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Table of Contents: Supplement No. 191 (2011)
Statistical Physics and Topology of Polymers with Ramifications
to Structure and Function of DNA and Proteins
Proceedings of the YITP Workshop: a Satellite Meeting of STATPHYS24
Ed. by T. Deguchi, H. Hayakawa, K. Shimokawa, A. Stasiak and K. Tsurusaki
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DNA Knots: Theory and Experiments
( De Witt Sumners)
pp.1-19
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How Broken DNA Finds Its Template for Repair: A Computational Approach
( Lutz R. Gehlen, Susan M. Gasser and Vincent Dion)
pp.20-29
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Chromatin Topological Transitions
( Christophe Lavelle, Aurélien Bancaud, Pierre Recouvreux, Maria Barbi, Jean-Marc Victor and Jean-Louis Viovy)
pp.30-39
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Mean-Field Theory of the Symmetry Breaking Model for X Chromosome Inactivation
( Antonio Scialdone, Mariano Barbieri, Deborah Pallotti and Mario Nicodemi)
pp.40-45
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Role of Topological Exclusion in Formation and Organization of Chromosomal Territories
( Julien Dorier and Andrzej Stasiak)
pp.46-54
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Taxonomy of DNA Conformations within Complex Nucleoprotein Assemblies
( Dorothy Buck and Kenneth Lee Baker)
pp.55-65
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Nullification of Small Knots
( Claus Ernst, Anthony Montemayor and Andrzej Stasiak)
pp.66-77
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Signed Unknotting Number and Knot Chirality Discrimination via Strand Passage
( Chris Soteros, Kai Ishihara, Koya Shimokawa, Michael Szafron and Mariel Vazquez)
pp.78-95
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Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility
( Jonathan Mitchell and Sarah Harris)
pp.96-108
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Evaluating Partition Functions for Multiscale Models of DNA
( Andreas Hanke, Stefan Giovan and Stephen D. Levene)
pp.109-129
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Dimension of Ring Polymers in Melt Studied by Monte-Carlo Simulation
( Jiro Suzuki, Atsushi Takano and Yushu Matsushita)
pp.130-134
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GPU Based Molecular Dynamics Simulations of Polymer Rings in Concentrated Solution: Structure and Scaling
( Daniel Reith, Leonid Mirny and Peter Virnau)
pp.135-145
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Universal Ratios in the Dynamics of Open and Closed Chains of Linked Ring Polymers in Solution via Brownian Dynamics
( Naoko Kanaeda and Tetsuo Deguchi)
pp.146-153
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General Polygonal Length Dependence of the Linking Probability for Ideal Random Polygons
( Naomi Hirayama, Kyoichi Tsurusaki and Tetsuo Deguchi)
pp.154-164
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Cumulative Shapes of Knotted Polymers
( Eric J. Rawdon, Kenneth C. Millett, Vy T. Tran and Andrzej Stasiak)
pp.165-171
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A Study of the Entanglement in Systems with Periodic Boundary Conditions
( Eleni Panagiotou, Christos Tzoumanekas, Sofia Lambropoulou, Kenneth C. Millett and Doros N. Theodorou)
pp.172-181
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The Length Scale of 3-Space Knots, Ephemeral Knots, and Slipknots in Random Walks
( Kenneth C. Millett)
pp.182-191
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Probing the Entanglement and Locating Knots in Ring Polymers: A Comparative Study of Different Arc Closure Schemes
( Luca Tubiana, Enzo Orlandini and Cristian Micheletti)
pp.192-204
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Knot Localization in a Flexible Polymer Confined in a Tube
( Chihiro H. Nakajima and Takahiro Sakaue)
pp.205-209
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Driven Translocation of Semi-Flexible Polymer under Strong Force
( Takuya Saito and Takahiro Sakaue)
pp.210-214
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Ideal, Best Packing, and Energy Minimizing Double Helices
( Jun O'Hara)
pp.215-224
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On Transforming a Spatial Graph into a Plane Graph
( Akio Kawauchi)
pp.225-234
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Entanglement of Embedded Graphs
( Toen Castle, Myfanwy E. Evans and Stephen T. Hyde)
pp.235-244
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Band Surgeries between Knots and Links with Small Crossing Numbers
( Kai Ishihara and Koya Shimokawa)
pp.245-255