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Mathematics of Materials and Macromolecules: Multiple Scales, Disorder, and Singularities, September 1, 2004 - June 30, 2005

IMA Special Workshop:

Modeling Sequence-Dependent DNA Dynamics:
The Third ABC Debriefing

May 7-8, 2005

Organizers:

Richard Lavery

CNRS
Richard.Lavery@ibpc.fr

John H. Maddocks

Swiss Federal Institute of Technology Lausanne
John.Maddocks@epfl.ch

Roman Osman

Mount Sinai School of Medicine
osman@inka.mssm.edu

 

Schedule Participants Feedback
Dining Guide Maps
Talk Materials Abstracts
Radisson Reservations

 

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. Having obtained the basic data the results are now being analyzed. 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.

WORKSHOP SCHEDULE
Saturday Sunday
SATURDAY, MAY 7
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00-9:45 David Beveridge
Wesleyan University
Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II. Sequence Context effects on the Dynamical Structures of the 10 unique Dinucleotide Steps
9:45-10:15 Rami Osman
Mount Sinai School of Medicine
Quantum Chemistry and Energetics in Pu-p-Pu
10:15-11:00 Jiri Sponer
Institute of Biophysics
Molecular dynamics simulations of RNA and noncanonical DNA molecules. Successes and troubles
11:00-11:45 Thomas E. Cheatham, III
The University of Utah
Do Longer or Bigger Simulations of DNA Actually Teach Us Anything New?
12:00-1:30
Lunch Break
1:30-2:15 Dave Case
Scripps Research Institute
Generalized Born Studies of ABC DNA Sequences
2:15-3:00 Richard Lavery
IBPC, Paris
CURVES+
3:00-3:45 Modesto Orozco
University of Barcelona
Exploring the Flexibility of Nucleic Acids
3:45-4:30 John H. Maddocks

Molecular Dynamics Simulations of DNA minicircles

Slides:   pdf

SUNDAY, MAY 8

MEMBERS OF THE CONSORTIUM WILL MEET IN CLOSED SESSION

Saturday Sunday

LIST OF CONFIRMED PARTICIPANTS

Name Department Affiliation
Arnaud Amzallag DMA Swiss Federal Institute of Technology at Lausanne (EPFL)
Douglas N. Arnold Institute for Mathematics and its Applications University of Minnesota
David L. Beveridge Department of Chemistry Wesleyan University
Thomas C. Bishop Center for Bioenvironmental Research Tulane University
David Case Department of Molecular Biology, TPC15 The Scripps Research Institute
Thomas Cheatham Medical Chemistry / Pharmaceutics University of Utah
Ludovica Cecilia Cotta-Ramusino SB-IMB-LCVMM Swiss Federal Institute of Technology at Lausanne (EPFL)
Antonio Di Carlo Department of Studies on Structures Universita` degli Studi Roma Tre
Surjit Dixit Department of Chemistry Wesleyan University
Ralf Everaers   Max-Planck-Institut for Physics of Complex Sys
Eugene C. Gartland Jr. Department of Mathematical Sciences Kent State University
Emmanuel Giudice Department of Physiology and Biophysics Mount Sinai School of Medicine
Leesa Maree Heffler Institut de Mathematiques Bernoulli Swiss Federal Institute of Technology Lausanne
Nara Jung Department of Mathematics University of Toronto
Filip Lankas Bernoulli Institute for Mathematics Swiss Federal Institute of Technology (EPFL)
Richard Lavery Laboratoire de Biochimie Theorique CNRS
Debra Lewis Institute for Mathematics and its Applications University of Minnesota
John H. Maddocks Institut de Mathématiques Bernoulli Swiss Federal Institute of Technology Lausanne
Karsten Matthies Institut fuer Mathematik I Freie University Berlin
Roman Osman Department of Physiology and Biophysics Mount Sinai School of Medicine
Andrew Pohorille   NASA Ames Research Center
Arnd Scheel Institute for Mathematics and its Applications University of Minnesota
Shagi-Di Shih Department of Mathematics University of Wyoming
John Sklenar Theoretical Biophysics Max-Delbruck-Center
Valery P. Smyshlyaev   University of Bath-UK
Jiri Sponer Institute of Biophysics Czechoslovakian Academy of Sciences
Luciano Teresi Mathematical Structures of Materials Physics Universita` degli Studi Roma Tre
Krystyna Zakrzewska Laboratoire de Biochimie Théorique CNRS

Mathematics of Materials and Macromolecules: Multiple Scales, Disorder, and Singularities, September 2004 - June 2005
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