User:Julius B. Lucks
I am a graduate student of David Nelson at Harvard University working on problems in biophysics related to viruses. We are 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.
At the moment I am in the OWW Publishing Working Group where we are discussing alternative publishing models and OWW involvement in them.
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.
Tools I Like
- Eric Raymond's thoughts on Python vs. 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.
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:
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
- 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.
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.
V. Vitelli, J. B. Lucks, D. R. Nelson. Crystallography on Curved Surfaces. PNAS, 103, 12323-12328, 2006.
J. B. Lucks, Y. Kafri. Dynamics of RNA Translocation through a Nanopore.
- Arxiv: q-bio.BM/0703028 (FREE)
My email address is firstname.lastname@example.org, or you can email me through OWW.