Knots and soft-matter physics


Aug. 26, 2008

9:30-9:40 Opening
9:40-10:20 Stu G. Whittington (Canada)
Counting almost unknotted embeddings of graphs and surfaces
10:20-10:50 coffee break
10:50-11:30 Akio Kawauchi (Osaka City Univ.)
On a complexity of a spatial graph
11:30-12:10 Yuanan Diao (USA)
Jones Polynomials of Knots Formed by Repeated Tangle Replacement Operations
12:10-13:40 Lunch
13:40-14:20 Chris Soteros (Canada)
14:20-15:00 Jason Cantarella (USA)
A new proof that every tight knotted tube (other than the unknot) has a self-contact
15:00-15:30 coffee break
15:30-16:10 Claus Ernst (USA)
The Linearity of the Ropelengths of Conway Algebraic Knots in Terms of Their Crossing Numbers
16:10-16:50 Eric Rawdon (USA)
The Effect of Knotting on the Size and Shape of Polymers
16:50-17:30 Cristian Micheletti (Italy)
Simulations of knotting in confined circular DNA

Aug. 27, 2008

9:00-9:40 Mitchell Berger (UK)
Magnetic Writhe and Braiding
9:40-10:20 S. Yamazaki (Okayama Univ.)
Topological mechanism of nucleation of cyclic polyethylene
10:20-10:40 coffee break
10:50-11:30 T. Okui (Tokyo Inst. of Tech.)
Topological Effect on Polymer Crystallization - Linear and Ring Polymers -
11:30-12:10 Atsushi Takano (Nagoya Univ.)
Chain dimension of ring polystyrenes in solutions
12:10-13:40 Lunch
13:40-14:20 A. Ikai (Tokyo Inst. of Tech.)
Stabilization of a protein structure by pseudo-knot formation
14:20-15:00 Peter Virnau (Germany)
Knots in globular polymers and proteins
15:00-15:30 coffee break
15:30-16:10 Todd O Yeates (USA)
Discovering, Engineering, and Exploring Knots in Proteins
16:10-16:50 Joanna I. Sulkowska (USA)
Dynamics of knots in proteins
16:50-17:30 Poster session

Aug. 28, 2008

9:00-9:40 K. Yoshikawa (Kyoto Univ.)
Packing a semi-flexible molecular chain
9:40-10:20 Giovanni Dietler (Switzerland)
Single Molecule Imaging Study of the Effects of Topology on the Statistical Properties of DNA
10:20-10:40 coffee break
10:50-11:30 Stephen Levene (USA)
DNA Topology Meets Nanotechnology: A New Approach to DNA Hybridization
11:30-12:10 Lynn Zechiedrich (USA)
Bullied no more; DNA bullies biology
12:10-13:40 Lunch
13:40-14:20 Andrzej Stasiak (Switzerland)
DNA supercoiling inhibits DNA knotting
14:20-15:00 Koya Shimokawa (Saitama Univ.)
Tangle analysis of DNA catenane unlinking by the Xer/FtsK system
15:00-15:30 coffee break
15:30-16:10 Julia Yeomans (UK)
Polymer dynamics in confined spaces
16:10-16.40 Takeaki Araki (Kyoto Univ.)
Monte Carlo simulation of nematic liquid crystal in porous media: The topological constraint and surface anchoring effect
16:40-17:00 S. Saka (Keio Univ.)
Average Structure of a Single Knotted Ring Polymer
17:00-17:20 Naoko Kanaeda (Ochanomizu Univ.)
Intrinsic viscosity of knots in solution evaluated through the Brownian Dynamics
17:20-17:30 Naomi Hirayama (Ochanomizu Univ.)
Linking probabilities of self-avoiding polygons
18:00 banquet

Aug. 29, 2008

9:00-9:40 Tom Kephart (USA)
Knots and Links in Semi-classical Systems
9:40-10:20 Olivier Pierre-Louis (UK)
Knots in stiff strings
10:20-10:40 coffee break
10:50-11:30 Attilio Stella (Italy)
Topological signatures of the thermodynamics of swollen and globular polymer rings
11:30-12:10 Kyoichi Tsurusaki (Kanagawa Industrial Tech. Inst.)
Analysis on topological effects of polymer systems using link and knot invariants
12:10-13:40 Lunch
13:40-14:20 Jun O'Hara (Tokyo Metropolitan Univ.)
Configuration space of small equilateral and equiangular n-gons (n < 6)
14:20-15:00 K. Taniyama (Waseda Univ.)
Unknotting numbers of diagrams of a given nontrivial knot are unbounded
15:00-15:30 coffee break
15:30-16:00 K. Ishihara (Saitama Univ.)
Minimal step number of knots with small crossing number
16:00-16:20 S. Araki (Kyoto Univ.)
The hierarchical structure of chromatin(by S. Araki, K. Hizume, K. Takeyasu, and K. Yoshikawa)
16:20-16:50 T. Deguchi (Ochanomizu Univ.)
Novel criticality of random knots at the theta temperature
16:50-17:00 Closing

Poster presentations / Aug. 27, 2008

1) Makoto Ozawa (Komazawa Univ.)
Rational structure on algebraic tangles and closed incompressible surfaces in the complements of algebraically alternating knots and links
2) Shinya Saka (Keio Univ.)
Relaxation of a Single Knotted Ring Polymer
3) Ryo Hanaki (Waseda Univ.)
On Psuedo Diagrams of Knots, Links and Spatial Graphs
4) Jiro Suzuki (J-PARC Center)
Topological effect in ring polymers studied by Monte Carlo Simulation
5) Shugo Yasuda (Kyoto Univ.)
Multi-scale hybrid simulation for softmatters
6) Naoko Kanaeda (Ochanomizu Univ.)
Diffusion of a circular DNA in solution by the Brownian Dynamics
7) Naoko Kanaeda (Ochanomizu Univ.)
Diffusion of a supercoiled DNA and the effect of base flipping by the Brownian dynamics
8) Naomi Hirayama (Ochanomizu Univ.)
Linking probabilities of self-avoiding polygons
9) Yoko Akita (Ochanomizu Univ.)
Distance distribution of random knots