Jun Lab -- Physical Biology at Harvard FAS Center for Systems Biology

THEORY

Suckjoon Jun and Nick Rhind, Just-in-time DNA replication,
Physics 1, 32 (2008) [read the article]
---read also the Editorial by Gene D. Sprouse on the launch Physics

David Boal and Suckjoon Jun, Entropy-driven shape change as a model for primitive cell division [preprint]

Q: What is the typical timescale of relaxation of a chain in a cylinder?
Youngkyun Jung, Suckjoon Jun, Bae-Yeun Ha, A self-avoiding polymer trapped inside a cylindrical pore: Flory free energy and unexpected dynamics, Phys Rev E (in press, 2009)

Towards understanding the bacterial cell cycle as a "dialogue" between physical and biological processes
Suckjoon Jun, Can entropy save bacteria?

Q: What is the free energy for deforming a chain/biomolecule in a cylinder?
Suckjoon Jun, D. Thirumalai and Bae-Yeun Ha, Compression and stretching of a self-avoiding chain in cylindrical nanopores,
Phys. Rev. Lett. 101, 138101 (2008) [PDF]

Q: What is the typical timescale of relaxation of biomolecules in a cylinder?
Axel Arnold, Behnaz Borzorgui, Daan Frenkel, Bae-Yeun Ha and Suckjoon Jun, Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement, J Chem Phys 127, 164903 (2007). [PDF] [arXiv:0708.2099] NOTE: reprinted in Nov 5, 2007 issue of Virtual Journal of Nanoscale Science & Technology.

Q: Is entropy-driven segregation in a cylinder fast enough?
Axel Arnold and Suckjoon Jun, Timescale of entropic segregation of flexible polymers in confinement: Implications for chromosome segregation in filamentous bacteria, Phys Rev E 76, 031901 (2007) [PDF] [arXiv:0704.3230v1 (cond-mat.soft)] NOTE: reprinted in Sept 15, 2007 issue of Virtual Journal of Biological Physics Research.

Q: Can we use a Flory-type free energy in a cylinder?
Bae-Yeun Ha and Suckjoon Jun, Remarks on Flory theory of a self-avoiding chain under cylindrical confinement. [PDF] [cond-mat/0702264 (2007)]

Q: What is the free energy cost to overlap multiple chains? What happens in a sphere?
Suckjoon Jun, Axel Arnold and Bae-Yeun Ha, Confined space and effective interactions of multiple self-avoiding chains, Phys. Rev. Lett. 98, 128303 (2007) [PDF] [physics/0702084]. NOTE: reprinted in April 1, 2007 issue of Virtual Journal of Biological Physics Research.

Q: Is chromosome segregation a physical process or a biological process? }Round 1.
Suckjoon Jun and Bela Mulder, Entropy-driven sptial organization of highly confined polymers: Lessons for the bacterial chromosome Proc. Nat. Acad. Sci. 103, 12388 (2006) [download]
See also "Segregation by entropy" in Journal of Cell Biology [link].

2005 and before: DNA replication and related physics

Suckjon JUN
Kinetic model of DNA replication and the looping of semiflexible polymers, PhD thesis 2004 [PDF]

Jun, S., Bechhoefer J., and Ha, B.-Y.
Ch. 3. Looping of Semiflexible Polymers: from Statics to Dynamics in
Molecular Interfacial Phenomena of Polymers and Biopolymers,
edited by Pu Chen (Woodhead Publishing Ltd, Cambridge, UK) (July, 2005)

Suckjoon Jun and John Bechhoefer
Nucleation and growth in one dimension
part II: Application to DNA replication kinetics
(cont-mat/0408297; Phys.Rev.E 71, 011909 (2005)) [PDF]
NOTE: reprinted in February 1, 2005 issue of Virtual Journal of Biological Physics Research.

Suckjoon Jun, Haiyang Zhang, and John Bechhoefer
Nucleation and growth in one dimension
part I: The generalized Kolmogorov-Johnson-Mehl-Avrami model
(cont-mat/0408260; Phys.Rev.E 71, 011908 (2005)) [PDF]
NOTE: reprinted in February 1, 2005 issue of Virtual Journal of Biological Physics Research.

S. Jun, Y. Hong, H. Imamura, B.-Y. Ha, J. Bechhoefer, and P. Chen
Self-Assembly of the Ionic Peptide EAK16:
the effect of charge distributions on self-assembly
Biophysical Journal 87, 1249-1259 (2004) [PDF]

Suckjoon Jun, John Herrick, Aaron Bensimon, and John Bechhoefer
Persistence length of chromatin determines origin spacing in Xenopus early-embryo
DNA replication: Quantitative comparisons between theory and experiment
Cell Cycle 3 (2), 223-229 (2004) [PDF].

Suckjoon Jun, John Bechhoefer, and Bae-Yeun Ha
Diffusion-limited loop formation of semiflexible polymers:
Kramers theory and the intertwined time scales of chain relaxation and closing
Europhys. Lett. 64 (3), 420-426 (2003) [PDF].

Suckjoon Jun and John Bechhoefer
Role of Polymer Loops in DNA replication
Physics in Canada 59 (2), pp. 85-92 (2003). [PDF]
(Invited review article for special issue on Polymer Physics)

John Herrick, Suckioon Jun, John Bechhoefer, and Aaron Bensimon
Kinetic model of DNA replication in eucaryotic organisms
J.Mol.Biol. 320, 741-750 (2002) [PDF].

M Luban, F Borsa, S Bud’ko, P Canfield, S Jun, JK Jung, P Kögler, D Mentrup, A Müller, R Modler, D Procissi, BJ Suh, and M Torikachvili.
Heisenberg spin-triangle in {V6}-type magnetic molecules: Experiment and theory.
Phys. Rev. B 66, 054407(1)-054407(12) (2002) [PDF].