Highlights

The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer
Brenda Youngren, Henrik Jork Nielsen, Suckjoon Jun, and Stuart Austin.
Genes & Development 28:71-84, 2014
[open access full article]
[see also 'The bacterial chromosome: a physical biologist’s apology. A perspective.']
At long last, and for the first time, we understand the organization, dynamics, segregation of the E. coli chromosome under all growth and cell-cycle conditions in vivo.
The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer
Physical manipulation of the bacterial chromosome reveals its soft nature
James Pelletier, Ken Halvorsen, Bae-Yeun Ha, Raffaella Paparcone, Steven Sandler, Conrad Woldringh, Wesley Wong, and Suckjoon Jun
PNAS Plus 109(40), E2649-E2656, 2012.
[open access full article] [PNAS highlight]
[Nature Methods highlight]
All chromosomes must fold to fit within cellular containers. Though strongly confined, the bacterial chromosome exhibits highly dynamic behavior during the cell cycle. Many models have been proposed, but few measurements have quantified the essential micromechanical properties of the bacterial chromosome. In this work, we experimentally demonstrated and quantified the fundamentally soft nature of the bacterial chromosome and the entropic forces that can cause fast compaction in a crowded intracellular environment. This 7-year work, experiment and theory combined, is a quantitative demonstration of the loaded entropic spring model of the bacterial chromosome.
Entropy as the driver of chromosome segregation
Suckjoon Jun and Andrew Wright
Nature Reviews Microbiology 8, 600-607 (2010).
[online] [PDF] [Small Things Considered]
In our PNAS 2006 article, we proposed conformational entropy- driven chromosome organization and segregation in bacteria. This work quantitatively discusses a set of minimal physical conditions the bacterial chromosomes should satisfy to segregate spontaneously, and goes beyond the original PNAS 2006 article. Furthermore, this article critically examines the existing models.
Robust growth of Escherichia coli,
Ping Wang, Lydia Rober, James Pelletier, Wei Lien Dang, Francois Taddei, Andrew Wright, and Suckjoon Jun
Current Biology 20, 1099-1103, 2010.
[online] [PDF] [F1000] [Small Things Considered]
[The Scientist Top 7 Biology]
[The Scientist Top 7 Biochemistry]
In this work, we introduce the mother machine for the first time. The mother machine allowed us to follow thousands of individual mother cells for hundreds of consecutive generations. The results were surprising. See the movie below.

Publications

[La Jolla, CA, 2013-]
  Single-cell physiology
Sattar Taheri*, Dustin McIntosh*, Gautam Reddy, Suckjoon Jun
[Review; 20 pages; Annual Review of Biophysics, to appear in 2015]
Bending stresses plastically deform growing bacterial cell walls

Q: How does E. coli control its shape?

Bending stresses plastically deform growing bacterial cell walls
Ariel Amir, Farinaz Babaeipour, Dustin McIntosh, David Nelson, and Suckjoon Jun
Proc. Nat. Acad. Sci. USA (Early Edition, 2014)
[open access full article]
The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer

See highlights on the right

The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer
Brenda Youngren, Henrik Jork Nielsen, Suckjoon Jun, and Stuart Austin.
Genes & Development 28:71-84, 2014
[open access full article]
[Cambridge, MA, 2007-2012]
Physical manipulation of the Escherichia coli chromosome reveals its soft nature.

See highlights on the right

Physical manipulation of the Escherichia coli chromosome reveals its soft nature
James Pelletier, Ken Halvorsen, Bae-Yeun Ha, Raffaella Paparcone, Steven Sandler, Conrad Woldringh, Wesley Wong, and Suckjoon Jun
PNAS Plus 109(40), E2649-E2656, 2012.
[open access full article] [PNAS highlight]
[Nature Methods highlight]
Intrachain ordering and segregation of polymers under confinement

Q: "superblobs"?

Intrachain ordering and segregation of polymers under confinement
Y. Jung, J. Kim, S. Jun and B.-Y. Ha
Macromolecules 45 (7), 3256-3262, 2012.
[online] [PDF]
Ring polymers as model bacterial chromosomes: confinement, chain topology, single chain statistics and how they interact.

Q: What is the behavior of two ring polymers in strong confinement?

Ring polymers as model bacterial chromosomes: confinement, chain topology, single chain statistics and how they interact.
Y. Jung, C. Jeon, J. Kim, H. Jeong, S. Jun and B.-Y. Ha
Soft Matter 8, 2095-2102, 2012.
[online] [PDF]
Entropy as the driver of chromosome segregation.

See highlights on the right

Entropy as the driver of chromosome segregation.
Suckjoon Jun and Andrew Wright
Nature Reviews Microbiology 8, 600-607 (2010).
[online] [PDF] [Small Things Considered]
Robust growth of Escherichia coli

See highlights on the right

Robust growth of Escherichia coli
Ping Wang, Lydia Rober, James Pelletier, Wei Lien Dang, Francois Taddei, Andrew Wright, and Suckjoon Jun
Current Biology 20, 1099-1103, 2010.
[online] [PDF] [F1000] [Small Things Considered]
[The Scientist Top 7 Biology] [The Scientist Top 7 Biochemistry]
A self-avoiding polymer trapped inside a cylindrical pore: Flory free energy and unexpected dynamics

Q: What is the typcal timescale of relaxation of a chain in a cylinder?

A self-avoiding polymer trapped inside a cylindrical pore: Flory free energy and unexpected dynamics
Youngkyun Jung, Suckjoon Jun, Bae-Yeun Ha
Phys. Rev. E 79, 061912 (2009).
[PDF]
Just-in-time DNA replication

Viewpoint article for Physics (APS)

Just-in-time DNA replication
Suckjoon Jun and Nick Rhind
Physics 1, 32 (2008).
[online]
Compression and stretching of a self-avoiding chain in cylindrical nanopores

Q: How to fix Flory’s mistake to obtain forcecompression curves in a cylindrical pore?

Compression and stretching of a self-avoiding chain in cylindrical nanopores
Suckjoon Jun, D. Thirumalai and Bae-Yeun Ha
Phys. Rev. Lett. 101, 138101 (2008).
[PDF]
[Paris & Amsterdam, 2004-2007]
Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement

Q: What is the real relaxation time of a selfavoiding chain in a cylinder?

Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement
Axel Arnold, Behnaz Borzorgui, Daan Frenkel, Bae-Yeun Ha and Suckjoon Jun
J. Chem. Phys. 127, 164903 (2007).
[online] [PDF]
Timescale of entropic segregation of flexible polymers in confinement: Implications for chromosome segregation in filamentous bacteria

Q: Is entropy-driven segregation in a cylinder fast enough?

Timescale of entropic segregation of flexible polymers in confinement: Implications for chromosome segregation in filamentous bacteria
Axel Arnold and Suckjoon Jun
Phys. Rev. E 76, 031901 (2007).
[online] [PDF]
Confined space and effective interactions of multiple self-avoiding chains

Q: What is the free energy of arbitrary number of overlapping self-avoiding chains?

Confined space and effective interactions of multiple self-avoiding chains
Suckjoon Jun, Axel Arnold and Bae-Yeun Ha
Phys. Rev. Lett. 98, 128303 (2007)
[online] [PDF]
Entropy-driven sptial organization of highly confined polymers: Lessons for the bacterial chromosome.

This papers introduces two novel ideas on bacterial chromosomes. 1. Conformational entropy can drive strongly confined DNA demix during replication, 2. Newly-replicated DNA will be extruded to the periphery of the bacterial chromosome in vivo.

Entropy-driven sptial organization of highly confined polymers: Lessons for the bacterial chromosome.
Suckjoon Jun and Bela Mulder
PNAS 103, 12388 (2006)
[online] [F1000] [JCB highlight]
[Vancouver, BC, 1999-2004]
Ch. 3. Looping of Semiflexible Polymers: from Statics to Dynamics
Jun, S., Bechhoefer J., and Ha, B.-Y.
Edited by Pu Chen (Woodhead Publishing Ltd, Cambridge, UK) (July, 2005)
[online]
Kinetic model of DNA replication and the looping of semiflexible polymers Kinetic model of DNA replication and the looping of semiflexible polymers
Suckjoon Jun
PhD Thesis (2004)
[PDF]
Nucleation and growth in one dimension part II: Application to DNA replication kinetics Nucleation and growth in one dimension part II: Application to DNA replication kinetics
Suckjoon Jun and John Bechhoefer
(Phys.Rev.E 71, 011909 (2005); cont-mat/0408297)
[PDF]
Nucleation and growth in one dimension part I: The generalized Kolmogorov-Johnson-Mehl-Avrami model Nucleation and growth in one dimension part I: The generalized Kolmogorov-Johnson-Mehl-Avrami model
Suckjoon Jun, Haiyang Zhang, and John Bechhoefer
(Phys.Rev. E 71, 011908 (2005); cont-mat/0408260)
[PDF]
Self-Assembly of the Ionic Peptide EAK16: the effect of charge distributions on self-assembly Self-Assembly of the Ionic Peptide EAK16: the effect of charge distributions on self-assembly
S. Jun, Y. Hong, H. Imamura, B.-Y. Ha, J. Bechhoefer, and P. Chen
Biophys. J. 87, 1249-1259 (2004)
[PDF]
Persistence length of chromatin determines origin spacing in Xenopus early-embryo DNA replication: Quantitative comparisons between theory and experiment Persistence length of chromatin determines origin spacing in Xenopus early-embryo DNA replication: Quantitative comparisons between theory and experiment
Suckjoon Jun, John Herrick, Aaron Bensimon, and John Bechhoefer
Cell Cycle 3(2), 223-229 (2004)
[PDF]
Diffusion-limited loop formation of semiflexible polymers: Kramers theory and the intertwined time scales of chain relaxation and closing Diffusion-limited loop formation of semiflexible polymers: Kramers theory and the intertwined time scales of chain relaxation and closing
Suckjoon Jun, John Bechhoefer, and Bae-Yeun Ha
Europhys. Lett. 64(3), 420-426 (2003)
[PDF]
Role of Polymer Loops in DNA replication Role of Polymer Loops in DNA replication
Suckjoon Jun and John Bechhoefer
Physics in Canada 59(2), pp. 85-92 (2003)
[PDF]
Kinetic model of DNA replication in eucaryotic organisms Kinetic model of DNA replication in eucaryotic organisms
John Herrick, Suckioon Jun, John Bechhoefer, and Aaron Bensimon
J. Mol. Biol. 320, 741-750 (2002)
[PDF]
Heisenberg spin-triangle in {V6}-type magnetic molecules: Experiment and theory Heisenberg spin-triangle in {V6}-type magnetic molecules: Experiment and theory
M Luban, F Borsa, S Budko, P Canfield, S Jun, JK Jung, P Kögler, D Mentrup, A Müller, R Modler, D Procissi, BJ Suh, and M Torikachvili
Phys. Rev. B 66, 054407 (2002)
[PDF]