International workshop on
Knots and Polymers:
Aspects of topological entanglement in DNA, proteins and graph-shaped polymers


Date : August 8-10, 2017

Venue : Inter-Faculty Building 2, Ochanomizu University, Tokyo, Japan

Aim :
Recently, various aspects in topological properties of polymers and biopolymers such as DNA and proteins have attracted much attention in many different fields of science. Statistical and dynamical properties of circular DNA which may be knotted or unknotted and pseudoknots of proteins are studied both experimentally and theoretically. Various polymers with complex chemical connectivity expressed by graphs have been synthesized, which we call topological polymers. Interestingly, symplectic geometry plays an important role in the statistical mechanics of ring polymers and topological polymers. In the present workshop we discuss various topological aspects of polymers through several different interdisciplinary approaches and seek a unified perspective among them.

Confirmed speakers :
Jason Cantarella (Univ. Georgia)
Clayton Shonkwiler (Colorado State Univ.)
Chris Soteros (Univ. Saskatchewan)
Eric Rawdon (Univ. St. Thomas)
Cristian Micheletti (SISSA)
Giovanni Dietler (EPFL)
Joanna Sulkowska (Univ. Warsaw)
Peter Virnau (JGU Mainz )
Nicholas Beaton (Univ. Melbourne)
Kenneth Millett (UC Santa Barbara)
Akio Kawauchi (Osaka City Univ.)
Atsushi Takano (Nagoya Univ.)
Jiro Suzuki (KEK)
Daichi Ida (Kyoto Univ.)
Takahiro Sakaue (Kyusyu Univ.)
Takuya Yamamoto (Hokkaido University)
Kai Ishihara (Yamaguchi University)
Erica Uehara (Ochanomizu University)
Tetsuo Deguchi (Ochanomizu Univ.)
Yasuyuki Tezuka (TIT)

Schedule : (PDF file)
August 8, 2017
9:00-9:50 Jason Cantarella (Univ. Georgia)
Optimal closures for equilateral polygons in any dimension
9:50-10:40 Clayton Shonkwiler (Colorado State Univ.)
The Geometry of Polygon Space: Acute Triangles, Convex Quadrilaterals, Flag Means, and More

10:40-11:10 Coffee break

11:10-12:00 Tetsuo Deguchi (Ochanomizu Univ.)
Statistical and Hydrodynamic Properties of Graph-Shaped Polymers and Quaternions

12:00-13:40 Lunch break

13:40-14:30 Takuya Yamamoto (Hokkaido University)
Topology for Polymeric Materials
14:30-15:20 Daichi Ida (Kyoto Univ.)
A Monte Carlo Study of Dilute Solution Properties of Semiflexible Ring Polymers

15:20-15:50 Coffee break

15:50-16:40 Eric Rawdon (Univ. St. Thomas)
Knotting transitions: the action of topoisomerase IV and glueball decay
16:40-17:30 Yasuyuki Tezuka (TIT)
Topological Polymer Chemistry Designing Complex Macromolecular Graph Constructions

18:00- Conference banquet

August 9, 2017
9:00-9:50 Chris Soteros (Univ. Saskatchewan)
Lattice models of Knot and Link Transition Probabilities in Polymers
9:50-10:40 Nicholas Beaton (Univ. Melbourne)
Knotting probabilities and pattern theorems for polygons in tubes

10:40-11:10 Coffee break

11:10-12:00 Erica Uehara (Ochanomizu University)
Statistical mechanics of theta-shaped and ring-shaped polymer chains

12:00-13:40 Lunch break

13:40-14:30 Jiro Suzuki (KEK)
Interactions between trivial-ring polymers studied by Monte Carlo simulation
14:30-15:20 Joanna Sulkowska (Univ. Warsaw)
New type of entanglement in protein structures - lassos and links

15:20-15:50 Coffee break

15:50-16:40 Akio Kawauchi (Osaka City Univ.)
Complexity of a knitting pattern

16:40-17:30 Poster session
Erika Nozawa (Ochanomizu Univ.) : Coupled Map Lattice for Spiral Arms and Stars in Cosmology as Dynamical Systems
Kayo Kinjo (Ochanomizu Univ.): Analysis of the 1D Bose Gas by the Bethe Ansatz Method
Yasuyoshi Ito (Saitama Univ.) : On 2-adjacency between two knots

August 10, 2017
9:00-9:50 Giovanni Dietler (EPFL)
Statistical properties of DNA in 2 dimensions and in channels
9:50-10:40 Kai Ishihara (Yamaguchi University)
Enzyme action for topological entanglement in DNA and knot theory

10:40-11:10 Coffee break

11:10-12:00 Peter Virnau (JGU Mainz)
Knots in DNA, Chromosomes and Polymer melts

12:00-13:40 Lunch break

13:40-14:30 Cristian Micheletti (SISSA)
Pore translocation of knotted polymers
14:30-15:20 Takahiro Sakaue (Kyusyu Univ.)
On topological glass in melt of non-concatenated ring polymers

15:20-15:50 Coffee break

15:50-16:40 Atsushi Takano (Nagoya Univ.)
Chain dimension of ring polymers in bulk
16:40-17:30 Kenneth Millett (UC Santa Barbara)
The viscoelastic effects of polymer entanglement in complex fluids: a topological analysis of a fluctuating hydrodynamic simulation

Organizers :
Tetsuo Deguchi (Ochanomizu University)
Yasuyuki Tezuka (Tokyo Institute of Technology)
Koya Shimokawa (Saitama University)

Supported by :
JSPS KAKENHI Grant numbers 26310206, 16H03928 and 17H06463.