Physics at Brandeis

One current undergraduate, and five alumni, from the Brandeis Sciences were honored with offers of National Science Foundation Graduate Research Fellowships in 2012. The fellowships, which are awarded based on a national competition, provide three full years of support for Ph.D. research and are highly valued by students and institutions. These students are:

• Samuel McCandlish ’12 (Physics) , a current student who did research with Michael Hagan and Aparna Baskaran, resulting in a paper “Spontaneous segregation of self-propelled particles with different motilities” in Soft Matter (as a junior). He then switched to work with Albion Lawrence for his senior thesis research. Sam will speak about “Bending and Breaking Time Contours: a World Line Approach to Quantum Field Theory” at the Berko Symposium on May 14.  Sam has been offered a couple of other fellowships as well, so he’ll have a nice choice to make. Sam will be heading to Stanford in the fall to continue his studies in theoretical physics.

• Briana Abrahms ’08 (Physics). After graduating from Brandeis, Briana followed her interests in ecological and conversation issues, and  in Africa as a research assistant with the Botswana Predator Conservation Trust, Briana previously described some of her experiences here in “Three Leopards and a Shower“. Briana plans to pursue as Ph.D. in Ecology at UC Davis.

• Sarah Robinson ’07 (Chemistry). Sarah did undergraduate research with Irving Epstein on “Pattern formation in a coupled layer reaction-diffusion system”. After graduating, Sarah spent time with the Peace Corps in Tanzania, returning to study Neurosciene at UCSF.

• Si Hui Pan ’10 (Physics) participated in a summer REU program at Harvard, and continued doing her honors thesis in collaboration with the labs at Harvard. Her award is to study condensed matter physics at MIT.

• Elizabeth Setren ’10 was a Mathematics and Economics double major who worked together with Donald Shepard (Heller School) on the cost of hunger in the US. She has worked as an Assistant Economist at the Federal Reserve Bank of New York and her award is to study Economics at Harvard.

• Michael Ari Cohen ’01 (Psychology) worked as a technology specialist for several years before returning to academia as  PhD student in the Energy and Resources Group at UC Berkeley.

Congratulations to all the winners!

On Monday, May 14, the Physics Department will hold the Twenty-first Annual Student Research Symposium in Memory of Professor Stephan Berko in Abelson 131. The symposium will end with talks by the Berko Prize winners. This year the prize is being shared by two graduating seniors, Yuri Levin-Schwartz and Sam McCandlish, and two graduate students, Andy Ward and Michael Giver. The whole department then gathers for a lunch of cold cuts, cookies and conversation. “It’s a great way to close out the academic year,” said Professor of Astrophysics and Department Chair John Wardle. “We come together to celebrate our students’ research and hear what the different research groups are doing.” The undergraduate speakers will describe their senior thesis honors research. This is the final step in gaining an honors degree in physics, and many of them will also be co-authors on a paper published in a mainline science journal. The graduate student speakers are in the middle of their PhD research, and will describe their progress and goals. The prize winners are nominated and chosen by the faculty for making particularly noteworthy progress in their research. Michael Giver’s talk is titled “Stochastic Chemical Oscillations on a Spatially Structured Medium.” He works with Professor Bulbul Chakraborty.  Andy Ward’s talk is titled “Friction Between Biological Filaments.” He works with Professor Zvonimir Dogic. Yuri Levin-Schwartz’ talk is titled “Going Towards the Light; Single Cell Phototaxis and Collective Dynamics of Algae.” He works with Professor Azadeh Samadani. The final talk is by Sam McCandlish and is titled “Bending and Breaking Time Contours: a World Line Approach to Quantum Field Theory.” Sam works with Professor Albion Lawrence. The schedule for Monday morning can be found on the Physics Department website. Abstracts of all the talks will be posted there shortly. This Student Research Symposium is now in its 21st year. The “First Annual…..” (two words which are always unwise to put next to each other) was initiated in 1992 by Wardle to honor Professor Stephan Berko, who had died suddenly the previous year. Family, friends and colleagues contributed to a fund to support and celebrate student research in his memory. This provides the prize money which the four students will share. Stephan Berko was a brilliant and volatile experimental physicist who was one of the founding members of the physics department. He was born in Romania in 1924 and was a survivor of both the Auschwitz and Dachau concentration camps. He came to the United States under a Hillel Foundation scholarship and obtained his PhD at the University of Virginia. He came to Brandeis in 1961 to establish a program in experimental physics and worked tirelessly to build up the department. Together with Professors Karl Canter (dec. 2006) and Alan Mills (now at UC Riverside) he established Brandeis as a world center for research into positrons (the anti-matter mirror image of ordinary electrons). In a series of brilliant experiments they achieved many “firsts,” culminating in election to the National Academy of Sciences for Steve, and, it has been rumored, in a Nobel Prize nomination for the three of them. Steve was as passionate about teaching as he was about research, and when he died, it seemed most appropriate to honor his memory by celebrating the research of our graduate and undergraduate students. During the coffee break on Monday, we will show a movie of Steve lecturing on “cold fusion,” a headline-grabbing but phony claim for producing cheap energy from 1989.

by Dapeng Bi

During this year’s annual March meeting of the American Physical Society, students from Professor Bulbul Chakraborty’s group presented recent research results in the area of granular materials and the jamming transition. In undergraduate student Michal Dichter’s talk titled “Jamming in Hopper Flows: Analysis of Survival Times,” Dichter presented results of numerical simulations of dense, gravity-driven, granular flows in a two-dimensional hopper with a tapered outlet. Graduate student Dapeng Bi presented recent results published in Nature 2011 in which a new paradigm was found for the jamming transition in physical granular materials. Interestingly, during the APS meeting, an application based on the jamming transition was proposed by Professor Heinrich Jaeger from University of Chicago.

Many alumni from Professor Chakraborty’s group also presented their current research. Silke Henkes (PhD ‘08), currently a researcher at Syracuse University, was given a prestigious slot at the invited talk session. Her talked titled “Active Jamming: Self-propelled particles at high density” attracted broad interest from soft condensed matter physicists and biophysicists alike. Ya Liu (PhD ‘10), currently a post-doctoral researcher at Lehigh University, presented a talk titled “Encapsulation by Janus Oblate Spheroids.” Mitch Mailman (PhD ‘11), currently a post-doctoral researcher at the University of Maryland, presented a talk titled “Cooperative rotations of 2d frictional disks under oscillatory shear.”

 

by Nate Tompkins

This was the second APS March Meeting I have attended and the turn out from Brandeis was phenomenal. Last year in Dallas there was a small dedicated team giving short descriptions of each major project but this year each project was supported by a full crew of personnel, both giving talks and discussing the topics afterwards in the corridors. Several different research groups were well-represented: Seth Fraden’s group (on multiple topics), Jane Kondev’s group (en masse), Bulbul Chakraborty’s group (past and present), and Zvonimir Dogic’s group (with fresh glamour publications). Having the conference in Boston this year certainly aided turnout but the emerging group of second year graduate students demonstrated their fresh projects as well. My own talk fell on curious ears due to an interesting choice of sectioning but you can all judge for yourself at the upcoming Berko Symposium on May 14 where I will be giving a talk of similar length and topic. In the end Brandeis was very well represented this year, making an impact in many different APS sections and continuing its tradition as a well-respected institution in the research community.

by Ning Li

This is the first time I attended an APS March meeting. The meeting this year was the largest meeting of soft condensed matter ever. Though there were too many interesting talks to enumerate, I found several talks particularly inspiring to my work on synchronization. Herbert Levine, UCSD, talked about chiral patterning in paenibacillus colonies under stress. His simulation with random lattices, successfully resolving his problem with anisotropy effect, gave me a hint on the current difficulty I’m having with finite element simulation. Raymond Goldstein and Eric Lauga each gave an interesting talk on synchronization of flagella. I was glad to see that the general rules of synchronization of chemical oscillators I learned were applicable to other fields. That’s actually one of the points that I tried to make during my talk. I also tried to explain to an audience of microfluidic experts that Belousov-Zhabotinsky solution is an interesting material to put in microfluidic devices and the difference (or advantage if you like) of nonlinear chemical oscillator from real biological oscillators like fireflies and neurons.

Biological Physics
by Matt Perkett and Sandeep Choubey

More than a quarter of this year’s March meeting covered various aspects of soft matter research with more than 170 sessions and 2,000 contributed talks. Brandeis faculty, postdocs, and graduate students contributed more than 20 of these talks. These speakers presented a diverse range of soft matter research interests.

Matt Perkett, a fourth year Physics graduate student, presented his work on virus capsid assembly. MS2 is a small bacteriophage that forms a spherical capsid with a diameter of about 27.5nm. The completed capsid is made of protein dimers that adopt one of two different conformations depending on their position in the completed capsid. The goal of his research was to determine the mechanism by which these dimers are placed into the correct conformation during assembly. Since the kinetics of virus assembly is difficult to determine experimentally, all atom simulations and enhanced sampling techniques were used. The free energy difference between the two different protein dimer conformations was found to be in agreement with experiments and future measurements with bound RNA will determine the selection mechanism during assembly.

Sandeep Choubey, a third year Physics graduate student, presented his work on the regulation of ribosomal genes. Upon adding more ribosomal genes to the E. coli cell, it adjusts the overall transcription of these genes by reducing the average transcription rate per gene, so as to keep constant the level of ribosomal RNA in the cell. It was observed that this reduction in the average transcription level per gene is accompanied by the generation of transcriptional bursts. The goal of his work was to understand the mechanistic basis of these bursts. He considers three possible mechanisms suggested in literature: Promoter proximal pausing by RNA polymerase, cooperative recruitment of RNA polymerase by DNA supercoiling, and competition between RNA polymerase and a transcription factor for binding regulatory DNA associated with ribosomal genes. The statistical properties of transcription initiation were computed and were compared with the distribution of distances between the polymerases transcribing the ribosomal genes, obtained from electron micrographs. It was shown that the three mechanisms can be discriminated by comparing the predictions for the mean and variance of interpolymerase distances with experimental data and further experiments were suggested.

Numerous Brandeis alumni were also present at this year’s meeting. Alvaro Sanchez, (PhD ’10) of MIT presented his work on population dynamics. Evolution has traditionally been viewed as a very slow process that happens over geological timescales. In contrast, changes in the size of a population are typically much faster, occurring in timescales of a few generations time. Therefore, it has been commonplace to assume that both evolution and population dynamics are independent processes. Recently, this view has been challenged, and examples where either population dynamics affect evolutionary change, or the other way around, have been documented. Using cooperatively growing yeast as a model system, we have showed that population dynamics and evolutionary dynamics are linked together through a feedback loop, which dominates both the outcome of the evolutionary competition between cooperators and cheaters, and the demographic fate of the population. This feedback loop saves the population from extinction when a population of cooperatively growing cells gets invaded by a cheater phenotype emerging from random mutation. While the population does not go extinct as a result of invasion by cheaters, it becomes less resilient to environmental changes, and has a higher chance of going extinct as a result of environmental deterioration. Our results were reproduced by simple model, which suggest that this type of coupling could be common in communities that rely on cooperation for their survival.

In addition to the presentations showcased here, a variety of exciting experimental soft matter work was also presented, some of which has already been discussed in greater detail on this blog (Sanchez, Zakhary).

 

by Rafael A. Cabañas

Every year in March, the American Physical Society holds an annual meeting where eleven thousand physicists get together to show and discuss the latest results in their research. Top shelf research talks outlining the latest developments in various fields mix with coffee breaks where more specific conversations happen. It is an art for each attendee to create a coherent schedule among the fifty four parallel sessions and thousand talks scheduled for each day. Ten minutes talks are packed in between thirty minute jewels of research expositions where lengthy introductions to various research areas provide a great first step for young researchers and an act of reminiscence for experienced professors.

The main focus of the March meeting is Condensed Matter Physics every year. Theory, simulation and experimental results allow the audience to see what is new in each sub field, start scientific discussions and exchange old and new ideas.

This year, that squishy part of physics known as Soft Matter has had significant weight at the meeting. Everything in between solid and liquid: gels, polymers, cells, etc. has been gaining weight as a study topic among physicists.

I presented our work in the Q47 session about DNA-coated colloidal particles.   At the Fraden Lab, as part of the Physics Department, the Quantitative Biology program at Brandeis University and MRSEC institute at Brandeis University, we study material properties at the interface of physics, chemistry and biology. Those three programs and structures complement each other to give the student a coherent formation in a highly interdisciplinary field. In my case, I use a bottom-up approach to study the physical properties of new self-assembled materials using basic biological material.   Self-assembly is a word commonly used among the scientific community, especially those who deal with the microscopic world, to describe the process of association, aggregation or cluster of particles, which leads to the appearance of a defined structure.  It assumes that no external force is used and particles just come together due to inter-particle interactions and thermal agitations.

For engineering applications, self-assembly needs to be reliable and useful.

At length scales of less than a few microns – a fraction of a human hair – self assembly is a powerful strategy to achieve ordered structures. Even the smallest of tweezers would be too large to organize these components.  Materials that have controllable structure present useful, interesting and new optical and mechanical properties.

The components or building blocks can be atoms, molecules, macromolecules or bigger particles such as colloids. Colloids are particles with sizes between nanometers and few microns. They are small enough so thermal motion prevents sedimentation and they are subject to Brownian motion in solution.

The driving force that produces self assembly of particles can have a diverse origin: charge, hydrophilicity, etc., but one might think that an attractive component between the building blocks is necessary to achieve association.  That is not necessarily true. Entropy plays an important role when it comes to producing ordered structures. The particles will organize themselves to minimize the excluded volume each particle occupies and maximize the number of states the system can be in, that is, maximize the entropy. The excluded volume of a particle is the effective volume that another particle cannot occupy because of the presence of that first particle. The excluded volume can be bigger than the actual physical volume of an object.

In absence of any attractive force, entropy tends to make the excluded volume as small as possible. This leads particles to adopt configurations in which they have more freedom of movement. In special circumstances, this results in making the particles organize themselves in ordered structures, or for elongated molecules, to be oriented in the same direction.

Since it is the volume that plays an important role in the transition to order, shape becomes a critical characteristic. Depending on the shape of the particle we may get one or another macroscopic ordered structure.

The main objective of studying self assembly is to determine how the particles’ physical characteristics, lead to certain macroscopic structures, and not others.

Colloidal rods, for example, are anisotropic particles that prefer to align in the same direction as we increase concentration called the nematic phase used in LC displays, or in layers called the smectic phase – the structure of lipids in cell membranes if we increase the concentration even more.  Molecules that present such phases are called liquid crystals.

At Brandeis, scientists  (D.L.D. Caspar, R.B. Meyer,  S. Fraden, Z. Dogic) have been studying colloidal liquid crystals and the properties that govern  self-assembly for over 50 years!  What distinguishes Brandeis liquid crystal research from other groups is the use of biological polymers.

The way to obtain colloidal particles with rod shape is using rod like viruses. TMV, fd or m13 are bacteriophage viruses with the shape of a straight stick.

Viruses are relatively easy to produce using biological techniques, and have many desirable properties. They have the size of a colloidal particle, are mono-disperse, rigid, electrically charged so they do not aggregate in solution and they can be modified using genetic and chemical techniques.

Caption figure1: Viruses in solution present liquid crystalline phases as we increase concentration. We can also get an idea of the size and shape from the electron micrograph on the right side.  The fd viruses are no more than a single stranded circular DNA plasmid coated by a capsid made of proteins.

Fd viruses display liquid crystalline phases, as we see on figure 1, and even more interesting structures when one adds interparticle attraction in the form of a depletant agent. Dextran polymer added to the suspension of viruses creates an effective attraction and a myriad of new ordered structures, as we see in figure2.

 

 

 

 

 

 

 

 

 

 

Our idea is to use these viruses’ colloidal particles and attach single strands of DNA on the exterior protein coat. We are using the anisotropic properties of the particles to create self-assembled ordered phases and are adding a tunable temperature dependent potential, since the hybridization process of DNA is dependent on temperature.

Those new particles, that we have created using chemical processes, can attach to others that contain the complementary DNA strain or to the same type of particles using DNA linkers.

In the actual state of our research, we have created these new particle made of virus and DNA and confirmed the success of our protocol to fabricate them through different methods. We have used a chemical linker to attach modified single strands of DNA to the amino groups present in the surface of the coat protein of the virus.

 

 

 

 

Caption figure3: Schematic of the structure of the coating protein VIII of the virus Fd. The amino groups at the surface have been highlighted in light blue and the chemical linker in dark blue. Finally a single strand of DNA is attached to show a model of the final result. Just approximately one quarter of the number of linkers will have a DNA strand attached at the end of the final process. Images are not in scale and just pretend to illustrate the linking process.

The idea and creation process of such virus-DNA particles were presented in the last American Physical Society meeting last March 2012. Up to now we have confirmed the success of the creation of the particles. In the near future we want to study the liquid crystalline behavior and self assembly properties of mixtures of such particles.

 

Another Brandeis NOW story covers the results of the 2012 Sprout Grant competition. Of 20 applications received, half were software related, half life sciences and physical science-related, so the groups were judged separately. Thirteen groups were asked to return for a second round of interviews, coaching and presentations to outside panels of industry judges.  Seven groups were awarded grants: 2012 Sprout Grant winners, life and physical sciences:

• 
Radiation detector, Wellenstein, PI $20,000
• Tuberculosis treatment, therapeutic, Hedstrom, PI $17,000
• Cold Stage for Light Microscopy, microscope tools, Turrigiano, PI $16,000
• Conditional gene silencing, research tool, Lau PI, $6,000

2012 Sprout Grant winners, software:

• Innermost Labs, social network. Sahar Massachi and Adam Hughes, $7,500
• Digital Learning Analytics, learning analytics, Larusson PI  $6,000
• Campus Bash, social network, Y. Sebag, and M. Jafferji $6,500

For more information about the projects and the judging process, read the story at Brandeis NOW.

On March 26, 2012, Professor Gregory A. Petsko wrote on behalf of the Strage Award Selection Committee:

It is with great pleasure that I announce the recipient of this year’s Strage Award for Aspiring Young Science Faculty, Dr. Michael Hagan of the Physics Department. Mike is one of Brandeis’ most accomplished young faculty members. His work has focused largely on the factors that govern self-assembly – the ability of macromolecular systems to form organized structures spontaneously. This is at the heart of the development of complexity, not just in living organisms but also in nanotechnology. Please join me in congratulating Mike on winning this award, and bring your students and postdocs to his Strage Award Lecture. The award ceremony and lecture will take place on Monday, April 16, in Abelson 131, at 12 :30 p.m. The title of the lecture is Mechanisms of Virus Assembly.