Highlights

Mechanistic origin of cell-size control and homeostasis in bacteria
Fangwei Si, Guillaume Le Treut, John T Sauls, Stephen Vadia, Petra Anne Levin and Suckjoon Jun
Current Biology, 29, 1-11 (2019)
[online][PDF][Google Scholar][UCSD news]

Video abstract explaining the mechanistic origin of adder.
Fundamental Principles in Bacterial Physiology - History, Recent progress, and the Future with Focus on Cell Size Control: A Review
Suckjoon Jun, Fangwei Si, Rami Pugatch and Matthew Scott
Reports on Progress in Physics (2018)
[online][PDF][arXiv Preprint (PDF)]
A comprehensive overview of bacterial physiology focusing on the fundamental problems of the field, with extensive reference to milestones that shaped the field from the inception of the field to the most up-to-date developmnent.
Invariance of initiation mass and predictability of cell size in Escherichia coli
Fangwei Si*, Dongyang Li*, Sarah E. Cox, John T. Sauls, Omid Azizi, Cindy Sou, Amy B. Schwartz, Michael J. Erickstad, Yonggun Jun, Xintian Li and Suckjoon Jun
Current Biology, 2017
[OPEN ACCESS (PDF)][Download full dataset][UCSD News][phys.org]
We proposed the "unit cell" as the fundamental building block of cell size and its invariance underlies the predictability of cell size using the general growth law.
Cell-size control and homeostasis in bacteria
S. Taheri-Araghi, S. Bradde, J. T. Sauls, N. S. Hill, P. A. Levin, J. Paulsson, M. Vergassola, and S. Jun
Current Biology 25(3), 385–391, 2015
[online] [PDF+extended SI] [Google Scholar] [news coverage] [download data]
Cell-size maintenance: universal strategy revealed
S. Jun & S. Taheri-Araghi
Trends in Microbiology 23(1), 4–6, 2015
[online] [PDF] [Google Scholar]
Cell-size Control and Maintenance We believe these two articles together establish a fundamental quantitative 'adder' principle for size control and homeostatis, one of the long-standing questions in biology.
Size convergence by the Adder principle
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] [Google Scholar]
[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] [Google Scholar]
[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] [Google Scholar]
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]
[Google Scholar]
[The Scientist Top 7 Biology]
[The Scientist Top 7 Biochemistry]
[download data]
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.

Just Published and Upcoming

2023_Boesen_bioRxiv Robust control of replication initiation in the absence of DnaA-ATP ⇋ DnaA-ADP regulatory elements in Escherichia coli
Thias Boesen, Godefroid Charbon, Haochen Fu, Cara Jensen, Michael Sandler, Suckjoon Jun, and Anders Lobner-Olesen, bioRxiv (2023)
[online]
  Temperature Compensation through Kinetic Regulation in Biochemical Oscillators
Haochen Fu, Chenyi Fei, Qi Ouyang, Yuhai Tu, arXiv (2024)
[online]
2023_Fu_PRXlife Bacterial Replication Initiation as Precision Control by Protein Counting
Haochen Fu, Fangzhou Xiao, Suckjoon Jun, PRX Life (2023)
[online][Viewpoint]
  Robust and resource-optimal dynamic pattern formation of Min proteins in vivo
Ziyuan Ren, Henrik Weyer, Laeschkir Würthner, Dongyang Li, Cindy Sou, Daniel Villarreal, Erwin Frey, Suckjoon Jun, bioRxiv (2023)
[online]
  Tools and methods for high-throughput single-cell imaging with the mother machine
Ryan Thiermann, Michael Sandler, Gursharan Ahir, John T. Sauls, Jeremy W. Schroeder, Steven D. Brown, Guillaume Le Treut, Fangwei Si, Dongyang Li, Jue D. Wang, Suckjoon Jun, bioRxiv (2023)
[online]
  Microbiology: How to Bridge Mechanisms and Phenomenology
Suckjoon Jun, Editorial for a special issue of JMB (2020)
[online]
  Single-cell data and correlation analysis support the independent double adder model in both Escherichia coli and Bacillus subtilis
Guillaume Le Treut, Fangwei Si, Dongyang Li and Suckjoon Jun, bioRxiv (2020)
[online][Jupyter notebook]
  Comment on ‘Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism’
Fangwei Si, Guillaume Le Treut, Dongyang Li and Suckjoon Jun, bioRxiv (2020)
[online][Jupyter notebook]
  Mother machine image analysis with MM3
John T. Sauls, Jeremy W. Schroeder, Steven D. Brown, Guillaume Le Treut, Fangwei Si, Dongyang Li, Jue D. Wang, Suckjoon Jun
bioRxiv (2019)
[online]
  Control of Bacillus subtilis Replication Initiation during Physiological Transitions and Perturbations
John T. Sauls, Sarah E. Cox, Quynh Do, Victoria Castillo, Zulfar Ghulam-Jelani, Suckjoon Jun
mBio, 10, e02205-19 (2019)
[online][PDF]
Si2019CurrBio Mechanistic origin of cell-size control and homeostasis in bacteria
Fangwei Si, Guillaume Le Treut, John T Sauls, Stephen Vadia, Petra Anne Levin and Suckjoon Jun
Current Biology, 29, 1-11 (2019)
[online][PDF][Google Scholar][UCSD news]
  Cell boundary confinement sets the size and position of the E. coli chromosome
Fabai Wu, Pinaki Swain, Louis Kuijpers, Xuan Zheng, Kevin Felter, Margot Guurink, Jacopo Solari, Suckjoon Jun, Thomas S. Shimizu, Debasish Chaudhuri, Bela Mulder* and Cees Dekker*
Current Biology, 29, 2131-2144.e4 (2019)
[online]
SaulsMSB2018 Synthesis and degradation of FtsZ quantitatively predicts the first cell division in starved bacteria
K. Sekar, R. Ruscon, JT Sauls, T. Fuhrer, E. Noor, J. Nguyen, VI Fernandez, MF Buffing, M. Berney, S. Jun, R. Stocker, U. Sauer
Mol. Sys. Biol., (2018) 14, e8623
[online][PDF][Google Scholar][ETHZ news]
  Promoting an "Auteur Theory" for Young Scientists: Preserving Excitement and Creativity
Arshad Desai and Suckjoon Jun
BioEssays, 1800147, (2018)
[PDF]
  Fundamental Principles in Bacterial Physiology - History, Recent progress, and the Future with Focus on Cell Size Control: A Review
Suckjoon Jun, Fangwei Si, Rami Pugatch and Matthew Scott
Reports on Progress in Physics (2018)
[online][PDF][Google Scholar][arXiv Preprint (PDF)]
  Protocol for Construction of a Tunable CRISPR Interference (tCRISPRi) Strain for Escherichia coli
Xintian Li, Cindy Sou, and Suckjoon Jun
BIO-PROTOCOL 7(19):e2574 (2017).
[online]
  A fundamental unit of cell size in bacteria
Suckjoon Jun and Michael Rust
TRENDS in Genetics 33, 433-435 (2017)
[online][PDF]
Unit Cell Invariance of initiation mass and predictability of cell size in Escherichia coli
Fangwei Si*, Dongyang Li*, Sarah E. Cox, John T. Sauls, Omid Azizi, Cindy Sou, Amy B. Schwartz, Michael J. Erickstad, Yonggun Jun, Xintian Li and Suckjoon Jun
Current Biology (2017)
[OPEN ACCESS (PDF)][Download full dataset][Google Scholar][UCSD News][phys.org][ScienceDaily][KENNISLINK (in Dutch!)][Commentary in Current Biology]
  tCRISPRi: tunable and reversible, one-step control of gene expression
Xintian Li, Yonggun Jun, Michael J. Erickstad, Steven D. Brown, Adam Parks, Donald L. Court, and Suckjoon Jun
Scientific Reports 6, 39076 (2016)
[PDF][Google Scholar][strain request]
  Adder and a coarse-grained approach to cell size homeostasis in bacteria
John T Sauls, Dongyang Li, and Suckjoon Jun
Current Opinion in Cell Biology 38:38-44 (2016)
[online][PDF][Google Scholar]
  Self-Consistent Examination of Donachie's Constant Initiation Size at the Single-Cell Level
Sattar Taheri
Frontiers in Microbiology 6:1349 (2015)
[online]
  Single-cell cultivation in microfluidic devices
Sattar Taheri-Araghi and Suckjoon Jun
Hydrocarbon and Lipid Microbiology Protocols, Springer Protocols Handbooks, doi:10.1007/8623_2015_68 (2015)
[online]
  Single-cell physiology
Sattar Taheri, Steven Brown, John T. Sauls, Dustin McIntosh, Suckjoon Jun
Annual Review of Biophysics 44, 123-142 (2015)
[download] [Google Scholar]
  Complete Genome Sequence of Escherichia coli NCM3722
S. D. Brown and S. Jun
Genome Announc 3(4):e00879-15. doi:10.1128/genomeA.00879-15. [online][Google Scholar][strain request]
Cell-size control and maintenance Cell-size control and homeostasis in bacteria
S. Taheri-Araghi, S. Bradde, J. T. Sauls, N. S. Hill, P. A. Levin, J. Paulsson, M. Vergassola, and S. Jun
Current Biology 25(3), 385–391, 2015
[online] [PDF+extended SI] [Google Scholar] [news coverage] [download data]
Cell-size maintenance: universal strategy revealed
S. Jun & S. Taheri-Araghi
Trends in Microbiology 23(1), 4–6, 2015
[online] [PDF] [Google Scholar]
Chromosome, cell cycle, and entropy Chromosome, cell cycle, and entropy
S. Jun.
Biophysical Journal 108(4), 785-786, 2015
[online] [PDF] [from the cover]

Publications

[La Jolla, CA, 2013-]
Bending stresses plastically deform growing bacterial cell walls

Q: How does E. coli control its shape?

Bending forces plastically deform growing bacterial cell walls
Ariel Amir, Farinaz Babaeipour, Dustin McIntosh, David Nelson, and Suckjoon Jun
Proc. Nat. Acad. Sci. USA 111, 5778-5783, 2014
[open access full article] [News in Nature Physics] [Google Scholar]
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] [Google Scholar]
[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] [Google Scholar]
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] [Google Scholar]
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] [Google Scholar]
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] [Google Scholar]
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] [Google Scholar] [Small Things Considered]
[The Scientist Top 7 Biology] [The Scientist Top 7 Biochemistry] [download data]
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] [Google Scholar]
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] [Google Scholar]
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] [Google Scholar]
[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] [Google Scholar]
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] [Google Scholar]
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] [Google Scholar]
[Vancouver, BC, 1999-2004]
Ch. 4. 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] [Google Scholar]
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] [Google Scholar]
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] [Google Scholar]
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] [Google Scholar]
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] [Google Scholar]
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] [Google Scholar]
Kinetic model of DNA replication in eucaryotic organisms Kinetic model of DNA replication in eucaryotic organisms
John Herrick, Suckjoon Jun, John Bechhoefer, and Aaron Bensimon
J. Mol. Biol. 320, 741-750 (2002)
[PDF] [Google Scholar]
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] [Google Scholar]
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