Division of Science Hosts the 2016 Undergraduate Science Symposium

Written by Jena Pitman-Leung.


The Division of Science Graduate Affairs group hosted the 2nd annual Brandeis University Undergraduate Science Symposium on Saturday 17th, 2016. More than 60 students representing institutions from Massachusetts, Rhode Island, and New Hampshire attended the event, which was held in the Shapiro Science Center. The morning session included research talks from faculty in the Life Sciences (Don Katz, Liz Hedstrom) and the Physical Sciences (Matt Headrick, Christine Thomas), followed by panel discussions with faculty in the Life Sciences (Liz Hedstrom, Bruce Goode, and Maria Miara) and Physical Sciences (Gabriella Sciolla, Isaac Krauss, Jordan Pollack) on how to apply to graduate school. The students then came together for a networking lunch with Brandeis students, postdocs, and faculty. Lunch was followed by a well attended poster session, where 38 students had the opportunity to present their independent research. The day ended by awarding prizes for the best posters in five disciplines. The winners were:

Biology: Rahim Hirani, Hampshire College, “The regulatory role of Beta-Arrestin 1 in prostate cancer cell proliferation”
Neuroscience: Paige Miranda, Wellesley College, “Metabolic Processes Driving Hippocampal Long Term Potentiatio”
Biochemistry: Myfanwy Adams, Wellesley College, “Expression of a Cardiac ATP-sensitive Potassium Channel in a Heterologous Cell Line”
Chemistry: Natsuko Yamagata, Brandeis University, “Exploring the Unexplored: Supramolecular Hydrogels of Retro-Inverso Peptides for 3D Cell Culture”
Physics: Jameson O’Reilly, Northeastern University, “A capillary-mimicking optical tissue phantom for diffuse correlation spectroscopy”

The Division of Science is committed to supporting local undergraduate research, and is excited about the possibility of these bright young scientist choosing Brandeis for their graduate study. We look forward to hosting similar events in the future!

REU Students Arrive for 2016 Summer Research


Amber Jones and Susan Okrah

Alongside the more than 100 Brandeis science undergrads doing research this summer, there are 19 students who are participating in our Research Experiences for Undergraduates (REU) programs. Some students are from Brandeis, but most call universities in Kansas, Virginia, Pennsylvania, New Jersey their academic homes. Eight students are from Hampton University as part of the Partnership for Research and Education in Materials (PREM) initiative between Hampton and Brandeis. The two universities are focused on fostering interest in research science in under-represented groups of undergraduates.

The two independent REU programs were each created 6 years ago with funding from the National Science Foundation (NSF) with a goal of providing a 10-week period of intensive lab research experience to rising sophomores and juniors interested in scientific careers. Professor Susan Lovett is the director of the Cell and Molecular Visualization REU and Dr. Anique Olivier-Mason is the director of the Material Research Science and Engineering Center (MRSEC) REU.

The online application process required each student to submit a transcript, two letters of recommendation and write two essays describing their research experience (if any) and their academic and research goals. This year, 8 students are participating in the MRSEC site; 11 students are working in the Biology-based Cell and Molecular Visualization REU.

Amber Jones, who is going to be a junior at Hampton University this fall, is working in the Avi Rodal lab where she is researching how proteins can be taken on and off of cell membranes. From here, she is hoping to target specific proteins that will ultimately aid in disease research.

Amber has worked in a lab before, but believes nothing could have prepared her for her experience at Brandeis. Her REU lab work has been very involved, but she wasn’t expecting the ups and downs that are a part of lab research. The graduate students and other lab members have been supportive. She has been told “it’s okay; it’s science!”

Returning REU student, Alex Cuadros is working in the Liz Hedstrom lab, says he can go to Cell and Molecular Visualization REU coordinators Cara Pina and Laura Laranjo for assistance. They “have more experience in the lab and they tell me that things don’t always work for them. They say that ‘it’s just part of the science’.”

Nicholas Martinez, who is working in Timothy Street’s lab said, “The biggest challenge I have encountered this summer with my research is being able to do cope with disappointment. Since I am working on a defined timetable and my time here at Brandeis is limited, I want to make as much progress as possible with my research.”

Susan Okrah is working in the Seth Fraden lab this summer. She believes this experience is different from a Chemistry class at Hampton University where you are given an experiment and the results are known. In the REU program, students are given a project that is a subset of their lab’s research. Unlike school, the outcome of their research is unknown. Susan said, “We are given a direction and told to see if it works.”

Alex said that in class he has learned how to do experiments, but at Brandeis he is “doing something that has not been done before so there’s no right method.” It’s also helpful to be able to ask advice about how to approach his research and “Then you go back and you figure out how to do it. You are forced to think independently.”

During the academic year, Alex works in a Biochemistry lab at UMass Amherst. He landed the job last fall as a direct result of his 2015 REU research. How did he get the job in a very competitive environment on the large UMass campus? He presented the poster that he prepared for SciFest 2015.

The most valuable lesson learned this summer? “Resilience” said Amber. Learning to cope with the changing tides of research is important. As Susan said, “people don’t really understand what goes into research until they’re here.”

Part of the REU program involves attending journal clubs and lab meetings, but the most valuable experience of this program is simply being in a lab. Both Amber and Susan agree that anyone thinking about a career in research should go through an intensive research experience such as this. Jones noted, “I wasn’t really expecting to get this type of understanding. I really appreciate that now that I’m here.”

Both Nicholas and Alex ultimately would like to attend graduate school. For Nicholas, “being able to participate in the Cell and Molecular Visualization REU program at Brandeis has been a great opportunity for me to diversify my knowledge and skill set in scientific research prior to applying for graduate school next year. This It has been a great way for me to gain experience in a new area of research that I am interested in and to become part of a different scientific community.”

The REU students are hard at work wrapping up their research and preparing their posters for the SciFest 2016 poster session that is scheduled for Thursday, August 4.

Using computer simulations to model bacterial microcompartment assembly

Bacterial microcompartments are protein shells found in bacteria that surround enzymes and other chemicals required for certain biological reactions.  For example, the carboxysome is a type of microcompartment that enables bacteria to convert the products of photosynthesis into sugars (thus taking carbon out of the atmosphere).  During the formation of a microcompartment, the outer protein shell assembles around hundreds of enzymes and chemicals required for the reaction.  Because the intermediates in this assembly process are small and short-lived, it is hard to study in detail using experiments. It is therefore useful to develop computational models that can help explain how proteins collect the necessary cargo, and then assemble into an ordered shell with the cargo on the inside.  The videos in this post show some examples of computer simulations of a model for bacterial microcompartment assembly, with each video corresponding to a different set of parameters that control the strengths of interactions among the proteins and cargo.

The study is described in the research article “Many-molecule encapsulation by an icosahedral shell” by Jason Perlmutter, Farzaneh Mohajerani, and Michael Hagan in eLife (eLife 2016;10.7554/eLife.14078).

Video 1: Multistep assembly of a microcompartment encapsulating hundreds of molecules (I) video1
Video 2: Multistep assembly of a microcompartment encapsulating hundreds of molecules (II)  video2
Video 3: Assembly of a microcompartment and encapsulation of hundreds of diffuse cargo molecules  video3

Yoshinori Ohsumi to Receive Rosenstiel Award Wednesday, April 6

ohsumi220Biologist Yoshinori Ohsumi will receive the 45th Rosenstiel Award for Distinguished Work in Biomedical Science this Wednesday, April 6th at 4:00 pm in Gerstenzang 123. At that time, he will present a lecture titled, “Lessons from yeast: Cellular recycling system, autophagy”.

Ohsumi is a cell biologist and professor at the Tokyo Institute of Technology’s Frontier Research Center in Japan. He is one of leading experts in the world on autophagy, a process that allows for the degradation and recycling of cellular components. The Rosenstiel Award is being given to Ohsumi in recognition of his pioneering discoveries in autophagy.

Learn more about Professor Ohsumi and his research at BrandeisNow.

DIY your own Programmable Illumination Microscope

The Fraden Group describes how to build your own Programmable Illumination Microscope in the American Journal of Physics

Have you ever marveled at the equipment used in a research lab? Have you ever wondered how a specialized piece of equipment was made? Have you ever wondered how much it would cost to build your own research microscope? Have you ever considered trying to make your own research microscope? The details on how the Fraden Group builds their Programmable Illumination Microscope for under $4000 was recently published in the American Journal of Physics.


The Programmable Illumination Microscope or PIM is a highly specialized microscope where the illumination for the sample being imaged comes from a modified commercial projector, nearly identical to the ones mounted in every classroom. For the PIM the lens that projects the image onto the screen is removed and replaced with optics (often the same lens in reverse) that shrinks the image down so that it can be focused through the microscope objective onto the sample. The light coming from the projector, which is the illumination source for the microscope, can be modified in realtime based on the image being captured by the camera. Thus the illumination is not only programmable but can also be algorithmic and provide active feedback.

This new publication in the American Journal of Physics, which is published by the American Association of Physics Teachers, is intended to help small teaching and research labs across the country develop their own PIMs to be built and used by undergraduate students. The paper includes schematics and parts lists for the hardware as well as instructions and demonstration code for the software. Any other questions can be directed to the authors Nate Tompkins and Seth Fraden.

Nature News Feature Highlights Dogic Lab Active Matter Research

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Biological material is constantly consuming energy to make things move, organize information such as DNA, or divide cells for reproduction; but building a fundamental theory which encompasses all of the features of biological matter is no easy task. The burgeoning field of active matter aims to understand these complex biological phenomena through physics. Active matter research has seen rapid growth over the last decade, but linking existing active matter theories with experimental tests has not been possible until recently. An explosion of biologically based and synthetic experimental systems as well as more detailed theories have arrived in recent years, and some of these foundational experiments have been conducted here at Brandeis University. Recently, a Nature News Feature (The Physics of Life) has highlighted work from Zvonimir Dogic’s lab in an article about the field of active matter and the physics which endeavors to understand biology.


Pairs of Supermassive Black Holes May Be Rarer Than Earlier Thought

Image by David Roberts

Image by David Roberts

Recent research by David H. Roberts, William R. Kenan, Jr. Professor of Astrophysics at Brandeis, has shown that pairs of supermassive black holes at the centers of galaxies are less common than previously thought. This suggests that the level of gravitational radiation from such systems is lower than earlier predicted. This work was in collaboration with Lakshmi Saripalli and Ravi Subrahmanyan of the Raman Research Institute in Bangalore, and much of the work was done by Brandeis undergraduate students Jake Cohen and Jing Liu. It has recently been published in a pair of papers in the Astrophysical Journal Supplements and Astrophysical Journal Letters.

Gravitational waves are ripples in space-time predicted by Einstein’s 1915 General Theory of Relativity. Propagating at the speed of light, they are produced in astrophysical events such as supernovae and close binary stars.

No direct experimental evidence of the existence of gravitational waves has been found to date. We know that they exist because they sap energy from the orbits of binary systems, and using ultra-precise radio astronomy it has been shown that the changes in binary orbits of pairs of pulsars (magnetized neutron stars) are precisely as predicted by General Relativity. Hulse and Taylor were awarded the Nobel Prize in Physics for their contributions to this work.

The largest source of gravitational waves is expected to be the coalescence of pairs of supermassive black holes in the centers of large galaxies. We know today that galaxies grow by mergers, and that every galaxy harbors a massive black hole at its center, with mass roughly proportional to the galaxy’s mass. When two massive galaxies merge to form a larger galaxy, it will contain a pair of black holes instead of a single one. Through a process involving the gravitational scattering of ordinary stars the two black holes migrate toward each other and eventually coalesce into a single even more massive black hole. The process of coalescence involves “strong gravity,” that is, it occurs when the separation of the two merging black holes becomes comparable to their Schwarzschild radii. Recent developments in numerical relativity have made it possible to study the coalescence process in the computer, and predictions may be made about the details of the gravitational waves that emerge. Thus direct detection of gravitational waves will enable tests of General Relativity not achievable any other way.

In order to predict the amount of gravitational radiation present in the Universe it is necessary to estimate by other methods the rate at which massive galaxies are colliding and their black holes coalescing. One way to do this is to examine the small number of radio galaxies that have unusual morphologies that suggest that they were created by the process of a spin-flip of a supermassive black hole due to its interaction with a second supermassive black hole. These are the so-called “X-shaped radio galaxies” (“XRGs”), and a naive counting of their numbers suggests that they are about 6% of all radio galaxies. Using this and knowing the lifetime of such an odd radio structure it is possible to determine the rate at which massive galaxies are merging and their black holes coalescing.

Roberts et al. re-examined this idea, and made a critical assessment of the mechanism of formation of XRGs. It turns out that other mechanisms can easily create such odd structures, and according to their work the large majority of XRGs are not the result of black hole-black hole mergers at all. They suggest as a result that the rate of supermassive black hole mergers may have been overestimated by a factor of three to five, with the consequence that the Universe contains that much less gravitational radiation than previously believed. In fact, recent results from searches for such gravitational waves have set upper limits below previous predictions, as might expect from this work.

For more information:


IGERT Summer Institute – July 27 to August 7, 2015

IGERTBrandeis is hosting a two-week summer institute for graduate students in the mathematical sciences from July 27-August 7.  This will combine the annual summer institute of Brandeis’ Geometry and Dynamics IGERT program, with a sequel to the US-India Advanced Studies Institute on thermalization, held two years ago in Bangalore.


  • Large deviation theory
  • Statistics of extreme events
  • The large N expansion in statistical and quantum physics
  • Statistical fluid dynamics
  • Quantum information and quantum gravity
  • Thermalization in Quantum Systems


Sumit Das (U. Kentucky)
Chandan Dasgupta (IISC, Bangalore)
Rajesh Gopakumar (HRI, Allahabad and ICTS)
Alex Maloney (McGill University)
Satya Majumdar (LPTMS, Paris)
Sanjib Sabhapandit (Raman Research Institute, Bangalore)
Peter Weichman (BAE systems)


Albion Lawrence
Bulbul Chakraborty


There will be no registration fee, but the venue will have limited capacity, so interested students should register by sending an email to Catherine Broderick (cbroderi@brandeis.edu) by July 4. Please list your affiliation, your year in graduate school, any publications, and the name of your PhD advisor.

Additional information can be found at www.brandeis.edu/igert/.

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