented. I will also present a case study in which we apply MTS MD to an enzyme system, the soluble guanylyl cyclase (sGC). While our aim is to reveal the science behind the phenomena, the MD trajectory analysis is more an art than anything else. I will present how we go about making analysis to infer the mechanism of allosteric activation of sGC.
Julie C. Mitchell (University of Wisconsin) Tutorial on basics of proteins
Abstract: This is an elementary introduction to the basics of proteins, intended for mathematicians with no background in biochemistry, with the objective of establishing a foundation for the workshop Experiments in Physical Biology, part II, May 16-20.
Modesto Orozco(University of Barcelona) Exploring the flexibility of nucleic acids
Abstract: Nucleic acids are very flexible structures whose conformation can be adapted in response to chemical and mechanical stress. Such perturbation can be of two types: i) large transitions that lead to helical unfolding and ii) small perturbations that can be fitted to harmonic deformation modes. I will present theoretical studies on both type of distortions, making an special emphasis on harmonic deformations, since these can be well represented by means of the analysis of covariance matrices (Cartersian, mass-weigthed Cartesian or helical) obtained from database analysis or from extended molecular dynamics simulations. I will show how these simple harmonic deformations can explain many physical and even biological properties of nucleic acids.
Roman Osman (Mount Sinai School of Medicine) Quantum chemistry and energetics in Pu-p-Pu
Abstract: Joint work with Elena Rusinova and Emmanuel Giudice.

The occurrence of interconversions in backbone angles present an interesting question as to its origin and frequency. Unlike the rather frequent BI-BII transitions characterized by the combination backbone angles epsilon and zeta, the transition due to an interconversion of the alpha and gamma pair is less frequent and in a simulation time span of 15 ns may occur at most once or twice. Two stable states have been identified ~V the canonical characterized by alpha/gamma (-g/+g) and the non-canonical with alpha/gamma (+g/t). The energetics and the barrier for the interconversion between these two states are not kn

We have conducted quantum chemical calculations on four Pu-p-Pu pairs using a PCM to represent the effect of the solvent. The canonical conformations are lower than the non-canonical and the barriers for the interconversion are in the range of 7.6 ~V 11.4 kcal/mol. We will discuss these results in the context of the observed transitions in the ABC simulations.

M. Thomas Record (University of Wisconsin) Wrapping of DNA on protein surfaces
Abstract: The organization of large regions of DNA on the surface of proteins is critical to many DNA 'transactions', including replication, transcription, recombination and repair, as well as the packaging of chromosomal DNA. Thermodynamic and structural studies of DNA binding by integration host factor indicate that the disruption of protein surface salt bridges (dehydrated ion pairs) dominates the observed thermodynamics of integration host factor binding and, more generally, allows the wrapping of DNA on protein surfaces. The proposed thermodynamic signature of wrapping with coupled salt bridge disruption includes large negative salt-concentration-dependent enthalpy, entropy and heat capacity changes and smaller than expected magnitudes of the observed binding constant and its power dependence on salt concentration. Examination of the free structures of proteins recently shown to wrap DNA leads us to hypothesize that a pattern of surface salt bridges interspersed with cationic sidechains provides a structural signature for wrapping and that the number and organization of salt bridges and cationic groups dictate the thermodynamics and topology of DNA wrapping, which in turn are critical to function.
M. Thomas Record (University of Wisconsin) Large-scale conformational changes in RNA polymerase and promoter DNA in transcription initiation
Abstract: Opening of the transcription start site and the adjacent regions of promoter DNA by RNA polymerase is accomplished thermodynamically using binding free energy. The mechanism of binding to and opening the promoter involves a sequence of large scale conformational changes. Bending and wrapping of the upstream DNA occur early in the process; coupled folding of regions of polymerase occurs late, and the kinetics are dominated by a slow conformational change once the duplex DNA is in the jaw-like structure of the polymerase. Kinetic and footprinting studies to eluciate the nature of this conformational change and of the intermediates will be discussed.
Robert Schleif (Johns Hopkins University) DNA looping: biology and mechanisms
Abstract: What it is.
Why Nature uses it.
How it was discovered.
Additional experiments demonstrating looping.
Role of supercoiling in looping.
How looping is controlled in the arabinose system.
Ronald Siegel (University of Minnesota) Rhythmic hormone delivery based on a gel/enzyme chemomechanical oscillators
Abstract: Polyelectrolyte gels swell and shrink due to the resolution of three forces: polymer elasticity, polymer-solvent interaction, and electrostatic/osmotic repulsion between pendant charge groups. The latter force can be modulated by local pH changes. For particular gel chemistries, swelling and shrinking occur as a first order phase transition, with a significant region of bistability and hence hysteresis in response. We will show how to couple a particular gel system to an enzyme (glucose oxidase), whereby the gel affects delivery of substrate (glucose) to the enzyme, and the product of the reaction (hydrogen ion) affects the swelling state and hence substrate permeability of the membrane. Negative feedback with hysteresis can be driven into a Hopf-type instability, and oscillations in gel swelling results. These oscillations are in turn harnessed to produce rhythmic, pulsed delivery of hormones, which is essential in treating certain disorders. In this seminar, we will discuss the fundamental principles, show some experimental results, and present two models of system behavior.
Jiri Sponer (Czechoslovakian Academy of Sciences) Molecular dynamics simulations of RNA and noncanonical DNA molecules. Successes and troubles
Abstract: Since 2000, we have carried out an extensive set of RNA simulations, with cumulative time scale at this moment above 2 microseconds and individual simulations expanded up to 100 ns, with 6 published and ca 5 in preparation papers. The aim of the project is MD analysis of distinct classes of RNA systems, including main rRNA non-Watson-Crick motifs. The studied systems include frameshifting pseudoknot, several RNA kissing complexes and related extended duplexes, wide range of ribosomal kink-turns, 5S rRNA Loop E and its complex with L25 protein, sarcin-ricin loop, hepatitis delta virus ribozyme and some other systems. The simulations appear to provide unique qualitative insights into the RNA dynamics, including role of tightly bound waters (residency times 1-25+ ns), unprecedented cation binding sites with up to 100% occupancy and frequent solute-bulk cation exchange, distinct mechanical properties of various classes of ribosomal RNA that can be related to the function, and others. In response to the recent observations of / transitions in B-DNA, we reanalyzed all our MD data. Since the RNA molecules have often a low resolution and there are many possible substates of backbone in RNA, the analysis is not always straightforward. Nevertheless, until now, we did not identify anything what could be considered as evident backbone pathology. If there are / switches, they are mostly reversible and often can be identified as being between two established RNA backbone conformations. Quality of backbone at the end of the simulations is comparable to the experimental data and there is no degradation of the structures in the course of the simulations. It is also notable that the nature of conformational variability in RNA allows to direct the research in a rather qualitative way, thus modest force field imbalances could often be tolerated. In addition, the simulations appear to very well reproduce many aspects of RNA molecules established by crystallography, including water-mediated dynamics of A-minor type I interaction (the most prominent RNA tertiary motif) in K-turns, correct prediction of topology of bulged out bases subsequently confirmed by crystallography, stability of specific backbone states such as S-turn, correct prediction of mutated structure of spinach chloroplast Loop E independently verified by NMR and others. We do not suggest that the force field is perfect but we can safely claim that it can be used very successfully to study many aspects of RNA structural dynamics. At the same time, we recently reported a large-scale failure of simulations to predict topology of d(GGGGTTTTGGGG)2 quadruplex loops, which halted all our advances in the G-DNA field. It appears to be accompanied by the same backbone / switch as noticed in ABC B-DNA simulations.
Jonathan Widom (Northwestern University) Sequence-dependent DNA mechanics in very small DNA circles and nucleosomes
Abstract: Part I of my lectures will summarize our recent studies on the spontaneous bending and twisting of double stranded DNA. We found that DNAs that are much shorter than the DNA persistence length easily form very small circles, whose inner diameters are only a few times larger than the diameter of the DNA from which they are formed. I will discuss our experiments that demonstrate that these small circles exist, summarize our current understanding of the bendability and twistability of the sharply bent DNA, and discuss striking effects of particular DNA sequences on the relative ability of the circles to form. Part II will focus on sharply bent DNA as it occurs in nucleosomes, the fundamental structural subunits of chromosomes in people and all other higher life forms. I will discuss a selection experiment for DNA sequences that make especially stable nucleosomes, unexpected sequence motifs discovered in these selected DNAs that are responsible for their facile nucleosome formation, the relation between nucleosome formation and spontaneous DNA cyclization, and current ideas for the molecular basis of sequence dependent DNA bendability.
Visitors in Residence
Amandine Aftalion Universite Pierre et Maris Curie (Paris VI) 5/8/2005 - 5/20/2005
Arnaud Amzallag Swiss Federal Institute of Technology at Lausanne (EPFL) 4/30/2005 - 5/11/2005
Irene Arias Polytechnic University Catalonia 5/1/2005 - 5/20/2005
Douglas N. Arnold University of Minnesota 7/15/2001 - 8/31/2006
Donald G. Aronson University of Minnesota 9/1/2002 - 8/31/2005
Marino Arroyo Polytechnic University of Catalunya 4/11/2005 - 5/20/2005
Gerard Awanou University of Minnesota 9/2/2003 - 8/31/2005
David L. Beveridge Wesleyan University 5/6/2005 - 5/8/2005
Thomas C. Bishop Tulane University 5/1/2005 - 5/8/2005
Zev Bryant Stanford University 5/3/2005 - 5/7/2005
Geoffrey Burr IBM Corporation 5/5/2005 - 5/6/2005
Maria-Carme Calderer University of Minnesota 9/1/2004 - 6/30/2005
David Case The Scripps Research Institute 5/6/2005 - 5/10/2005
Thomas Cheatham University of Utah 5/3/2005 - 5/9/2005
Qianyong Chen University of Minnesota 9/1/2004 - 8/31/2006
Ae-Gyeong Cheong Clemson University 5/13/2005 - 5/22/2005
Rustum Choksi Simon Fraser University 4/30/2005 - 5/6/2005
Patricia Cladis Advanced Liquid Crystal Technologies 5/23/2005 - 5/26/2005
Ludovica Cecilia Cotta-Ramusino Swiss Federal Institute of Technology at Lausanne (EPFL) 4/10/2005 - 5/10/2005
Antonio DeSimone SISSA-Italy 3/10/2005 - 7/15/2005
Antonio Di Carlo Universita` degli Studi Roma Tre 4/10/2005 - 6/12/2005
Brian DiDonna University of Minnesota 9/1/2004 - 8/31/2006
Qiang Du Pennsylvania State University 5/8/2005 - 5/29/2005
Yuhua Duan University of Minnesota 5/16/2005 - 5/20/2005
Ryan S. Elliott University of Michigan 1/1/2005 - 6/30/2005
Nikolaus Ernsting Humboldt University of Berlin 5/1/2005 - 5/6/2005
Ralf Everaers Max-Planck-Institut for Physics of Complex Sys 4/28/2005 - 5/9/2005
Petri Fast Lawrence Livermore National Laboratories 5/23/2005 - 5/25/2005
Eliot Fried Washington University - St. Louis 5/23/2005 - 5/25/2005
Carlos Garcia-Cervera University of California - Santa Barbara 5/23/2005 - 5/25/2005
Tim Garoni University of Minnesota 8/25/2003 - 8/31/2005
Eugene C. Gartland Jr. Kent State University 1/10/2005 - 6/30/2005
Ziomara P. Gerdtzen University of Minnesota 5/2/2005 - 5/6/2005
Ziomara P. Gerdtzen University of Minnesota 5/16/2005 - 5/20/2005
Antoine Gloria CERMICS - ENPC 5/28/2005 - 6/12/2005
Dmitry Golovaty University of Akron 5/23/2005 - 5/27/2005
Alexander Grosberg University of Minnesota 5/16/2005 - 5/20/2005
Robert Gulliver University of Minnesota 9/1/2004 - 6/30/2005
Rohit Gupta University of Minnesota 5/16/2005 - 5/20/2005
Chuan-Hsiang Han University of Minnesota 9/1/2004 - 8/31/2005
Leesa Maree Heffler Swiss Federal Institute of Technology Lausanne 4/30/2005 - 5/11/2005
Chun-Hsiung Hsia Indiana University 5/2/2005 - 5/6/2005
Nicholas Hud Georgia Institute of Technology 5/1/2005 - 5/6/2005
Chris Hunter University of Sheffield 5/1/2005 - 5/6/2005
Richard D. James University of Minnesota 9/1/2004 - 6/30/2005
Robert L. Jerrard University of Toronto 4/20/2005 - 5/24/2005
Shi Jin University of Wisconsin 1/4/2005 - 6/30/2005
Sookyung Joo University of Minnesota 9/1/2004 - 8/31/2006
Hem Raj Joshi Xavier University 5/15/2005 - 5/20/2005
Nara Jung University of Toronto 4/20/2005 - 5/24/2005
Jason Kahn University of Maryland 5/1/2005 - 5/6/2005
Vladimir Kamotski University of Bath-UK 5/24/2005 - 6/14/2005
Chiu Yen Kao University of Minnesota 9/1/2004 - 8/31/2006
Yiannis Kaznessis University of Minnesota 5/16/2005 - 5/20/2005
Sarah L. Keller University of Washington 5/15/2005 - 5/20/2005
Daniel Kern University of Nevada - Las Vegas 5/15/2005 - 5/20/2005
David Kinderlehrer Carnegie Mellon University 4/1/2005 - 6/30/2005
Richard Kollar University of Minnesota 9/1/2004 - 8/31/2005
Matthias Kurzke University of Minnesota 9/1/2004 - 8/31/2006
Filip Lankas Swiss Federal Institute of Technology (EPFL) 4/30/2005 - 5/11/2005
Richard Lavery CNRS 5/6/2005 - 5/10/2005
Claude Le Bris CERMICS 4/7/2005 - 5/20/2005
Deborah Leckband University of Illinois - Urbana-Champaign 5/15/2005 - 5/20/2005
Frederic Legoll University of Minnesota 9/3/2004 - 8/31/2006
Benedict Leimkuhler University of Leicester 2/1/2005 - 6/2/2005
Stephen Levene University of Texas - Dallas 4/30/2005 - 5/6/2005
Adrian Lew Stanford University 5/29/2005 - 6/11/2005
Debra Lewis University of Minnesota 7/15/2004 - 8/31/2006
Xiantao Li University of Minnesota 8/3/2004 - 8/31/2005
Chun Liu Pennsylvania State University 9/1/2004 - 6/30/2005
Hailiang Liu Iowa State University 1/1/2005 - 6/30/2005
John Lowengrub University of California - Irvine 5/23/2005 - 5/25/2005
Tom C. Lubensky University of Pennsylvania 5/23/2005 - 5/25/2005
Mitchell Luskin University of Minnesota 9/1/2004 - 6/30/2005
Marc Q. Ma New Jersey Institute of Technology 5/14/2005 - 5/21/2005
John H. Maddocks Swiss Federal Institute of Technology Lausanne 4/9/2005 - 5/11/2005
Patrick T. Mather Case Western Reserve University 5/23/2005 - 5/25/2005
Karsten Matthies Freie University Berlin 5/1/2005 - 6/15/2005
Robert B. Meyer Brandeis University 5/23/2005 - 5/26/2005
Julie C. Mitchell University of Wisconsin 4/1/2005 - 5/14/2005
Bagisa Mukherjee Penn State Worthington Scranton 5/8/2005 - 6/9/2005
Sharareh Noorbaloochi University of Minnesota 5/1/2005 - 5/6/2005
Duane Nykamp University of Minnesota 5/2/2005 - 5/6/2005
David Odde University of Minnesota 5/2/2005 - 5/6/2005
David Odde University of Minnesota 5/16/2005 - 5/20/2005
Roman Osman Mount Sinai School of Medicine 5/6/2005 - 5/8/2005
Peter Palffy-Muhoray Kent State University 3/27/2005 - 5/25/2005
Alexander Panchenko Washington State University 5/6/2005 - 5/30/2005
Jinhae Park University of Minnesota 5/16/2005 - 5/20/2005
Jinhae Park University of Minnesota 5/2/2005 - 5/6/2005
Peter Philip University of Minnesota 8/22/2004 - 8/31/2006
Daniel Phillips Purdue University 5/22/2005 - 5/27/2005
Robert Phillips California Institute of Technology 5/15/2005 - 5/20/2005
Robert Phillips California Institute of Technology 5/2/2005 - 5/6/2005
Harald Pleiner Max Planck Institute for Polymer Research 5/10/2005 - 6/18/2005
Andrew Pohorille NASA Ames Research Center 5/2/2005 - 5/11/2005
Thomas D. Pollard Yale University 5/19/2005 - 5/19/2005
Lea Popovic University of Minnesota 9/2/2003 - 8/31/2005
Ashok Prasad Brandeis University 5/1/2005 - 5/7/2005
M. Thomas Record University of Wisconsin 5/4/2005 - 5/6/2005
Alejandro Rey McGill University, Canada 5/15/2005 - 5/30/2005
Rolf Ryham Pennsylvania State University 9/1/2004 - 6/30/2005
Arnd Scheel University of Minnesota 7/15/2004 - 8/31/2006
Robert Schleif Johns Hopkins University 5/4/2005 - 5/6/2005
Tim P. Schulze University of Tennessee 5/1/2005 - 5/31/2005
Jonathan V. Selinger Naval Research Laboratory 5/23/2005 - 5/25/2005
George R Sell University of Minnesota 9/1/2004 - 6/30/2005
Shaun Sellers Washington University - St. Louis 5/23/2005 - 5/25/2005
Paul Selvin University of Illinois - Urbana-Champaign 5/15/2005 - 5/20/2005
James P. Sethna Cornell University 5/30/2005 - 6/12/2005
Michael J. Shelley New York University 5/23/2005 - 5/25/2005
Vivek Shenoy Brown University 5/10/2005 - 6/20/2005
Tien-Tsan Shieh Indiana University 9/1/2004 - 6/30/2005
Shagi-Di Shih University of Wyoming 5/1/2005 - 7/2/2005
Devashish Shrivastava University of Minnesota 5/16/2005 - 5/20/2005
Devashish Shrivastava University of Minnesota 5/2/2005 - 5/6/2005
Ronald Siegel University of Minnesota 5/13/2005 - 5/13/2005
Peter Smereka University of Michigan 5/27/2005 - 6/12/2005
Valery P. Smyshlyaev University of Bath-UK 4/10/2005 - 6/16/2005
Christopher Spillman Naval Research Laboratory 5/23/2005 - 5/25/2005
Daniel Spirn University of Minnesota 9/1/2004 - 6/30/2005
Jiri Sponer Czechoslovakian Academy of Sciences 5/5/2005 - 5/9/2005
Jaideep Srivastava University of Minnesota 5/2/2005 - 5/6/2005
Jaideep Srivastava University of Minnesota 5/16/2005 - 5/20/2005
Peter J. Sternberg Indiana University 8/15/2004 - 6/15/2005
Vladimir Sverak University of Minnesota 9/1/2004 - 6/30/2005
Luciano Teresi Universita` degli Studi Roma Tre 4/10/2005 - 6/12/2005
Florian Theil University of Warwick 4/4/2005 - 6/11/2005
Gabriel Turinici CERMICS 5/22/2005 - 6/10/2005
Qi Wang Florida State University 1/31/2005 - 5/15/2005
Stephen J. Watson Northwestern University 9/1/2004 - 6/30/2005
Jonathan Widom Northwestern University 5/2/2005 - 5/6/2005
Paul Wiggins California Institute of Technology 5/1/2005 - 5/6/2005
Jon Wilkening New York University 5/23/2005 - 5/25/2005
Doug Wright University of Minnesota 2/15/2005 - 8/31/2005
Baisheng Yan Michigan State University 9/1/2004 - 6/30/2005
Jie Yan University of Illinois - Chicago 5/1/2005 - 5/6/2005
Aaron Nung Kwan Yip Purdue University 1/16/2005 - 6/30/2005
Emmanuel Yomba University of Ngaoundéré 10/6/2004 - 8/31/2005
Krystyna Zakrzewska CNRS 5/1/2005 - 5/10/2005
Giovanni Zanzotto University of Padua 4/8/2005 - 5/5/2005
Yongli Zhang University of California - Berkeley 5/1/2005 - 5/6/2005
Wei Zhu New York University 5/23/2005 - 5/25/2005
Johannes Zimmer Max-Planck-Institute for Math in the Sciences 5/29/2005 - 6/12/2005
Legend: Postdoc or Industrial Postdoc Long-term Visitor

Participating Institutions: Carnegie Mellon University, Consiglio Nazionale delle Ricerche (CNR), Georgia Institute of Technology, Indiana University, Iowa State University, Kent State University, Lawrence Livermore National Laboratories, Los Alamos National Laboratory, Michigan State University, Mississippi State University, Northern Illinois University, Ohio State University, Pennsylvania State University, Purdue University, Rice University, Sandia National Laboratories, Seoul National University (BK21), Seoul National University (SRCCS), Texas A & M University, University of Chicago, University of Cincinnati, University of Delaware, University of Houston, University of Illinois - 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 Texas - Austin, University of Wisconsin, University of Wyoming, Wayne State University
Participating Corporations: 3M, Boeing, Corning, ExxonMobil, Ford Motor Company, General Electric, General Motors, Honeywell, IBM Corporation, Johnson & Johnson, Lockheed Martin, Lucent Technologies, Motorola, Schlumberger-Doll Research, Siemens, Telcordia Technologies