Home Department: Physics 

Email: arajan@ks.uiuc.edu

Telephone: 217-244-1613

Fax: 217-244-6078

Theoretical and Computational Biophysics Group
Beckman Institute, Room 3161
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801

One of the very interesting theoretical projects is the study of optical properties of single walled carbon nanotubes. Optical properties of carbon nanotubes are becoming increasingly widely studied, with these materials showing a lot of promise for use as optical sensors. We recently showed that excitons in carbon nanotubes exhibit stochastic diffusional behaviour. I am now involved in developing microscopic models to understand what causes this diffusional behaviour observed. More information about nanotubes can be found at our Nanotube website.

Since, full scale Quantum mechanical simulations are computationally expensive, we are investigating whether Quantum Mechanical PMFs (Potential of Mean Force) can be approximately evaluated using the CHARMM force field and thermodynamic perturbation theory. We are currently working on deca-alanine. More information about constructing PMFs for deca-alanine can be found in our Stretching deca-alanine tutorial.

There has been a lot of focus on molecular dynamics (MD) simulations of protein folding to gain insight into the long-elusive, fundamental problem of how proteins fold. As computer technologies advance, increasingly longer MD simulations are now possible. Our group has recently performed a 10-microsecond simulation of a downhill folding WW domain mutant. It has become necessary to develop methods to obtain a reduced representation for the data obtained from such very long trajectories. One of our goals is to develop a robust clustering technique, which can form a framework for analysing conformational transitions in the protein folding pathways.

(Talk) Diffusion limited optical effects in Single Walled Carbon Nanotubes. Aruna Rajan, Michael S. Strano, Tobias Hertel and Klaus Schulten. American Physical Society Meeting, 2008. New Orleans, LA.

(Invited Lecture) Length dependent optical effects in Single Walled Carbon Nanotubes. Condensed Matter Seminar, Institute of Mathematical Sciences, Madras, India,2007.

(Invited Lecture) Steady State Thermodynamics. Physics Department Seminar, Indian Institute of Technology, Madras, India, 2007.

School on Biomolecular Simulations. Bangalore, India, Nov. 2007.
Designed material, delivered various lectures, and taught hands-on sessions. Workshop was attended by students of varying background and experience in MD simulations, from all over India.

Physics 211, Univ Physics, Classical Mechanics. Spring, 2006. Fall, 2005. Spring, 2005..
A second level course for engineers and science majors in classical mechanics. Taught both discussion and labs.

Physics 102, Electricity and Magnetism, and Modern Physics. Fall, 2004.
A first level course for pre-meds in electricty, magnetism and modern physics. Taught discussion sections.