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Category: List of Bases 2009 2009 ICTP activities in Trieste ICTP activities in Trieste
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lecture

Cosponsor(s):

co-sponsored by: Wellcome Trust, London, U.K.

Start Time:

1 June 2009 at 09:00

Ends On:

5 June 2009

Location:

Trieste - Italy

Venue:

LB (Main Lecture Hall)

Organizer(s):

Directors: A.A. Kornyshev, W.K. Olson, V.A. Parsegian. Local Organizer: R. Gebauer

Description:

PLEASE NOTE:

CHANGE OF VENUE

THIS CONFERENCE WILL NOW TAKE PLACE AT THE
LEONARDO da VINCI BUILDING - MAIN LECTURE HALL

REGISTRATION WILL TAKE PLACE AT THE
LEONARDO da VINCI BUILDING - RECEPTION AREA
from 8.30 am - 9.30 am

Material:

MONDAY, 1 JUNE 2009

Room: Leonardo da Vinci Building Main Lecture Hall

1 June 2009
08:30
09:30
REGISTRATION / ADMINISTRATIVE FORMALITIES
01h00'
(Leonardo da Vinci Building - reception area)
09:30
10:50
SESSION 1 - OPENING SESSION
01h20'
CHAIR: Alexei KORNYSHEV

Greetings from ICTP
09:35
09:50
Preamble: can one always judge the book by its cover?
15'
Alexei KORNYSHEV
Imperial College London, U.K.
09:50
10:20
From disciplinary borders to frontiers of science
30'
Arturo FALASCHI
SNS, Pisa & ICGE, Trieste, Italy
10:20
10:50
The devil in the details: how DNA structure, sequence and counterions drive biology
30'
Lynn ZECHIEDRICH
Baylor College, Houston, U.S.A.
10:50
11:20
Coffee Break
30'
Room: Leonardo da Vinci Building, Lobby
11:20
12:50
SESSION 2 - DNA MECHANICS
01h30'
CHAIR: Jorge LANGOWSKI
11:20
11:50
Approaches to understanding the origin and management of DNA stiffness
30'
Jim MAHER
Mayo Clinic College, Rochester, U.S.A.
11:50
12:20
DNA micromechanics and macromolecular organization
30'
Wilma OLSON
Rutgers University, U.S.A.
12:20
12:50
Nanomechanics of single and double stranded DNA
30'
Piotr MARSZALEK
Duke University, Durham, U.S.A.
12:50
15:00
Lunch Break
02h10'
Room: Leonardo da Vinci Building Cafeteria
15:00
16:00
SESSION 3 - DNA MECHANICS
01h00'
CHAIR: Jorge LANGOWSKI
15:00
15:30
Multi-scale modelling of sequence-dependent DNA mechanics
30'
John MADDOCKS
EPFL, Lausanne, Switzerland
15:30
16:00
Geometry and mechanics of condensed DNA: Toroids and beyond
30'
Evgueni STAROSTIN
University College London, U.K.
16:00
16:30
Coffee Break
30'
Room: Leonardo da Vinci Building, Lobby
16:30
18:15
SESSION 4 - DNA STRUCTURE, INTERACTIONS AND AGGREGATION
01h45'
CHAIR: Adrian PARSEGIAN
16:30
17:00
Electrostatic interactions between DNA double helices
30'
Sergey LEIKIN
NIH, Bethesda, U.S.A.
17:00
17:30
Generalizations and ramifications induced by counterion structure in the strong and weak-coupling electrostatic interactions between macromolecules
30'
Rudi PODGORNIK
University of Ljubljana, Slovenia
17:30
18:00
Counterion-mediated DNA-DNA interactions
30'
Brian TODD
Purdue University, West Lafayette, U.S.A.
18:00
18:15
Correlations and helical coherence in DNA structure: "straightening" the helix upon crystal packing
15'
Aaron WYNVEEN
University of Duesseldorf, Germany
19:00
21:00
WELCOME RECEPTION
02h00'
Room: Leonardo da Vinci Building Terrace
TUESDAY, 2 JUNE 2009 (Republic's Day)

Room: Leonardo da Vinci Building Main Lecture Hall

2 June 2009
09:00
10:30
SESSION 5 - DNA STRUCTURE, INTERACTIONS AND AGGREGATION
01h30'
CHAIR: Richard LAVERY
09:00
09:30
Simulations of DNA condensation
30'
Malek KHAN
Uppsala University, Sweden
09:30
09:45
Mediating role of Alkaline earth metal ions in electrostatics of DNA: The long-range effects of solvent dielectric saturation
15'
Sergei GAVRYUSHOV
RAS, Engelhardt Institute of Molecular Biology, Moscow, Russia
09:45
10:00
How does helical structure influence correlation forces between DNA?
15'
Dominic LEE
Max-Planck-Institute for Complex Systems, Dresden, Germany
10:00
10:15
DNA from the polymer physics point of view: Topology and dimensionality effects
15'
Giovanni DIETLER
EPFL, Laussane, Switzerland
10:15
10:30
Kinetics of force-induced DNA melting
15'
Ioulia ROUZINA
University of Minnesota, Minneapolis, U.S.A.
10:30
11:00
Coffee Break
30'
Room: Leonardo da Vinci Building, Lobby
11:00
12:45
SESSION 6 - RECOGNITION OF HOMOLOGOUS GENES
01h45'
CHAIR: Jim MAHER
11:00
11:30
How can two homologous needles find each other in the genomic haystack?
30'
Adi BARZEL
University of Tel Aviv, Israel
11:30
12:00
Is recognition between homologous DNA double helices an intrinsic property of DNA?
30'
Geoff BALDWIN
Imperial College London, U.K.
12:00
12:30
Single molecule studies of homolog pairing
30'
Mara PRENTISS
Harvard University, Cambridge, U.S.A.
12:30
12:45
Homology recognition funnel
15'
Alexei KORNYSHEV
Imperial College London, U.K.
12:45
15:00
Lunch Break
02h15'
Room: Leonardo da Vinci Building Cafeteria
15:00
18:30
SESSION 7 - CONFORMATIONAL DYNAMICS, SUPERCOILING AND PACKING
03h30'
CHAIR: David BENSIMON
15:00
15:30
Conformation and dynamics of single molecules of DNA in solution
30'
Adam COHEN
Harvard University, Cambridge, U.S.A.
15:30
16:00
Dynamics of supercoiled DNA: some recent insights from single-molecule experiments
30'
Aurelien CRUT
LASIM, Villeurbanne, France
16:00
16:30
Compactness and apparent circularization of ssRNA
30'
Avinoam BEN-SHAUL
Hebrew University of Jerusalem, Israel
16:30
17:00
Coffee Break
30'
Room: Leonardo da Vinci Building, Lobby
17:00
17:30
DNA supercoiling and the lambda bacteriophage epigenetic switch
30'
Laura FINZI
Emory University, Atlanta, U.S.A.
17:30
18:00
Computer simulations of DNA supercoiling at the atomic level
30'
Sarah HARRIS
University of Leeds, U.K.
18:00
18:30
Unravelling the organization of bacterial chromatin
30'
Remus DAME
Leiden University, Leiden & VU, Amsterdam, The Netherlands
WEDNESDAY, 3 JUNE 2009

Room: Leonardo da Vinci Building Main Lecture Hall

3 June 2009
09:00
12:30
SESSION 8 - CONFORMATIONAL DYNAMICS, SUPERCOILING AND PACKING
03h30'
CHAIR: Wilma OLSON
09:00
09:30
The organization and topology of chromatin
30'
Andrew TRAVERS
MRC-LMB, Cambridge, U.K.
09:30
10:00
Stacking plates and wedges: the physics of DNA compaction
30'
Helmut SCHIESSEL
University of Leiden, The Netherlands
10:00
10:30
DNA and chromatin dynamics studied by single molecule methods and computer modelling
30'
Jorg LANGOWSKI
GSRC, Heidelberg, Germany
10:30
11:00
Coffee Break
30'
Room: Leonardo da Vinci Building, Lobby
11:00
11:30
DNA, chromatin and remodeling factors
30'
David BENSIMON
ENS, Paris, France
11:30
12:00
DNA and chromatin dynamics: Discovery of a novel ATP-dependent DNA rewinding motor
30'
James KADONAGA
UCSD, La Jolla, U.S.A.
12:00
12:30
Modelling chromatin with explicit ions: ion correlation effects and like charge attraction. Comparison with new experiments
30'
Lars NORDENSKIOLD
Nanyang Technological University, Singapore
12:30
12:45
Modeling the hysteretic behavior of chromatin fibers under magnetic tweezers: why are nucleosomes left handed?
15'
Maria BARBI
Universite Pierre et Marie Curie, Paris,France
12:45
15:00
Lunch Break
02h15'
Room: Leonardo da Vinci Building Cafeteria
15:00
16:30
SESSION 9 - DNA COMPACTIZATION IN VIRUSES
01h30'
CHAIR: Helmut SCHIESSEL
15:00
15:30
DNA ejection from bacterial and mammalian viruses
30'
William GELBART
UCLA, Los Angeles, U.S.A.
15:30
16:00
Menagerie of viruses: diverse chemical sequences or simple electrostatics?
30'
Murugappan MUTHUKUMAR
University of Massachusetts, Amherst, U.S.A.
16:00
16:30
DNA structure and phase transitions in the bacteriophage capsid
30'
Francoise LIVOLANT
CNRS, Orsay, France
16:30
17:00
Coffee Break
30'
Room: Leonardo da Vinci Building, Lobby
17:00
18:00
SESSION 10 - FEATURE PRESENTATION
01h00'
CHAIR: Helmut SCHIESSEL
17:00
17:30
Charge transport of cancer-related genes
30'
Rudolf ROEMER
University of Warwick, Coventry, U.K.
17:30
19:30
POSTER FAIR - Wellcome Trust Prizes for the best works of young participants
02h00'
Room: Leonardo da Vinci Building, Lobby
POSTER GALLERY (behind the Main Lecture Hall)

refreshments available
THURSDAY, 4 JUNE 2009

Room: Leonardo da Vinci Building Main Lecture Hall

4 June 2009
09:00
13:00
SESSION 11 - DNA-PROTEIN INTERACTION AND RECOGNITION
04h00'
CHAIR: Laura FINZI
09:00
09:30
Mechanisms of direct and indirect readout
30'
Loren WILLIAMS
Georgia Tech., Atlanta, U.S.A.
09:30
10:00
A singular view of DNA transactions
30'
Gijs WUITE
VU, Amsterdam, The Netherlands
10:00
10:30
Single-molecule manipulation of DNA
30'
Ching-Hwa KIANG
Rice University, Houston, U.S.A.
10:30
11:00
Coffee Break
30'
Room: Leonardo da Vinci Building, Lobby
11:00
11:30
DNA mechanics and protein-DNA recognition
30'
Richard LAVERY
BCP, Lyon, France
11:30
12:00
How proteins find their Targets on DNA
30'
Anatoly KOLOMEISKY
Rice University, Houston, U.S.A.
12:00
12:30
Topoisomerase I equilibrates metastable secondary structure in relaxed supercoiled DNA's
30'
Michael SCHURR
University of Washington, Seattle, U.S.A.
12:30
12:45
Binding of HU-proteins and DNA elasticity
15'
Yitzhak RABIN
Bar Ilan University, Ramat-Gan, Israel
12:45
13:00
The effect of HU on DNA looping
15'
Luke CZAPLA
University of Uppsala, Sweden
13:00
14:30
Lunch Break
01h30'
Room: Leonardo da Vinci Building Cafeteria
14:30
18:30
Group and Project Meetings Networking
04h00'
18:30
22:30
CONFERENCE DINNER
04h00'
FRIDAY, 5 JUNE 2009

Room: Leonardo da Vinci Building Main Lecture Hall

5 June 2009
09:00
12:00
SESSION 12 - DNA IN CONFINEMENT
03h00'
CHAIR: Sergey LEIKIN
09:00
09:30
Subtitles of nanoconfined DNA
30'
Theo ODIJIK
TU Delft, The Netherlands
(talk presented by Marc EMANUEL)
09:30
10:00
DNA capture in nanoscale pores - How does it happen?
30'
Amit MELLER
Boston University, U.S.A.
10:00
10:30
Origin of the electrophoretic force on DNA in solid state nanopores
30'
Serge LEMAY
TU Delft, The Netherlands
10:30
11:00
Coffee Break
30'
Room: Leonardo da Vinci Building, Lobby
11:00
11:30
Amphiphile-DNA complexes: adsorption, delivery and release
30'
Yan LEVIN
IF-UFRGS, Porto Alegre, Brazil
11:30
12:00
Backtracking by RNA polymerase: single molecule experiments vs theory
30'
Stephen GRILL
Max-Planck-Institute for Complex Systems, Dresden, Germany
12:00
14:30
Lunch Break
02h30'
Room: Leonardo da Vinci Building Cafeteria
14:30
16:00
SESSION 13 - SMART DNA
01h30'
CHAIR: Rudi PODGORNIK
14:30
15:00
What is it like to be a molecular robot based on DNA?
30'
Milan STOJANOVIC
Columbia University, New York, U.S.A.
15:00
15:30
Synthetic DNA Holliday junctions as controllable nanoswitch systems
30'
Andrew MOUNT
University of Edinburgh, U.K.
15:30
16:00
On the theory of cholesteric ordering in solutions of macromolecules
30'
Mikhail OSIPOV
University of Stratchclyde, U.K.
16:00
16:30
Coffee Break
30'
Room: Leonardo da Vinci Building, Lobby
16:30
18:15
SESSION 14 - PANEL-LED GENERAL DISCUSSION
01h45'
PANEL CHAIR: Adrian PARSEGIAN

PANEL MEMBERS - T.B.C.
18:15
18:30
CLOSING SESSION
15'
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