User:Julius B. Lucks

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 arXiv.org project, where I am the lead developer of the applications programming interface. You can reach me at jblucks at berkeley dot edu.

Research/Projects

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 drugs. 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 arXiv.org API, which allows easy, programmatic access to the vast amounts 'open source' scientific information housed at arXiv.org. The API allows software developers to include arXiv.org 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

CV

Julius B. Lucks

Miller Fellow
Department of Bioengineering
University of California Berkeley
309 Hildebrand Hall
mailcode 5230
Berkeley, CA 94720
510-643-5683
jblucks at berkeley dot edu

Education

• Miller Fellow, University of California Berkeley (2008)
  • Mentor: Adam Arkin
• PhD, Harvard University (2002-2007)
  • Chemical Physics
  • Advisor: David Nelson
  • Committee: Dudley Herschbach, Eric Heller, Eugene Shakhnovich
  • Thesis: Biophysics of Polynucleotide Unzipping, Viral Codon Usage and Crystalline Defects
• MPhil Cambridge University Churchill College (2001-2002)
  • Theoretical Chemistry
  • Advisor: Nicholas Handy
  • Committee: Ali Alavi, David Tozer
• BS University of North Carolina at Chapel Hill (1997-2001)
  • Chemistry, Highest Honors
  • Mathematics Minor
  • GPA 3.97

Fellowships

Honors and Awards

Publications

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

OWW: Article Page (FREE)

Arxiv: arXiv:0803.1838 (q-bio.QM) (FREE)

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.

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)

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