CDSAGENDA V.5 Conference on Knots and other Entanglements in Biopolymers: Topological and Geometrical Aspects of DNA, RNA and Protein Structures

Conference on Knots and other Entanglements in Biopolymers: Topological and Geometrical Aspects of DNA, RNA and Protein Structures

Start Time:

15 September 2008 at 08:00

Ends On:

19 September 2008

Location:

Trieste - Italy

Venue:

AGH (Kastler Lecture Hall)

Organizer(s):

Directors: H-S. Chan, C. Micheletti, A. Stasiak, L. Zechiedrich. Local Organizer: M. Marsili

Description:

Material:

no notes available

Registration and Administrative Formalities

Location: Adriatico Guest House Lower Level

15 September 2008

08:00
09:15

01h15'

TOPIC: Evolution + folding of Knotted Proteins

Room: Adriatico Guest House Kastler Lecture Hall

15 September 2008

09:30
10:00

Welcome address

30'

recording

10:00
11:00

Life -- A result of evolution or design? + 15' discussion

01h00'

recording

Peter Schuster
President Austrian Academy of Sciences

The lecture will discuss the probability issues and, in particular, the Levithal paradox

11:05
11:50

Evolutionary Optimisation of Proteins on a Fitness Landscape with Entangled Traits

45'

recording

Erich Bornberg-Bauer
University of Muenster

11:50
12:35

Capturing knots in polymers and proteins

45'

recording

Peter Virnau
Johannes Gutenberg-Universität Mainz

12:35
14:15

Lunch

01h40'

14:15
15:00

Stretching of proteins and dynamics of knots

45'

recording

Marek Cieplak
Polish Academy of Sciences

15:00
15:45

The Folding Pathways of Knotted Proteins

45'

Sophie Jackson
University of Cambridge

15:45
16:00

Break

15'

Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)

16:00
16:45

Disentangling the folding mechanics of a knotted protein: kinetics vs thermodynamics

45'

Stefan Wallin
Lund University

No recording is available for this lecture due to copyright restrictions.

16:45
17:30

Protein topology and knots

45'

recording

William Taylor
The National Institute for Medical Research London

19:00
20:30

Welcome drink

01h30'

Room: Adriatico Guest House (Terrace)

TOPIC: DNA

Room: Adriatico Guest House Kastler Lecture Hall

16 September 2008

09:00
09:45

An Electrostatic/Geometric Mechanism for Compact Chromatin Stabilization Revealed by Mesoscale Modeling

45'

abstract

Tamar Schlick
New York University

No recording is available for this lecture due to copyright restrictions.

09:45
10:30

DNA replication fork repair by RecG protein: A propagating front model

45'

Somendra Bhattacharje
Institute of Physics Bhubaneswar

10:30
10:55

Coffee break

25'

Room: Adriatico Guest House (Terrace)

11:00
11:45

Interplay of DNA supercoiling and catenation during the segregation of sister duplexes

45'

Jorge Schvartzman
Centro de Investigaciones Biológicas (CSIC) Madrid

11:45
12:30

Single DNA molecule micromanipulation: a tool to investigate replication enzymes

45'

Vincent Croquette
Ecole Normale Supérieure Paris

12:30
13:45

Lunch

01h15'

13:45
14:30

DNA tangles

45'

Isabel Darcy
University of Iowa

14:30
15:15

Modeling DNA unlinking by Xer recombination

45'

Mariel Vazquez
San Francisco State University

15:15
15:30

Break

15'

Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)

15:30
16:15

Computer Simulations of DNA Topology at the Atomic Level

45'

Sarah Harris
University of Leeds

16:15
17:00

The statistical mechanics of how recognition of local DNA juxtaposition geometry may underlie the disentangling actions of type-II topoisomerases

45'

recording

Hue Sun Chan
University of Toronto

TOPIC: Polymers

Room: Adriatico Guest House Kastler Lecture Hall

17 September 2008

09:00
09:45

Monte Carlo simulation on the conformational statistics of worm-like DNA chains: effect of DNA juxtaposition and topoisomerase action

45'

Zhirong Liu
Peking University

09:45
10:30

The effect of knotting on the shape of polymers

45'

recording

Kenneth Millett
University of California at Santa Barbara

10:30
10:55

Coffee break

25'

Room: Adriatico Guest House (Terrace)

11:00
11:45

Topological signatures of the thermodynamics of knotted polymer rings

45'

Attilio Stella
Università degli Studi di Padova

11:45
12:30

Polymers, polygons and pattern theorems

45'

Stuart Whittington
University of Toronto

12:30
13:45

Lunch

01h15'

13:45
15:15

Poster session

01h30'

Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)

15:15
15:30

Break

15'

Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)

15:30
16:15

Bullied no more- DNA takes an active role in biology

45'

recording

Lynn Zechiedrich
Baylor College of Medicine Houston

16:15
17:00

DNA knotting in spooling like conformations in bacteriophages

45'

Javier Arsuaga
San Francisco State University

TOPIC: Knot Theory

Room: Adriatico Guest House Kastler Lecture Hall

18 September 2008

09:00
09:45

DNA supercoiling inhibits DNA knotting

45'

recording

Andrzej Stasiak
Université de Lausanne

09:45
10:30

Entanglement Complexity of Systems of Self-Avoiding Walks in Lattice Tubes

45'

Christine Soteros
University of Saskatchewan

10:30
10:55

Coffee break

25'

Room: Adriatico Guest House (Terrace)

11:00
11:45

Knotting in stretched polymers

45'

recording

Carla Tesi
Università di Bologna

11:45
12:30

Writhe Descriptors for Macromolecular Structure

45'

De Witt Sumners
Florida State University Tallahassee

12:30
14:15

Lunch

01h45'

14:15
15:00

Predicting RNA pseudoknot folding and ribosomal frameshifting

45'

recording

Shi-Jie Chen
University of Missouri Columbia

15:00
15:45

Pseudoknots in RNA

45'

recording

Henri Orland
CEA Gif-sur-Yvette

15:45
16:00

Break

15'

Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)

16:00
16:20

Molecular Dynamics simulation of hepatitis C virus IRES IIId domain. Effects of mutations in electrostatic and structural properties

20'

recording

Angel Gonzalez
Pontificia Universidad Catolica de Chile

16:20
16:40

Dodging the crisis of folding proteins with knots

20'

recording

Joanna I. Sulkowska
The University of California, San Diego

16:40
17:00

Modeling filament kinematics for proteic coding and viral spooling

20'

Francesca Maggioni
University of Bergamo

TOPIC: Proteins + Knot Theory

Room: Adriatico Guest House Kastler Lecture Hall

19 September 2008

09:00
09:45

Soft Entropic forces between approaching polymers with prescribed topology: possible implications on the physics of interphase chromosomes

45'

Enzo Orlandini
Istituto Nazionale di Fisica Nucleare Padova

09:45
10:30

Scaling aspects in the probability of random knots and links and the dynamics of ring polymers in solution

45'

abstract

Tetsuo Deguchi
Ochanomizu University Tokyo

10:30
10:55

Coffee break

25'

Room: Adriatico Guest House (Terrace)

11:00
11:45

Structural motifs of biomolecules

45'

Trinh Xuan Hoang
Pennsylvania State University

11:45
12:05

Statistical properties of intrinsically curved polymers

20'

Surya K. Ghosh
Indian Institute of Technology Bombay

12:05
12:25

Topological methods for measuring the entanglement of polymers

20'

recording

Eleni Panagiotou
National Technical University, Athens

12:25
12:45

Numerical simulations of DNA catenanes: energetic and topological influence of supercoiling

20'

recording

Guillaume Witz
Ecole Polytechnique Fédérale de Lausanne

12:45
14:15

Lunch

01h30'

14:15
15:00

Confined biopolymers: DNA packaging and chromosome territories

45'

recording

Davide Marenduzzo
University of Edinburgh

15:00
15:45

Size, Shape and Correlations of Topologically Constrained DNA

45'

recording

Giovanni Dietler
Ecole Polytechnique Fédérale de Lausanne

15:45
16:00

Concluding remarks

15'

recording

Cristian Micheletti
SISSA, Trieste