IGERT Summer Institute

 The Brandeis IGERT program is hosting its first summer institute starting Wednesday, July 31 and running weekdays through Friday, August 9. This will be a series of lectures by experts inside and outside of Brandeis, together with some student seminars, aimed at graduate students across the sciences, especially (but not exclusively!) those doing theoretical work.

The lectures will run from 9:30-4 every day, with coffee at 9am, and ample time between lectures for questions and conversations.  They will be held in room 055 of the Lemberg Academic Center (note that Domenic’s will be open at that time, so lunch is available nearby).  Those interested in attending should RSVP to Tony Bottaro (bottaro@brandeis.edu) so that we can get a head count for coffee.

The lecturers are:

Parongama Sen (University of Calcutta, Kolkata, India), lecturing on applications of statistical physics to social science problems.
Henry Cohn (Microsoft Research, New England), lecturing on symmetry and optimization.
Ben Allen (Emmanuel College and Harvard), lecturing on evolutionary dynamics
Paul Miller (Brandeis), lecturing on aspects of theoretical neuroscience.
Blake LeBaron (Brandeis), lecturing on empirical puzzles in financial data, and applications of agent-based modeling.
Albion Lawrence (Brandeis), lecturing on fiber bundles (“gauge theory”) and their applications to deformable bodies (falling cats, swimming bacteria).

In addition, we will have seminars by IGERT students:

Sumantra Sarkar
Blake Stacey
Daniel Goldstein

and a schedule can be found on this webpage:


IGERT Video Poster Competition Voting Open

Tony Ng (a grad student in Paul Miller’s lab in Neuroscience) writes:

I’m entering a nationwide video/poster competition organized by the National Science Foundation (NSF) under the IGERT program.  There are over 100 three-minute-videos/posters in the competition.  The videos/posters are divided into 18 fields, all of which are multidisciplinary.  Mine covers cognition/biology/physics.

The competition has a Public Choice award.  Winning the award requires Facebook “likes” on my page.  I need on the order ~1000 “likes” to be in contention.  The bar has been raised from last year’s.  The competition is fierce.  Each/every vote from the Brandeis community counts!

The competition opens today (5/21) and ends Thursday (5/23) at 10pm.  For a vote to count, it is imperative to click on the “Public Choice” button, which would then trigger a Facebook “like” sign-in.  Anyone with an existing Facebook account can contribute.

Here’s the link to my 3-minute video/poster:


Act now! Tthe competition closes on Thursday at 10pm!

Hope you enjoy the videos!

Update (2 pm):

Andrew Russell from the Petsko-Ringe lab also has a poster in the competition on studying Aβ oligomers to understand Alzheimer’s Disease – check it out — vote early, vote often?


Video Poster: One Dimensional Rings of Coupled Oscillators

Brandeis Physics grad students (IGERT trainees) Michael Giver and Nathan Tompkins have a “video poster” in the NSF IGERT Video & Poster Competition on “One Dimensional Rings of Coupled Oscillators – Turing’s Theory Realized”. You can check out and comment on their poster on-line at http://posterhall.org/igert2012/posters/244.

award ribbonUpdate: Michael and Nathan’s poster received a Judge’s Choice award ($2,000.00) in the competition!

Geometry and Dynamics IGERT Awarded

Brandeis has just been awarded an NSF Integrative Graduate Education and Research Traineeship (IGERT) grant in the mathematical sciences.  The grant, titled Geometry and Dynamics: integrated education in the mathematical sciences, is designed to foster interdisciplinary research and education by and for graduate students across the mathematical and theoretical sciences, including chemistry, economics, mathematics, neuroscience, and physics.  It is structured around a number of themes common to these disciplines: complex dynamical systems, stochastic processes, quantum and statistical field theory; and geometry and topology. We believe that it is the first IGERT awarded for the theoretical (as opposed to laboratory) sciences, and are very excited about what we believe to be a highly novel program which will cement existing interdepartmental relationships and encourage exciting new collaborations in the mathematical sciences, including collaborations between the natural sciences and the International Business School (IBS).

The resolution of a singularity that develops along Ricci flow, understood mathematically by Grigori Perelman.  If the red manifold represents the target space of a string, it is conjectured that the corresponding two-dimensonal field theory describing the string undergoes confinement and develops a mass gap for the degrees of freedom corresponding to the singular regime.

The award, for $2,867,668 spread out over five years, provides funds for graduate student stipends, travel, seminar speakers, and interdisciplinary course development.  It contains activities and research opportunities in partnership with the New England Complex Systems Institute (NECSI) in Cambridge, MA.  It also provides opportunities for research internships at the International Center for the Theoretical Sciences in Bangalore.

The PIs on the grant are: Bulbul Chakraborty (Physics); Albion Lawrence (Physics: lead PI); Blake LeBaron (IBS); Paul Miller (Neuroscience); and Daniel Ruberman (Mathematics).  There are 11 additional affiliated Brandeis faculty across biology, chemistry, mathematics, neuroscience, physics, and psychology.  Contact Albion Lawrence (albion@brandeis.edu) for more information about the program.

Arrays of repulsively coupled Kuramoto oscillators on a triangular lattice organize into domains with opposite helicities in which phases of any three neighboring oscillators either increase or decrease in a given direction. Fig. (a) illustrates these two helicities in which cyan, ma- genta and blue vary in opposite directions. In Fig. (b), white and green regions represent domains of opposite helicities. The red regions indicate the frequency entrained oscillators, which are predominantly seen in the interior of the domains.

Admission to the program is handled through the Ph.D programs in the various disciplines:

A lattice of interacting chemical oscillators

At Brandeis, there is a long tradition of interesting experiments on the Belousov-Zhabostinsky reaction system, with the legendary Zhabotinsky himself having been a part of the fraternity. This reaction system shows interesting oscillatory and stable patterns (see videos on Youtube). In the Fraden lab, an oil emulsion of micron-sized water droplets containing the BZ reactions, was shown to show interesting synchronization properties and complex spatial patterns [Toiya et al, J. Phys. Chem. Lett. 1, 1241 (2010)]. A coupling between the droplets due to preferential diffusion of an inhibitory reactant (bromine) in the oil medium was seen to be responsible for these collective phenomena.

In a new paper titled “Phase and frequency entrainment in locally coupled phase oscillators with repulsive interactions” in Phys. Rev. E, Physics Ph. D student Michael Giver, postdoc Zahera Jabeen and Prof. Bulbul Chakraborty show that neighboring oscillators can be modeled as Kuramoto phase oscillators, coupled nonlinearly to its nearest neighbors. The form of the coupling chosen is repulsive, which favors out of phase synchronization. They show using linear stability analysis as well as numerical study that the stable phase patterns depend on the geometry of the lattice. A linear chain of these repulsively coupled oscillators shows anti-phase synchronization, in which neighboring oscillators show a phase difference of π The phase difference between the neighboring oscillators when placed on a ring however depends on the number of oscillators. In such a case, the locally preferred phase difference of π is ruled out for an odd number of oscillators, as this may lead to frustration. When these oscillators are placed on a triangular lattice in two dimensions, the geometry of the lattice constrains the phase difference between two neighboring oscillators to 2 π /3. Interestingly, domains with different helicities form in the lattice. In each domain, the phases of any three neighboring oscillators can vary continuously in either clockwise or an anti-clockwise direction. Hence, phase difference between the nearest neighbors are seen to be ±2π /3 in the two domains (See figure). A phase difference of π is seen at the interfaces of these domains. These domains can grow in time, resembling domain coarsening in other statistical studies. At large coupling strengths, the domains freeze in size due to frequency synchronization of all the oscillators. Hence, an interplay between frequency synchronization and phase synchronization was seen in this system. Ongoing studies in the BZ experimental setup at the Fraden Lab, find correlations with the above results. Hence, insights into a complex system like the BZ oscillators could be gained using the phase oscillator formalism.

The research was supported by the ACS Petroleum Research Fund and the Brandeis MRSEC. Michael Giver is a trainee in the Brandeis NSF-sponsored IGERT program Time, Space & Structure: Physics and Chemistry of BIological Systems

The importance of sniffing

Matt Wachowiak from the University of Utah’s Department of Physiology and Brain Institute will speak about Seeing what the nose tells the brain: order coding and processing in the awake animal on November 29th in the IGERT Neuroscience Seminar Series. The talk, hosted by Don Katz, will take place at 4:00 PM in Gerstenzang 121. Refreshments will be available at 3:45 PM.

This seminar will focus on understanding olfaction in the context of active sensing – in particular, on the importance of sniffing in shaping odor representations and processing. Wachowiak’s lab has found that changes in sniffing behavior can transform both temporal and identity codes for odors even at the level of sensory neurons, and that sniffing – like visual saccades – reflects directed attention towards a particular sensory target. Using a combination of awake imaging, electrophysiology, optogenetics and behavioral analyses they are investigating these bottom-up as well as top-down pathways by which sensory codes are actively shaped by the behaving animal.

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