Movies

Periodic production of green fluorescent-fusion division proteins.
Size convergence by the Adder principle.
Fluorescent E. coli growing in the mother machine. Wang et al, Current Biology, 2010.
JT Sauls talks about what he does for qBio and the Jun Lab. See more at the qBio homepage.
James Pelletier is a Hertz Fellow :)
Lysis of exponential phase E. coli cells.
Chromosome compression in the micropiston.
How to make the mother machine.
How to make an oxygen plasma cleaner under $500 (we paid about $10K).
How to duplicate the mother machine using epoxy.

Jun Lab in Quantitative Biology at UCSD


Are you interested in joining the lab? Read this.

[December, 2023] It has been some time since we updated the research section of our website, so I’m writing this note to give you a general idea of how my lab operates and the type of people we welcome. First and foremost, my lab consistently attracts top students and postdocs who are exceptional in their unique ways. They go on to secure fulfilling positions in both academia and industry, ranging from top students in China to a former Googler who chose to leave his prestigious job for graduate school. If you’re passionate about science and eager to pioneer new research frontiers, I encourage you to reach out to me, regardless of your background, training, gender, or skin color.

Regarding our research: You might not find the most current information on this page. On any given day, we’re tackling several groundbreaking, high-risk/high-reward research problems. By the time our findings are published, it’s likely we’ve already been working on something new for several years. The impact of our work is clear from the number of citations each of our papers receives.

If you’re a prospective graduate student: This dynamic can pose a challenge. Therefore, the best—and perhaps only—way to learn about what our junior researchers are doing is by speaking with us directly. Almost all the students in my lab initially came to UCSD Physics with different intentions but chose to stay after experiencing a rotation in my lab. Once you join the lab, expect to find that your lab mates will become lifelong friends. You’ll be engaged in a challenging yet intriguing problem, chosen collaboratively by you and me, after experimenting with various mini-projects. My role is to create a safe and supportive environment, encouraging you to fearlessly pursue ‘crazy’ ideas in research.

If you’re a prospective postdoc: You probably already have some insight into our lab. Most postdocs here aspire to become professors or research group leaders, and our lab has a strong track record in facilitating these career paths. If you’re interested, I invite you to contact me for an informal discussion and inquiry.

Examples of our current interest:
  • We have been revisiting some of the classic problems in biological physics using a physiological framework. This allows us to ask new kinds of questions, which sometimes leads to fundamental scientific discoveries.
  • We are also very interested in problems of resource allocations. The current paradigm is based on the model bacterial organism Escherichia coli. In the past 5+ years, we have been learning that E. coli represents a special case of far more general and fundamental principles of cellular resource allocation.
  • We have been working on eukaryotes for almost 5 years! You will need to contact us for more information.
  • We also work with minimal cells with a collaborator at JCVI.
  • We also develop tools and methods when we need them but they don’t exist yet. Well-known examples include our invention of the mother machine and image analysis pipeline or the high-precision tunable CRISPRi method.
  • Just Published and Upcoming


    "Fundamental decoupling of proteome partitioning and metabolic flux in bacteria"
    Ryan Thiermann*, Jin Yang*, Taylor Rytlewski, Aniket Zodage, Farshad Abdollah-Nia, Fangzhou Xiao, John T. Sauls, Sarah Cox, Zulfar Ghulam-Jelani, Victoria Castillo, James R. Williamson, David M. Stevenson, Daniel Amador-Noguez, Jue D. Wang**, Suckjoon Jun** [in preparation, 2024]
    "Temperature Compensation through Kinetic Regulation in Biochemical Oscillators"
    Haochen Fu*, Chenyi Fei, Qi Ouyang, and Yuhai Tu**  [PNAS (2024)]
    "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** [Elife (2024)]
    "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, 2024]
    "Bacterial Replication Initiation as Precision Control by Protein Counting"
    Haochen Fu*, Fangzhou Xiao*, Suckjoon Jun** [PRX Life (2023)] [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]
    "Deriving principles of precision control in biology from replication initiation in bacteria"
    Haochen Fu*, Dongyang Li*, Fangzhou Xiao, Xintian Li, Suckjoon Jun** [in preparation]
    "Quantitative examination of five stochastic cell-cycle and cell-size control models for Escherichia coli and Bacillus subtilis"
    Guillaume Le Treut, Fangwei Si, Dongyang Li, and Suckjoon Jun [Frontiers in Microbiology (2021)]
    "Microbiology: How to Bridge Mechanisms and Phenomenology"
    Editorial for a special issue of JMB
    Suckjoon Jun (2020)
    [in press]
    "Comment on ‘Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism"
    Guillaume Le Treut, Fangwei Si, Dongyang Li, and Suckjoon Jun (2020) [bioRxiv]
    -- Updated version [bioRxiv] [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 and Suckjoon Jun (2019)
    [bioRxiv] - this is our lab's main image analysis pipeline
    "Control of Bacillus subtilis Replication Initiation during Physiological Transitions and Perturbations" John T. Sauls, Sarah E. Cox, Quynh Do, Victoria Castillo, Zulfar Ghulam-Jelani and Suckjoon Jun, mBio, 10, e02205-19 (2019)
    [online][PDF]
    "Mechanistic origin of cell-size control and homeostasis in bacteria"
    Fangwei Si, Guillaume Le Treut, John T Sauls, Stephen Vadia, Petra A. Levin and Suckjoon Jun, Current Biology, 29, 1-11 (2019)
    [Google Scholar][online][PDF][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)
    "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 and U. Sauer, Mol. Sys. Biol. 14, e8623 (2018)
    [Google Scholar][online][PDF][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)
    [Google Scholar][online][PDF][arXiv]
    "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. [online]
    "A fundamental unit of cell size in bacteria," Suckjoon Jun and Michael Rust, TRENDS in Genetics 33, 433-435, (2017). [online][PDF]
    "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 27, 1278–1287 (2017).
    [Google Scholar][OPEN ACCESS (PDF)][UCSD News][phys.org][ScienceDaily][KENNISLINK (in Dutch!)][Commentary in Current Biology]
    [ Download full dataset ]
    Unit cell
    "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).
    [Google Scholar][PDF][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).
    [Google Scholar][online][PDF]

    Select Recent Publications


    "Single-cell physiology," Sattar Taheri, Steven Brown, John T. Sauls, Dustin McIntosh, Suckjoon Jun, Annual Review of Biophysics, 44, 123-42 (2015). [download] [Google Scholar]
    S. Taheri-Araghi, S. Bradde, J. T. Sauls, N. S. Hill, P. A. Levin, J. Paulsson, M. Vergassola, and S. Jun, Current Biology (2014)

    [Google Scholar][online] [PDF+extended SI]
    [news coverage] [download data]

    Size convergence
    "Cell-size maintenance: universal strategy revealed," S. Jun & S. Taheri-Araghi, Trends in Microbiology (2014) [Google Scholar][online][PDF]
    "Bending forces plastically deform growing bacterial cell walls," A. Amir, F. Babaeipour, D. McIntosh, D. R. Nelson, S. Jun, Proc. Nat. Acad. Sci. USA (2014).
    Bending forces plastically deform growing bacterial cell walls
    "The bacterial chromosome: a physical biologist’s apology. A perspective." Appeared in Small Things Considered [click] (2014).
    The bacterial chromosome: a physical biologist’s apology. A perspective.
    [Link to David Goodsell’s new high-resolution E. coli illustration]
    "The multi-fork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer,"
    B. Youngren, H. J. Nielsen, S. Jun, and S. Austin, Genes & Development (2014).
    The multi-fork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer
    "Physical manipulation of the Escherichia coli chromosome reveals its soft nature," Pelletier & Halvorsen et al., PNAS Plus (2012).
    Physical manipulation of the Escherichia coli chromosome reveals its soft nature
    "Entropy as the driver of chromosome segregation," S. Jun and A. Wright, Nat. Rev. Microbiol. (2010)
    [Google Scholar] [online] [PDF] [Small Things Considered]
    Entropy as the driver of chromosome segregation
    "Robust growth of Escherichia coli," Wang et al., Curr. Biol. (2010)
    [Google Scholar][online] [PDF] [F1000] [Small Things Considered][The Scientist Top 7 Biology]
    [The Scientist Top 7 Biochemistry] [download data]
    Robust growth of Escherichia coli

    News

    [pinned] Our lab is the 2022 laureate of the Biophysical Society's Bárány award 2022!(October 4, 2021); We are most proud of and happy for Fangwei Si (2015-present), who will start his own lab at Carnegie Mellon University in summer 2022 as an assistant professor of physics.  (June 14, 2021)

    We welcome a new grad student, Michael Sandler, to our lab. In the era of “doom and gloom” and “goodbye academia,” Michael left his job at Google last year to become a graduate student. He will be exploring minimal cells with John Glass at JCVI. (September, 2022)

    We welcome our new postdoc Fangzhou! He recently graduated from Caltech, and will conduct experiments to test his fantastic theories. (July, 2022)

    Thias, a PhD student of Anders Lobner Olesen (U. Copenhagen) has arrived to do cool experiments! (March, 2022)

    We have been awarded Chan Zuckeberg Initiative's napari plugin project grant. This will allow us to distribute our mother machine analyzer to a broad research community via the napari ecosystem. We will add Jupyter notebook and video tutorials. Give us max 6 months. (November, 2021)

    We will be at the GRC Stochastic Physics in Biology to present new results from multiple projects.(September 21, 2021)

    We are organizing a meeting on quantitative microbial physiology in June, 2022 in its birth place -- Copenhagen, Denmark. (September 21, 2021)

    We have multiple postdoc positions. See JOIN US below for more information.(June, 2021)

    We are sad that Dongyang is leaving us after 5 years, but happy that he will be joining Michael Elowitz's lab at Caltech as a postdoc. We have been lucky that JT and Dongyang - our first two PhD students - have set a very high standard in intellect/creativity, fearlessness, and collegiality. (March, 2021)

    Best wishes to Fangwei and Guillaume, who revealed the mechanistic principles of size control in bacteria. Fangwei has moved to our neighbor friend's lab, Lisa Racki at TSRI across the street. And Guillaume a little farther to Chan Zuckerberg Biohub in San Francisco as a scientist. They both will remain as close collaborators of the lab. (November, 2020)

    Congratulations to Saransh Umale, who has just been selected for the Ray Thomas Edwards Award based on his excellent performance in research by the division of Biological Sciences at UCSD. Very well deserved!  (September 14, 2020)

    Great news for the lab: the first Ph.D from our lab, JT, has become Head of Bioengineering at the research-centric startup in Cambridge, MA, PhAST. We are really proud of JT! 

    We also welcome two new exceptionally strong PhD students in physics to the lab, Aaron Ren and Haochen Fu! Will update lab members page hopefully soon. (September, 2020)

    Congratulations to Orianna, she is one of the 33 recipients of 2019-2020 UC San Diego Physical Sciences Dean’s Undergraduate Award for Excellence, out of nearly 4,000 undergraduate majors in the Departments of Chemistry and Biochemistry, Mathematics, and Physics! (Nov, 2019)
    JT has defended and officially become a PhD. Congratulations Dr. Sauls! (Sept, 2019)
    BREAKING NEWS: We have made our image analysis package for mother machine experiments publicly available. See MOTHER-MACHINE IMAGE ANALYSIS on the top of our site. More information to follow in the 2nd half of 2019. (Aug, 2019)
    Welcome aboard Saransh Umale! Saransh is a PhD student in the biology graduate program at UCSD. (May, 2019)
    Welcome Tejal Agarwal as a visiting PhD student from IISER Pune (India)! Tejal will be working on chromosome organization here for six months. (March, 2019)
    Dongyang defended his PhD thesis! (December, 2018)
    We welcome new graduate student Ryan Thiermann to join the lab! We welcome Liyana Valiya Peedikakkal to come back as a postdoc! (October, 2018)
    We welcome Mikkel Svenningsen from Niels Bohr Institute in Denmark for a 3-month visit. (February, 2018)
    Our review on bacteria physiology is accepted to Reports on Progress in Physics (ROPP), check it out on our publication page! (January, 2018)
    The lab had a road trip to San Francisco! (December, 2017)
    Our undergrad lab alumni are moving on to the next stage in their academic lives. Eden Aklile will start at Northwestern and Zulfar Ghulam-Jelani at Duke in their respective top programs. We wish them all the very best! (August, 2017)
    We now have a revamped research webpage. (June, 2017)
    Suckjoon has been promoted to Associate Professor with tenure. Congratulations! (May, 2017)
    We welcome our new postdoc Guillaume Le Treut, from Commissariat à l'énergie atomique et aux énergies alternatives (CEA, Paris, France). (February, 2017)
    We welcome Jacopo Solari, a PhD student from AMOLF for a 3-month visiting. (January, 2017)
    Congratulations to graduating senior Amy Schwartz. She has been awarded the UCSD Physics Dept's John Holmes Malmberg Prize. Amy will enter graduate school here at UCSD in the fall. (June, 2016)
    Dr. Ashley Cadby arrived from the University of Sheffield, UK for a 6-month sabbatical with us. (February 1, 2016)
    We welcome Kazuki Yoda, a visiting undergraduate from the University of Tokyo, for a 3-month internship. (January 19, 2016)
    Many congratulations to Sattar! He will join California State University Northridge in the Fall as an Assistant Professor in Physics. (July, 2015)
    We welcome two new postdocs, Jia-Wei from Cornell and Fangwei from Johns-Hopkins. They will start in September. (July, 2015)
    Many congratulations to Yonggun Jun! After considering multiple offers, he has decided to join National Central University in Taiwan as a faculty member in biophysics in 2016. We are happy for his new chapter in life and career. (May, 2015)
    Benjamin just arrived from École Normale Supérieure (Paris, France) for 6-month internship. (February 20, 2015)
    Suckjoon has been selected as a Scialog Fellow for Scialog: Molecules Come to Life by Research Corporation and Gordon & Betty Moore Foundation. (July 16, 2014)
    Suckjoon has been awarded a 5-year NSF CAREER Award (MCB, $1.15M) Cell cycle and cell size control in bacteria. (July 22, 2013)
    Suckjoon has been named one of the 22 Pew Scholars. [UCSD News] [Press Release] (June 13, 2013)
    Our lab alumnus (at Harvard), James Pelletier (now at MIT), has been named a Hertz Fellow. Congratulations! (April 15, 2013)
    Thanks to the Paul G. Allen Foundation, Suckjoon is one of the five Allen Distinguished Investigators. [UCSD News] [Seattle Times] [Xconomy] (February 28, 2013)
    Thanks to Brendan at UCSD Physics IT, the beta version of our web site is ready for public. (November 13, 2012)
    Our lab has officially moved from Harvard to UCSD. The new lab space at UCSD is currently under construction in Urey Hall 6249-6253, to be completed before next year. (October 4, 2012)
    James' paper has just appeared online at PNAS. Highlight or full article. (September 14, 2012)
    Jean-Yves Bouet (CNRS) visited us. (June 8-12, 2012)
    Another brave theoretical physicist, Ariel Amir (Harvard Junior Fellow), will start his adventure in experimental physical biology. (May 2, 2012)
    Stuart Austin (NCI) and Henrik Nielsen will be visiting us to discuss bacterial chromosomes. (April 25-28, 2012)
    Please visit The Cost of Knowledge (boycott Elsevier), and sign, if you agree.
    It will take some serious courage, especially for junior scientists, since Elsevier owns Cell, Current Biology, and many others.
    For background information, read the blogposts by Tom Gowers , Terence Tao, HMS; articles in the Guardian, NYT, the Boston Globe.
    If you want to have a good laugh, investment firms seem to know a lot about Open Access Movement -- read this. (April 22, 2012)
    Suckjoon will be giving a keynote speech at the Chemical Biophysics Symposium in Toronto, Canada. (April 13-15, 2012)
    Sattar has been accepted to Advanced Bacterial Genetics course at Cold Spring Harbor Laboratory.
    Intense 3 weeks in June! (April 2, 2012)
    Petra Levin (Washington Univ., St Louis) visited us to discuss bacterial cell cycle in E. coli and B. subtilis. (January 6-7, 2012)
    The complete data sets for the mother machine paper are available for download.
    Please see here or here before writing us with requests. Thanks. (November 28, 2011)
    Muyoung Heo has been selected as one of the 15 Fellows in natural sciences awarded by the President of Korea.
    It is a great deal and it comes with a very generous package for his future research. (August 30, 2011)

    Current Lab Members [link]

    • • Aaron Ren
        graduate student, Physics; B.Sc, UC San Diego
    • • Aman Sharma
        graduate student, Physics; B.Sc, IIT Bombay
    • • Aniket Zodage
        graduate student, Physics
    • • Cara Jensen (UG, physics/biophysics)
    • • Fangzhou Xiao
         postdoc; Ph.D, John Doyle group @ Caltech
    • • Haochen Fu
        graduate student, Physics; B.Sc, Peking Univ.
    • • Michael Sandler
        graduate student, Physics; previously at Google/YouTube
    • • Ryan Thiermann
        graduate student, Physics; B.Sc, U. of Chicago
    • • Saransh Umale
        graduate student, Physics; B.Sc, IIT Madras
    • • Suckjoon Jun (Professor of Physics)
    • • Taylor Rytlewski (UG, physics/biophysics)
    •  

    RECENT ALUMNI

    • • Gursharan Ahir (Computer Science, MSc 2022')
        Present: Google
    • • Fangwei Si (Ph.D, Johns Hopkins 2016; Postdoc 2016-2022)
        Present: Assistant Professor of Physics
        Carnegie Mellon University
    • • Guillaume Le Treut (Ph.D., Saclay 2017; Postdoc 2017-2021)
        Present: Scientist, Chan Zuckerberg Biohub
    • • Dongyang Li (PhD 2018’ + postdoc 2018-20')
         Present: Postdoc (Elowitz lab)
        California Institute of Technolgy
    • • John T. Sauls (PhD 2019', Jun Lab)
        Present: Head Of Engineering - PhAST

    Join Us

    Interested students and postdocs should contact Prof. Jun.

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