Page 26 - CBAC Newsletter 2017

that. Dr. Rudy said his lab was heading into that kind of work. He did not have a lot of publications on this but that is
what he is trying to do now and that I should look it up.

Later on, I wrote to Dr. Rudy and said that I was interested. Dr. Rudy said come on over. Tom O’Hara was there and
got me started in the lab. He was mentoring her [Jiajing Xu]. I really liked it because it was different than the other
labs. Back then, Dr. Rudy’s lab was a big lab and there were a lot of people. If I needed something, everybody was
nice and wanted to help. It was a happy environment.

So when you both first came here, how many more people were there?

Xu: So the first year when I came here, there was: Subham Ghosh, Yong Wang, Junjie Zhang, Ramya Vijayakumar, me,
Thomas Hund, Jordi Heijman, Keith Decker, Leonid Livshitz, Ali Nekouzadeh, and about two more people from the
medical school. In the summer of 2009, Subham and Yong left, then Smiruthi came and Jordi left.

According to Jiajing and Smiruthi, in 2009, the Rudy Lab was one of the largest in the BME department. At one time,
including clinicians, the lab had about twenty people in it. The lab was full, like every computer was occupied. During
meetings, they had to pull chairs to in the lab conference room and it would take around two hours to get through
everybody’s presentations.

Jiajing: in the first year, the lab was not divided into two groups. Right before Smiruthi came, the size of the lab was
too big to fit into the conference room so that was one of the reasons why Dr. Rudy decided to split the lab into two
groups to have two lab meetings.

“You know destiny? That was what it was!”
- Smiruthi Ramasubramanian

Jiajing Xu and Smiruthi Ramasubramanian’s Research: Cardiac Excitation and Arrhythmias

Xu: We are working on the same general problem and aim but our solutions and approaches are different.

The overall objective is to provide a mechanistic understanding of the relationships between the dynamic molecular
structure of cardiac ion-channel proteins during gating and their function as charge carriers during the whole cell
action potential (AP).

Below is a broad description of the protein research the Rudy Lab is working on using resources at the
Center for High Performance Computing (CHPC), Mallinckrodt Institute of Radiology:

Voltage-gated ion channels are massive proteins with thousands of amino acids. Experimental techniques such as
crystallography and NMR can provide valuable information about a frozen protein conformation. However,
experimental techniques are limited in their ability to visualize structural changes at an atomistic resolution. Thus far,
the best adaptation of experimental techniques has not been able to quantify the structural changes of the protein
during activation, deactivation and inactivation.

Atomistic simulation of voltage-gated membrane proteins will help scientists to better understand normal channel
behavior and mechanisms of disease paradigms due to malfunction, thus aid in drug design. Extensive biomolecular
simulations such as protein dynamics require intensive calculations. The problem is exacerbated with the size of the

21 | CBAC Center Heartbeat