Sep 07

Despite centuries of studying the atom and the particles within it, the mysteries of matter continue to elude scientists. What are we really made of?

An Electron-Ion Collider would probe the inner microcosm of protons to help scientists understand how interactions among quarks (colored spheres) and glue-like gluons (yellow) generate the proton’s essential properties and the large-scale structure of the visible matter in the universe today.
To solve such an enigma and better understand the building blocks of our universe, Stony Brook University and the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory (BNL) have partnered to establish the Center for Frontiers of Nuclear Science, bolstered by a new $5 million grant from the Simons Foundation.

“The Center for Frontiers in Nuclear Science will bring us closer to understanding our universe in ways in which it has never before been possible,” said Samuel L. Stanley Jr., MD, President of Stony Brook University. “Thanks to the vision of the Simons Foundation, scientists from Stony Brook, Brookhaven Laboratory and many other institutions are now empowered to pursue the big ideas that will lead to new knowledge about the structure of everything in the universe today.”

Establishing the Center is a big step toward discovering the unknown essentials of matter for Stony Brook and BNL, which already have internationally renowned programs in nuclear physics. But before solving such a mystery, one must first know the clues. Here’s a quick breakdown.

Matter is any substance that has mass and takes up space. An atom is the smallest unit of matter. At an atom’s core is its nucleus, made of protons of neutrons — subatomic particles collectively called nucleons. Looking deeper, nucleons are made of elementary particles called quarks and gluons, and this is where the trail goes cold.

“The role of quarks and gluons in determining the properties of protons and neutrons remains one of the greatest unsolved mysteries in physics,” said Doon Gibbs, Ph.D., Brookhaven Lab Director.

Solving this mystery is the focus of quantum chromodynamics (QCD), a branch of theoretical physics that investigates how quarks and gluons interact as fundamental elements of matter.

Stony Brook and BNL’s new center is slated to become a leading international research and educational hub for QCD over the next several decades, uniting our faculty, students and researchers with BNL staff and scientists from around the world in an effort to crack the quantum case.

One key aspect of the Center’s launch is a proposed Electron Ion Collider (EIC), a powerful new particle accelerator that would create rapid-fire, high-resolution “snapshots” of quarks and gluons contained in nucleons and complex nuclei — crucial to QCD progress.

Abhay Deshpande, PhD, Professor of experimental nuclear physics in the Department of Physics and Astronomy in the College of Arts and Sciences at Stony Brook University
“An Electron Ion Collider would reveal the internal structure of these atomic building blocks, a key part of the quest to understand the matter we’re made of,” Gibbs said.

Abhay Deshpande, professor of experimental nuclear physics in the Department of Physics and Astronomy, has been named Director of the Center, as well as Director of Electron Ion Collider Science at BNL.

A champion of the EIC for decades, Deshpande is positioned to lead development of the collider, which was deemed highest priority for new facility construction by the National Science Foundation’s Nuclear Science Advisory Committee in an effort to strengthen and expand U.S. leadership in nuclear physics and stimulate economic benefits well into the 2040s.

Like most mysteries, collaboration is the key to success, so Deshpande is focused on uniting QCD and EIC experts from around the globe with Stony Brook students who will serve as the next generation of researchers in the field.

“Overall, I want the worldwide community of EIC enthusiasts to see the Center for Frontiers in Nuclear Science as their ‘home away from home,’ where they can come and work on EIC-related research,” Deshpande said. “My hope is that within a short time, the students at Stony Brook will have more opportunities to work with researchers at Brookhaven, and vice-versa.”

Despite the complexity of nuclear physics and related areas of study, the results of such research could reveal the most basic aspects of our very existence.

“Nuclear physics is a deep and important discipline, casting light on many poorly understood facets of matter in our universe,” said Jim Simons, chairman of the Simons Foundation. “It is a pleasure to support research in this area conducted by members of the outstanding team to be assembled by Brookhaven Lab and Stony Brook University.”

Through major funding, the Simons Foundation is bonding a partnership between Stony Brook and BNL perhaps as strong as the interaction between quarks and gluons.

“Basic science research seeks to improve our understanding of the world around us, and it can take human understanding to wonderful and unexpected places,” said Marilyn Simons, president of the Simons Foundation. “Exploring the qualities and behaviors of fundamental particles seems likely to do just that.”

— By Brian Smith

Sep 07

Scientists have yet to understand and explain how life’s informational molecules – proteins and DNA and RNA – arose from simpler chemicals when life on earth emerged some four billion years agoScientists have yet to understand and explain how life’s informational molecules – proteins and DNA and RNA – arose from simpler chemicals when life on earth emerged some four billion years ago. Now a research team from the Stony Brook University Laufer Center for Physical and Quantitative Biology and the Lawrence Berkeley National Laboratory believe they have the answer. They developed a computational model explaining how certain molecules fold and bind together to grow longer and more complex, leading from simple chemicals to primitive biological molecules. The findings are reported early online in PNAS.

Ken Dill
Ken Dill explains the computational model that shows how certain molecules fold and bind together in the evolution of chemistry into biology, a key step to explain the origins of life.
Previously scientists learned that the early earth likely contained the basic chemical building blocks, and sustained spontaneous chemical reactions that could string together short chains of chemical units. But it has remained a mystery what actions could then prompt short chemical polymer chains to develop into much longer chains that can encode useful protein information. The new computational model may help explain that gap in the evolution of chemistry into biology.

“We created a computational model that illustrates a fold-and-catalyze mechanism that amplifies polymer sequences and leads to runaway improvements in the polymers,” said Ken Dill, lead author, Distinguished Professor and Director of the Laufer Center. “The theoretical study helps to understand a missing link in the evolution of chemistry into biology and how a population of molecular building blocks could, over time, result in the emergence of catalytic sequences essential to biological life.”

In the paper, titled “The Foldamer Hypothesis for the growth and sequence-differentiation of prebiotic polymers,” the researchers used computer simulations to study how random sequences of water-loving, or polar, and water-averse, or hydrophobic, polymers fold and bind together. They found these random sequence chains of both types of polymers can collapse and fold into specific compact conformations that expose hydrophobic surfaces, thus serving as catalysts for elongating other polymers. These particular polymer chains, referred to as “foldamer” catalysts, can work together in pairs to grow longer and develop more informational sequences.

This process, according to the authors, provides a basis to explain how random chemical processes could have resulted in protein-like precursors to biological life. It gives a testable hypothesis about early prebiotic polymers and their evolution.

“By showing how prebiotic polymers could have become informational ‘foldamers’, we hope to have revealed a key step to understanding just how life started to form on earth billions of years ago,” explained Professor Dill.

Co-authors of the paper include Elizaveta Guseva of the Laufer Center and Departments of Chemistry and Physics & Astronomy at Stony Brook University, and Ronald N. Zuckermann of the Lawrence Berkeley National Laboratory in Berkeley, Calif.

The research was supported in part by the National Science Foundation.

Aug 25

Researchers from Stony Brook University, Brookhaven National Laboratory and the Hebrew University of Jerusalem have discovered new effects of an important method for modulating semiconductors.


The method, which works by creating open spaces or “vacancies” in a material’s structure, enables scientists to tune the electronic properties of semiconductor nanocrystals (SCNCs) — semiconductor particles that are smaller than 100 nanometers. This finding will advance the development of new technologies like smart windows, which can change opaqueness on demand.

Anatoly Frenkel, a professor in Stony Brook’s Department of Materials Science and Chemical Engineering in the College of Engineering and Applied Sciences, holds a joint appointment at Brookhaven National Laboratory and was the lead BNL researcher on this study.

Scientists use a technique called “chemical doping” to control the electronic properties of semiconductors. In this process, chemical impurities — atoms from different materials — are added to a semiconductor in order to alter its electrical conductivity. Though it is possible to dope SCNCs, it is very difficult due to their tiny size. The amount of impurities added during chemical doping is so small that in order to dope a nanocrystal properly, no more than a few atoms can be added to the crystal. Nanocrystals also tend to expel impurities, further complicating the doping process.

Seeking to control the electronic properties of SCNCs more easily, researchers studied a technique called vacancy formation. In this method, impurities are not added to the semiconductor; instead, vacancies in its structure are formed by oxidation-reduction (redox) reactions, a type of chemical reaction where electrons are transferred between two materials. During this transfer, a type of doping occurs as missing electrons, called holes, become free to move throughout the structure of the crystal, significantly altering the electrical conductivity of the SCNC.

“We have also identified size effects in the efficiency of the vacancy formation doping reaction,” said Uri Banin, a nanotechnologist from the Hebrew University of Jerusalem. “Vacancy formation is actually more efficient in larger SCNCs.”

In this study, the researchers investigated a redox reaction between copper sulfide nanocrystals (the semiconductor) and iodine, a chemical introduced in order to influence the redox reaction to occur.

“If you reduce copper sulfide, you will pull out copper from the nanocrystal, generating vacancies and therefore holes,” said Frenkel.

The researchers used the x-ray powder diffraction (XPD) beamline at the National Synchrotron Light Source II (NSLS-II)—a DOE Office of Science User Facility—to study the structure of copper sulfide during the redox reaction. By shining ultra-bright x-rays onto their samples, the researchers are able to determine the amount of copper that is pulled out during the redox reaction.

Based on their observations at NSLS-II, the team confirmed that adding more iodine to the system caused more copper to be released and more vacancies to form. This established that vacancy formation is a useful technique for tuning the electronic properties of SCNCs.

Still, the researchers needed to find out what exactly was happening to copper when it left the nanocrystal. Understanding how copper behaves after the redox reaction is crucial for implementing this technique into smart window technology.

“If copper uncontrollably disappears, we can’t pull it back into the system,” Frenkel said. “But suppose the copper that is taken out of the crystal is hovering around, ready to go back in. By using the reverse process, we can put it back into the system, and we can make a device that would be easy to switch from one state to the other. For example, you would be able to change the transparency of a window on demand, depending on the time of day or your mood.”

Aug 25

The U.S. has a population of more than 50 million seniors for the first time in history. As that number climbs, Stony Brook University has received a three-year $1 million grant from the W.M. Keck Foundation to fund research that uses brain imaging data to understand how the nutrition of brain neurons affects cognition in aging humans. The research could provide a critical first step toward personalized medicine in neurology for aging patients.

This collaborative project is led by Associate Professor Lilianne R. Mujica-Parodi.
The project, “Protecting the Aging Brain: Self-Organizing Networks and Multi-Scale Dynamics Under Energy Constraints,” is led by Lilianne R. Mujica-Parodi, Associate Professor of Biomedical Engineering at Stony Brook University School of Medicine. The work involves interdisciplinary research and collaboration between Stony Brook University and the Martinos Center for Biomedical Imaging at Harvard Medical School and Massachusetts General Hospital.

“This prestigious grant from the Keck Foundation supports innovative imaging research that will help transform the way scientists study the aging brain,” said Stony Brook University President Samuel L. Stanley Jr. “The funding also comes at a crucial time, as the aging of America will continue and the importance of dietary and other interventions to protect the aging brain are more vital than ever.”

Dr. Mujica-Parodi and co-investigators will integrate human neuroimaging data – from 7-Tesla fMRI and positron emission tomography – with multi-scale biomimetic modeling to test hypotheses with respect to how energy constraints based on diet and mitochondria affect neural efficiency in the aging brain.

“The collaborative work of Stony Brook faculty on the aging brain with scientists from other leading medical research institutions provides a strong basis for advancing this important area of 21st-century medicine,” said Kenneth Kaushansky, Senior Vice President for the Health Sciences and Dean of the School of Medicine. “Using extremely sophisticated imaging algorithms to trace neural pathways, coupled to metabolic interventions seen under stress, Dr. Mujica-Parodi will likely gain practical insights into methods to improve cognition in elderly individuals.”

The research builds on the pilot work of Mujica-Parodi and colleagues at Stony Brook University’s Laufer Center for Physical and Quantitative Biology and the Martinos Center for Biomedical Imaging. The team approaches brain network connectivity, assessed by fMRI and associated cognitive function, as a dynamic emergent phenomenon. They developed a metabolic-neuron hybrid model that can be used in the imaging research to identify and gauge energy input via glucose, glycogen and ketone kinetics.

“By using the imaging and biomimetic modeling techniques, we will investigate the use of exogenous ketones, a fuel source that is an alternative to glucose, as a way to ameliorate age-related effects,” explained Mujica-Parodi. “We hope our findings prove that personalized medicine for neurology is within our reach and that our methods can be a model toward that goal.”

The research team will use their approach to predict how neural networks self-organize in response to changes in energy supply and demand, and then compare those results to data on individuals to better understand the exact connection between nutrition to brain neurons and cognitive capacity.

May 03

The New Fringe Rates have been approved and are in effect 5/2/17. They Can be seen at

Apr 05

As of April 1, 2017, the Policy on Tuition Remission for Graduate Students Supported by Sponsored Projects has been updated to charge six (6) credits per semester per supported student at the in-state rate prevailing at the time the proposal is submitted, with this rate continuing for the life of the grant. Currently, six (6) credits at the in-state rate is $2,718 per semester. In addition, the policy now allows pro-rated charges for graduate students who are supported part-time on a grant. Additional information can be found here.

Apr 27

The P209 Investigator Conflict of Interest Policy has been revised to enable the transition from a submission-based paper process to an online Annual Certification process through the new myResearch portal (Huron Click).

Therefore, beginning May 1st, the Conflict of Interest (COI) PDF forms will no longer be required for any faculty, staff and students that have previously been required to submit paper COI forms to the Office of Sponsored Programs for COEUS proposals submissions, PHS annual awards, changes/additions of investigators to current/new awards and/or to the Office of Research Compliance for participation as study personnel on IRB applications.

All Annual Certifications are required to be submitted in myResearch no later than May 31st.

During the May transition month,all faculty and staff (as required above) must have completed an Annual Certification in myResearch for new awards received in this month, for PHS award anniversaries and for new IRB submissions for COI review in accordance with the campus and federal policies.

Please direct any questions you may have regarding this change you may visit the Conflict of Interest Website or contact Susan Gasparo, in the Office of Research Compliance,, 631-632-1954

Mar 21
Key Dates
Release Date:   March 17, 2017


The Department of Health and Human Services (HHS), including NIH, operates under the “Further Continuing and Security Assistance Appropriations Act, 2017,” (Public Law 114-254) signed by President Obama on December 10, 2016.  This Act (CR) continues government operations through April 28, 2017 at 99.8099 percent of the FY 2016 enacted level.

Continuing the procedures identified under NOT-OD-17-001 and NOT-OD-16-046 and consistent with NIH practices during the CRs of FY 2006 – 2016, the NIH will issue non-competing research grant awards at a level below that indicated on the most recent Notice of Award (generally up to 90% of the previously committed level). Upward adjustments to awarded levels will be considered after FY 2017 appropriations are enacted, but NIH expects institutions to monitor their expenditures carefully during this period.  All legislative mandates that were in effect in FY 2016 (see NOT-OD-16-044 and NOT-OD-16-048) remain in effect under this CR.  Per NOT-OD-17-049, the salary limitation set at Executive Level II of the Federal Pay Scale, was increased from $185,100 to $187,000, effective January 8, 2017. The Ruth L. Kirschstein National Research Service Award postdoctoral stipend levels and tuition/fees for FY 2017 are described in NOT-OD-17-003. Until further notice, the undergraduate and predoctoral stipends and tuition/fees will remain at the levels announced in NOT-OD-16-062.





Mar 21


Since 1990, Congress has legislatively mandated a limitation on direct salary for individuals under NIH grant and cooperative agreement awards (referred to here as a grant). The mandate appears in the annual appropriation act that provides authority for NIH to incur obligations for a given Fiscal Year (FY). At this time NIH has not received a FY 2017 appropriation, and is operating under a Continuing Resolution "the Further Continuing and Security Assistance Appropriations Act, 2017" (Public Law 114-254) that applies the terms and conditions of the Consolidated Appropriations Act, 2016.

The Consolidated Appropriations Act, 2016, restricts the amount of direct salary to Executive Level II of the Federal Executive pay scale. The Executive Level II salary was previously set at $185,100, and increased to $187,000 effective January 8, 2017.

For awards issued in those years that were restricted to Executive Level II (see Salary Cap Summary, FY 1990 – FY 2016), including competing awards already issued in FY2017, if adequate funds are available in active awards, and if the salary cap increase is consistent with the institutional base salary, grantees may rebudget to accommodate the current Executive Level II salary level. However, no additional funds will be provided to these grant awards.

Once the Department of Health and Human Services Appropriation for FY 2017 is enacted, NIH will publish the annual Notice of legislative mandates to provide information on any statutory provisions that limit the use of NIH grant funds in FY 2017. Additional guidance on the salary cap will also be provided at that time.

For a historical record of the salary cap, including effective dates see:


Please direct all inquiries to:

Questions about specific awards may be directed to the Grants Management Specialist identified on the Notice of Award.

Jan 24

On January 30, 2017, the National Science Foundation (NSF) will release updates to FastLane that may impact the way you work. NSF will implement the following changes in FastLane to support the policy updates in the Proposal & Award Policies & Procedures Guide (PAPPG) (NSF 17-1) and to run new and enhanced automated compliance checks on proposals:
Proposal Submission

• Two new types of proposals will be incorporated into the PAPPG with new required supporting documents and automated proposal compliance checks.

o Grant Opportunities for Academic Liaison with Industry (GOALI): GOALI is a type of proposal that seeks to stimulate collaboration between academic research institutions and industry. The new GOALI automated compliance checks will
require hat at least one Co-Principal Investigator (PI) exists on the proposal and the “GOALI-Industrial PI Confirmation Letter” is uploaded at the time of proposal submission. All automated compliance checks applicable to Research proposals
will apply to GOALI proposals. GOALI proposals were previously submitted via a program solicitation.

o Research Advanced by Interdisciplinary Science and Engineering (RAISE): The RAISE proposal type supports bold, interdisciplinary projects. The new RAISE automated compliance checks will require that a “RAISE-Program Officer
Concurrence Email” is uploaded at the time of proposal submission, the proposal award budget is less than or equal to $1 million, and the proposal duration is less than or equal to 5 years. All automated compliance checks applicable to
Research proposals will apply to RAISE proposals.

• The Facilitation Awards for Scientists and Engineers with Disabilities (FASED) type of proposal will be included on the FastLane dropdown menu. All automated compliance checks applicable to Research proposals will apply to FASED proposals.

Deadline Submission

• Organizations that are unable to submit a proposal prior to a deadline due to a natural or anthropogenic disaster will be required to submit a new Single Copy Document, “Nature of Natural or Anthropogenic Event,” when attempting to submit a late proposal using the “Special Exception to the Deadline Date Policy” box on the NSF Cover Sheet.

Updated References and Terminology

• The PAPPG (NSF 17-1) has been modified in its entirety, to remove all references to theGrant Proposal Guide (GPG) and Award & Administration Guide (AAG). The document will now be referred to solely as the NSF Proposal & Award Policies & Procedures Guide and is sequentially numbered from Chapter I-XII. All system references and links to the GPG and AAG will be updated to corresponding references and links in the PAPPG (NSF 17-1).
• “International Travel” type of proposals will be renamed to “Travel” and will be expanded to include domestic and international travel.
• “Facility/Center” type of proposals will be renamed to “Center/Research Infrastructure.”

Enhanced Automated Compliance Checks

• In addition to the new compliance checks for the GOALI, RAISE, and FASED types of proposals, FastLane will run enhanced automated compliance checks across several proposal types and will generate errors or warnings when the submission or deadline validation compliance checks are not met.
• Checks are run during “Check Proposal,” “Forward to SPO,” and “Submit Proposal.” The complete list of FastLane automated compliance checks effective January 30, 2017, is available here.

Note About Proposal File Update (PFU):

The automated compliance checks also apply when a PFU is performed on a proposal. The compliance checks will be run on all sections of the proposal, regardless of which section was updated during the PFU. Proposers should be aware that if a proposal was previously submitted successfully, a PFU performed on the proposal will be prevented from submission if the proposal does not comply with the compliance checks in effect at the time.

For system-related questions,please contact FastLane User Support at 1-800-673-6188 or Policy-related questions should be directed to


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