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DOE OSTI2021

Solar Photovoltaic Module Recycling: A Survey of U.S. Policies and Initiatives

Industry stakeholders, regulators, and policymakers in the United States are starting to develop policies for PV module recycling. Well-designed policies could reduce negative environmental impacts and resource constraints while opening new market and employment opportunities. This paper summarizes drivers, barriers, and enablers related to PV module recycling, which might be addressed via policy. It then analyzes existing and proposed U.S. policies that may affect PV module recycling. Among the global and national voluntary industry stewardship standards related to EoL PV management, this paper discusses a Solar Energy Industries Association program encouraging PV recycling among its U.S. membership. The paper concludes with a synthesis of policy-related factors that may encourage effective EoL PV module management.

14 SOLAR ENERGY↗

DOE OSTI2017

Synthesis and Crystal Structures of Volatile Neptunium(IV) β- Diketonates

Production of certified reference materials in support of domestic nuclear forensics programs require volatile precursors for introduction into electromagnetic isotopic separation instruments. β-diketone chelates of tetravalent actinides are known for their high volatility, but previously developed synthetic approaches require starting material (NpCl 4 ) that is prohibitively difficult and hazardous to prepare. An alternative strategy was developed here that uses controlled potential electrolysis to reduce neptunium to the tetravalent state in submolar concentrations of hydrochloric acid. Four different β-diketone ligands of varying degrees of fluorination were reacted with an aqueous solution of Np 4+ . Products of this reaction were characterized via X-ray diffraction and infrared spectroscopy, and were found to be neutral 8-coordinate complexes that adopt square antiprismatic crystal geometry. Synthesis of Np β-diketonates by this approach circumvents the necessity of using NpCl 4 in tetravalent Np coordination compound synthesis. The volatility of the complexes was assessed using thermogravimetric analysis, where the temperature of sublimation was determined to be in the range of 180° to 205° C. The extent of fluorination did not appreciably alter the sublimation temperature of the complex. Thermal decomposition of these compounds was not observed during sublimation. High volatility and thermal stability of Np β-diketonates make them an ideal candidate for gaseous introduction into isotopic separation instruments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

Molecular Genetic Traits Influencing Maize Endosperm Development and Value

Development of the endosperm in cereal grasses entails different phases characterized by cell division, endoreduplication, accumulation of storage metabolites and cell death, which need to be carried out in an orderly fashion. While correct regulation of the cell cycle plays an essential role in endosperm development, the key regulatory factors and how the cell cycle interfaces with other pathways in this developmental context are largely unknown. We investigated the cyclin-dependent kinase (CDK)-retinoblastoma pathway and how it controls the cell cycle and coordinates it with other processes during maize endosperm development. Retinoblastoma-related (RBR) proteins may be inactivated through CDK-mediated phosphorylation, but the identity of the responsible kinase in maize is unknown. We have previously shown that down-regulation of CDKA;1 severely inhibits the endoreduplication cell cycle and suggested that CDK may be an up-stream regulator of the retinoblastoma pathway. We discovered two types of maize RBR genes, RBR1 and RBR3, which differ in terms of structure, regulation and function. Phylogenetic analyses indicate that these genes may be distinctive features of the Poaceae. We found that RBR3 plays a positive rather than a negative role in DNA replication, cell transformation, and the expression of the minichromosome maintenance (MCM)2-7 family of DNA replication factors. These features are a paradigm shift in RBR gene function and appear to be unique within the RBR gene family. They suggest the existence in maize and related cereal crops of specific RBR/E2F-dependent pathways impinging on the cell cycle and development. RBR1 was down-regulated in transgenic endosperm using RNAi approaches. This resulted in the de-repression of a number of down-stream E2F targets, including RBR3, the MCM2-7 gene family, DNA methyltransferase (MET)1, CDKB;1, and the recently identified RBR4 gene. It also increased endosperm ploidy levels, stimulated the production of a larger number of cells, reduced the average cell size, and promoted programmed cell death. To test whether CDKA;1 inhibits RBR1 (through phosphorylation) in the pathway that leads to DNA synthesis and endoreduplication, the two CDKA;1 and RBR1 down-regulated mutants were crossed and their progeny analyzed. Our results indicate that CDKA;1 controls endoreduplication through an RBR1-dependent pathway. However, the ability of RBR1 to repress gene expression programs is independent from CDKA1, suggesting the presence of two differently regulated RBR1 activities in developing endosperm. One type of RBR1 activity controls E2F-dependent gene expression and is largely independent from CDKA;1, while another suppresses endoreduplication and can be inhibited by CDKA;1. In addition, RBR1 is part of a regulatory feedback loop that impinges on CDK activity. Together, these results indicate that the CDKA;1-RBR1 pathway integrates and controls different processes associated with endosperm development. Genome-wide analyses of the transcriptome, metabolome, and epigenetic mechanisms to understand how the cell cycle is coordinated with other pathways at a systems biology level are currently underway.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Quantum logic gate synthesis as a Markov decision process

Reinforcement learning has witnessed recent applications to a variety of tasks in quantum programming. The underlying assumption is that those tasks could be modeled as Markov decision processes (MDPs). Here, we investigate the feasibility of this assumption by exploring its consequences for single-qubit quantum state preparation and gate compilation. By forming discrete MDPs, we solve for the optimal policy exactly through policy iteration. We find optimal paths that correspond to the shortest possible sequence of gates to prepare a state or compile a gate, up to some target accuracy. Our method works in both the absence and presence of noise and compares favorably to other quantum compilation methods, such as the Ross–Selinger algorithm. This work provides theoretical insight into why reinforcement learning may be successfully used to find optimally short gate sequences in quantum programming.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Catalytic oxidative coupling of arenes and alkanes: applications for efficient chemical synthesis and for hydrocarbon oligomerization. Progress Report 2016-7. Final report

This is the final report for DE-FG02-08ER15997 with a grant period of 8/15/2008-8/14/2018 (plus 1 year NCE); Program: Basic Energy Sciences; PI: Melanie S. Sanford; co-PI: Adam J. Matzger. The project resulted in 20 publications, 12 supported entirely by this grant and 8 supported substantially by this grant. The overall goals of this project were design catalysts (both homogeneous catalysts and MOF-supported catalysts) to control reactivity and selectivity in energy relevant C–H bond functionalization reactions. The proposed research led to a variety of new catalysts and catalytic processes which are currently finding application in organic synthesis. These efforts were well aligned with the goals of the DOE BES Catalysis Science Program. C–H functionalization reactions have extensive applications in energy-related industries, including petroleum and biofuels processing. The research activities also matched many of the priority areas identified by the Catalysis Science Program, including: investigating problems at the interface of heterogeneous and homogeneous catalysis as a means to derive new catalysts; incorporating 2° interactions to modulate catalyst stability, reactivity, and selectivity; using these new catalysts to tune molecular-level catalytic activity and selectivity; and studying structure-reactivity relationships of inorganic, organic, or hybrid catalytic materials in solution.

02 PETROLEUM↗

DOE OSTI2012

Ring Walking/Oxidative Addition Reactions for the Controlled Synthesis of Conjugated Polymers

Power conversion efficiencies of plastic solar cells depend strongly on the molecular weight characteristics of the semiconducting polymers used for their fabrication. The synthesis of these materials typically relies on transition metal mediated catalytic reactions. In many instances, the ideal structures cannot be attained because of deficiencies in these reactions, particularly when it comes to being able to achieve high number average molecular weights and narrow molecular weight distributions. Another important conjugated polymer structure of interest is one in which a single functional group is attached at the end group of the chain. Such systems would be ideal for modifying surface properties at interfaces and for labeling biomolecular probes used in fluorescent biosensors. To respond to the challenges above, our efforts have centered on the design of homogenous transition metal complexes that are easy to prepare and effective in carrying out living, or quasi-living, condensative chain polymerization reactions. The key mechanistic challenge for the success of this reaction is to force the insertion of one monomer unit at a time via a process that involves migration of the transition metal-containing fragment to one terminus of the polymer chain. Chain growth characteristics are therefore favored when the metal does not dissociate from the newly formed reductive elimination product. We have proposed that dissociation is disfavored by the formation of a -complex, in which the metal can sample various locations of the electronically delocalized framework, a process that we term ring-walking , and find the functionality where oxidative addition takes place. Success has been achieved in the nickel-mediated cross coupling reaction of Grignard reagents with aromatic halides by using bromo[1,2-bis(diphenylphosphino)ethane]phenylnickel. This reagent can yield poly(thiophene)s (one of the most widely used type of polymer in plastic solar cells) with excellent stereoregularity and molecular weight distributions with polydispersities that are consistent with a living polymerization sequence. Another important objective of this program concerned the use of these new catalysts and improved mechanistic insight for the synthesis of specific polymeric materials with prespecified properties.

14 SOLAR ENERGY↗

DOE OSTI2016

Streamlining the Design-to-Build Transition with Build-Optimization Software Tools

Scaling-up capabilities for the design, build, and test of synthetic biology constructs holds great promise for the development of new applications in fuels, chemical production, or cellular-behavior engineering. Construct design is an essential component in this process; however, not every designed DNA sequence can be readily manufactured, even using state-of-the-art DNA synthesis methods. Current biological computer-aided design and manufacture tools (bioCAD/CAM) do not adequately consider the limitations of DNA synthesis technologies when generating their outputs. Designed sequences that violate DNA synthesis constraints may require substantial sequence redesign or lead to price-premiums and temporal delays, which adversely impact the efficiency of the DNA manufacturing process. In this paper, we have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. BOOST incorporates knowledge of DNA synthesis success determinants into the design process to output ready-to-build sequences, preempting the need for sequence redesign. The BOOST web application is available at https://boost.jgi.doe.gov and its Application Program Interfaces (API) enable integration into automated, customized DNA design processes. Finally, the herein presented results highlight the effectiveness of BOOST in reducing DNA synthesis costs and timelines.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Electron- and Thermal-Stimulated Synthesis of Water on Boehmite (y-AlOOH) Nanoplates

Utilizing a combination of electron stimulated desorption, infrared spectroscopy and temperature program desorption measurements, we show that molecular water is synthesized during electron irradiation on boehmite nanoplates and postulate that the reaction proceeds first through decomposition of the hydroxyl to produce trapped hydrogen atoms. Once released, these hydrogen atoms can react with a neighboring hydroxyl resulting in adsorbed water. In addition, molecular water is readily formed on the surface of the boehmite nanosheets through thermal induced recombinative desorption. Peak water production via recombinative desorption occurs at 750 K in agreement with previous studies. We have also identified a weak desorption feature near 400 K which is likely strongly adsorbed water. The derived experimental desorption activation energy of water assuming full coverage is 98.6 kJ mol-1.

Jones, Brant M.↗

DOE OSTI2014

Effects of K and Pt promoters on the performance of cobalt catalyst supported on CNTs

This paper presents a comparative study on the effects of incorporation of potassium (K) and platinum (Pt) as promoters on the physicochemical properties of cobalt catalyst. The catalyst was prepared by a wet impregnation method on a CNTs support. Samples were characterized using transmission electron microscopy (TEM), H{sub 2}-temperature-programmed reduction (TPR) and X-ray photoelectron spectroscopy (XPS) techniques. Fischer-Tropsch Synthesis (FTS) was carried out in a fixed-bed microreactor at 543 K and 1 atm, with H{sub 2}/CO = 2v/v and space velocity, SV of 12 L/g.h for 5 hours. The K-promoted and Pt-promoted Co catalysts have different physicochemical properties and catalytic performances compared to that of the un-promoted Co catalyst. XPS analysis revealed that K and Pt promoters induced electronic modifications as exhibited by the shifts in the Co binding energies. Incorporation of 0.06 wt% K and 0.06 wt% Pt in Co/CNTs catalyst resulted in an increase in the CO conversion and C{sub 5+} selectivity and a decrease in methane selectivity. Potassium was found to be a better promoter for Co/CNTs catalyst compared to platinum.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2016

Polynuclear Aromatic Hydrocarbons with Curved Surfaces: Buckyballs

The discovery of a new allotropic form of elemental carbon – the fullerenes – and subsequently other novel forms of elemental carbon with pyramidalized surfaces, most notably single-walled and multi-walled carbon nanotubes, introduced a novel structural motif to the polycyclic aromatic hydrocarbons (PAHs) with nonplanar surfaces. Our research program supported by BES DOE grant DE-FG02-04ER15514 has dealt with the synthesis, structural studies, and chemistry of the novel curved-surface PAHs with carbon frameworks structurally related to fullerenes. They are referred to as “buckybowls”. We prepared several new buckybowls and, even more importantly, developed the efficient, gram-scale synthetic methodologies for the preparation of small buckybowls, most notably corannulene (C20H10) and its derivatives. In addition, the employment of the corannulene-based synthons previously developed in our laboratory led to a number of highly nonplanar molecular architectures with two or more corannulene subunits with a potential for the applications as novel materials in separation sciences, nanoelectronics, photovoltaics and catalysis. In collaboration with Professor Angelici (Iowa State) we prepared and characterized several transition metal complexes of corannulene, providing the first structural characterization of η6 metal complexes of buckybowls by a single crystal X-ray diffraction. In addition to the definitive structural characterization of the complexes we demonstrated that the (η6-C6Me6)Ru2+ unit in some relatively stable complexes activate the corannulene ligand to react with proper nucleophiles suggesting that such complexex may be used in catalysis. (Section C). We have explored the efficiency of the dispersion-based interactions of curved-surface conjugated carbon networks by high-level computational models. We showed that the curvature of such networks does not reduce the van der Waals attractions as compared to the planar systems of similar size. We than concentrated on the design, synthesis and testing of the previously unknown molecular receptors with corannulene pincers which are capable of forming the strong ball-and-socket inclusion complexes with fullerenes in solution and in the solid state. Buckycatcher I (a molecular receptor with two corannulene pincers preorganized on a tetrabensocyclooctatetraene tether) inclusion complexes with fullerenes provided the first experimental evidence for the importance of concave-convex π – π interactions in the supramolecular chemistry of fullerene carbon cages with buckybowls. C60@Buckycatcher I has become the prototypical supramolecular system formed by the relatively weak (on the atom-to-atom bases) and has been extensively used by the computational community to test the quality of the theoretical models. In addition, Buckycatcher I shows an exceptional ability to adopt other guest molecules and several its inclusion complexes and/or solvates have been structurally characterized. These unusual structures show the potential of the buckycatchers to be tested as novel organic materials. “Intelligent design” of molecular receptors with corannulene receptors using computational approach allowing for a priori prediction of their binding potentials led to the preparation of other buckycatchers. Both bi- and tridentate corannulene pincers were tested and two of the bidentate receptors (Buckycatchers II and III) exhibited the outstanding affinity toward fullerenes, significantly exciding Buckycatcher I performance. Careful tailoring of the tethers resulted in the optimization of binding energies of the receptors with guest carbon cages and in the reduction of the entropy/solvation penalties. Practical preparation of dicorannulenopentacene opens a new avenue for the synthesis of a pool of bis-corannulene receptors possessing polar groups on their dibenzobarrelene tether. The polar “anchors” can be used to attach these efficient fullerene receptors to solid supports in order to modify their surfaces with the potential applications in separation sciences, catalysis and photovoltaic materials. additionally, the presence of such groups will improve the solubility of the receptors in polar solvents, expanding the scope of their supramolecular chemistry in solutions. Rigorous studies of thermodynamics of host-guest association of molecular clips and tweezers in organic solvents with C60/C70 inclusion complexes with Buckycatcher I as a model system have provided a full set of thermodynamical data including ΔG, ΔH, and –TΔS, for the formation of the inclusion complexes over a range of temperatures and in several solvents. Both 1H NMR and Isothermal Calorimetry (ITC) titrations provide virtually identical association constants, confirming the reliability of the results. WE have shown that thermodynamics of the host-guest complex formation is more complicated than anticipated and proposed by the existing computational models. These data are of premium importance for the testing of the computational solvation models and for a deeper understanding of the supramolecular interactions in organic solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Mesoscale Design of Magnetoelectric Heterostructures and Nanocomposites

Multiferroic materials have a coexistence of at least two ferroic orders. The coupling interaction between the different order parameters can produce new phenomena, such as the magnetoelectric (ME) effect. The ME response is the appearance of an electric polarization P upon applying a magnetic field H, and/or vice versa. Magnetoelectricity has been observed as an intrinsic effect in some natural materials at low temperature; however, such single phase materials suffer from extremely weak ME exchange. Better alternatives are two-phase composites consisting of magnetostrictive and piezoelectric phases, which have been shown to have large ME coefficients. Said composites exploit a unique product ME tensor property that depends upon the individual strictions of the piezoelectric and magnetostrictive phases, the elastic stiffness and integrity of the interphase interfaces, the phase distribution and the dimensionality of its connectivity, and any elastic constraint; amongst other things. This research program between D. Viehland PI and S.Priya at Virginia Tech investigated the mesoscale physics and chemistry of such two-phase ME heterostructures. The results of the proposed research are relevant to new generations of multifunctional materials involving heterogeneous components. How the product ME property be optimized? The answers lies with the interphase-interfaces, where the atomic layers coordinate stress transfer from one phase to another. It was the primary goal of this research program to discover such fundamental relationship for two phase ME heterostructures and nanocomposites. This research program integrated all the components required to fully investigate the ME phenomenon: starting from synthesis of nanomaterials with diversified interfacial characteristics; to full electrical, magnetic, and structural characterizations.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Characterization of MC&A for the Molten Salt Fuel Cycle

Advanced reactor developers are exploring diverse reactor designs, including molten salt reactors (MSRs). These advanced reactors are considered for wider applications and a range of deployment locations, including supporting the integration of renewable energy sources in the grid. There are three main types of MSRs: (1) reactors in which the fuel salt freely circulates within the core; (2) reactors with the fuel salt contained within vented fuel tubes; and (3) reactors that use molten salt solely as a coolant, with the fuel in a separate, solid form. In this document, the term MSR refers specifically to the first two types, which use fuel salt—special nuclear material (enriched uranium, plutonium, and 233 U) in chloride or fluoride form mixed with chloride- or fluoride-based carrier salt in a peritectic mixture—as the primary medium for fission. The composition of fuel salt, both at startup and for makeup or refueling, varies depending on the MSR design and the chosen fuel cycle approach, which can be either once-through or closed. For MSRs, a variety of fuel cycle approaches (e.g., U, U–Pu, U–Pu–TRU, U–Th, U–Pu–Th) are being considered. Fuel in MSRs is much different than traditional solid fuel, including its preparation. The uniqueness warrants investigation into characterizing fuel preparation processes, known as fuel salt synthesis . This effort characterized major fuel preparation and synthesis processes, identifying temperature, equipment, and environmental requirements for uranium-, plutonium-, and thorium-based fuel preparation and synthesis. Because MSR fuel salt synthesis facilities handle special nuclear material in loose, bulk form, a material control and accounting plan will be required for licensing from the US Nuclear Regulatory Commission or under the US Department of Energy authorization. This effort serves as a foundation to investigate material control and accounting approaches for synthesis facilities, including determining measurement points and techniques. Because several MSR developers are planning demonstration facilities in the coming years, this effort will support stakeholders with preparing or reviewing material control and accounting plans for providing assurance that all special nuclear material is accounted for at fuel salt synthesis facilities. This report was produced for Materials Protection, Accounting, and Control Technologies (MPACT) program under the US Department of Energy (DOE), Office of Nuclear Energy, Nuclear Fuel Cycle and Supply Chain.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2017

Biomass to Liquid Fuels and Electrical Power

This research program provided data on immediate applicability of forest biomass production and logistics models. Also, the research further developed and optimized fractionation techniques that can be used to separate biomass feedstocks into their basic chemical constituents. Finally, additional research established systematic techniques to determine economically feasible technologies for production of biomass-derived synthesis gases that will be used for clean, renewable power generation and for production of liquid transportation fuels. Moreover, this research program continued our efforts to educate the next generation of engineers and scientists needed to implement these technologies.

09 BIOMASS FUELS↗

DOE OSTI2017

Synthesis and Crystal Structures of Volatile Neptunium(IV) β-Diketonates

There is a large need for neptunium certified reference materials to support domestic nuclear forensics programs. These reference materials are required for quantification of Np forensic related samples. Isotopic separation is required to produce this material; traditional isotopic separation methods use electromagnetic separation techniques. Such methods require a gaseous introduction of Np into the separation source. This work sought to produce a volatile Np compound that would be suitable for the purpose of certified reference material production. ß-diketonates were identified as compounds likely able to serve this purpose. However, previously described synthesis requires NpCl4, which is not commercially available and prohibitively difficult to produce. A novel and facile procedure was developed here to successfully synthesize several tetravalent ß-diketonates of Np. They were characterized using FTIR and single crystal x-ray diffraction. The volatility of these compounds at elevated temperatures was then analyzed, and discussed. The synthesis procedure developed here presents a facile platform for further Np organometallic studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Assessing the cumulative effects of nearshore habitat restoration actions for multiple populations of juvenile salmon in Whidbey Basin, Washington: foundation and approach for synthesis and evaluation

Ecosystem restoration is a common tool for re-establishing ecosystem processes, structures, and functions to improve biodiversity and services in coastal and estuarine ecosystems. In the Salish Sea, salmon habitats have been fragmented, reduced in size, and diminished in quality, and the ecosystem processes that form and sustain these habitats have been degraded and disrupted as well. This loss is especially prevalent in estuaries, where up to 90% of former salmon habitat has been lost or compromised. Salmon species are integral to the identities and cultures of people in the Pacific Northwest, yet salmon abundances remain at historic lows, especially in urbanized areas. Recent investments in restoration are creating rearing habitat and repairing lost ecosystem function. However, restoration efforts in this region have largely proceeded at the site scale, with less attention to big-picture thinking regarding how restoration will effectively recover degraded or lost habitats for target species. As a result, no landscape-scale evaluation program exists, and the cumulative benefits of multiple interventions are unknown. We describe innovative methods for science synthesis related to the evaluation of cumulative effects of ecosystem restoration for Pacific salmon, using years of existing, but disparate data. Building from previous work on cumulative effects evaluation and incorporating a hierarchy of hypotheses approach, we propose using causal inference across numerous hypotheses in a framework to assess the cumulative benefits to Pacific salmon from multiple estuarine restoration projects. We present the framework as a method that can be used to address many complex questions and provide examples from the Salish Sea where the approach is being implemented. The framework draws on science synthesis from numerous fields and uses a hierarchy of hypotheses, causal analysis at multiple scales, and a new hierarchy of synthesis for assessing multiple lines of evidence documenting restoration effects on Pacific salmon. We propose causal inference to synthesize dissimilar data streams, in our case, to identify various manifestations of cumulative effects of restoration and benefits to salmon, and to further inform restoration and recovery planning. A unifying framework would allow for the detection of thresholds at which restoration provides measurable improvement and would greatly advance understanding of the effects of restoration on ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Towards On-Chip Learning for Low Latency Reasoning with End-to-End Synthesis

The Software Defined Architectures (SODA) Synthesizer is an open-source compiler-based tool able to automatically generate domain-specialized systems targeting Application-Specific Integrated Circuits (ASICs) or Field Programmable Gate Arrays (FPGAs) starting from high-level programming. SODA is composed of a frontend, SODA-OPT, which leverages the multilevel intermediate representation (MLIR) framework to interface with productive programming tools (e.g., machine learning frame-works), identify kernels suitable for acceleration, and perform high-level optimizations, and of a state-of-the-art high-level synthesis backend, Bambu from the PandA framework, to generate custom accelerators. One specific application of the SODA Synthesizer is the generation of accelerators to enable ultra-low latency inference and control on autonomous systems for scientific discovery (e.g., electron microscopes, sensors in particle accelerators, etc.). This paper provides an overview of the flow in the context of the generation of accelerators for edge processing to be integrated in transmission electron microscopy (TEM) devices, focusing on use cases from precision material synthesis. We show the tool in action with an example of design space exploration for inference on reconfigurable devices with a conventional deep neural network model (LeNet). Finally, we discuss the research directions and opportunities enabled by SODA in the area of autonomous control for scientific experimental workflows.

Castellana, Vito G.↗

DOE OSTI2018

Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation

Peptoids are peptide-mimetic biopolymers that are easy-to-synthesize and adaptable for use in drugs, chemical scaffolds, and coatings. However, there is insufficient information about their structural preferences and interactions with the environment in various applications. We conducted a study to understand the fundamental differences between peptides and peptoids using molecular dynamics simulations with semi-empirical (PM6) and empirical (AMBER) potentials, in conjunction with metadynamics enhanced sampling. From studies of single molecules in water and on surfaces, we found that sarcosine (model peptoid) is much more flexible than alanine (model peptide) in different environments. However, the sarcosine and alanine interact similarly with a hydrophobic or a hydrophilic. Finally, this study highlights the conformational landscape of peptoids and the dominant interactions that drive peptoids towards these conformations. ACKNOWLEDGMENT: MD simulations and manuscript preparation were supported by the MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory (PNNL), a multi-program national laboratory operated by Battelle for the U.S. Department of Energy. CJM was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by the US Department of Energy, Office of Basic Energy Sciences, Biomolecular Materials Program at PNNL. Computing resources were generously allocated by University of Washington's IT department and PNNL's Institutional Computing program. The authors greatly acknowledge conversations with Dr. Kayla Sprenger, Josh Smith, and Dr. Yeneneh Yimer.

alanine↗

DOE OSTI2013

Tailored fatty acid synthesis via dynamic control of fatty acid elongation

Medium-chain fatty acids (MCFAs, 4-12 carbons) are valuable as precursors to industrial chemicals and biofuels, but are not canonical products of microbial fatty acid synthesis. We engineered microbial production of the full range of even-and odd-chain-length MCFAs and found that MCFA production is limited by rapid, irreversible elongation of their acyl-ACP precursors. To address this limitation, we programmed an essential ketoacyl synthase to degrade in response to a chemical inducer, thereby slowing acyl-ACP elongation and redirecting flux from phospholipid synthesis to MCFA production. Our results show that induced protein degradation can be used to dynamically alter metabolic flux, and thereby increase the yield of a desired compound. The strategy reported herein should be widely useful in a range of metabolic engineering applications in which essential enzymes divert flux away from a desired product, as well as in the production of polyketides, bioplastics, and other recursively synthesized hydrocarbons for which chain-length control is desired.

Torella, JP↗