Physics at Brandeis Alumni Profiles
Mara Rosenberg, BS ’12
Background: At first a typically undecided liberal arts freshman, I quickly found my niche in the Physics Department at Brandeis University and graduated with a Bachelor of Science in physics in 2012. I began to explore the intersection of physics and medical research during the summer of sophomore year through an internship in a biophotonics laboratory at Oregon Health and Science University (OHSU) where I studied the effect of alcohol cerebral blood flow in mice. The following summer, I continued to pursue research in this multidisciplinary area as an American Association of Physicists in Medicine Fellow, placed with Dr. James Tanyi, a medical physicist in the radiation oncology department at OHSU. I furthered this research under the guidance of Prof. Robert Meyer at Brandeis, and published our findings on optimal dose delivery conformations in treatment of primary lung cancer. While at Brandeis I also had the opportunity to branch into other departments, assisting as a computer programmer in the neuroscience lab of Dr. Van Hooser and also studying the Spanish language leading to a semester abroad in Granada, Spain. Further, I was a member of the Brandeis Equestrian Team, competing with schools across Massachusetts.
Update: Since graduating from Brandeis in 2012, I have been honored to work as an Associate Computational Biologist under the guidance of Dr. Gad Getz at the Broad Institute of MIT and Harvard in Cambridge, MA. There I apply the critical analytical skills learned while studying physics at Brandeis to gain insight into the genetic composition of cancer tumors. In addition to researching many different tumor types, I have helped lead the investigation of the mutational landscape in lung adenocarcinoma through a national collaboration of upwards of fifty scientists under The Cancer Genome Analysis, funded by the National Cancer Institute and the National Human Genome Research Institute. Recently, I have begun to focus research on circulating tumor cells (CTCs) and am part of a paper that demonstrated the feasibility of identifying of mutations in CTCs from a metastatic prostate cancer patient. This finding would suggest the possibility of cancer progression monitoring and therapy decisions through a simple blood draw, and, as we currently scale up to multiple samples, I am excited by the possibilities it may provide. I plan to remain at the Broad for another year and then pursue a degree in medicine starting fall of 2015. Ultimately, I hope to straddle the clinical and research worlds, translating novel findings from laboratory benchside directly into improved patient care. Outside of the Broad, I have been working to climb all 4,000-foot mountains in New Hampshire and also take lessons in flying trapeze.
Daniel Beller, BS ’10
Background: I studied physics and math at Brandeis for four wonderful years from 2006 to 2010. As a sophomore and junior, I worked in Zvonimir Dogic’s lab on creating a model colloidal liquid crystal with tunable chirality. I’m proud that this system has proved useful in some of the amazing work produced by the Dogic lab more recently, helping to identify new roles for microscopic chirality in mesoscale self-assembly. Moving into theoretical research as a senior, I wrote an honors thesis under the guidance of Prof. Dogic and Prof. Robert Meyer on liquid crystalline monolayers of chiral colloidal rods, examining the signatures of chirality in the thermal fluctuations of these newly discovered objects. I benefited greatly from the supportive and enthusiastic mentorship of Profs. Dogic and Meyer, and of graduate students Nadir Kaplan and Ed Barry. The founding of the Materials Research Science and Engineering Center (MRSEC) made this an especially exciting time to study soft matter physics at Brandeis. I was also active in the Physics Department as an Undergraduate Departmental Representative and in the Physics Club, where I enjoyed working with fellow students outside the classroom in mentoring and community service roles.
Update: My interest in soft matter physics, and liquid crystals in particular, continues in my graduate studies in physics at the University of Pennsylvania. Presently, I am a Ph.D. candidate in the group of Prof. Randall Kamien. My research focuses on modeling liquid crystals in nontrivial confining geometries. We have shown, for example, how patterned boundaries can give rise to customized, controllable arrays of self-assembled defect structures in smectic liquid crystals, creating a newly expanded class of micro-patterned materials. We continue to study the geometrically complex ways in which the material accommodates these defect structures. Another area of interest is the burgeoning subfield of colloidal self-assembly in liquid crystals, where we are investigating how defects and the equilibrium arrangements of suspended colloids change when we alter the shapes of colloids and boundaries. As at Brandeis, close collaboration between theoretical and experimental groups provides a seemingly endless source of inspiration.
Netta Engelhardt, BS ’11
Background: I first became interested in high energy physics prior to starting college. In my time at Brandeis, I was presented with numerous opportunities to pursue and develop the skills and background that I would need for research in theoretical high energy physics. These opportunities included both experiential research and individualized instruction on topics tailored to my interests; in particular, string theory and mathematical topics that pertain to it. I was introduced to the basics of string theory via this form of personalized instruction by Matthew Headrick, who subsequently advised my senior thesis on numerical methods in string theory. I took advantage of similar learning methods at the mathematics department, where I studied topics in topology and differential geometry under the guidance of Bong Lian. Understanding of these topics proved instrumental to my later research.String theory is an attempt to reconcile quantum theory and Einstein’s theory of gravity, which describe matter on the smallest and largest scales, respectively. The two theories are at odds with each other, and much research in theoretical high energy physics centers on resolving this contradiction. My research at Brandeis focused on developing a numerical algorithm for solving a set of equations in a particular type of string theory known as heterotic string theory, which has the potential to give a phenomenologically accurate description of our universe.
Update: I am currently a graduate student at the University of California, Santa Barbara physics Ph.D. program. I work on gravitational aspects of string theory under the guidance of Gary Horowitz. Analysis of gravitational systems can shed light into certain potentially observable physics by studying a correspondence suggested by string theory called gauge/gravity duality. Many difficult calculations in the gauge side of the correspondence are more tractable in the gravity side, and this duality thus offers a a way of analyzing many properties of physics systems which are not yet well understood. As examples, the gauge side describes certain condensed matter systems such as superconductors and Fermi liquids, and early-universe constituents like the quark-gluon plasma
Lacramioara Bintu, BS ’05
Background: I arrived at Brandeis at the end of August 2001. From the first semester, I found a new home in the Science Complex. My first semester I took mainly Math and Physics courses while I improved my English speaking and writing with private tutoring (which Brandeis offered to me for free!). Between these classes, doing my homework in the computer rooms (I didn’t own a computer yet), and working 20 hours in the Science Library, I spent most of my waking time in the Science buildings. I really enjoyed my Physics courses. The classes were really small, which meant that I could ask questions, and get to know the faculty quite well. This of course, meant great opportunities: during my sophomore year, Prof. Meyer, hired me as a teaching assistant for Modern Physics. OK, I was mainly a grader, but he gave me the space to hold a few office hours every week, and I really loved it! During the second year, I also started looking for research openings. Initially I was attracted to astrophysics, and started thinking about working with Dr. David Roberts. However, after taking a course on Physical biology with Jane’ Kondev, I was totally won over. I really liked how he thought about science, and the biophysics field seemed so fresh and just ripe for discovery. I took an independent course with Jane’, and we started thinking about the statistical mechanics of gene regulation. We used partition functions to calculate the probabilities of a promoter to be occupied by RNA polymerase, given its competition with repressor proteins or its affinity for activators. Through this work, I got to meet Rob Phillips from Caltech, who is a long-time collaborator of Jane’. I spent two summers at Caltech with Rob, and learned a great deal about physical biology, but also about how to write and present, and how to work together with another student (Hernan Garcia). We finished and published this work on gene regulation during my senior year (Bintu et al. 2005a, Bintu et al. 2005b). During my time at Brandeis I also met and got engaged to my current husband, Anton Geraschenko, who was a Math and Physics major. Looking back at my time at Brandeis I am amazed by the opportunities that I had! I am still going back every time I visit the Boston area, and it really feels like returning home.
PhD work at U.C. Berkeley: After graduating from Brandeis in 2005, I moved out to California and started my PhD in Physics at Berkeley. I decided to work with Carlos Bustamante, looking at a very straight forward experimental question in biophysics: what happens when one RNA polymerase encounters a nucleosome. How does this molecular motor deal with such an obstacle on the DNA template it’s supposed to read and copy into RNA? We hoped that understanding the details of this mechanism would offer insight on how cells can use nucleosomes to regulate transcription. I arrived at just the right time in the Bustamante lab: previous postdoctoral students in the lab had figured out how to work with the polymerase at the single-molecule level and how to assemble nucleosomes in vitro. So I just had to put the two techniques together. Carlos thought I was the perfect person to do it, as I had a background on transcription from working with Jane’ Kondev and Rob Phillips. Of course, my background was theoretical, and I had barely touched a pipette before. Fortunately, Carlos’s lab was very big, and the people in his lab amazing, so they helped me learn very quickly. I still keep in touch with many of them. We used optical tweezers to hold onto single polymerases and follow their behavior as they met the nucleosome. We found out that the polymerase is a bit of a wimpy motor, and it can’t strip the DNA from the histones to remove the nucleosome from its path. Instead, it has to wait for fluctuations that open the nucleosome temporarily, and then it acts a ratchet to prevent the DNA from rewrapping (Hodges and Bintu, Science 2009). In a follow-up work we showed that these fluctuations of the nucleosome, and hence the probability of the polymerase to make it past the nucleosomal barrier, are controlled by modifications of the histone tails (Bintu and Ishibashi, Cell 2012). We then asked what happens with the nucleosome after the polymerase passes it. We used Atomic Force Microscopy to image nucleosomes, and found that the answer depends on the speed of the polymerase.
My time in Berkeley was really good: I became aware of many social and political issues, found some of the best food, hiked and windsurfed. Moreover, Anton, who was also a student in the Math Department at Berkeley, and I got married.
Postdoctoral work at Caltech: As postdoctoral scholar at Caltech, I am still thinking about gene regulation. However, I decided to move to the next experimental level: from in vitro biochemistry to working with live cells. I work with Michael Elowitz, who also has a Physics, quantitative background. He is well known for constructing gene circuits, and examining the behavior of gene expression at the single-cell level. Using the techniques established in the Elowitz lab, genetic engineering and time-lapse microscopy, I proceeded to investigate the regulation modes that different types of chromatin modifiers enable in mammalian cells. Since time evolution and cell-to-cell variations are very important in epigenetic gene control during cell differentiation and response to the environment, we decided to focus on these aspects. We engineered a system that allows us to control gene expression by systematically recruiting chromatin modifiers at a defined gene locus and directly measuring their effects on expression in real time, at the single-cell level.