Julius B. Lucks

As a Miller Fellow, I have become interested in RNA-based mechanisms that regulate gene expression, and in particular how the interplay between RNA structure and function can be engineered to create a platform for the scalable control of gene expression.  One of the most thrilling aspects of this work is that it is at the interface between basic science and engineering.  On the basic science side, we use computational structure prediction and in-vivo mutation analysis and screening to uncover RNA-RNA binding and folding pathways that are at the core of these regulatory mechanisms.  Information gleaned from these mechanistic studies are then used to develop more general engineering principles, where we make targeted changes to the RNA molecules to design RNA motifs that have tunable function, can act orthogonally inside the same cell, are both physically and functionally composable, and that ultimately facilitate the design and construction of scalable genetic architectures for controlling gene expression.

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

1. •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. 
   

2. •I am also wrote the first code for 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.  It has already been integrated into several iPhone applications and literature searching software applications.
   

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

1. •Unzipping DNA at a constant force
   

2. •Translocating RNA through nanopores
   

3. •Geometrical Defects in curved, two-dimensional crystals (related to viral capsids)
   

4. •Phage genome landscapes - a way to visualize important genomic features related to comparative genomics of bacteriophages