Welcome to the Biophysics Department undergraduate newsletter. We have articles about courses, alumni, faculty, and department programs. Biophysics Mentoring Program The Biophysics Mentoring Program is designed to connect students considering the biophysics major with current biophysics majors. If you are interested in learning more about biophysics, and would like to hear a current student’s perspective, email Dr. Fleming (karen.fleming@jhu.edu) to sign-up for the Biophysics Mentoring Program. She will connect you with a current student, so that you can learn more about the major, ask any questions you may have, and get inside advice from current majors. All mentors and mentees meet at least once a semester as a group. Check out a picture from our last Mentoring party!

Undergraduate Research Guidelines Interested in joining a research laboratory? Students often have many questions regarding independent research. How do I contact professors? What kind of research satisfies the Biophysics major requirement? To make the process easier for undergraduate students, Dr. Karen Fleming, the Director of Undergraduate Studies, has assembled a comprehensive online guide for students. The guide elucidates key procedures for obtaining research credit and explains the Department’s research philosophy. http://biophysics.jhu.edu/ResearchRequirements.pdf

Course Profile Biophysics 250.265 Introduction to Bioinformatics Taught by Patrick Fleming, PhD From a seemingly simple concept - the form and function of biomolecules depends on their respective amino acid or nucleotide sequences - a very complex, multifaceted body of knowledge is emerging: Bioinformatics. This area of study is especially complex because of the exponentially increasing torrent of molecular sequences available (now several billion bases of DNA).

Bioinformatics is the use of computing tools to manage and analyze this biomolecular sequence information and associated data. In this course we learn the most important bioinformatic algorithms through simple computer programs written by students. The use of these algorithms to extract information from global databases is then practiced using webservers around the world.

Equally important to learning algorithms is learning how to address the tough questions on how genomic sequence information is used in our society. At the end of the course all students present their research into the ethical uses of genomic information.

Updates from Young Alumni Name: Jonathan Zuckerman Hometown: Los Angeles, CA When/Why did you decide to major in Biophysics? I switched from biology to biophysics at the beginning of my sophomore year. I wanted to study biological systems from a more quantitative angle. What was your favorite thing about the Biophysics Major? The faculty was really wonderful, they seemed to really enjoy the process of teaching and the material they taught. What are you doing now? How has your biophysics background come in handy? I am currently a graduate student in the laboratory of Dr. Mark Davis at Caltech in my third year of the combined MD/PhD program between UCLA and Caltech. I just completed my second year of medical school and I am starting the PhD phase. The biophysics background has given me good grounding in both the physical and biological sciences which allows me to think about problems from both angles.

What was your favorite Biophysics class? The intermediate physics classes Wave Phenomena with Biophysical Application (171.309) and Biological Physics (171.310). These courses focused on applying mathematical models or descriptions to biological phenomena. I gained a lot of insight into the basic principles governing biological systems from these classes, which even today I find myself remembering when thinking about biological problems. Where do you see yourself in 10 years? I would like to be a Principal Investigator at a medical institution working on projects that directly translate basic science understandings of biological systems to real treatments for patients. What advice do you have for budding biophysicists and students considering the major? For the budding biophysicist, I suggest they engage themselves in research early and often; so that they can directly apply the concepts they learn in class to real biophysical problems. I think few things are as satisfying as creating or discovering something new. Undergraduate Research Spotlight Name: Deepak Atri Hometown: Yardley, PA Let me begin with a confession: on my first day in Dr. Quinones-Hinojosa’s laboratory, I knew so little that didn’t know how to pipette. If you’re like I was, there’s still no need to be anxious about research. Initially, I assisted in the projects of others, but through this period I learned techniques and grasped an understanding of the relevant literature. More importantly, I learned the thought processes of science and ultimately found that research is my cup of tea. That helped me to gain independence in the lab. With regard to the particulars of my work, I’m carrying two projects focused on cancers of the brain in the Department of Neurosurgery at the School of Medicine. In my first project, I’m examining the role of normal neural stem cells in brain cancer aggression. It’s been found that brain tumors that are closer to the stem cell niches of the brain come back more quickly and more aggressively, so we think that normal neural stem cells are somehow involved in exacerbating the cancer. In the second, I’m trying to find a small molecule “phenotype” of cancer stem cells by NMR spectroscopy. As has been shown in other cancers, if we can interfere with the cancer on the metabolic level, we might slow its progression and fight malignant cells without hurting normal cells. Details aside, my suggestion in picking a lab is to find an environment with good teachers, and that’s not limited to the PI. The question is less important than the thought processes acquired through research: these come with mentorship. Fortunately, our department is filled with brilliant scientists who are also first-rate teachers. If your passions lead you elsewhere for your research, you can use most other forms of wet lab-work to fulfill your undergrad requirements.

Faculty Interview Name: Doug Barrick, PhD Hometown: Boulder, CO What is your definition of Biophysics? Essentially, it’s the use of physical sciences to understand biology. But biophysics comes in many different flavors depending on the problem: the physical framework changes with the size of the problem. For example, the type of biophysics relevant to my work is most concerned with physical chemistry, which naturally relates to systems of purified proteins and substrates. Different physical tools, however, are necessary to study cell and neurobiology. The disciplines of science often have blurry divisions; biophysics is no exception.

What is it like to teach every Biophysics major in Biophysical Chemistry (250.372)? It’s great. I’ve taught the course twelve times and I look forward to it every year. It never gets old. It’s great to get to know all the students—who have unique bonds as majors in this department—and to watch them develop through the years. In teaching, I also learn a lot because I’m always finding new ways of thinking about and explaining these concepts. I would never plan not to teach that class.

What are your areas of research? My lab focuses on three topics: protein folding, the Notch signaling pathway, and the synthesis of biofuels. I originally focused on the Notch pathway—a pathway that is important in animal development as well as a number of diseases—as I started my laboratory. My background in protein folding sparked some novel work as we learned more about the Notch proteins. The repetitive nature of the Notch receptor makes it a great candidate to study folding in parallel because it greatly simplifies the folding problem.

In a separate project, we’re working on protein engineering to see if we can use cellulose to create biofuels. One billion tons of cellulosic waste are available for recycling each year in the U.S. If we could cheaply convert it into transportation fuel, we could decrease our fossil fuel consumption by 25%. All three of these projects involve fundamental biophysical concepts, especially thermodynamics and kinetics, while employing many different physical techniques.

What do you like to do outside of academics? I love being a parent. Aside from that, I like to play the electric guitar, athletics (especially running and yoga), and cooking.

Important Announcements

Mark your calendars! The Spring Mentoring Party will be taking place during the first week of February.

Attention seniors! Graduation will be here soon. In order to receive Department honors, students must write an Honors Thesis. Information regarding the paper can be found online at:

http://biophysics.jhu.edu/BiophysicsHonors09.pdf.