User:Julius B. Lucks

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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 cells 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 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

Education

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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