Listed below are some examples of the research being carried out by the nearly 600 Stony Brook faculty and students at Brookhaven Lab. If you are interested in having your research listed on our website, please contact Laura Lyons.
I have had two substantive projects with BNL, and numerous other contacts. In the mid-1990's, we worked with Bill Studier and John Dunn on an effort to sequence the bacterium which causes Lyme Disease (borrelia Burgdorferi). My then-student Ting Chen (now a professor at USC) and I developed the sequence assembler program used in the project, which jump started my involvement in bioinformatics.
More recently, we have worked on an interesting metagenomics project with Niels van der Lelie. Here my then student Dimitris Papamichail (now a professor at the Univ. of Miami) and I worked to classify bacterial DNA sequences extracted from soil samples to determine changes in species distributions under high and low CO2 concentrations.
For the past six years Prof. Thomas Robertazzi of Stony Brook’s Dept. of Electrical and Computer Engineering has collaborated with Dr. Dantong Yu of BNL’s Computational Science Center on scheduling algorithms and performance prediction for grid systems. Grids are distributed networks of large scale computer resources applied to large scale computational problems. Such computational resources include supercomputers, cluster computers, mass storage systems and remote experimental equipment. The computing power of grids is applied to outstanding large scale computing problems in science and end engineering. Work by Yu and Robertazzi has resulted in tractable mathematical means of scheduling and evaluating the performance of grid systems. Other work with Dantong Yu, Dimitrios Katramatos and Kunal Shroff has involved scheduling for BNL’s high speed networking Terapaths project led by Dr. Yu. This latter project received a best paper award from the Internet 2009 conference.
Robert C. Liebermann, Department of Geosciences and Mineral Physics Institute
Brookhaven affiliation: National Synchrotron Light Source [NSLS]
Distinguished Service Professor and President of COMPRES [COnsortium for Materials Properties Research in Earth Sciences].
Research at BNL
A. Research in sound velocities at high pressures and temperatures
Over the past 20 years, our research group has pioneered the development of ultrasonic techniques to measure sound velocities of mantle minerals at high pressures and temperatures in multi-anvil, high-pressure devices. These experiments can now be performed at simultaneous conditions of 25 GPa [250,000 atmospheres] of pressure and 2000K of temperature.
Most of these sound velocity experiments are now conducted at the Brookhaven and Argonne National Laboratories in conjunction with synchrotron X-radiation to interrogate the structure and densities of specimens under high P & T.
These projects are conducted in collaboration with Professor Baosheng Li of the Mineral Physics Institute.
Details of these experimental techniques may be found at:
B. Role of COMPRES at the NSLS of BNL
COMPRES supports the operation of high-pressure facilities at the superconducting wiggler beamline at X17C and the ultraviolet beamline at U2A.
Details of these operations may be found at:
Miguel Garcia-Diaz, Pharmacological Sciences
Phone: (631) 444-3054
Fax: (631) 444-3218
X-ray crystallography of protein-nucleic acid complexes.
Nucleic acids are constantly subject to endogenous and environmental insults. The resulting DNA damage may be encountered by the protein machinery of several fundamental cellular processing pathways, including replication, transcription and DNA repair. These events can potentially lead to mutagenesis, which underlies the etiology of sporadic diseases such as cancer. In addition, subtle defects in the protein machinery that synthesizes and processes nucleic acids can be inherited and are the cause of a large number of genetic pathologies with a broad spectrum of symptoms, ranging from mental retardation to light sensitivity. Our laboratory takes advantage of the NSLS protein crystallography beamlines at Brookhaven National Laboratory to determine the structure of different protein-nucleic acid complexes to understand the molecular details of different nucleic acid processing pathways. This information is then used to characterize how these pathways are affected by DNA damage and other environmental exposures, and ultimately to understand how alterations in normal nucleic acid biology can result in human disease.
Collaborative project between:
Andrew Tucci (SBU Undergraduate Student), Peter Thanos (BNL-Medical, faculty),Brenda Anderson (SBU-Psychology, faculty), John Robinson (SBU, Psychology, faculty)and Nora Volkow (BNL & NIDA, faculty)
Our Biopsychology facebook page is below:
Empirical studies on addicts and in animals suggest a dysfunction of the dopamine system. Lower levels of dopamine d2 receptors (D2R) have been proposed to increase addiction and drug abuse vulnerability. In contrast, physical exercise increasesdopamine and D2R density. The possibility that exercise upregulates the system integral in reinforcement leads us to hypothesize that exercise reduces the vulnerability to drug abuse. We have found that exercise training in male rats reduces cocaine seeking. These findings are consistent with the hypothesis that exercise, by increasing dopaminergic transmission, serves to reduce cocaine seeking and cocaine self-administration through its actions ondopaminergic transmission and D2R. We are currently conducting carefully controlled studies with sensitive behavioral and neuroimagingmeasures (in-vitro D2R autoradiography and in-vivo brain activity using microPET) in rats to evaluate whether chronic exercise can reduce the risk for drug abuse, increase D2R receptor density, and alter brain activity during cocaine exposure.
"The Use of Supercritical Carbon Dioxide for Environmentally Green Polymer Surface Processing"
My group focuses on the development of new “green” process environments for polymer surface using supercritical carbon dioxide (scCO2). At temperatures and pressures above the critical point values, one-component fluids can have densities and solvent properties approaching those of the corresponding liquid. Fluids in this regime are defined as “supercritical fluids”. In particular, scCO2 is appealing because it is inexpensive, nontoxic, and environmentally benign and has an easily accessible critical temperature and pressure. The goals of our research are (i) to understand the novel phenomena (swelling, plasticization, phase separation and crystallization) induced at the polymer/scCO2 interface on the nanometer scale and (ii) to utilize the fundamental understandings for nanofabrication of functional polymer surfaces to be used as biogas membranes, solar cells, low-k films, conductive nanowires. In order to characterize the nanometer structures, my group has been integrating a variety of surface-sensitive X-ray scattering techniques at the x10A&B beamlines of NSLS. The successful achievement of the collaborative research would profoundly impact the fields of environmentally green technology for polymer surface processing. The research is currently supported by a National Science Foundation CAREER award (2009-2014).
Graduate Student, Biopsychology
Department of Psychology
Stony Brook University, Stony Brook, NY 11794-2500
In collaboration with,
Brookhaven National Laboratory
Bldg 490, Upton, NY 11793-5000
The neurpsychoimaging group at BNL conducts translational research in the study of addiction. Having access to the unlimited resources (first class scientists, facilities, technology, computer systems) at Brookhaven allows us to explore many different avenues and perspectives. So to accomplish this, we use a multi-modal approach, combining data from physiological measures such as functional magnetic resonance (fMRI), electroencephalogram recordings (EEG), positron emission tomography (PET), neuropsychological and behavioral testing, clinical interviewing, and genetic assays. The particular focus is on cocaine dependence, as it serves as one of the best models dopamine dysfunction, and consequently addiction. The goal of translational approaches in the study of psychological conditions is to extend basic scientific findings to the general understanding of the disease and development of appropriate drug and social-psychological treatments. Current/ongoing work includes research [questions] related to the following: reward processing, emotional response to salient stimuli, structural abnormalities, dopamine function, genetic contribution, co-morbidity, aggression, etc.
For more information, please visit: http://www.bnl.gov/neuropsychology/
Prasad Kerkar1, Kristine Horvat2, Keith Jones3, Devinder Mahajan4
1Graduate Student, Material Science and Engineering Department, Stony Brook University; 2Undergraduate Researcher, Chemical and Molecular Engineering, Stony Brook University; 3Environmental Sciences Department, Brookhaven National Laboratory; 4Joint Appointment, Chemical and Molecular Engineering, Stony Brook University and Energy Sciences & Technology Department, Brookhaven National Laboratory.
Imaging time-resolved methane hydrate growth in porous media using X-ray computed microtomography
Methane hydrates are clathrates in which water molecules form a cage to encapsulate methane molecules under conditions of low temperatures (< 5oC) and high pressures (> 5 MPa). Gas hydrates are known to occur worldwide in locations such as the permafrost regions of Siberia, the Mackenzie Delta, and the North Slope of Alaska though abundant but mostly dispersed hydrates are beneath the ocean floor, making these a potential source of methane to supplant our gas supply. The structural properties of methane hydrates can greatly affect the elastic properties of their host, the hydrate-bearing matrix. An understanding of the sediment-hydrate interaction is of importance to quantify changes that may accompany changes in the seafloor’s elastic properties in the event of a rapid release of methane. We are developing the use of synchrotron x-ray computed microtomography (CMT) technique at NSLS / BNL in the study of gas hydrate behavior. Our recently reported study (Kerkar et al., 2009. Appl. Phy. Lett. 95 024102) was aimed at understanding a surrogate THF-Hydrate system. The individual tomogram data collected at Beamline X-2B was reconstructed to produce 2-D and 3-D images. One such 3-D image after 78 hours (FIG. 1) show relative hydrate saturation and suggests, for the first time, that the hydrates formation is patchy and follows pore-filling growth. A follow-up study of methane hydrate growth in porous media is now nearing completion (Kerkar et al, manuscript in preparation, 2009) that may help understand the implication of sudden methane release in predicting seafloor stability and impact on climate change.
Gary V. Lopez
Department of Chemistry at Stony Brook University / Department of Chemistry at BNL
Advisor: Dr. Trevor Sears
Our group at Stony Brook University focuses on developing techniques that involve lasers to study molecules. These techniques are applied to prototype molecular systems in order to understand their structure and dynamics in the gas phase. Using high resolution photoelectron methods like the resonance enhanced multiphoton ionization (REMPI), we study the vibrational structure of the first excited states (S1) and cation ground state (D0) of aromatic molecules like phenylacetylene and fluorene. The slow electron velocity mapping (SEVM) technique helps us to study their photoelectron angular distributions. Theoretical methods using electronic structure and vibronic interaction programs are been developed to predict the vibrational structure of an electronic transition. We are involved in comparing our experimental spectra with those we calculated in an effort to validate our theoretical results. Our group is also working on implementing a new technology developed in 2005 by T. Hänsch, J. Hall and co-workers. Using this new technology known as the optical femtosecond frequency comb, we are trying to measure with high accuracy and precision the frequency lines of the 1.5 m bands of acetylene trying to exceed the best measurement of these lines to date which are to about 1012 accuracy. Once we have successfully characterized the 1.5 μm region of acetylene we will be able to use our technique to probe other molecules such as phenylacetylene and PbF.
Baosheng Li, Mineral Physics Institute, Research Professor
Research at X17B2, NSLS BNL
My research utilizes the large volume high pressure apparatus installed on this super wiggler beamline for studying structure and physical properties of solids and liquids up to 200 kbar in pressure and 2000K in temperature. X17B2 is the beamline where I led a team and pioneered the techniques for sound velocity measurements at high pressure and temperature. The most significant impact of such measurements is that we can measure the velocity of Earth minerals and compare with that of the Earth derived from Earthquake studies to constrain the mineralogical composition of the deep interior. Funding from DOE/NNSA has also enabled applications of such measurements on metals, ceramics, BMG for understanding their behavior under extreme conditions, from atomic structure to bulk properties.
Research at X17B3, X17C, U2A, NSLS BNL
Projects conducted on these beamlines involve the use of diamond anvil cell at pressures as high as those in the core of the planet Earth. Examples include probing iron and its alloys at high pressures to investigate the likelihood of minor elements in the core (Ph.D Thesis, Matthew Whitaker, 2009), discovering and exploring the structural behavior of new energy materials (thermoelectric, piezoelectric, etc.) at high pressures. The optical transparency of the diamond allows for other spectroscopic investigations in addition to X-ray, such as inferred, and Raman spectroscopes at U2A.
Details of these experimental techniques may be found at:
Andrew Tucci, Stony Brook University Psychology Major '11, BNL Medical Dept. Bldg. 490
Thanos Lab. Research Associate
Since September 2008 I have been working on the effects of exercise and addiction under Dr. Peter Thanos' mentoring at Brookhaven National Laboratory. My first completed experimented was titled "The Effects of Chronic Adolescent Forced Exercise on Cocaine Conditioned Place Preference in Male and Female Lewis Rats". This experiment lasted 16 consecutive weeks and examined how treadmill exercise will affect female and male adolescent rats' preference for cocaine. In mid October I presented this experiment as a poster at the 2009 Society for Neuroscience Conference in Chicago. My abstract was selected as a "Hot Topic" and was one of a few to be published into the media books as a lay language article. Following SFN I was invited to present at the inauguration of the new President of Stony Brook University, Dr. Stanley Samuel. I had the privilege to meet the President and present my poster and findings. I love doing addiction research at Brookhaven. In recent months exercise has been pushed to the forefront of addiction research and the work we are doing at my lab will continue to open eyes in the neuroscience and addiction research communities.
Stefan Judex, PhD, BME Department at SBU and Lisa Miller, PhD, Synchrotron Light Source at BNL
The strength of bone is a product of the quantity and quality of the tissue. In this work, we propose that the compromise in bone strength that cannot be fully explained by a decrease in bone quantity is propagated by inherent defects in the material, resulting in an increased susceptibility to fracture. Similarly, antiresorptive (e.g., bisphosphonates) and anabolic (e.g., PTH) treatments for musculoskeletal diseases may influence both the quantity and quality of the bone matrix, and thus can ultimately improve (or compromise) bone’s ability to resist load, but the manner in which this is achieved remains unclear. The underlying hypothesis of this work is that subtle modulation of bone’s matrix properties, as manifested in chemical composition (e.g., mineral/matrix ratio, calcium/phosphorus ratio, collagen structure, crystallinity) and/or structure will markedly influence the quality of bone, and will result in direct effects on bone structural behavior under mechanical load (e.g., bone stiffness, strength, resilience, toughness). Using a unique combination of state of the art chemical, mechanical, morphological, and histological assays at both BNL and SBU, the primary aim of this study is to identify the principal matrix and architectural factors that define bone quality. These relations will be derived from the rat skeleton defined through aging as well as in situations when the remodeling balance is altered (withdrawal of estrogen) and treated with anti-catabolic or anabolic treatments. These conditions will establish a large range of microscopic and macroscopic tissue properties which will be quantified by in situ synchrotron infrared microspectroscopy and small-angle x-ray scattering to determine chemical properties, synchrotron nano-CT and micro-CT to determine the structure, and nano-indentation and macroscopic mechanical testing regimes to determine mechanical properties. Taken together, these systematic studies present a unique opportunity to first identify and then test precise interrelationships between biochemical, mechanical, and structural factors during aging, hormonal imbalances, and anti-catabolic/anabolic treatment at different hierarchical levels. Identification of these potential chemical targets will provide critical information for improved diagnostic, prophylactic, and therapeutic means of addressing bone quality defects induced by aging, disease, and treatment.
Vasso (Bessy) Alexandratos came to Stony Brook with a passion for the environment. It turned out to be no small wonder when she decided to pursue research to identify how contaminants such as arsenic can be removed from water supplies using relatively simple and cost-effective means. It had been known that one of the common dissolved forms of arsenic, AsO43-, has an affinity for reacting with calcium carbonate, which is an abundant mineral found in limestone. What wasn’t known, however, was how the arsenic reacted with calcium carbonate and whether the process could be effective in removing this contaminant from sources of drinking water. Bessy wanted to solve these problems and joined Prof. Richard Reeder’s environmental geochemistry group that was taking advantage of the unique X-ray spectroscopy facilities at the National Synchrotron Light Source at Brookhaven National Laboratory. Bessy used a technique called X-ray absorption fine structure spectroscopy to identify how dissolved AsO43- reacted with calcium carbonate. She performed experiments in the geochemistry lab at Stony Brook and analyzed the reaction products at the National Synchrotron Light Source. Bessy learned that this form of arsenic sorbs strongly to the surface of the calcium carbonate in a way that effectively removes it from the water and retains it at the surface, even when the chemistry of the water changes. Bessy published her research in a leading geochemistry journal, and won praise for having one of the journal’s most highly viewed papers.
Lingling Wu, Graduate Student in Applied Mathematics and Statistics
Working with Prof. Roman Samulyak, a scientist in Computational Science Center of BNL.
Our recent research project is "structure of plasma liners for plasma jets induced magneto inertial fusion", started from September 2009. We use BNL bluegene supercomputer to simulate a 3 dimensional formation evolution of plasma liners for plasma jets. These plasma jets are highly supersonic with Mach number 60. M144 uniformly distributed jets are studied, mainly focus on detached process and the oblique shock waves during merging process. Our code solve time dependent hydrodynamic Partial differential equations in parallel way with c language.
The most important result is the prediction of the average Mach number reduction and description of liner structure and properties, including density, pressure, temperature etc. We also compare the convergence by increasing mesh resolution. The
biggest parallel processes number for our research is 16384 with 3d 1024^3 grid, and the code runs smoothly. The visualization cluster of BNL bluegene also help us a lot in data analysis part.
I am happy to have this chance to show my appreciation to BNL. My advisor update some newest research information in:
Meng Li, Graduate student in Materials Science department
Working with Dr. Radoslav Adzic, a senior scientist in Chemistry Department, Brookhaven National Laboratory.
Electrocatalysts for Ethanol-Powered Fuel Cells
Nowadays human beings are facing energy crisis because we running out fossil fuels. Fuel cells could convert the chemical energy of various fuels, such as hydrogen, methanol, ethanol, etc., directly to electrical energy; and hence have been widely recognized as an excellent alternative energy source. The high cost and low efficiency of current existing electrocatalysts now have hindered commercializing fuel cells. Our group is dedicated to develop electrocatalysts for both anode reaction (including methanol and ethanol oxidation) and cathode reaction (oxygen reduction reaction) in fuel cells.
My own research is about the electrocatalysts for ethanol oxidation reaction. Ethanol is an ideal fuel for fuel cell applications, and the major hurdle is the molecule’s slow, inefficient oxidation. Specifically, the suitable electrocatalyst should be able to break carbon-carbon bond in the ethanol molecule. We synthesized a ternary PtRhSnO2/C electrocatalyst by depositing platinum and rhodium nanoparticles on tindioxide nanoparticles on a high-surface-area carbon support. This electrocatalyst effectively splits the C-C bond in ethanol at room temperature in acid solutions, so facilitating its oxidation predominantly to CO2 at low potentials. The origin of the enhanced activity was identified through a combination of experimental methods, employing electrochemical techniques, in situ X-ray absorption spectroscopy, in situ infrared spectroscopy, transmission electron microscope, and density functional theory calculations.
These studies reveal that the high catalytic activity results from the synergy between all three constituents and these findings may open up new possibilities for studies of C-C bond splitting in variety of important reactions.
Minghua Zhang, Professor and Director, Institute for Terrestrial and Planetary Atmospheres, Associate Dean, School of Marine and Atmospheric Sciences
Project 1 Title: Nested Modeling of Regional Climate Change under Global Warming
I am collaborating with BNL scientists Drs. Wuyin Lin and Andrew Vogelmann to study regional climate change as a result of increasing greenhouse gases in the atmosphere. Current global climate models cannot resolve or poorly represent many energetic atmospheric systems, such as convection and hurricanes, because the grid sizes are on the order of a hundred kilometers. Due to limitation of computer powers, it is still unfeasible to refine the resolutions of global climate models to several kilometers in the foreseeable future. With funding from the US Department of Energy, we are studying methods of nesting high-resolution mesoscale models inside global models, with two-way interactions, in critical regions over the globe to carry out climate change simulations. This will enable us to better represent convection and to more accurately infer characteristics of climate change that are specific to regions of interests. We use the NY BlueGene supercomputer for this research.
Project 2 Title: Study and Verification of Fast Physics in Climate Models
I am collaborating with Dr. Yangang Liu and a group of scientists at BNL, GFDL/Princeton University, JPL/Caltech, and GISS/NASA to evaluate and improve physical processes in climate models on time scales of days or shorter. These processes include cloud nucleation, particle growth through condensation and collision, radiative transfer, turbulence, cloud macrophysics, and atmospheric convective transports of moisture, heat and momentum. We use measurements from the DOE Atmospheric Radiation Measurement Program and the various NASA satellite missions to constrain our models and to find better ways to describe them in climate models.
BNL scientists: Alla Zelenyuk and Dan Imre (formerly at BNL Environmental Sciences Department, now at PNL) Stony Brook PhD students: Hyunjung Lee, EunJu (Julia) Nam, Yiping Han, Peter Imrich (sequential involvement since project start in 2002)
Stony Brook faculty: Klaus Mueller (Computer Science Department)
ClusterSculptor: Software for Expert-Steered Classification of Single Particle Mass Spectra
To take full advantage of the vast amount of highly detailed data acquired by single particle mass spectrometers it is required that the data be organized according to some rules that have the potential to be insightful. Most commonly cluster analysis methods are used to classify the individual particle mass spectra on the basis of their similarity. Cluster analysis is a powerful strategy for the exploration of high-dimensional data in the absence of a-priori hypotheses or data classification models. However, more often than not, the examination of the data clustering results reveals that many clusters contain particles of different types and that many particles of one type end up in a number of separate clusters. Our experience with cluster analysis shows that we have a vast amount of non-compiled knowledge and intuition that if brought to bear in this effort has the potential to greatly improve it. ClusterSculptor is a software package designed to provide a comprehensive and intuitive visual framework to aid scientists introduce their vast knowledge into the data classification process. ClusterSculptor offers a wide variety of tools that are necessary for a high-dimensional, expert-driven activity we call cluster sculpting. ClusterSculptor is designed to be coupled to SpectraMiner, our data mining and visualization software package. The data are first visualized with SpectraMiner and identified problems are exported to ClusterSculptor, where the user steers the reclassification and recombination of clusters of tens of thousands of particle mass spectra in real-time. The resulting sculpted clusters can be then imported back into SpectraMiner.
Abhay Deshpande, Associate Professor, Dept. of Physics & Astronomy, Stony Brook University
Sr. Fellow & Dep. Group Leader (Experiments), RIKEN BNL Research Center, Brookhaven National Laboratory
Almost fifty years have passed since the discovery, that protons and neutrons, the nucleons, are made up of quarks and gluons. Yet, we understand neither the origin of their mass fully nor the constitution of their spin. Quarks contribute less than 1% of their mass, and less than a third of its spin. Scientists believe the gluons self-interactions generate the mass, but there is no intuition for the spin contribution from the quarks and gluons and their internal dynamics. A world-wide effort to understand the internal spin structure of the nucleons (i.e. to solve the Spin Puzzle/Crisis) was initiated in 1990s employing polarized high energy scattering of electrons and muon beams off stationary nucleons (polarized Deep Inelastic Scattering, pDIS). A complementary (& novel) technique of high-energy polarized proton-proton scattering using the polarized proton beams of the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory (BNL) was realized in 2001.
Prof. Abhay Deshpande and his group use the polarized RHIC and the PHENIX detector (seen in the background in the picture above) at BNL to study the internal spin structure of the proton. In recent past, the group has led the measurements of the gluons contribution to the proton spin using collisions at 200 GeV center-of-mass. Recently a significant increase in the center-of-mass (500 GeV) of the RHIC was achieved to look deeper in to the proton and to measure the anti-quark & quark polarizations contribution to the nucleon spin. Novel aspects of transverse spin dynamics of the quarks discovered at RHIC recently will also be part of the spin studies in near future.
Prof. Abhay Deshpande was one of the early proposers of the future Electron Ion Collider (EIC) in which a high energy polarized electrons would collide with a high-energy polarized proton & nuclei and enable an unprecedented study of Quantum Chromodynamics (QCD) through precise investigations of role of the gluons in nucleons and nuclei. One of the two proposals of this future facility, eRHIC at BNL, utilizes the existing RHIC beams and a new polarized electron beam facility to be built next to it.