Advanced spectroscopy reveals mechanism of vectorial action in a membrane pump

Judith Herzfeld research imageSome proteins in cell membranes are responsible for actively pumping desired molecules in or unwanted molecules out. Since their discovery, it has been expected that their vectorial action involves the existence of two protein conformations, one in which the active site has a low affinity for substrate and is open to the discharge side of the membrane and the other in which the active site has a high affinity for substrate and is open to the uptake side of the membrane. The driver of the pump is a source of energy that converts the pump from the lower energy state to the higher energy state, from which it can relax back and begin the cycle anew.

However, this model has never fit the longest-studied pump, the light-driven ion pump bacteriorhodopsin. At rest, the active site has a high proton affinity but is open to the discharge side of the membrane. Disruption of the active site by light reduces the proton affinity, but it has been a decades-long mystery how this occurs while maintaining access to the discharge side of the membrane. This mystery has now been solved through advanced spectroscopic studies of photocycle intermediates trapped at low temperatures. Obtained collaboratively by Judith Herzfeld’s group at Brandeis and Robert Griffin’s group at MIT, the spectra trace the establishment of an essential U-shaped pathway to the discharge side of the membrane. The results also explain how this pathway is broken as soon as the proton is released, thereby preventing back flow and enforcing the vectorial action of the pump.

“Primary transfer step in the light-driven ion pump bacteriorhodopsin: an irreversible U-turn revealed by DNP-enhanced MAS NMR.” Qing Zhe Ni, Thach Van Can, Eugenio Daviso, Marina Belenky, Robert G. Griffin, and Judith Herzfeld. J. Am. Chem. Soc., DOI: 10.1021/jacs.8b00022. Publication Date (Web): February 28, 2018

Papaemmanouil Receives Funding from Huawei Technologies

Olga PapaemmanouilShenzhen-based Huawei Technologies, the largest manufacturer of telecom equipment in the world, is supporting Associate Professor of Computer Science Olga Papaemmanouil‘s efforts to develop machine learning approaches for managing the performance of data management systems. The grant will support research on workload management, that is the task of query placement, query scheduling and resource allocation for database applications. Workload management is an extremely critical task for database systems as it can impact the execution time of incoming processing tasks as well as the overall perceived performance of the database  and the quality of the service (QoS) offered to end-clients. The complexity of the problem increases for applications that involve dynamically changing workloads and concurrently executing queries sharing the same underlying resources, as well as applications that are deployed on data clusters with fluctuating resource availability.

Dr. Papaemmanouil’s research aims to design frameworks that can be trained on application-specific properties and performance metrics  to automatically learn how to effectively dispatch incoming queries across a cluster of servers, implicitly solving the resource allocation challenge. These techniques will rely on machine learning algorithms (reinforcement learning and deep learning)  that model the interaction of concurrently running queries  as well as the relationship between database performance and the underlying resource availability in the cluster. The project will lead the way towards the development of workload management solutions that eliminate ad-hoc heuristics often used by database administrators to address these challenges and replace them with software modules capable of providing custom workload management strategies to end-clients.

Jonathan Touboul is new Associate Professor in Mathematics

Jonathan Touboul is a new associate professor in the Department of Mathematics. He is also associated to the Neuroscience program, and member of the Volen National Center for Complex Systems. His research deals with mathematical equations modeling the behavior of neurons and networks of the brain. He is also interested in understanding how the brain is interconnected and if or how these interconnection patterns play a role information processing, learning and memory.

Prior to joining Brandeis, Jonathan Touboul led for a research team at Collège de France in Paris, within the Center for Interdisciplinary Research in Biology. He received his PhD in Mathematics from École Polytechnique (Paris) and spent some time as a postdoc at Pittsburgh University with Bard Ermentrout and at the Rockefeller University with Marcelo Magnasco.

At Brandeis, he intends to pursue his researches in models of large-scale neural networks, learning, memory and synchronized oscillations in Parkinson’s disease.

Summer MRSEC Undergraduate Research Fellowships

In 2018, the Division of Science will offer seven Summer MRSEC Undergraduate Research Fellowships (SMURF) for Brandeis students doing undergraduate research, sponsored by the Brandeis Materials Research Science and Engineering Center.

The fellowship winners will receive $5,000 stipends (housing support is not included) to engage in an intensive and rewarding research and development program that consists of full-time research in a MRSEC lab, weekly activities (~1-2 hours/week) organized by the MRSEC Director of Education, and participation in SciFest VIII on Aug 2, 2018.The due date for applications is March 1, 2018, at 6:00 PM EST.

To apply, the application form is online and part of the Unified Application (Brandeis login required).


Students are eligible if they will be rising Brandeis sophomores, juniors, or seniors in Summer 2018 (classes of ’19, ’20 and ’21). No prior lab experience is required. A commitment from a Brandeis MRSEC member to serve as your mentor in Summer 2018 is however required. The MRSEC faculty list is:

Conflicting Commitments
SMURF recipients are expected to be available to do full time laboratory research between May 29 – August 3, 2018. During that period, SMURF students are not allowed to take summer courses, work another job or participate in extensive volunteer/shadowing experiences in which they commit to being out of the lab for a significant amount of time during the summer. Additionally, students should not be paid for doing lab research during this period from other funding sources.

Application Resources
Interested students should apply online (Brandeis login required). Questions that are not answered in the online FAQ may be addressed to Steven Karel <divsci at>.

Summer Research Funding For Undergrads in 2018

The Division of Science announces the opening of the Division of Science Summer Undergraduate Research Fellowship competition for Brandeis students doing undergraduate research in Summer 2018.  These fellowships are funded by generous alumni donations and by grants.

New this year is the Dan Getz Endowment for Cardiovascular Research Fellowship. This fellowship is for a student working with a Brandeis faculty member on a topic relevant to cardiovascular health. See the Div Sci website for details of additional programs which fund students across all the sciences. We expect to fund at least 30 students this summer.

The due date for applications  is March 1, 2018,  at 6:00 PM EST.

Students who will be rising Brandeis sophomores, juniors, or seniors in Summer 2018 (classes of ’19, ’20, and ’21), who in addition are working in a lab in the Division of Science at the time of application, are eligible to apply. A commitment from a Brandeis faculty member to serve as your mentor in Summer 2017 is required.

The Division of Science Summer Program will run from May 29 – Aug 3, 2018. Recipients are expected to be available to do full time laboratory research during that period, and must commit to presenting a poster at the final poster session (SciFest VIII) on Aug 2, 2018.

Interested students should apply online (Brandeis login required). Questions that are not answered in the online FAQs may be addressed to Steven Karel <divsci at>.

Grant funding for undergraduates doing Computational Neuroscience

The Division of Science is pleased once again to announce the availability of Traineeships for Undergraduates in Computational Neuroscience through a grant from the National Institute on Drug Abuse. Traineeships will commence in summer 2018 and run through the academic year 2018-19.

Please apply to the program by March 1, 2018 at 6 pm to be considered.

Computational Neuroscience undergraduate trainees were first authors on 2 papers in 2017; figure above from Christie et al., J. Neurophysiol., 2017

Traineeships in Computational Neuroscience are intended to provide intensive undergraduate training in computational neuroscience for students interested in eventually pursuing graduate research. The traineeships will provide approximately $5000 in stipend to support research in the summer, and $3000 each for fall and spring semesters during the academic year. Current Brandeis sophomores and juniors (classes of ’19, ’20) may apply. To be eligible to compete for this program, you must

  • have a GPA > 3.0 in Div. of Science courses
  • have a commitment from a professor to advise you on a research project related to computational neuroscience
  • have a course work plan to complete requirements for a major in the Division of Science
  • complete some additional requirements
  • intend to apply to grad school in a related field.

Interested students should apply online (Brandeis login required). Questions that are not answered in the online FAQ may be addressed to Steven Karel <divsci at> or to Prof. Paul Miller.

Protected by Akismet
Blog with WordPress

Welcome Guest | Login (Brandeis Members Only)