User:Julius B. Lucks

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I am a recent(!) PhD from Harvard, where I worked on problems in biophysics related to viruses with David Nelson. During my PhD, I became interested in problems ranging from structural properties of viral capsids (and the underlying theory of geometrical defects in curved lattices that is required), to understanding phage genomics.

Currently, I am about to start a position at the Physics Preprint arXiv at Cornell with Paul Ginsparg, where I will stay until I start a Miller Fellowship with Adam Arkin in January '08. In addition to reading up on potential post-doc projects, I am a co-chair of the OWW Outreach Effort where we are coordinating local outreach officers to actively recruit new members to the OWW community. Interested in becoming a local outreach member? - contact us!

I am spending most of my free time writing a game for the $100 Laptop as part of the One Laptop Per Child Project.

Academics

Check out my oww home page for more info on the projects I am working on.

Interests

In addition to biophysics, I am becoming more and more fascinated with how the internet can be used to make some of the common tasks in science more efficient. I enjoy thinking about topics such as:

How to make the literature system more efficient through better user interfaces to searching. To address this, a group of friends and I got together and made mapLit. mapLit is a new way to visualize literature search results that uses nested tree views for displaying related articles in context. There are also convenience features that allow easy annotation of search results, saving of search results to work offline and share results, and the ability to connect saved searches online at a later date. We appreciate any feedback on mapLit!
Low-overhead customizable databases for quick and flexible organization of data. If you are interested in this topic, please add your comments to OpenWetWare:Software/Flexible_Science_Databases.
Using the internet for fast publication of results.
- Broad community ranking of the usefulness/integrity of such results.

I hope to continue working on some of these ideas at the arXiv.

I recently started a project (with the same group of friends) making a game for the $100 Laptop as part of the One Laptop Per Child Project. The game is a generalization of classic Number Munchers, with question content derived from a whole range of topics including learning numbers, arithmetic, spelling, vocabulary, you name it!

Tools I Like

Python
- Eric Raymond's thoughts on Python vs. Perl
Perl
- Perl-CGI - check out The Pica Literature Database
Ruby on Rails
- If you haven't seen the screencasts, they will blow your mind.

I have always wanted to write a series of articles on great scientific tools. I have started one, Scientific Pipelines, that I hope turns into a nice resource for someone just entering into scientific programming.

Despite the languages listed above, I recently took the 'Which Programming Language Are You?' quiz, and found out that <html> <a href="http://www.bbspot.com/News/2006/08/language_quiz.php"><img src="http://www.bbspot.com/Images/News_Features/2006/08/language/lisp.jpg" width="300" height="90" border="0" alt="You are Lisp. Very few people like you (Probably because you use too many parenthesis (You better stop it (Reallly)))"><br>Which Programming Language are You?</a> </html> Lisp has been on my list to learn for a while now - even more reason to do so.

Inspiration

There are some really great thinkers out there ...

Paul Graham's essays are fantastic. He has a lot to say about young people full of creative energy - from how they like to work, to common pitfalls they encounter. If any of you have a need to hear some advice from someone who understands the way you think and work, check these out. In particular I like:

OpenWetWare

My Contributions

Science

Research

My specific projects deal with

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

Ph. D. candidate in chemical physics at Harvard University.
M. Phil. in theoretical physics at the CUC3 at Cambridge University (Churchill College).
B.S. in chemistry (Math minor) at the University of North Carolina at Chapel Hill.

Publications

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)

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

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

J. B. Lucks, D. R. Nelson, G. Kudla, J. B. Plotkin. Genome landscapes and bacteriophage codon usage.

Arxiv: arXiv:0708.2038v1 (q-bio.GN) (FREE)