Research in Medical Robotics

– written by Cenk Baykal, BS Computer Science and Mathematics

When I started at UNC, I didn’t have the slightest idea what undergraduate research was. As a freshman, I heard about research opportunities, but given my inexperience, I was hesitant on pursuing them until my sophomore year. That year, I began to work as a research assistant in Enabling Technologies under the supervision of Dr. Gary Bishop. During this time, I helped develop and enhance tarheelreader.org, a website designed to provide a collection of easy-to-read books, and created an online game designed for visually impaired students. I was able to see the positive impact this work had, and wanted to continue conducting research afterwards.

I then became a research assistant in the Computational Robotics Group led by Dr. Ron Alterovitz. In the robotics group, I’ve been researching concentric tube robots – medical robots that have potential to enable novel and minimally-invasive surgical procedures. One challenge that we’ve faced is allowing for intuitive control of these robots by physicians. Hence, I have worked with graduate student Luis Torres and developed a multi-component system architecture that bridges real-time motion planning with an interactive user interface and visualization. Concurrently with my robotics work, I conducted research with Dr. Ming Lin and graduate student David Wilkie on participatory route planning, which culminated in the creation of a mobile system, similar to Google Maps, that was able to generate optimal route plans by considering the impact of the system’s own plans on future traffic conditions.

An image of the cocentric tube robot used in Cenk's project.

An image of the cocentric tube robot used in Cenk’s project.

During Summer 2014, I continued my research on concentric tube robots with the help of the Summer Undergraduate Research Fellowship (SURF) and my advisor Dr. Ron Alterovitz. Namely, I have been investigating the optimization of the design of these medical robots on an application- and patient-specific basis. More specifically, I have been developing a software program that is capable of computing the optimal design under which the robot can feasibly maneuver to clinical regions of interest and simultaneously avoid damage to surrounding tissue. This has been an extremely exciting project and a great experience as it not only combines my passion for Computer Science and Math, but also has potential to facilitate the use of concentric tube robots for early diagnosis of lung cancer, the leading cause of cancer-related deaths in the United States. Thanks to the Dunlevie Honors Undergraduate Research Award, I will be extending my work and writing an honors thesis on the design optimization for concentric tube robots during my senior year.

In retrospect, undergraduate research has definitely been a highlight of my experience at Carolina. I had the opportunity to work on fascinating projects and collaborate with outstanding professors, graduate students, and mentors, to whom I am extremely grateful. Conducting research has exposed me to a wide variety of notions and concepts that I would not otherwise be introduced to in a classroom setting alone. Participating in undergraduate research has also motivated me to apply to graduate schools this fall in pursuit of a PhD in Computer Science, something that had never crossed my mind when I first came to Carolina. I would definitely encourage every undergraduate student to give research a try and not be demotivated by qualms concerning lack of experience or skill. As I look back on my research experience, the only regret I have is not starting any sooner.

For more information about these projects please see:

http://robotics.cs.unc.edu/
http://tarheelreader.org/

http://gamma.cs.unc.edu/

 

In With the New – OUR Welcomes New Ambassadors

UNC - Chapel Hill with Graham Memorial in the background

The University of North Carolina – Chapel Hill
with Graham Memorial in the background

written by Daijha J. Copeland

As nine ambassadors turned their tassels to officially become Carolina alumni in May, we welcome a new group of highly-qualified and enthusiastic undergraduate researchers. With experiences ranging in disciplines from Art History to Biology to Political Science, our new ambassadors offer a diversity of experiences to share with the Carolina community. These ambassadors have worked on timely projects such as: how specific RNA molecules distribute controls the division of zygotes, the role of suicide in the plays of William Shakespeare, further development in C. elegans, and the development of a thermoelectric vaccine cooler. Check out the ambassadors’ page to get to know all of our ambassadors and the other enriching projects that they have been a part of.

The ambassadors program was created for undergraduate researchers to be used as a resource to advocate for undergraduate research to university leaders and to serve as peer mentors. Ambassadors frequently host meet-and-greets with fellow students and give presentations on research opportunities offered through OUR and the greater university. And of course ambassadors are here to provide information, make faculty introductions, or answer any questions, so feel free to contact them for any assistance navigating Carolina’s research filled world.

If you have research experiences that you would like to share with other undergraduates and would like to apply to be an OUR ambassador, look for the call to apply in early spring. Below are the OUR ambassadors for 2014-2015.

Lauren Askew Biology /Spanish for the Medical Professions Minorlaskew@live.unc.edu

Jordan Bishop Chemistryjwbishop@live.unc.edu

Emily Cerciello Health Policy and Management & Economicscerciello@live.unc.edu

Sarah Cooley Geoscience-Geophysics/ Math and Religious Studies Minorsswcooley@live.unc.edu

Clark Cunningham Chemistry & Biologychcunnin@live.unc.edu

Sarah Faircloth History & Art Historyscfaircl@live.unc.edu

Blake Hauser Environmental Health Sciences & Biologybmhauser@live.unc.edu

David Joyner Political Science & Englishdbjoyner@live.unc.edu

Sloane Miller Environmental Health Science & Engineeringskm0709@live.unc.edu

Rizul Naithani Clinical Laborarory Science/ Chemistry Minor

Layla Quran Global Studies/ Journalism Minorlaylaquran@gmail.com

Sam Resnick Biology/ Chemistry Minor sresnick@live.unc.edu

Jay Zhang Biostatistics & Quantitative Biology/ Chemistry Minorjczhang@email.unc.edu

Zijian (Larry) Zhou Chemistry/ Computer Science Minorzzhou1@live.unc.edu

 

My Experience as a 2013 SMART Scholar’s Mentor

Written by Nick Battista, graduate student in the Department of Mathematics

As a Ph.D. student in applied mathematics, when I heard I was going to be a mentor to a SMART student I felt a little nervous. It was not immediately clear to me how much a SMART Scholar would be able to contribute to or understand about my project but, more importantly, I was not sure how effective a mentor I could be. However, within the first few days of meeting Andrea Lane, it was evident that we were going to mutually benefit from one another. 

At first it was a challenge since my research requires extensive knowledge of mathematical modeling and scientific computing/numerical analysis, as well as computer programming across multiple languages and platforms. Andrea started the program not having a strong background, or in some cases any experience, in these things. This was a blessing in disguise. It forced me to learn how to communicate the essential ideas for working on this project and thereby how to transfer my knowledge to Andrea in a way that made sense to her. Furthermore I wrote many tutorials and summaries to describe the basic programming ideas, how to use various software and programming platforms, and the big picture of what research is in general.

Due to Andrea’s unprecedented work ethic, she quickly learned the necessary skills to perform various numerical simulations and analyze their data to produce meaningful results, interesting plots and images, and high quality videos of the simulations. She ran numerical experiments pertaining to the flow of blood, including red blood cells, within embryonic heart tubes for various volume fractions of the red blood cells. She analyzed average flow velocities, pressure, and shear within the heart tube. All of these quantities are thought to be important to the morphogenesis of the heart itself. The simulations that she made, ran, and analyzed helped me answer questions that are pertinent to the aims of my own Ph.D. thesis work.

Beyond the actual embryonic heart modeling research, Andrea expressed an interest in learning more about general scientific computing and programming. Throughout the summer, we made sure to set some time aside to discuss advanced topics in numerical analysis. The goal was for her to see what it is like to develop her own code from the ground up. Eventually Andrea developed her own backward stable nonlinear ordinary differential equation solver, where she had to blend together a bunch of different algorithms she had previously coded with me during the course of the summer.

This was important because, even though the code we use for the heart tube simulations is extremely sophisticated and complex, we could use the ideas she learned from writing her own codes to help her better understand how our heart tube code worked and actually runs simulations.  It was an unparalleled feeling seeing her actually physically finally understand the big picture behind these type of mathematical models and simulations.

All in all, it was a great experience being a SMART scholar’s mentor this summer. It taught me a lot about being an effective mentor and how to competently communicate high level mathematical ideas to someone who hasn’t had as much formal training (or any) in mathematical modeling and scientific computing.  I only hope Andrea got as much out of this research experience as I did.

At the AACR: Attending a Scientific Meeting

Written by Patrick Short, OUR Ambassador, Applied Mathematics and Quantitative Biology major

I had the unique opportunity to attend the American Association for Cancer Research Annual Meeting in Washington D.C. in early April as a part of the Thomas J. Bardos Program for Undergraduates.  The program is structured to provide the opportunity to attend two consecutive annual meetings for undergraduates interested in a career in research, particularly those interested in working in cancer research.  Walking into my very first session of the long weekend I witnessed one of the most impressive speaking feats I have seen to this day.  Dr. Donald S. Coffey, a researcher in Oncology, Urology, and Pharmacology at Johns Hopkins University, gave the entire history of cancer research in just under twenty minutes.  His delivery included dozens of creative metaphors, sparing a lot of detail to get to the root of the issues.  Dr. Coffey described the cell cycle as a Xerox machine, the phenomenon of transposons and genetic repeats as Indian Corn (in contrast to a non-aberrant genome, which he asserts is much more like yellow corn), even the early distinction between benign tumors which he described as “like a tangerine you can just pluck out” and malignant tumors which were messy, asymmetric, and look like crabs, hence the etymology of ‘cancer’ from the Greek for crab.Patrick Short aacr_photo

Dr. Coffey’s presentation was a perfect case study in the art of explaining what could undoubtedly be extremely technical and opaque science in an interesting an accessible way.  In addition, the colorful metaphors provided a bird’s eye view of the complexity in cancer research without getting too entrenched in the details.  This speech was a perfect primer for what lay ahead.  The AACR annual meeting is meant to be broad in scope with topics ranging from imaging to experimental therapeutics to advances in genetics and personalized medicine, as well as providing depth through poster presentations and breakout sessions.  While personalized medicine is my main area of personal interest, the meeting provided ample opportunities to get exposure to virtually all of the topics relevant to cancer.  With nearly 18,000 researchers from around the globe in attendance, there were sessions with attendance in the thousands, all the way down to more intimate ‘meet and greet’ sessions with attendance in the dozens.  This program is one example of the many available opportunities for undergraduates to get involved in research.  Many scientific meetings like the AACR Annual Meeting provide these sorts of opportunities for undergraduates to present original research in poster sessions as well as network with leading scientists in the field.  For students in science and engineering, the scientific research society Sigma Xi hosts a biannual event in RTP for students to present research, explore summer internship opportunities, and network with professionals in the field.  Here are other resources for opportunities for undergraduate presentation or journal publication.

Undergraduate Presentation Opportunities:
http://www.unc.edu/depts/our/symposia.html
http://www.cur.org/resources/students/presentation_opportunities/

List of Undergraduate Journals:
http://www.cur.org/resources/students/undergraduate_journals/