User:Julius B. Lucks

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Revision as of 22:47, 2 December 2008 by Julius B. Lucks (talk | contribs) (CV: added pycon 2008 presentation)
Julius B. Lucks

I am a Miller Fellow at the University of California, Berkeley. With Adam Arkin, I am working on developing genetic systems that compute. I am also part of the project, where I am the lead developer of the applications programming interface. You can reach me at jblucks at berkeley dot edu.


As a recent Miller Fellow, I have become interested in studying and developing biological genetic circuits that can perform programmable computations. While I don't think cellular based computing can rival the speed of silicon computing, I do believe that a cellular system that can be programmed is an extremely powerful tool for applications we can only begin to imagine. In its simplest incarnation, programmatic control of gene expression would be an invaluable tool for metabolic engineers trying to coax bacteria into producing therapeutics. More creatively, we might see bacterial cells that can form patterns with each other, and carry out instructions once specific patterns are formed.

Recent work suggests that these goals are indeed feasible, but that we are in the exciting beginnings of this adventure! For more information, see the work of Jay Keasling on producing anti-malarial drugs inside bacteria, and Ron Weiss on pattern-forming bacteria.

In addition to scientific research, I am involved in projects aimed at improving the general science landscape.

  • With Lorrie LeJeune, I helped to start OpenWetWare's Open Writing Projects. As a first article, I have written an introduction to the Python programming language for scientists - Python, All A Scientist Needs.
  • I am also the lead developer of the API, which allows easy, programmatic access to the vast amounts 'open source' scientific information housed at The API allows software developers to include information, thereby giving scientists easy to use tools to access scientific literature. It also paves the way for creative uses of the information, and the creation of better search interface tools.

For my PhD, I worked in the area of biophysics with David Nelson, where we used theoretical physics to study problems related to

  • Unzipping DNA at a constant force
  • Translocating RNA through nanopores
  • Geometrical Defects in curved, two-dimensional crystals (related to viral capsids)
  • Phage genome landscapes - a way to visualize important genomic features

Keeping Up to Date


Julius B. Lucks

Miller Fellow
Department of Bioengineering
University of California Berkeley
309 Hildebrand Hall
mailcode 5230
Berkeley, CA 94720
jblucks at berkeley dot edu



Honors and Awards

  • Robert Karplus Prize in Chemical Physics, Harvard University (2002)
  • Francis P. Venable Medal, University of North Carolina Chapel Hill (2001)
  • Academic Excellence in Physical Chemistry, University of North Carolina Chapel Hill (2001)
  • Phi Beta Kappa, University of North Carolina Chapel Hill, 2000
  • American Chemical Society Undergraduate Research Award, University of North Carolina Chapel Hill (1999)


J. B. Lucks, L. S. Qi, W. Whitaker, A. P. Arkin. Toward scalable parts families for predictable design of biological circuits., Current Opinion in Microbiology, 11, 567-573, 2008.

DOI: 10.1016/j.mib.2008.10.002 (Not Free)

J. B. Lucks Python - All a Scientist Needs, 2008.

OWW: Article Page (FREE)
Arxiv: arXiv:0803.1838 (q-bio.QM) (FREE)
Video (Pycon 2008 Presentation)

J. B. Lucks, D. R. Nelson, G. Kudla, J. B. Plotkin. Genome landscapes and bacteriophage codon usage, PLoS Computational Biology, 4, 1000001, 2008.

DOI: 10.1371/journal.pcbi.1000001 (FREE)
Arxiv: arXiv:0708.2038v1 (q-bio.GN) (FREE)

J. B. Lucks, Y. Kafri. Dynamics of RNA Translocation through a Nanopore, 2007.

Arxiv: q-bio.BM/0703028 (FREE)

V. Vitelli, J. B. Lucks, D. R. Nelson. Crystallography on Curved Surfaces. PNAS, 103, 12323-12328, 2006.

DOI: 10.1073/pnas.0602755103 (FREE)
Arxiv: cond-mat/0604203 (FREE)

J. D. Weeks, J. B. Lucks, Y. Kafri, C. Danilowicz, D. R. Nelson and M. Prentiss. Pause Point Spectra in DNA Constant-Force Unzipping, Biophysical Journal, 88, 2752-2765, 2005.

DOI: 10.1529/biophysj.104.047340,
Arxiv: cond-mat/0406246 (FREE)


J. B. Lucks Python - All a Scientist Needs, Pycon 2008, Chicago. (Video)

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