Modeling Sequence-Dependent DNA Dynamics: The Third ABC Debriefing

May 07 - 08, 2005

Content

Overview

Organizers:

Richard Lavery	Centre National de la Recherche Scientifique (CNRS)
John Maddocks	École Polytechnique Fédérale de Lausanne (EPFL)
Roman Osman	Mount Sinai School of Medicine, CUNY

The Ascona B-DNA Consortium (ABC) was established in 2001 with the aimof creating a database describing the dynamics of DNA as a function ofits base sequence. The method chosen was Molecular Dynamicscarried out on a series of DNA fragments containing multiple copies ofthe 136 unique tetranucleotide sequences. The calculations werecarried out by a consortium of nine laboratories, four european andfive in the USA. Having obtained the basic data the results are nowbeing analyzed. The day long meeting on May 7 will have a number of talksdescribing results arising from, and pertinent to, the ongoing ABCproject.On May 8 members of the consortium will meet in closed session.

Schedule

Saturday, May 07, 2005

9:00 am - 9:45 am	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 David Beveridge (Wesleyan University)	EE/CS 3-180
9:45 am - 10:15 am	Quantum chemistry and energetics in Pu-p-Pu Roman Osman (Mount Sinai School of Medicine, CUNY)	EE/CS 3-180
10:15 am - 11:00 am	Molecular dynamics simulations of RNA and noncanonical DNA molecules. Successes and troubles Jiri Sponer (Czechoslovakian Academy of Sciences)	EE/CS 3-180
11:00 am - 11:45 am	Do longer or bigger simulations of DNA actually teach us anything new? Thomas Cheatham (The University of Utah)	EE/CS 3-180
12:00 pm - 1:30 pm	Lunch
1:30 pm - 2:15 pm	Generalized Born studies of ABC DNA sequences David Case (Scripps Research Institute)	EE/CS 3-180
2:15 pm - 3:00 pm	CURVES+ Richard Lavery (Centre National de la Recherche Scientifique (CNRS))	EE/CS 3-180
3:00 pm - 3:45 pm	Modesto Orozco, University of Barcelona Exploring the flexibility of nucleic acids Douglas Arnold (University of Minnesota, Twin Cities)	EE/CS 3-180
3:45 pm - 4:30 pm	MD Simulations of DNA Minicircles John Maddocks (École Polytechnique Fédérale de Lausanne (EPFL))	EE/CS 3-180

Sunday, May 08, 2005
			Video
12:01 am	Modeling Sequence-Dependent DNA Dynamics: The Third ABC Debriefing (Closed session)	Lind 409

Participants

Name	Department	Affiliation
Arnaud Amzallag	DMA	École Polytechnique Fédérale de Lausanne (EPFL)
Douglas Arnold	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
David Beveridge	Department of Chemistry	Wesleyan University
Thomas Bishop	Center for Bioenvironmental Research	Tulane University
David Case	Department of Molecular Biology	Scripps Research Institute
Thomas Cheatham	Department of Medical Chemistry	The University of Utah
Ludovica Cotta-Ramusino	EPFL SB MATHGEOM LCVMM	École Polytechnique Fédérale de Lausanne (EPFL)
Antonio DiCarlo	Department of Studies on Structures	Universita` degli Studi Roma Tre
Surjit Dixit		Wesleyan University
Ralf Everaers		Max-Planck-Institut für Physik Komplexer Systeme
Eugene Gartland Jr.	Department of Mathematical Sciences	Kent State University
Emmanuel Giudice		Mount Sinai School of Medicine, CUNY
Leesa Heffler	Institut de Mathematiques	École Polytechnique Fédérale de Lausanne (EPFL)
Nara Jung	Department of Mathematics	University of Toronto
Filip Lankas	Institute for Mathematics	École Polytechnique Fédérale de Lausanne (EPFL)
Richard Lavery	Laboratoire de Biochimie Théorique	Centre National de la Recherche Scientifique (CNRS)
Debra Lewis	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
John Maddocks	SB IMB (Bernoulli Institute for Mathematics) LCVMM	École Polytechnique Fédérale de Lausanne (EPFL)
Karsten Matthies	Institut für Mathematik	Freie Universität Berlin
Roman Osman	Department of Physiology and Biophysics	Mount Sinai School of Medicine, CUNY
Andrew Pohorille		NASA Ames Research Center
Arnd Scheel	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Shagi-Di Shih	Department of Mathematics	University of Wyoming
John Sklenar		Stiftung Max-Delbrück-Centrum für Molekulare Medizin (MDC)
Valery Smyshlyaev	Department of Mathematical Sciences	University of Bath
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	Centre National de la Recherche Scientifique (CNRS)