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.

Sep 18

In 2017, Stony Brook graduate student and ethnomusicologist Jay Loomis and assistant professor of computer science Roy Shilkrot teamed up to secure a grant to create 3D printed replicas of ancient wind instruments.

Assistant Professor of Computer Science Roy Shilkrot, left, and grad student and ethnomusicologist Jay Loomis collaborate on creating 3D replicas of ancient wind instruments.

The goal? To give museum-goers an opportunity to interact with rare instruments rather than merely viewing them through a glass enclosure.

Loomis had been interested in wind instruments since he was a boy in Wisconsin, when he was struck deeply by flute music wafting from his car radio. After he moved to Long Island, his thirst for playing dovetailed with an insatiable curiosity about indigenous musical instruments. He hoped to build such instruments, as a way of sharing aspects of Native American culture with the public.

In his travels as an academic, he encountered musical virtuosos, acoustic experts and computer scientists who shared his passion. That passion gained momentum when Loomis became a teaching assistant at cDACT, the Stony Brook-based Consortium for Digital Art, Culture and Technology.

Through cDACT Director Margaret Schedel, Loomis connected first with Shilkrot and later Hideo Sekino, a visiting professor from Tokyo Institute of Technology, who is associated with the Institute for Advanced Computational Science at Stony Brook.

In spring 2017, Loomis and Shilkrot developed a 3D scanner and used desktop and professional 3D printers to recreate playable replicas of wind instruments, including flutes, ceramic ocarinas and whistles of different shapes and sizes. An integral part of the process was to recreate the sound of the original instrument and mirror its physical characteristics as well.

The greatest challenge the collaborators experienced was in designing the cavity of the instrument, which was essential to recreating the authentic sound.

The results were encouraging but weren’t as precise as Loomis wanted. Schedel recommended collaborating with Sekino due to his interest in the traditional Japanese flute known as a shakuhachi. After she introduced the two musicians, Loomis was inspired to feature the instrument in an electronic piece he co-composed with Timothy Vallier.

Aug 11

Researchers in the Departments of Computer Science, and Applied Mathematics and Statistics awarded $449k through the National Science Foundation’s NeTS program.

Anshul Gandhi, left, and Zhenhua Liu

Even for the personal smartphone or home computer user there is no avoiding the use of cloud computing. Cloud computing is low in cost, easily available, and offers access to useful services that would otherwise be out of reach. Services such as Netflix, Amazon Fire, and Expedia are only some of the popular online services being hosted on the cloud. On the backend, dynamic applications in the cloud are more lucrative if their deployments grow through dynamic capacity provisioning. Software deployments must be carefully provisioned to meet their performance requirements without wasting resources.

Most resource provisioning solutions today employ predictions to estimate demand and provide resources, accordingly. At times, this process could be fraught with errors. With the support of a National Science Foundation (NSF) Networking Technology and Systems (NeTS) award of $449k researchers Anshul Gandhi and Zhenhua Liu, seek to bridge the gap between predictors and provisioning solutions.

The goal of their NeTS project, Demystifying the Role of Prediction Models: Bridging Prediction Algorithms and Resource Provisioning, is to develop and leverage error models to fully realize the potential of predictors. According to Gandhi, “Our research will allow businesses to maximize resource utilization despite prediction errors.”

“This is the kind of cross-cutting research we encourage among our faculty, to advance technologies that push the boundaries and challenge traditional thinking,” said Fotis Sotiropoulos, Dean of the College of Engineering and Applied Sciences. “I applaud Professors Gandhi and Liu on their collaborative approach to this research, and congratulate them on this recognition from the NSF. I look forward to following the progress of their research.”

Gandhi and Liu will investigate the prediction error model which includes constructing models that capture the structure of prediction errors; developing an algorithmic framework; and designing systems to exploit the new prediction error-aware algorithms.

Joseph Mitchell, chair of the Department of Applied Mathematics and Statistics, said, “This is a compelling project that requires collective expertise from computer science, optimization, probability, and statistics, and represents an ideal collaboration between Computer Science and Applied Mathematics and Statistics, both in research and in educational impact.”

Gandhi and Liu will realize additional benefits of their research through technology transfer opportunities with industrial partners.

NSF identified this NeTS project as “transformative research” related to fundamental scientific and technological advances in networking as well as systems research. NSF funds projects such as these in the hope that it will lead to “the development of future-generation, high-performance networks and future internet architectures”.

Arie E. Kaufman, chair of the Department of Computer Science, said, “In addition to finding the answer to network performance challenges, this project is especially interesting because it will directly contribute to interdisciplinary courses taught in two major departments on campus.”

About the Researchers
Anshul Gandhi is an assistant professor in the Department of Computer Science and he is affiliated with the Department of Applied Mathematics and Statistics, and Stony Brook University’s Smart Energy Technologies Cluster. He earned his PhD in computer science from Carnegie Mellon University, where he was advised by Prof. Mor Harchol-Balter. Prior to joining Stony Brook, he spent a year as a post-doctoral researcher in the Cloud Optimization and Analytics group at the IBM T.J. Watson Research Center.

Assistant Professor Zhenhua Liu is currently based in the Department of Applied Mathematics and Statistics, and he is affiliated with Department of Computer Science, and Smart Energy Technology Cluster. He was recently on leave for the ITRI-Rosenfeld Fellowship in the Energy and Environmental Technology Division at Lawrence Berkeley National Laboratory during the year 2014-2015. Dr. Liu earned his PhD in computer science at the California Institute of Technology.

Gandhi and Liu also recently received another NSF award, titled Enhancing the Parasol Experimental Testbed for Sustainable Computing, as part of an infrastructure grant led by Rutgers University to study sustainable computing in datacenters, which is aligned with the Smart Energy Technology cluster’s objectives.

Both the Department of Computer Science and the Department of Applied Mathematics and Statistics are part of the College of Engineering and Applied Sciences at Stony Brook University.

–Christine Cesaria

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.

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 28

Two Stony Brook University Department of Physics and Astronomy faculty in the College of Arts and Sciences recently received the Department of Energy (DOE) Early Career Award for their individual research projects related to the discovery of dark energy and dark matter.  

Marilena Loverde, left, and Anja von der Linden

Assistant Professor Anja von der Linden was awarded for her project, “Towards Precision Cluster Cosmology with Large Synoptic Survey Telescope (LSST)”; Assistant Professor Marilena Loverde, also appointed in the Yang Institute for Theoretical Physics,  was awarded for “Discovering Dark Energy, Dark Matter, and Neutrino Properties with Cosmic Structure.”  Each will receive $750,000 over five years to develop their research.

“This is a wonderful distinction for both Professors von der Linden and Loverde, whose research programs will greatly help us further understand the origin and evolution of the Universe,” said Stony Brook University President Samuel L. Stanley Jr. “The Department of Physics is fortunate to have these scientists among its faculty, both of whom are well deserved of the prestigious Department of Energy Early Career Award.”

The Early Career Research Program, now in its eighth year, supports the development of individual research programs of outstanding scientists during the crucial early career years and simulates research careers in the disciplines supported by the DOE Office of Science.

“Marilena Loverde and Anja von der Linden’s work exemplifies the world-class research being conducted by our outstanding faculty,” says Michael A. Bernstein, Provost and Senior Vice President for Academic Affairs at Stony Brook University. “We are tremendously pleased about this much-deserved recognition for two of our rising stars.”

Both von der Linden’s and Loverde’s research programs address the mystery of the composition of the Universe: less than five percent is in a form of matter familiar to us – planets, stars, gas, photons, and neutrinos. The vast majority of the Universe is in the form of dark matter (about 25 percent) and dark energy (about 70 percent). While dark matter is a form of matter that does not interact with us apart from gravity, dark energy is even more mysterious — it describes the puzzling fact that the expansion of the Universe is accelerating, rather than slowing down due to gravity.  Prof. von der Linden compares it to ”throwing a ball up in the air, and, after initially slowing down, seeing it accelerate upwards.”  

The Department of Energy is involved in several large cosmic surveys, which will provide precision maps of the Universe on the largest scales. These maps themselves are snapshots of the Universe over the past several billion years of cosmic history. From them, we can study the origin and evolution of structure in our Universe and learn about dark energy, dark matter, and the elusive neutrino. Professor Loverde’s research focuses on the theoretical framework for modeling and interpreting cosmic structure; Professor von der Linden’s research focuses on measurements of the distribution of the largest objects in the Universe, clusters of galaxies, as a way of quantifying cosmic structure.

Marilena Loverde

“My research will develop the theory of structure formation in the presence of cosmic neutrinos and other novel types of matter,” Professor Loverde said. “Despite being the second most abundant particle in the known universe, we don’t know how much the neutrino weighs. This is something we hope to learn from cosmic surveys, but we need a more complete theory of cosmic structure formation.  My primary goal is to make sure that our models are sufficiently accurate to detect the neutrino mass, but this work will also generate new tools to study dark matter, dynamical dark energy, and structure formation in the Universe.”

“Solving the puzzle of dark energy requires precision measurements of the expansion history and evolution of structure of the Universe,” Professor von der Linden said. “Clusters of galaxies provide particularly powerful measurements of the Universe,  as the number of clusters as a function of mass and its evolution with time is very sensitive to the details of the inner workings of the Universe, including the properties of dark energy, dark matter, and the masses of neutrinos.  The challenge for cluster cosmology lies in accurately measuring the masses of clusters, and the most promising technique to determine the absolute mass calibration of clusters is through weak gravitational lensing.”

Loverde’s research aims to develop theoretical templates for several large DOE projects, including the Large Synoptic Survey Telescope (LSST), the Dark Energy Spectroscopic Instrument (DESI), and a Stage IV Cosmic Microwave Background (CMB-S4) survey. von der Linden’s project aims to provide the precision measurements necessary to compare to theoretical predictions; in this case, cluster mass estimates based on the weak-lensing capabilities of LSST.  The 8.4-meter LSST is currently being constructed in Chile, and will feature the largest digital camera ever built, with over 3200 megapixels (the sensors for the camera are being developed at nearby Brookhaven National Lab).  

“Professors  von der Linden and Loverde are pursuing one of the central questions in cosmology:  95% of the matter in the Universe is unaccounted for,” says Sacha Kopp, Dean of the College of Arts and Sciences. “Their studies bring us closer to understanding the make-up and origin of the Universe.”

Starting in 2023, LSST will image the entire night sky once every three nights, and continue to do so for 10 years.

Anja von der Linden

This will create the deepest image of the Universe over half of the entire sky.  LSST will sensitively measure the shapes and distances of billions of galaxies.  “Weak lensing” refers to the statistical analysis of these in order to infer the distortion of space-time due to the matter distribution of the Universe. The purpose of von der Linden’s project is to develop and test techniques necessary to utilize LSST weak-lensing data for cluster cosmology, and apply them to targeted pre-cursor as well as LSST data.  

“This award is fantastic news for our research group, and I am grateful to the DOE for supporting our work,”  von der Linden says. “LSST will be a tremendously exciting project, and I look forward to Stony Brook taking part in it. The results of our project will enable cluster surveys to harness their tremendous statistical potential and be a leading probe of cosmology in the next decade.”

“I am absolutely thrilled to receive this award,” Loverde says. “I’m extremely grateful to the Department of Energy for this support. This is a huge boost for the cosmology group here at Stony Brook University, and I’m excited about the work ahead.”

Prior to joining the College of Arts and Sciences Department of Physics and Astronomy in 2015, Professor von der Linden was a Tycho Brahe fellow at the DARK Cosmology Centre in Copenhagen and the Kavli Institute for Particle Astrophysics and Cosmology (KIPAC), Stanford University. She received her PhD in astrophysics from the Max-Planck-Institute for Astrophysics, Garching, Germany, and the Ludwig-Maximilians-Universität, München, Germany.

Professor Loverde joined Stony Brook College of Arts and Sciences in 2015, holding a joint appointment in the C.N. Yang Institute for Theoretical Physics (YITP) and the Department of Physics and Astronomy. She received a BA in Mathematics and Physics from the University of California, Berkeley, in 2003, and a PhD in Physics from Columbia University in 2009. Prior to joining Stony Brook University she was a postdoctoral fellow at the University of Chicago and at the Institute for Advanced Study.

— Rachel Rodriguez

Aug 03

Alum Bryan Perozzi, now a research scientist at Google, won the Association of Computing Machinery SIGKDD, KDD 2017 Doctoral Dissertation award for his work at Stony Brook University. The annual award acknowledges excellent doctoral research in the field of data mining and knowledge discovery.

Bryan Perozzi and Steven Skiena

Perozzi thesis, Local Modeling of Attributed Graphs: Algorithms and Applications, was recognized as the best dissertation of the year in the data science community. His work involves graph embeddings — ways of representing the knowledge encoded in the structure of networks to make them accessible for machine learning models.

Focused on developing scalable algorithms and models for attributed graphs, Perozzi presented an online learning algorithm utilizing recent advances in deep learning to result in rich graph embeddings. The applications of this research are far reaching for the fields of data mining, information retrieval, profiling and demographic inference, online advertising and fraud detection.

Perozzi, whose advisor was Stony Brook Professor Steven Skiena, defended his thesis in May 2016. Upon learning of the award, he said, “Wow, what an honor! I’m humbled to have my work recognized by this prestigious early career award, and I am looking forward to giving a talk during the Doctoral Dissertation Award session on August 15.” The KDD 2017 Conference takes place in Nova Scotia, August 13-17.

Professor Skiena is especially proud of Perozzi’s research accomplishments, and they are collaborators on a number of published works. Their paper on DeepWalk graph embeddings has already been cited 270 times in Google Scholar since its publication in 2014.

“Bryan was a very creative, hardworking and independent graduate student here at Stony Brook, and his work on DeepWalk has proven extremely influential in the data science and machine learning communities. They got the right man for this award,” said Skiena.

At Google, Perozzi’s research relates to the intersection of data mining, machine learning, graph theory, and network science with a particular focus on local graph algorithms. In January 2017, he published and presented Ties that Bind: Characterizing Classes by Attributes and Social Ties, a collaboration with Stony Brook PhD student Aria Rezaei and Carnegie Melon faculty Leman Akoglu.

Perozzi is the first PhD student in the Department of Computer Science, which is part of the College of Engineering and Applied Sciences at Stony Brook University, to receive this award.

About the Association for Computing Machinery
Founded in 1947, the ACM is the largest and oldest scientific and industrial computing society. SIGKDD is the ACM’s Special Interest Group on Knowledge Discovery and Data Mining. SIGKDD selects one winner and two runner-ups each year to receive the award. Selections are based on the relevance to KDD, originality, scientific significance, technical depth and soundness, and overall presentation and readability.

Jul 10

Stony Brook Linguistics PhD candidate Paola Cepeda has been recognized with a 2017 Mellon/American Council of Learned Societies (ACLS) Dissertation Completion Fellowship for her thesis research entitled “Negation and Time. Against expletive negation in temporal clauses.” Cepeda is an international student from Peru.

Scholars previously thought that this type of negation, which is present in a variety of natural languages, had no meaning (e.g., a speaker saying, “I missed not seeing you last summer” when he/she actually missed was “seeing you” and not “not seeing you”). Cepeda’s groundbreaking research suggests otherwise. In addition to addressing an open question in her field, her findings could have broader impacts on language processing by artificial personal assistants like Siri or Cortana.

Cepeda’s advisor, Professor Richard Larson from the Department of Linguistics, explains further: “The artificial languages of logic and computer science have the property that expressions written in them are meaningful in all their parts — they contain no extraneous symbols. As such, one might describe such artificial languages as ‘perfectly’ interpreted. They show a perfect match up between form and meaning. Cepeda’s results suggest that when speakers say a ‘not’ they really do convey a negative meaning, even when it doesn’t seem so. If she is correct, then speakers are more logical and systematic, and natural language more perfect, than initially appears.”

It is a great honor for Cepeda — and Stony Brook — to be recognized with this prestigious award. Only 65 fellows were selected from a pool of more than 1,000 applicants through a rigorous, multi-stage peer-review process. The fellowship offers promising graduate students a year of support to focus their attention on completing projects that form the foundations of their careers and that will help shape a generation of humanistic scholarship. The program, which is made possible by a grant from The Andrew W. Mellon Foundation, also includes a faculty-led academic job market seminar, hosted by ACLS, to further prepare fellows for their postgraduate careers.

“The fellows are completing their degrees at 36 different US universities, and their work represents the broad range of disciplines that this program supports, including literature, philosophy, media studies, ethnic studies, linguistics, sociology, and archaeology,” said ACLS Program Officer Rachel Bernard.

When asked what advice she has for other graduate students pursuing prestigious awards, Cepeda emphasized the importance of crafting one’s proposal with a particular audience in mind. “It’s a delicate balance,” she said, “you want to appear knowledgeable while still ensuring that the subject is approachable for non-experts.” Cepeda carefully tailored her application materials so that a panel of humanists and social scientists unfamiliar with her topic could grasp the significance of her research.

Click here for more information about the Mellon/ACLS Dissertation Completion Fellowship.

Jul 11

New research reveals that sulfur dioxide, a major contributor to air pollution, is removed from the air by concrete surfaces. Stony Brook University researcher Alex Orlov, PhD, and colleagues discovered how concrete interacts and eliminates sulfur and nitrogen oxides. Their findings, published in the July edition of the Journal of Chemical Engineering, could be a significant step toward the practice of using waste concrete to minimize air pollution.

Alexander Orlov, PhD

According to the World Health Organization, as many as seven million premature deaths of people worldwide may be linked to poor air quality and pollution. Sulfur dioxide emissions are among the most common pollutants into the air globally, with power plants emitting the most sulfur dioxide. Cement kilns also produce approximately 20 percent of all sulfur dioxide industrial emissions.

“Even though producing concrete causes air pollution, concrete buildings in urban areas can serve as a kind of sponge adsorbing sulfur dioxide to a high level,” explained Dr. Orlov, Associate Professor of Materials Science and Chemical Engineering in the College of Engineering and Applied Sciences, and a faculty member of the Consortium for Inter-Disciplinary Environmental Research at Stony Brook University. “Our findings open up the possibility that waste concrete coming from building demolitions can be used to adsorb these pollutants.”

He added that concrete remains the most widely used material in the world and is inexpensive.  Because of this, Dr. Orlov emphasized that “the strategy of using pollution causing material and turning it into an environmental solution could lead to new thinking in urban design and waste management.”

This electron microscopy image of concrete includes a model of sulfur dioxide interactions with concrete surface – represented by the colored spheres. (photo: Marija Illoska)

Dr. Orlov cautioned that the capacity for concrete to adsorb pollutants diminishes over time as the material ages. Crushing concrete, however, can expose new surfaces and restore its pollution removing properties.

The researchers used various cement and cement-based building materials to conduct their experiments, details of which are in the paper, titled “Reactions of SO2  on hydrated cement particle system for atmospheric pollution reduction: A DRIFTS and XANES study.” They employed Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) and X-ray absorption Near Edge Spectroscopy (XANES) to identify the levels of sulfur dioxide adsorption on the materials.

Experiments were conducted at Stony Brook University, Brookhaven National Laboratory’s National Synchrotron Light Source and Center for Functional Nanomaterials, and the National University of Singapore.

Co-authors on the paper are Girish Ramakrishnan and Qiyuan Wu of Stony Brook University, and Juhyuk Moon at the National University of Singapore.

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


Go to top