Maria V. Fernandez-Serra, Department of Physics & Astronomy (SBU) and Deyu Lu (BNL)

"Theoretical and Computational Approaches to Accurately Compute van der Waals Interactions: Method Development and Application"

Abstract:The discovery of new materials for renewable energy applications can be expedited by effective use of the first principle computational tools. In this regard, DFT and its time-dependent (TD) variant have become the workhorse in the past several decades to provide atomic details as well as the underlying electronic structure of complex materials to successfully supplement the experimental results. However, DFT under the local or semi-local approximation has well known deficiencies including the self-interaction error due to the lack of long-range correlation effect, and the poor description of the electron-hole interaction in the excited states. As a result, it remains computationally challenging to address several fundamental problems related to renewable energy applications. Examples are structural characterization of materials bound by van der Waals (vdW) forces, optical absorption spectra calculation for novel photovoltaic materials, and energy level alignment at inorganic/liquid interfaces in photo-catalytic reactions for liquid fuel generation. From a material point of view, water plays a critical role in most applications. The understanding of the electrochemical interface, necessary to design efficient hydrogen fuel cells, requires atomistic modeling capable of accurately reproducing the polarizability and network structural relaxations of water molecules interacting with charged surfaces. One of the most promising sources of clean energy is the use of 100% sun-driven fuel cells to store energy inH2 and O2 produced from photo-catalytic water splitting redox reactions. Research in this area is progressing thanks to strong collaborations between experimental and theoretical teams. However, an important limiting factor is that only modeling is capable of predicting atomistic mechanisms for the reactions. The prediction of thermodynamic and kinetic barriers is limited by the quality of the simulations, which need very accurate characterization of bulk water and interfacial water structure and dynamics.

Jon Patrick Longtin, Department of Mechanical Engineering (SBU) and Thomas Butcher (BNL)

"Improved Refrigeration Efficiency Using a Two-phase Thermo Syphon, Sky Cooling and Phase Change Materials"

Abstract: U.S. households consume >150 billion (B) kWh of electricity per year for residential refrigerators (left). At a national average electrical cost of $0.12/kWh, this represents an annual cost of $18B and 180B lb of CO2 per year. In virtually all applications, the refrigerator resides in a conditioned environment maintained at 20-22 oC (68-72 oF) and uses electricity to move heat from the refrigerated space at a temperature of 2.8-4.4 0C (37-40 oF) to the conditioned space at 68-72 F. In many parts of the U.S., however, the outside temperature falls below the 3–4o C refrigerated-space temperature for several months out of the year, particularly in the northern half of the country. A natural choice then is to use the low outside temperatures for cooling to reduce electricity usage for residential refrigerators. One approach to using cool outside tempera-tures is to place heat exchangers in the refrigerator compartment and outside, and pump a cool-ant through the system. Such approaches have not been very successful because they (1) are expensive, (2) use pumps and fans that require electricity and can fail, (3) require significant temperature differences between the refrigerated space and outdoor space in order to be effective. This last point is critical: as the minimum temperature difference between the refrigerated space and the outside required for a supplemental cooling system to work, the fewer days out of the year will be available for it to operate.

Andriy Lyakhov, Department of Geosciences (SBU) and Mark Hybertsen (BNL)

 "SBU-BNL Workshop on Frontier Computational Materials Science”

Abstract: The "Materials Genome Initiative for Global Competitiveness" highlights the critical role of computer-based theory and modeling not only for the research frontier but also as a critical component of industrial research and development. In many fields, the theory and modeling effort is a significant partner with experiment to advance the frontiers of knowledge. Enhanced use of computer-based theory and more effective development of targeted databases in support of rapid discovery of new materials with specified properties exemplify the leading edge of   Genome Initiative. Research directed to adapt this approach to discover new materials, for example with utility in catalysis and energy storage, will be a critical component in fulfillment of the Brookhaven National Laboratory Energy Strategy and will rely on the on-going developments in High Performance Computing under the SBU-BNL umbrella. The Materials Genome Initiative also presents a compelling educational challenge. The Materials Genome Initiative has grown out of pioneering research efforts in diverse research groups around the world. Expansion of this nascent effort to have impact on multiple classes of materials and functional applications will require training of a much broader swath of young research students and post-doctorals as well as experienced researchers. Students learn the fundamentals of their field through the curriculum for their discipline. While these curricula advance to include new developments, the vision of the Materials Genome Initiative requires a concentrated training in cross-disciplinary concepts and methodologies that is not easily realized within traditional curricula in the universities. Also the needs for additional training for practicing researchers require a different approach. We plan to organize a series of educational workshops on Frontier Computational Material Science, motivated by the vision of the Materials Genome Initiative, in Stony Brook and BNL. These workshops are aimed at young scientists from different fields: physics, chemistry, geoscience and material science. The workshops will provide the cross-disciplinary training needed for successful research in materials discovery by focusing on key methodological advances and providing the supporting framework of opportunities for application to leading problems in targeted areas of Materials Science. The proposed seed grant will play a key role to nucleate this program.

 Alexander Orlov, Department of Materials Science (SBU) and Yan Li (BNL)

"Understanding Extraordinary Water Splitting Activity of Sub-nm Noble Metal Particles of Different Sizes and Shapes; a First-Principle Investigation and Model Systems Study"

Abstract: Generating chemical fuels in a clean and sustainable way by harnessing sunlight, for example   by splitting water using photocatalysts, has enormous economic, environmental and energysustainability benefits. The proposed research is motivated by a recent finding in Orlov's lab (SBU PI)on the extraordinary activity of sub-nm gold nanoparticles for photocatalytic hydrogen production. One of the focuses of this proposal is to apply an advanced set of first-principles computational tools to investigate the structural, electronic and optical properties of both bare and ligand-protected noble metal nanoparticles. We will also carry out mechanistic studies on the interactions between nanoparticles and semiconductor catalyst surfaces, such as the charge exchange and energy level alignment at the interface. In addition, a set of model systems of noble metal nanoparticles deposited on single crystal substrates will be probed using Scanning Tunneling Microscopy (STM) and X-ray Photoelectron Spectroscopy (XPS) in order to establish relations between the shape/dimensions of supported sub-nm catalysts and their photoactivity. By utilizing advanced computational and experimental techniques, we will explore the combined choices of nanoparticles and catalyst materials to optimize efficiency for hydrogen production. Overall, we aim to provide a fundamental understanding of the physics that underlies this dramatic enhancement of photoactivity, and ultimately enable rational designs for water splitting in a predictable and controllable fashion.-

Sam Parnia, Department of Medicince (SBU) and Anat Biegon (BNL/SBU)

 “A Pilot Positron Emission Tomography Study Evaluating the Role of N-methyl-D-aspartate (NMDA) Receptor Activation and Neuro-inflammation in Cognitive Impairment following Anoxic Brain Injury”

Abstract: Anoxic brain injury following cardiac arrest is associated with significant mortality and morbidity. Studies have shown that up to 50% of cardiac arrest survivors suffer with cognitive deficits which include disturbances in memory. Reduction in NMDA receptor function and neuro-inflammation have in been demonstrated in human subjects with and experimental models of head trauma, stroke and meningitis, but the role of NMDA receptors in long term cognitive and memory deficits arising following anoxic brain injury in humans has not been fully established to date. This study will be the first to examine regional changes in NMDA receptor function in anoxic brain injury survivors with cognitive deficits compared to healthy subjects in vivo; in correlation with their cognitive performance and the intensity of neuro-inflammation. This will be accomplished using non invasive PET imaging with selective radiotracers for NMDAR and neuro-inflammation ([11C]CNS5161 and [11C]PK11195 respectively). The results will shed light on the role of this receptor in anoxic brain injury and provide a subject selection tool for further clinical trials with NMDAR agonists and/or anti-inflammatory agents in the treatment of cognitive deficits related to anoxic brain injury following cardiac arrest.

Dmitri Tsybychev, Department of Physics and Astronomy (SBU) and Zheng Li (BNL)

“Development of 3D Trench Detectors for Radiation Hard Collider Physics and Photon Science Applications”

Abstract: The Large Hadron Collider (LHC) at CERN, Geneva, Switzerland is the next energy frontier at 7-14 TeV center of mass energy, where beams of protons collide with unprecedented luminosity. Thus, the LHC and its experiments will provide excellent opportunities to shed light on the origin of electroweak symmetry breaking and to make fundamental discoveries. The LHC has recently begun to deliver large amounts of data, probing the universe at energies that have never been directly accessible to experimenters before. A very high collision rate of protons at the LHC will make the present pixel detectors of ATLAS and CMS (the two largest general purpose experiments at the LHC) inoperable due to high radiation damage and in turn will affect the physics program pursued by the experimental collaborations. Next generation High Energy Physics Collide experiments require radiation hard pixel detectors for efficient tracking closest to the interaction point. A number of groups, both in the U.S. and abroad, are undertaking research and design of detector upgrades to preserve and enhance the detector performance in the face of increased beam intensity. However, a completely satisfactory detector for the innermost regions has yet to emerge. In addition, new photon science facilities such as the National Light Source II project will require improved detectors for Imaging and Spectroscopy applications. In this proposal, we are proposing to develop a new 3-D silicon detector concept in collaboration with our BNL colleagues that will be capable of addressing the needs of these disparate fields. This concept, called the Trench 3-D detector [1,2], was recently proposed and prototyped by the BNL scientists, but has yet to be tested. The prototyped design features multiple variants of 3-D Trench detectors that were fitted and fabricated on a single silicon wafer. All of these variants use the same concept of "Trench" electrodes, but differ in geometry. The geometric pixel variations lead to detectors suitable for different applications. The goal of the proposal is to validate the Trench concept itself, through the systematic test and measurement of fabricated test structures. The work will also include preparations for bump bonding of fabricated test structures to ATLAS pixel front end readout chips, studies of the charge collection efficiency with cosmic rays and/or lasers.

This proposal requests one academic year of funding for an SBU graduate student who will carry out measurements on a probe station at Stony Brook and perform additional simulations for new test structures and a second generation detector design. We will collaborate with our colleagues from Instrumentation and Physics departments at BNL and will leverage existing infrastructure at Stony Brook and BNL.

Stanislaus Wong, Department of Chemistry (SBU) and Jason Graetz (BNL)

“Novel Nanostructures for Energy Storage Applications”

Abstract: In recent years, there has been an ever growing demand for reliable, inexpensive and environmentally sustainable methods for energy storage. This need is underscored by the limited supply of fossil fuels, uncertainty in the global economic climate, and the inherent challenges of climate change. Moreover, an efficient and inexpensive energy storage network will be required to store the energy produced from transient renewable sources such as solar and wind power.In this light, the continued development of battery technology has become a crucial element in meeting the need for reliable energy storage.  Of the multitude of battery technologies, Li-ion batteries have become increasingly important owing to their unique advantages such as their high operating potentials, high energy densities, proven reliability and significant commercial penetration into the portable power (e.g. cellular phones, cameras and laptops) and hybrid electric vehicle industries. However, many challenges remain in optimizing the commercialization of Li-ion batteries. For one thing, reliance upon cobalt-based metal oxides (LiCoO2) as a cathode material is problematic, as these materials are toxic, relatively expensive,and possess relatively low abundance, as compared with other potential battery materials. This realization has inspired a search for alternative cathode materials such as LiFePO that are not only non-toxic and abundant but also maintain the potential for high capacity and stability that is typically observed in cobalt oxide based materials.

 Dave Jackson (CSHL) and Suzanne Scarlata (SBU)

 "Testing Interactions of a Plant Receptor and the G-alpha Signaling Protein in Stem Cell Maintenenace "

Abstract: Plant development depends on stem cell populations called meristems, which regulate their size by balancing stem cell proliferation with the incorporation of daughter cells into primordia. This balance is controlled by the CLAVATA receptor-signaling pathway, which acts in a feedback loop with the WUSCHEL homeodomain transcription factor. However, little is known about the downstream events that transmit the CLAVATA receptor- mediated signals. The Jackson lab recently cloned a maize mutant compact plant2 (ct2), which exhibits meristem proliferation defects similar to CLAVATA mutants, such as maize FASCIATED EAR2 (FEA2). CT2 encodes the a subunit of a predicted heterotrimeric G protein, a well-known membrane-signaling complex. Heterotrimeric G proteins are well characterized in yeast and mammalian systems, where they transmit signals from G protein coupled receptors (GPCRs), which are typically 7-pass transmembrane proteins. Our results in plants challenge the dogma that heterotrimeric G proteins are regulated only by 7-pass GPCRs, because the CLAVATA receptors are predicted to be single pass proteins. The aim of this proposal is to use advanced imaging and biophysical methods to test the hypothesis that Ga interacts directly with a CLAVATA receptor in plants, using the complementary expertise of the Jackson lab in plant stem cell signaling and the Scarlata lab in imaging and biophysical characterization of G protein-receptor interactions.

 Hiro Fukuyama (CSHL) and Lonnie Wollmuth (SBU)

 "Biogenesis of Ionotropic Glutamate Receptors"

Abstract: In the nervous system, cell-to-cell communication is mediated by specialized structures called synapses. Most fast excitatory synaptic transmission in the nervous system is mediated by the neurotransmitter glutamate through its interactions with ionotropic glutamate receptors. Perturbations in glutamatergic neurotransmission – including variations in the membrane expression of ionotropic glutamate receptors – have been implicated in a wide variety of nervous system dysfunctions including psychiatric (e.g., schizophrenia and mood disorders), developmental (e.g., Autism spectrum disorders), acute excitotoxic (e.g., epilepsy and stroke) and chronic neurodegenerative (e.g., Parkinson’s and Alzheimer’s diseases) disorders. The goal of the present proposal is to define mechanisms of iGluR biogenesis – the transition from immature polypeptides to functional tetrameric receptors that can be inserted into the plasma membrane to carry out synaptic functions. Our experiments will focus mainly on newly discovered interactions in the transmembrane region of ionotropic glutamate receptors. The proposed experiments will aid in resolving controversies regarding iGluR assembly and will help define the fundamental principles of biogenesis and dynamic regulation of iGluRs in both normal and disease states.

Steve Skiena (SBU) and Michale Schatz (CSHL)

"Assembly algorithms for single-molecule DNA sequencing"

Abstract: We propose to develop algorithms for assembling genomic sequence data from the long-read, single-molecule DNA sequencing technologies of PacBio and Oxford Nanopore.  In principle, assembling a genome with single molecule sequencing technology reduces the complexity considerably - instead of assembling a jigsaw puzzle with a billion tiny tiles, we only need a few million tiles that are 100 times larger.  However, the challenge with single molecule sequencing is the error rate is much greater than the 1st or 2nd generation sequencers. Under this joint SBU/CSHL proposal, we will develop the needed algorithms and software packages to be able to assemble genomes directly from the high error long reads. This will include developing novel spaced-seed algorithms for overlapping the high error reads to be able to rapidly identify overlaps between the sequences, and novel algorithms for the multiple alignment and consensus generation of high error long reads.  We will be able to benchmark the success of our software against the available reference genomes and against the recently published parrot genome. We will also develop read simulation software to evaluate our algorithms in anticipation of the release of sequencing devices from Oxford Nanopore.

 

Pending proposal

Lei Zuo, Department of Mechanical Engineering, SBU; BNL Co-PI Thomas Butcher

“Ocean Wave Energy Harvesting”

Abstract: The potential for electricity generation from ocean wave energy in the US is estimated to be 64%of the total electricity generated from all sources in 2010 . Over 53% of the US populationlives within 50 miles of the coast (NOAA), so ocean waves offer ready opportunity forharvesting power. However, wave energy harvesting is still in its infancy worldwide .The objective is to develop an innovative technology of ocean wave energy harvesting withadvantage of high efficiency and reliability. We hope to create a solution to addressing thefundamental challenge of wave energy harvesting through converting the irregular up-and-downmotion of the ocean waves into unidirectional rotation of the electrical generator.