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Future directions for active matter on ordered substrates

Active matter is a term encompassing particle-based assemblies with some form of self-propulsion, including certain biological systems as well as synthetic systems such as artificial colloidal swimmers, all of which can exhibit a remarkable variety of new kinds of nonequilibrium phenomena. A wealth of non-active condensed matter systems can be described in terms of a collection of particles coupled to periodic substrates, leading to the emergence of commensurate-incommensurate effects, Mott phases, tribology effects, and pattern formation. It is natural to ask how such phases are modified when the system is active. Here we provide an overview and future directions for studying individual and collectively interacting active matter particles coupled to periodic substrates, where new types of commensuration effects, directional locking, and active phases can occur. Importantly, further directions for exploration include directional locking effects, the realization of active solitons or active defects in incommensurate phases, active Mott phases, active artificial spin ice, active doping transitions, active floating phases, active surface physics, active matter time crystals, and active tribology.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Using Bacteria to Determine Protein Kinase Specificity and Predict Target Substrates

The identification of protein kinase targets remains a significant bottleneck for our understanding of signal transduction in normal and diseased cellular states. Kinases recognize their substrates in part through sequence motifs on substrate proteins, which, to date, have most effectively been elucidated using combinatorial peptide library approaches. Here, we present and demonstrate the ProPeL method for easy and accurate discovery of kinase specificity motifs through the use of native bacterial proteomes that serve as in vivo libraries for thousands of simultaneous phosphorylation reactions. Using recombinant kinases expressed in E. coli followed by mass spectrometry, the approach accurately recapitulated the well established motif preferences of human basophilic (Protein Kinase A) and acidophilic (Casein Kinase II) kinases. These motifs, derived for PKA and CK II using only bacterial sequence data, were then further validated by utilizing them in conjunction with the scan-x software program to computationally predict known human phosphorylation sites with high confidence.

59 BASIC BIOLOGICAL SCIENCES↗

Microbial Community Responses to Organophosphate Substrate Additions in Contaminated Subsurface Sediments

Background: Radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. Methodology/Principal Findings: Uranium-contaminated sediments from the U.S. Department of Energy Oak Ridge Field Research Center (ORFRC) Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P)] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P) and 20 day (G3P) amended treatments, maximum phosphate (PO4 32) concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5) treatments and greatest with G3P (pH 6.8) treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%–50% and 3%–17% of total detected Archaea and Bacteria, respectively. Conclusions/Significance: This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium, strategies that harness microbial phosphate metabolism to promote uranium phosphate precipitation could offer an alternative approach for in situ sequestration.

54 ENVIRONMENTAL SCIENCES↗

Computational Investigation of the Interplay of Substrate Positioning and Reactivity in Catechol O-Methyltransferase

Catechol O-methyltransferase (COMT) is a SAM- and Mg 2+ -dependent methyltransferase that regulates neurotransmitters through methylation. Simulations and experiments have identified divergent catecholamine substrate orientations in the COMT active site: molecular dynamics simulations have favored a monodentate coordination of catecholate substrates to the active site Mg 2+ , and crystal structures instead preserve bidentate coordination along with short (2.65 Å) methyl donor-acceptor distances. We carry out longer dynamics (up to 350 ns) to quantify interconversion between bidentate and monodentate binding poses. We provide a systematic determination of the relative free energy of the monodentate and bidentate structures in order to identify whether structural differences alter the nature of the methyl transfer mechanism and source of enzymatic rate enhancement. We demonstrate that the bidentate and monodentate binding modes are close in energy but separated by a 7 kcal/mol free energy barrier. Analysis of interactions in the two binding modes reveals that the driving force for monodentate catecholate orientations in classical molecular dynamics simulations is derived from stronger electrostatic stabilization afforded by alternate Mg 2+ and surrounding ligands is permitted. SQM/MM free energy barriers for methyl transfer from bidentate and monodentate catecholate configurations are comparable at around 21–22 kcal/mol, in good agreement with experiment (18–19 kcal/mol). Overall, the work suggests that both binding poses are viable for methyl transfer, and accurate descriptions of charge transfer and electrostatics are needed to provide balanced relative barriers when multiple binding poses are accessible, for example in other transferases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of the T. brucei kinetoplastid RNA editing substrate-binding complex core component, RESC5

Kinetoplastid protists such as Trypanosoma brucei undergo an unusual process of mitochondrial uridine (U) insertion and deletion editing termed kinetoplastid RNA editing (kRNA editing). This extensive form of editing, which is mediated by guide RNAs (gRNAs), can involve the insertion of hundreds of Us and deletion of tens of Us to form a functional mitochondrial mRNA transcript. kRNA editing is catalyzed by the 20 S editosome/RECC. However, gRNA directed, processive editing requires the RNA editing substrate binding complex (RESC), which is comprised of 6 core proteins, RESC1-RESC6. To date there are no structures of RESC proteins or complexes and because RESC proteins show no homology to proteins of known structure, their molecular architecture remains unknown. RESC5 is a key core component in forming the foundation of the RESC complex. To gain insight into the RESC5 protein we performed biochemical and structural studies. We show that RESC5 is monomeric and we report the T . brucei RESC5 crystal structure to 1.95 Å. RESC5 harbors a dimethylarginine dimethylaminohydrolase-like (DDAH) fold. DDAH enzymes hydrolyze methylated arginine residues produced during protein degradation. However, RESC5 is missing two key catalytic DDAH residues and does bind DDAH substrate or product. Implications of the fold for RESC5 function are discussed. This structure provides the first structural view of an RESC protein.

59 BASIC BIOLOGICAL SCIENCES↗

Development of a Low Cost Insulated Foil Substrate for Cu(InGaSe) 2 Photovoltaics

The project validated the use of stainless steel flexible substrate coated with silicone-based resin dielectric, developed by Dow Corning Corporation, for Cu(InGaSe) 2 based photovoltaics. The projects driving force was the high performance of Cu(InGaSe) 2 based photovoltaics coupled with potential cost reduction that could be achieved with dielectric coated SS web substrate.

14 SOLAR ENERGY↗

High Quality, Low Cost Bulk Gallium Nitride Substrates Grown by the Electrochemical Solution Growth Method

The objective of this project was to develop the Electrochemical Solution Growth (ESG) method conceived / patented at Sandia National Laboratory into a commercially viable bulk gallium nitride (GaN) growth process that can be scaled to low cost, high quality, and large area GaN wafer substrate manufacturing. The goal was to advance the ESG growth technology by demonstrating rotating seed growth at the lab scale and then transitioning process to prototype commercial system, while validating the GaN material and electronic / optical device quality. The desired outcome of the project is a prototype commercial process for US-based manufacturing of high quality, large area, and lower cost GaN substrates that can drive widespread deployment of energy efficient GaN-based power electronic and optical devices. In year 1 of the project (Sept 2012 – Dec 2013) the overall objective was to demonstrate crystalline GaN growth > 100um on a GaN seed crystal. The development plan included tasks to demonstrate and implement a method for purifying reagent grade salts, develop the reactor 1 process for rotating seed Electrochemical Solution Growth (ESG) of GaN, grow and characterize ESG GaN films, develop a fluid flow and reaction chemistry model for GaN film growth, and design / build an improved growth reactor capable of scaling to 50mm seed diameter. The first year’s project objectives were met in some task areas including salt purification, film characterization, modeling, and reactor 2 design / fabrication. However, the key project objective of the growth of a crystalline GaN film on the seed template was not achieved. Amorphous film growth on the order of a few tenths of a micron has been detected with a film composition including Ga and N, plus several other impurities originating from the process solution and hardware. The presence of these impurities, particularly the oxygen, has inhibited the demonstration of crystalline GaN film growth on the seed template. However, the presence of both Ga and N at the growth surface indicates that the reactor hardware physics is all functioning properly; achieving film growth is a matter of controlling the chemistry at the interface. The impurities originating from the hardware are expected to be straightforward to eliminate. Activities were defined for an extension of budget period 1 to eliminate the undesired impurities originating from the reactor hardware and interfering with crystalline GaN film growth. The budget period 1 extension was negotiated during the 1st half of 2014. The budget period 1 extension spanned approximately from August 2014 to August 2015. The project objective for this extension period was to demonstrate at least 0.5um crystalline GaN film on a GaN seed in the lab scale reactor. The focus of the budget 1 extension period from August 2014 to August 2015 was to eliminate oxygen contamination interference with GaN film growth. The team procured the highest purity lowest oxygen salt for testing. Low oxygen crucible materials such as silicon carbide were installed and evaluated in the laboratory reactor. Growth experiments were performed with high purity salt, high purity hardware, and optimized oxide removal from the seed surface. Experiments were characterized with methods including UV inspection, profilometry, x-ray diffraction (XRD) to determine crystalline structure, optical and scanning electron microscopy, photoluminescence, x-ray photon spectroscopy (XPS), transmission electron microscopy (TEM), and secondary ion mass spectroscopy (SIMS). Despite successfully integrating the low oxygen materials in the laboratory reactor, the goal of depositing 0.5um of crystalline GaN on the MOCVD GaN seed was not met. Very thin (ca. 10nm) cubic phase GaN deposition was observed on the hexagonal MOCVD GaN seeds. But there was a competing etching reaction which was also observed and thought to be related to the presence of metallic lithium, a byproduct of the LiCl-KCl salt used as the process medium. The etching reaction could potentially be addressed by alternate salts not containing lithium, but would necessitate starting all over on the reactor and process design. Further, controlling the reaction of Ga and N in the bulk salt to favor deposition on the seed has proved to be very difficult and unlikely to be solved within the scope of this project in a manner consistent with the original objective for wafer or crystal scale thickness for GaN deposition on a GaN seed. Upon completion of the budget 1 extension period in August 2015 the project partners and DOE agreed to stop work on the project.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Electrochemical Solution Growth of Bulk GaN for Power Electronics Substrates, Final Report

This project focused on developing a novel, scalable, and economic growth technique for bulk gallium nitride (GaN), a critical material for next-generation high-temperature power electronics. Large area, high-quality bulk GaN is required as a substrate material in order to grow highly efficient bipolar transistors for inverters and power conditioning. Attempting to grow GaN in bulk by traditional precipitation methods forces extreme thermodynamic and kinetic conditions, putting these techniques at the extremes of experimental science, which is unsuitable for large-area, cost-effective substrate growth. The Electrochemical Solution Growth (ESG) technique is a novel concept that addresses these issues in a unique way, and was developed at Sandia National Laboratories (SNL), in part under this program. The crucial step in demonstrating the technique’s feasibility was to deposit high-quality GaN on a seed crystal. The bulk of SNL’s activities were focused on developing conditions for deposition of GaN on a seed crystal (a thin film of GaN grown by metal organic chemical vapor phase deposition (MOCVD) on c-axis oriented sapphire) in a molten salt electrolyte solution using a rotating disk reactor (RDR) ESG apparatus. This project was actively funded from FY08 to FY12 by the Energy Storage Program and GaN Initiative for Grid Applications (GIGA) program of the Office of Electricity Delivery and Energy Reliability (OE) in the U.S. Department of Energy (DOE). Some activities focused on silicon doping of GaN occurred in FY13 but only through the use of carryover funds.

36 MATERIALS SCIENCE↗

Manufacturable Corrugated Substrates for High Efficiency Organic Light-Emitting Diodes (OLEDs)

In this project, we start with optical simulation of an OLED to have a basic understanding of the mode dispersion inside the device. We first fabricated 1-D photonic crystals’ (PhCs) for corrugated green OLED devices observed enhanced EQE from 20% to 27%, which has the drawbacks of angular color shift. To resolve this issue, we fabricated poly crystalline PhCs (poly PhC) devices and observed alleviated angular color shift. The outcoupling efficiency is enhanced from 30% to 35%, which can be further enhanced to 60% by extracting the substrate mode. To further enhance the efficiency, we used RCWA (rigorous coupled-wave analysis) simulation to study the optical property in the corrugated device. We found out the corrugation reduces the reflectance of the Al cathode, lowers the cavity resonance and weakens the cavity emission. To preserve the cavity effect, we insert a low index Teflon layer (n = 1.3) between the ITO anode and the corrugated substrate, which increased the index contrast and hence the reflectance of the bottom electrode. As a result, the corrugated OLED with a Teflon layer shows a maximum outcoupling efficiency of 75%.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Impacts of Substrate Thinning on FPGA Performance and Reliability [Slides]

Substrate thinning is necessary in devices with flip-chip BGA packages to enable both radiation testing and component qualification and high-spatial resolution beam-based failure analysis methods. We investigated three factors affecting device performance: subsurface damage from the thinning process, reduced heat spreading in thin substrates, and changes in device switching speed. We conclude subsurface damage to crystalline Si caused by the thinning process is removable with sufficient SiO 2 slurry polishing. Local temperature differences increase minimally in devices thinned to 3 μm. Compressive stress in the Si increases globally after device thinning and leads to slowing of ring oscillator frequency by about 0.5% compared to full-thickness devices. Future work will include extending the results to submicron Si thickness values, which also has important benefits for failure analysis, debug, and security assessments. We also plan to extend this type of work to other FPGAs and other devices like memory and processors.

36 MATERIALS SCIENCE↗

Sapphire substrate qubit-based detector for light dark matter search

Harnessing sub-eV energy excitations from light dark matter interaction with a target material is one of the challenges in exploring promising novel materials for dark matter searches. In polar materials like sapphire, dark matter interaction can excite sub-eV optical phonon modes. Furthermore, the anisotropy of sapphire crystal could provide a signature of daily modulation of the dark matter scattering rate, making it a promising target material. We plan to utilize superconducting qubits on a sapphire substrate to take advantage of the excitation of phonons, which scatter and further down-convert to lower-energy phonons. A good fraction of these phonons are expected to reach the qubit superconductor on the substrate and break Cooper pairs. Such a process can cause qubit decoherence, which can be measured using standard qubit readout protocol. In this talk, we describe our ongoing attempt to build such a prototype detector.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

GaN MOCVD Growth on Native substrates for High Voltage (15-20 KV) Vertical Power Devices

This project aims to develop metalorganic chemical vapor deposition (MOCVD) homoepitaxy of GaN on native substrates with fast growth rate (15-20 μm/hr), low background doping (low-10 15 cm -3 ) and smooth surface morphology via comprehensive understanding of the crystal growth process including high quality GaN substrate development and surface preparation, impurity and native defects control, and their impacts on the breakdown field. The team successfully developed a new growth process by introducing the laser-assisted MOCVD (LA-MOCVD) process to address the limited growth rates of GaN in the traditional MOCVD process. Specifically, the use of the CO2 laser with lasing wavelength of 9.219 μm, the strong coupling between the laser beam with the ammonia (GaN MOCVD precursor) leads to efficient decomposition of NH3 which significantly increases the effective group V/III molar ratio and thus suppresses C impurity incorporation in MOCVD GaN. The reduction in C incorporation in LA-MOCVD GaN is especially prominent when the GaN growth rate is fast (> 10 μm/hr), which allows to develop thick GaN films with high crystalline quality and low controllable doping needed for vertical high power device applications. The results of this project lead to the demonstration of vertical GaN PN diodes with record breakdown voltage of ~ 8kV with high Baliga’s figure of merit.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Measuring Loss Tangents of Substrates for Superconducting Qubits with Part-per-Billion Precision

We report precision measurements of dielectric loss tangents in substrates for superconducting qubits using an ultra-high quality factor niobium SRF cavity operating at millikelvin temperatures and low electric fields. Multiple substrate types and surface treatments are compared to assess how processing impacts microwave dissipation. The RF results are correlated with materials analysis, including ToF-SIMS and XPS, to identify dominant loss mechanisms. This combined study links microscopic surface chemistry to macroscopic performance and provides a framework for materials-driven improvements in qubit coherence and device design.

Bafia, Daniel [Fermilab]↗

Measuring Loss Tangents of Substrates for Superconducting Qubits with Part-per-Billion Precision

We report precision measurements of dielectric loss tangents in substrates for superconducting qubits using an ultra-high quality factor niobium SRF cavity operating at millikelvin temperatures and low electric fields. Multiple substrate types and surface treatments are compared to assess how processing impacts microwave dissipation. The RF results are correlated with materials analysis, including ToF-SIMS and XPS, to identify dominant loss mechanisms. This combined study links microscopic surface chemistry to macroscopic performance and provides a framework for materials-driven improvements in qubit coherence and device design.

Bafia, Daniel [Fermilab]↗

Sonic Wafering of III-V substrates for High Efficiency Cells: A path to <$0.50/W

This project developed and demonstrated Sonic Lift-off, a novel technology that enables the reuse of expensive semiconductor substrates used to manufacture high-efficiency solar cells. By using sound waves to precisely separate thin layers of material, the process significantly reduces manufacturing costs while maintaining the performance of advanced III–V solar cells. These solar cells are among the most efficient in the world and are used in space, aerospace, and emerging terrestrial applications. The results of this work show that substrate reuse can be achieved without degrading device performance, offering a pathway to more affordable, high-performance solar technologies. This advancement supports U.S. clean energy goals by enabling broader deployment of renewable energy systems and strengthening domestic manufacturing capabilities in advanced photovoltaics.

14 SOLAR ENERGY↗

Thin Semiconductor Films of Fullerene C{sub 70} Nanoaggregates on the Surface of a Plane Glass Substrate

It was shown for the first time that, in the volume of an evaporating drop of a fullerene C{sub 70} solution in toluene located on the surface of a glass substrate, the self-organization of C{sub 70} molecules occurs and crystalline nC{sub 70} nanoaggregates of a spherical shape are synthesized. Films of nC{sub 70} nanoaggregates are deposited on a plane surface of a glass substrate. The physical mechanism of the self-organization of C{sub 70} molecules and the formation of large nC{sub 70} nanoaggregates are proposed, namely, Ostwald ripening, according to which relatively large nC{sub 70} nanoaggregates grow through smaller ones. The possibility of using thin films as solar transducers is discussed.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies

Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the life-history strategies of microorganisms influence their processing of organic carbon, which may affect microbial interactions and carbon cycling in soils. Here, we characterized the genomic traits, exometabolite profiles, and interactions of soil bacteria representing copiotrophic and oligotrophic strategists. Isolates were selected based on differences in ribosomal RNA operon ( rrn ) copy number, as a proxy for life-history strategies, with pairs of “high” and “low” rrn copy number isolates represented within the Micrococcales, Corynebacteriales, and Bacillales. We found that high rrn isolates consumed a greater diversity and amount of substrates than low rrn isolates in a defined growth medium containing common soil metabolites. We estimated overlap in substrate utilization profiles to predict the potential for resource competition and found that high rrn isolates tended to have a greater potential for competitive interactions. The predicted interactions positively correlated with the measured interactions that were dominated by negative interactions as determined through sequential growth experiments. This suggests that resource competition was a major force governing interactions among isolates, while cross-feeding of metabolic secretion likely contributed to the relatively rare positive interactions observed. By connecting bacterial life-history strategies, genomic features, and metabolism, our study advances the understanding of the links between bacterial community composition and the transformation of carbon in soils.

59 BASIC BIOLOGICAL SCIENCES↗

Green microalga Chromochloris zofingiensis conserves substrate uptake pattern but changes their metabolic uses across trophic transition

The terrestrial green alga Chromochloris zofingiensis is an emerging model species with potential applications including production of triacylglycerol or astaxanthin. How C. zofingiensis interacts with the diverse substrates during trophic transitions is unknown. To characterize its substrate utilization and secretion dynamics, we cultivated the alga in a soil-based defined medium in transition between conditions with and without glucose supplementation. Then, we examined its exometabolite and endometabolite profiles. This analysis revealed that regardless of trophic modes, C. zofingiensis preferentially uptakes exogenous lysine, arginine, and purines, while secreting orotic acid. Here, we obtained metabolomic evidences that C. zofingiensis may use arginine for putrescine synthesis when in transition to heterotrophy, and for the TCA cycle during transition to photoautotrophy. We also report that glucose and fructose most effectively inhibited photosynthesis among thirteen different sugars. The utilized or secreted metabolites identified in this study provide important information to improve C. zofingiensis cultivation, and to expand its potential industrial and pharmaceutical applications.

59 BASIC BIOLOGICAL SCIENCES↗