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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Multi-phase characterization of pitch-carbon coated nano-silicon anodes for lithium-ion batteries

Silicon (Si) is a leading next-generation Li-ion battery anode candidate that meets rigorous performance demands for portable power including enhanced power and energy density with robust cycling performance. However, a series of complex and interrelated reactions lead to reduced calendar life in Si-containing systems and therefore challenge practical adoption. In the present work, we probe the mechanisms underlying observed performance improvements by adding a pitch-carbon coating onto nano-Si material. We pair solid-phase (X-ray photoemission spectroscopy, Fourier-transform infrared), semi-volatile phase (solid-phase microextraction-gas chromatography-mass spectrometry), and gas-phase (gas chromatography-flame-ionization detector) characterization signals to comprehensively evaluate the impact of pitch-carbon coating on the evolution of the Si solid-electrolyte interphase (SEI) and the associated impacts on electrode/electrolyte reactivity. The pitch-carbon is found to serve as a physicochemical barrier, reducing the electro-active surface area for Si/electrolyte reactivity and preventing Si oxidation. Further, the pitch-carbon coating promotes the evolution of a more-favorable SEI by subsuming substantial functionality typically associated with the fluoroethylene carbonate (FEC) electrolyte additive - such as alkoxide scavenging and suppression of transesterification pathways - and by shifting the competitive electrolyte degradation pathways' favorability. The multi-phase characterization approach enables holistic end-products evaluation from complex (electro)chemical interfacial reactions, which informs a robust interpretation of the carbon coating's role in electrochemical performance improvements. The present mechanistic evaluation aids the rational design for improved nano-Si materials.

25 ENERGY STORAGE↗
NASA NTRS1998

Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA

3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

Lietzke, Susan E↗
DOE OSTI2026

Nitrogenated Graphene Quantum Dot-Derived Copper Single-Atom Catalyst for Oxygen Reduction Reaction

Despite the promise of fuel cells as sustainable energy conversion technologies, their widespread adoption is hindered by the high cost of platinum group metal (PGM) catalysts, particularly for catalyzing the oxygen reduction reaction (ORR) at the cathode. Here, we report copper-based single-atom catalysts (Cu-SACs) as cost-effective non-PGM alternatives for ORR. The catalysts were synthesized via simple pyrolysis of pyrene-derived amine-terminated graphene quantum dots (GQDs) in the presence of nitrogen and metal precursors. The abundant nitrogen functionality in GQDs effectively stabilized isolated Cu atoms during their conversion to porous carbon. A subsequent acid-washing step yielded a high density of atomically dispersed Cu active sites. X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and high-resolution scanning transmission electron microscopy (HR-STEM) confirmed the effective incorporation of isolated Cu atoms into the carbon matrix through copper–nitrogen (Cu-N) coordination. Electrochemical measurements revealed excellent ORR activity with a dominant four-electron pathway. This synthetic strategy provides a practical route to developing economically viable, non-precious metal catalysts.

catalysts↗
NASA NTRS2011

A Technology Pathway for Airbreathing, Combined-Cycle, Horizontal Space Launch Through SR-71 Based Trajectory Modeling

Access to space is in the early stages of commercialization. Private enterprises, mainly under direct or indirect subsidy by the government, have been making headway into the LEO launch systems infrastructure, of small-weight-class payloads of approximately 1000 lbs. These moderate gains have emboldened the launch industry and they are poised to move into the middle-weight class (roughly 5000 lbs). These commercially successful systems are based on relatively straightforward LOX-RP, two-stage, bi-propellant rocket technology developed by the government 40 years ago, accompanied by many technology improvements. In this paper we examine a known generic LOX-RP system with the focus on the booster stage (1st stage). The booster stage is then compared to modeled Rocket-Based and Turbine-Based Combined Cycle booster stages. The air-breathing propulsion stages are based on/or extrapolated from known performance parameters of ground tested RBCC (the Marquardt Ejector Ramjet) and TBCC (the SR-71/J-58 engine) data. Validated engine models using GECAT and SCCREAM are coupled with trajectory optimization and analysis in POST-II to explore viable launch scenarios using hypothetical aerospaceplane platform obeying the aerodynamic model of the SR-71. Finally, and assessment is made of the requisite research technology advances necessary for successful commercial and government adoption of combined-cycle engine systems for space access.

Kloesel, Kurt J.↗
DOE OSTI2026

Electrochemically mediated disproportionation for selective formaldehyde upcycling in acid

Formaldehyde (FA) electrolysis is attractive for paired production of value‑added chemicals. However, conventional electrolysis adopts alkaline electrolytes, which triggers FA self-disproportionation and severe feed loss. Here we introduce a sustainable and selective strategy for valorizing FA through electrochemically mediated disproportionation in acidic electrolytes. By leveraging a dual-electrode system consisting of a hydrophobic copper tetraminophthalocyanine layer (CuTAPc-layer) cathode and a Pt 2 Ru bimetallic anode, we efficiently convert FA into methanol and formic acid at high Faradaic efficiencies of 93.2% and 91.3%, respectively. Compared with alkaline FA oxidation, which can lose up to 76% FA and complicate downstream separation, the acidic system suppresses side reactions to ensure high product purity. Mechanism studies reveal that the hydrophobic microenvironment of CuTAPc-layer suppresses hydrogen evolution, while the stronger oxophilicity of Pt 2 Ru enhances FA activation and lowers the key deprotonation barrier for FA oxidation. The integrated device demonstrates application potential in polyoxymethylene upgrading, delivering 374.2 mA at 4 V with ~90% single-pass conversion, establishing a scalable and eco-friendly electrochemical pathway for chemical upcycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Prime Time for Model-Predictive Control? Assessing the Technical and Market Readiness of Advanced Controls in Buildings

Despite three decades of extensive research and field testing that have consistently validated the benefits of Model Predictive Control (MPC) in building applications, the technology has seen limited market adoption. This paper evaluates the readiness of MPC for widespread deployment, showcases recent demonstrations and field tests across diverse building types, including residential, small commercial, large commercial, and campus settings. Our results demonstrate that MPC can optimize system operations to achieve load shifting, minimize curtailment of on-site generation, and reduce energy costs by up to 80 %, while maintaining or improving occupant comfort. We also show that MPC can effectively control large assets, such as MW-sized thermal storage systems, and respond to dynamic pricing signals. However, achieving scale remains difficult due to labor-intensive workflows, reliance on a “PhD-in-the-loop” for MPC design and maintenance, susceptibility to fragile data infrastructure, and persistent workforce education and acceptance barriers. To bridge this gap, we outline a transition from bespoke, labor intensive prototypes toward streamlined, segment-targeted deployment strategies that leverage model templates, semantic tools, and generative AI. By automating control configuration and reducing engineering effort, these recommendations provide a pathway for transforming successful research demonstrations into scalable, market ready solutions for MPC-based controls.

Pritoni, Marco↗
DOE OSTI2026

Residential Vehicle-to-Home Backup Power Capabilities: Key Findings from a ComEd Beneficial Electrification R&D Pilot

This report summarizes key findings from a collaborative technical study of residential, non-grid-tied vehicle-to-home (V2H) backup power systems in Commonwealth Edison’s (ComEd’s) service territory. The work integrates (1) a feeder-level technoeconomic analysis (TEA) using historical outage-event data and simulated electric-vehicle (EV) driving/charging profiles to estimate potential reliability and customer interruption-cost impacts under V2H and vehicle-to-grid (V2G) adoption scenarios; (2) controlled laboratory performance testing of a representative V2H backup ecosystem to characterize transfer-to-backup behavior, sustained power delivery, efficiency trends, and repeatable reliability limitations; and (3) a cybersecurity assessment aligned with NIST Cybersecurity Framework (CSF) 2.0 and ISO/SAE 21434 to evaluate interface-level risk drivers and identify program-relevant mitigations. Results indicate that V2H can provide measurable resilience value, but outcomes are strongly context dependent on outage patterns and the share of events that are “V2H-applicable.” Typical transfer-to-backup behavior clustered on the order of minutes, but rare long-delay edge cases were observed (including an event approaching 30 minutes) and should be treated as a reliability risk. High-power testing showed that peak-rated output is not necessarily continuously deliverable; stable operation may require operation below nameplate ratings and attention to thermal and installation constraints. The cybersecurity assessment highlights a broad attack surface spanning commissioning, home networks, embedded services, and cloud/OTA pathways, motivating minimum controls for secure onboarding, signed updates, patch cadence, and coordinated vulnerability response for any scaled deployment.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Unlocking Energy Efficiency: Debunking Myths on the Road to Decarbonization

Energy efficiency is widely recognized as the foundational and most critical strategy for decarbonizing the manufacturing sector. Misconceptions surrounding energy efficiency measures often hinder their widespread adoption. This article aims to debunk five common myths and provides data and resources to help implement efficiency projects faster and more effectively to achieve greater decarbonization. First, the article challenges the myth that organizations have exhausted all possible energy efficiency opportunities by achieving voluntary energy intensity goals or energy performance certification. Second, it also addresses the misconceptions that efficiency projects are capital-intensive, require many qualified specialists, and have long investment return periods. By presenting real-world case studies and referencing commonly found efficiency opportunities, the article illustrates that energy-savings opportunities are ubiquitous. Organizations can use various contracting mechanisms as well as financial and technical resources from utility companies and government programs to lessen their burden. The notion that efficiency measures can be implemented solely in proprietorship facilities is dispelled. This article emphasizes the importance of green leases and explains that aligning decarbonization goals between the lessor and lessee can help drive savings for both parties. Finally, using unbundled renewable energy certificates as the sole pathway to decarbonization is strongly discouraged. By debunking these prevalent myths, this article aims to foster a deeper understanding of energy efficiency’s potential as a cornerstone of decarbonization efforts and to embrace it as a critical pathway toward a sustainable future.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

The path to 2060: Saudi Arabia's long-term pathway for GHG emission reduction

Saudi Arabia, as part of its Saudi Green Initiative, has announced its goal to achieve net zero green-house gas emissions by 2060. This ambitious target underscores the nation's dedication to address-ing climate change. However, there is a significant gap in comprehensive analysis regarding the long-term effects of Saudi Arabia's climate policies and their collective contribution towards the net-zero objective. This study endeavors to bridge this gap through a detailed examination using the GCAM-KSA, a specialized version of the Global Change Analysis Model tailored for Saudi Arabia, employing a multi-sectoral methodology that integrates economic, energy, and land use systems within a coherent framework to assess the impact of climate policies on GHG emissions. Our anal-ysis reveals that reaching net-zero GHG emissions by 2060 is a complex challenge requiring con-certed efforts across all sectors of the economy. While transitioning to low-carbon electricity and improving energy efficiency offer considerable emission reductions, fully decarbonizing the indus-trial and transportation sectors poses a significant hurdle. Our findings suggest that Saudi Arabia must triple its emission reduction commitments in its next Nationally Determined Contributions (NDCs) update to align with its 2060 net-zero goal. Early action and increased ambition could avoid the chances of getting locked into the high emission assets and give enough time to transform the energy system. Furthermore, the adoption and integration of Carbon Dioxide Removal (CDR) tech-nologies are identified as crucial for offsetting residual emissions, especially in sectors that might continue to rely on fossil fuels.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

Crystal structures of Salmonella enterica FraB deglycase reveal a conformational heterodimer with remarkable structural plasticity at the active site

Abstract Thefralocus ofSalmonella entericaencodes five genes for metabolism of fructose‐asparagine, an Amadori product formed by condensation of asparagine with glucose. In the last step of this pathway, the FraB deglycase cleaves 6‐phospho‐fructose‐aspartate into glucose‐6‐phosphate and aspartate. In homology models, FraB forms a homodimer with two equivalent active sites located at the dimer interface. E214 and H230, two invariant residues essential for catalysis, project into each active site cleft from opposing subunits of the dimer. Here, we have determined six crystal structures of FraB, three of a variant containing an N‐terminal His 6 tag and two mutations needed for crystallization (hereafter referred to as WT′), two with additional mutations to active site residues (E214A and P232A), and one of a variant with C‐terminal residues 313–325 deleted. Surprisingly, in the WT′ FraB structure, the two catalytic residues, E214 (general base) and H230 (general acid), are positioned ~22 Å apart. In the E214A and C‐terminus‐truncated FraB variants, however, a conformational change in the E214‐residing helix brings E214 and H230* to ~7 Å (* indicates residue from the second protomer that creates the inter‐subunit catalytic center). The loop bearing H230 also exhibits significant variation, ranging from being completely disordered to adopting open or closed states, with the nearby P232* residue being eithercisortrans. The C‐terminal residues 313–325 form a flexible “C‐tail” that can be fully disordered, bind in the active site to block access of substrate, or angle across the active site to wrap across the other subunit of the dimer and potentially close over substrate. Collectively, these structures reveal that FraB is a conformational heterodimer with two chemically identical subunits that are constrained to adopt different structures as they come together for catalysis. This plasticity likely involves correlated opening and closure of the two active sites for their respective binding and release of substrates and ligands.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Optimizing enzymes for plastic upcycling using machine learning design and high throughput experiments

Plastic use is ubiquitous in the modern world, and polyethylene terephthalate (PET) is one of the most abundantly produced plastics (and the most highly produced polyester), with ~65 million metric tons manufactured annually. To the consumer, PET is likely most recognizable as the plastic used to make beverage bottles. Like many plastics, traditional mechanical or chemical means of PET deconstruction and upcycling are costly and inefficient. Because of these challenges, recycled plastic is generally of lower quality and is more expensive to produce than virgin plastic derived from petroleum. Ultimately, this results in most plastic ending up as waste. We view plastic waste as an underutilized resource which, with the development of more efficient and high-quality recycling processes, could (1) generate significant economic value while (2) decreasing petroleum usage and greenhouse gas emissions, as well as (3) minimizing its negative environmental and health impacts. Biocatalytic recycling, or biomanufacturing the basic building blocks of new plastic from plastic waste, is a promising approach to plastic reuse that complements existing recycling technologies. Recently, biological enzymes capable of breaking down PET have garnered significant attention as an attractive means of dealing with the plastic problem. These enzymes are currently undergoing pilot studies for implementation in industrial-scale enzyme-based recycling. However, there are significant limitations to current enzymes, including the need to perform costly pre-processing of the plastic waste before the enzymes are able to work. Further optimization of these enzymes is necessary to make these technologies competitive, and ultimately incentivise industry-wide adoption of this biology-based green recycling technology. n this work we demonstrate a means to design and generate performant biological enzymes, capable of efficiently deconstructing plastic waste. Specifically, we applied recent advances in artificial intelligence, machine learning, and statistical analysis to design new versions and discover natural enzymes capable of breaking down PET. We focused on optimizing key properties that are important for industrial-scale enzymatic recycling such as pH and thermotolerance. Normal testing of enzymatic plastic-deconstruction is extremely labor intensive and so through this work we also developed a robotic-assisted experimental pipeline capable of characterizing thousands of candidate enzymes. The results of this iterative, AI-guided, multi-discipline approach have led to increases in enzymatic breakdown of over 150X over starting enzymes. This work supports the rapidly developing and transformative field of biocatalytic solutions to environmental problems beyond the discovery and predictive understanding of enzymes for polymer recycling, and has wide implications for tackling numerous energy problems such as carbon capture and fixation (e.g., engineering carbon monoxide dehydrogenase and the rubisco-pathway), biomining (e.g., design of lanthanide-binding proteins) and biomanufacturing (e.g., lignin-deconstruction enzymes).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Computational Methods for Multi-Physics Simulation of Melting in Steelmaking

Iron and steel production accounts for approximately 8% of global carbon dioxide (CO) emissions. Pathways to decarbonize include replacing fossil fuels in iron ore reduction and electrifying other steelmaking processes. Iron pellets produced by hydrogen, called Hydrogen Direct Reduced Iron (HDRI), have property differences from those produced using conventional DRI processes. These differences may impact melting in electric arc furnaces (EAF) and other downstream processes. The physical properties of iron pellets vary significantly with temperature during heating, complicating predictions of their behavior. In this project, we seek to develop an integrated simulation, including the fluid flow and convective thermal transport around the pellet particle. We also examine conduction and phase changes within the particle as they impact the melting process. We use adaptive mesh refinement (AMR) to resolve both the changing size of the particle and the complex physics of the interaction between the pellet and the surrounding fluid. We base our simulations on the AMReX-incflo module, which allows large-scale Navier-Stokes simulation while resolving the changing particle size during melting. As we advance our numerical tools, we anticipate an improved understanding of the dynamics of HDRI melting, which will, in turn, accelerate the adoption of low-carbon technologies in the steelmaking industry.

AMReX↗
DOE OSTI2025

Pultrusion and Vitrimer Composites: Emerging Pathways for Sustainable Structural Materials

Pultrusion is a manufacturing process used to produce fiber-reinforced polymer composites with excellent mechanical, thermal, and chemical properties. The resulting materials are lightweight, durable, and corrosion-resistant, making them valuable in aerospace, automotive, construction, and energy sectors. However, conventional thermoset composites remain difficult to recycle due to their infusible and insoluble cross-linked structure. This review explores integrating vitrimer technology a novel class of recyclable thermosets with dynamic covalent adaptive networks into the pultrusion process. As only limited studies have directly reported vitrimer pultrusion to date, this review provides a forward-looking perspective, highlighting fundamental principles, challenges, and opportunities that can guide future development of recyclable high-performance composites. Vitrimers combine the mechanical strength (tensile strength and modulus) of thermosets with the reprocessability and reshaping of thermoplastics through dynamic bond exchange mechanisms. These polymers offer high-temperature reprocessability, self-healing, and closed-loop recyclability, where recycling efficiency can be evaluated by the recovery yield retention of mechanical properties and reuse cycles meeting the demand for sustainable manufacturing. Key aspects discussed include resin formulation, fiber impregnation, curing cycles, and die design for vitrimer systems. The temperature-dependent bond exchange reactions present challenges in achieving optimal curing and strong fiber–matrix adhesion. Recent studies indicate that vitrimer-based composites can maintain structural integrity while enabling recycling and repair, with mechanical performance such as flexural and tensile strength comparable to conventional composites. Incorporating vitrimer materials into pultrusion could enable high-performance, lightweight products for a circular economy. The remaining challenges include optimizing curing kinetics, improving interfacial adhesion, and scaling production for widespread industrial adoption.

Fiber composites↗
DOE OSTI2024

Best Practices for Equitable Solar Workforce Development

The Midwest Renewable Energy Association (MREA) was selected to serve as a lead organization for the U.S. Department of Energy Solar Energy Technology Office’s Equitable Solar Communities of Practice initiative. This project, facilitated through a partnership with ENERGYWERX, aimed to develop strategies to support the expansion of equitable benefits in solar adoption across the U.S. Specifically, the MREA was chosen to lead the solar workforce development community of practice, focusing on scaling the U.S. solar workforce, to meet growing industry demands and ensure that these opportunities are accessible and beneficial to all communities. For the purpose of this initiative, we define the solar workforce in line with the National Solar Jobs Census, which defines a solar worker as someone who spends a majority of their time on solar-related work. This also includes workers who spend a plurality of their time on solar tasks. It’s important to note that manufacturing jobs were not included in this research, as the focus is primarily on solar installation, development, and related roles. To achieve the goals of the Equitable Solar Communities of Practice initiative, the MREA leveraged existing resources and engaged a diverse core team and group of stakeholders including industry professionals, educators, policymakers, and community leaders. The MREA began with a literature review and gap analysis to identify existing best practices and gaps in the solar workforce. This was followed by a community convening to gather insights from a wide range of stakeholders. The findings informed the best practices and pathways to scale the benefits of solar workforce development, focusing on training programs, workforce services, apprenticeship, and justice, inclusion, and sustainability. This report outlines the background, methodology, findings, and conclusions drawn from the landscape and gap analysis, providing valuable insights into workforce needs and training program capacities across the U.S. The outcomes of this research are presented in this report and contain recommendations for optimizing workforce development and training funding to support the equitable growth of the solar industry, ensuring that the transition to solar energy is inclusive and beneficial for all communities.

14 SOLAR ENERGY↗
DOE OSTI2025

Enterprise Artificial Intelligence Strategy for Los Alamos National Laboratory

In the 1984 martial arts drama film, The Karate Kid, a young Daniel LaRusso is unexpectedly placed in an adversarial environment unable to eYectively adapt to a series of new threats and limitations. Fortunately for the main character, once placed under the tutelage of a Mr. Miyagi, he finds resiliency not through the adoption of new tools, but a re-focused set of fundamentals. Much in the same way that Daniel learns waxing on and buYing oY car wax by hand has rewards for Karate, LANL is choosing the harder path of self-hosting Large Language Models (LLMs) for enterprise use instead of only relying on buying access to a hosted AI service like Azure’s OpenAI Application Programming Interface (API). We also are not willing to wait for software-as-a-service (SAAS) AI services to meet us where we need to be from a FedRAMP accreditation standpoint. Our operations regularly depend on access at CUI, UCNI, ITAR and other FIPS-199 moderate-impact data levels and hosting our own services gives us the right security and compliance posture to be useful across the broad range of our work at LANL. With the rise in threats to critical infrastructure, cloud service providers (CSPs), and supply chain attacks from both state and non-state actors, we are not placing the bet that SAAS hosted AI services will be available when we need them. Should a major event occur, we do not want our staY and operations left without a pathway for us to fix the problem and resume the use of AI tools.

42 ENGINEERING↗
DOE OSTI2025

Enhancing heat pump water heater performance with embedded phase change materials thermal energy storage: First hour rating improvement and demand response operation

The increasing global emphasis on energy efficiency and sustainability has put heat pump water heaters (HPWHs) in the spotlight as an energy-efficient alternative to traditional water heating systems. However, their widespread adoption is limited by challenges such as insufficient First Hour Rating (FHR), suboptimal control mechanisms, and limited flexibility for demand response operations. Here, to address these limitations, this study proposes an innovative HPWH system integrated with embedded phase change material (PCM)-based thermal energy storage (TES). The research introduces a novel design and control strategy that leverages optimized PCM integration to enhance thermal storage capacity, improve hot water delivery during peak demand, and increase load-shifting potential. A combination of system modeling, performance simulation, and demand response control strategy evaluation was employed to quantify the benefits of PCM integration. Results demonstrate that the proposed PCM-TES HPWH system significantly enhances FHR, with an optimal 7.0 lb. of PCM increasing FHR by over 26 %—from 62 to 78 gal—for a standard 50-gal HPWH. Additionally, under advanced demand response operation using a preheat strategy, the system reduces the percentage of control temperature out-of-band time from 65 % (conventional HPWH) to just 11.6 %, enabling a more stable and efficient hot water supply. This research contributes a novel PCM-embedded HPWH design and control framework that addresses both performance and grid-interactivity challenges. The findings offer a viable pathway to enhancing the operational efficiency, flexibility, and grid responsiveness of residential water heating systems.

Demand response control↗
NASA NTRS2017

Exploring Connectivity in Sequence Space of Functional RNA

Emergence of replicable genetic molecules was one of the marking points in the origin of life, evolution of which can be conceptualized as a walk through the space of all possible sequences. A theoretical concept of fitness landscape helps to understand evolutionary processes through assigning a value of fitness to each genotype. Then, evolution of a phenotype is viewed as a series of consecutive, single-point mutations. Natural selection biases evolution toward peaks of high fitness and away from valleys of low fitness. whereas neutral drift occurs in the sequence space without direction as mutations are introduced at random. Large networks of neutral or near-neutral mutations on a fitness landscape, especially for sufficiently long genomes, are possible or even inevitable. Their detection in experiments, however, has been elusive. Although a few near-neutral evolutionary pathways have been found, recent experimental evidence indicates landscapes consist of largely isolated islands. The generality of these results, however, is not clear, as the genome length or the fraction of functional molecules in the genotypic space might have been insufficient for the emergence of large, neutral networks. Thorough investigation on the structure of the fitness landscape is essential to understand the mechanisms of evolution of early genomes. RNA molecules are commonly assumed to play the pivotal role in the origin of genetic systems. They are widely believed to be early, if not the earliest, genetic and catalytic molecules, with abundant biochemical activities as aptamers and ribozymes, i.e. RNA molecules capable, respectively, to bind small molecules or catalyze chemical reactions. Here, we present results of our recent studies on the structure of the sequence space of RNA ligase ribozymes selected through in vitro evolution. Several hundred thousands of sequences active to a different degree were obtained by way of deep sequencing. Analysis of these sequences revealed several large clusters defined such that every sequence in a cluster can be reached from any other sequence in the same cluster through a series of single point mutations. Sequences in a single cluster appear to adopt more than one secondary structure. The mechanism of refolding within a single cluster was examined. To shed light on possible evolutionary paths in the space of ribozymes, the connectivity between clusters was investigated. The effect of length of RNA molecules on the structure of the fitness landscape and possible evolutionary paths was examined by way of comparing functional sequences of 20 and 80 nucleobases in length. It was found that sequences of different lengths shared secondary structure motifs that were presumed responsible for catalytic activity, with increasing complexity and global structural rearrangements emerging in longer molecules.

Wei, Chenyu↗