Directing Uphill Strand Displacement with an Engineered Superhelicase
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
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Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA
Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S preribosomal RNA. This structure reveals that Nop9 brings together a carboxy-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional amino-terminal module recognizing the central double-stranded stem region. We further show that the 3' single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA–Nop9 interaction. Both the amino- and carboxy-terminal modules retain the characteristic sequence-specific recognition of PUF proteins, but the amino-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.
59 BASIC BIOLOGICAL SCIENCES↗
Advanced Oxygen-Free Electrolyzer for Ultra-Low-Cost H 2 Storage for Fossil Plants (Final Technical Report)
DOE’s Office of Fossil Energy and Carbon Management has determined that long-duration energy storage solutions co-located with fossil energy assets offer significant benefits to the fossil industry, electric utilities, and customers. T2M Global has developed an Advanced O 2 -Free Electrolyzer System (AES) Technology for low-cost, long-duration H 2 energy storage for fossil plants. The MW-class AES Module conceptual design aims to upgrade stranded assets (dilute/waste syngas streams, excess electricity, and waste heat) at fossil plants to higher value H 2 for additional revenue and greater sustainability. The H 2 energy storage equips fossil plants with the load following capability needed for the lucrative grid-support services market created by Variable Renewable Energy resources.
08 HYDROGEN↗
Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio
The cellular response to ionizing radiation continues to be of significant research interest in cancer radiotherapy, and DNA is recognized as the critical target for most of the biologic effects of radiation. Incident particles can cause initial DNA damages through physical and chemical interactions within a short time scale. Initial DNA damages can undergo repair via different pathways available at different stages of the cell cycle. The misrepair of DNA damage results in genomic rearrangement and causes mutations and chromosome aberrations, which are drivers of cell death. This work presents an integrated study of simulating cell response after proton irradiation with energies of 0.5–500 MeV (LET of 60–0.2 keV/µm). A model of a whole nucleus with fractal DNA geometry was implemented in TOPAS-nBio for initial DNA damage simulations. The default physics and chemistry models in TOPAS-nBio were used to describe interactions of primary particles, secondary particles, and radiolysis products within the nucleus. The initial DNA double-strand break (DSB) yield was found to increase from 6.5 DSB/Gy/Gbp at low-linear energy transfer (LET) of 0.2 keV/µm to 21.2 DSB/Gy/Gbp at high LET of 60 keV/µm. A mechanistic repair model was applied to predict the characteristics of DNA damage repair and dose response of chromosome aberrations. It was found that more than 95% of the DSBs are repaired within the first 24 h and the misrepaired DSB fraction increases rapidly with LET and reaches 15.8% at 60 keV/µm with an estimated chromosome aberration detection threshold of 3 Mbp. The dicentric and acentric fragment yields and the dose response of micronuclei formation after proton irradiation were calculated and compared with experimental results.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Storing Affordability: Battery Storage as an Asset to Reduce Data Center Cost Shifts
This report examines how battery energy storage systems (BESS) can help utilities accommodate large load growth while protecting affordability for existing ratepayers. Rapid growth in electricity demand from artificial intelligence (AI) data centers is straining the U.S. grid. Furthermore, many new data centers are entering rural markets, which could offer economic benefits but may also pose implementation challenges for smaller utilities. At the same time, retail electricity prices are increasing faster than inflation, elevating customer affordability as a key challenge. While data centers have not been the primary driver of increases in residential prices to date, they have pushed wholesale energy and capacity prices higher in several markets. Fundamental utility cost-allocation principles show that data center growth can be rate-positive for existing customers only if new peak demand grows faster than the costs a utility must incur to serve it. Several factors, including a utility’s degree of wholesale market exposure, forecast uncertainty and stranded-asset risk, and tariff design can determine the outcome of load growth on retail rates. Energy storage can make several affordability contributions in the face of this landscape of uncertainty and market volatility, including deferral of higher-cost grid investments through improved utilization of existing assets and flexibility of new large loads, insulation from volatile wholesale prices through peak shaving, and reliability support to address grid risks stemming from the behavior of AI data center loads. Different potential BESS deployment pathways—utility-scale front-of-the-meter systems, aggregated small-scale storage installations, and data center-sited behind-the-meter storage—are compared against each other and against conventional capacity alternatives. This framework is intended as a conceptual resource to utilities, particularly smaller public utilities with rural service territories, who may be considering the role that energy storage can play in insulating existing ratepayers from data center cost shifts.
25 ENERGY STORAGE↗
De novo design of small beta barrel proteins
Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy–based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.
59 BASIC BIOLOGICAL SCIENCES↗
Significant reduction in the low-field magnetization of Nb 3 Sn superconducting strands using the internal oxidation APC approach
Nb 3 Sn superconductors are promising for building accelerator magnets for future energy-frontier circular colliders. A critical factor for this application is the low-field persistent-current magnetization because it leads to several critical issues: e.g. low-field instability (including flux jumps), hysteresis loss, and field errors in magnet bores. Suppression of low-field magnetization requires reduction of low-field critical current density (J c ) or effective subelement size (d eff ). However, reduction of deff of state-of-the-art Nb 3 Sn conductors—the restacked-rod-process (RRP ® ) type—below 40–50 μm without a pronounced decrease in high-field J c is difficult. On the other hand, the internal oxidation method which forms artificial pinning centers (APC) in Nb 3 Sn offers an alternative approach to reducing the low-field magnetization. Compared with a conventional Nb 3 Sn conductor whose flux pinning force versus field (F p –B) curve peaks at ~20% of its irreversibility field (B irr ), the F p –B curve peaks of APC conductors shift to higher fields due to the point pinning effect, leading to flattening of the J c –B curves. The goal of this paper is to quantitatively study how much the APC approach can reduce the low-field magnetization. Here we measured the J c –B curves of an RRP ® conductor and two APC conductors (reacted at 700 °C) from zero field to B irr using a high-field vibrating sample magnetometer. Here the results showed that the APC conductors have higher non-Cu J c at high fields (e.g. 32%–41% higher at 16 T) and simultaneously lower non-Cu Jc at low fields (e.g. 28%–34% lower at 1 T) compared with the RRP ® . This effect is due to a competition between their Nb3Sn layer fraction ratios and layer F p ratios. Suppose they reach the same 16 T non-Cu J c , then the 1 T non-Cu J c and magnetization of the APC conductors are only half or even less compared with the RRP ® conductor.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Electrolyte formulations for electrochemical cells containing a silicon electrode
Additives to electrolytes that enable the formation of comparatively more robust SEI films on silicon anodes. The SEI films in these embodiments are seen to be more robust in part because the batteries containing these materials have higher coulombic efficiency and longer cycle life than comparable batteries without such additives.
25 ENERGY STORAGE↗
Electrolyte formulations for electrochemical cells containing a silicon electrode
Additives to electrolytes that enable the formation of comparatively more robust SEI films on silicon anodes. The SEI films in these embodiments are seen to be more robust in part because the batteries containing these materials have higher coulombic efficiency and longer cycle life than comparable batteries without such additives. The additives preferably contain a nitrate group.
25 ENERGY STORAGE↗
How Fisheries Biologists Can Facilitate the Clean Energy Transition
Abstract Fisheries and aquatic biologists play a critical role in creating environmentally protective hydropower flow requirements that govern flow timing, frequency, magnitude, and rate of change. Hydropower's role in the U.S. electrical grid is expected to evolve in response to increased wind and solar generation as hydropower will be called upon to quickly ramp up and down in response to changes in wind and solar generation. For this reason, hydropower is expected to have increased value as fossil generation is phased out, even as rapid flow fluctuations linked with hydropower flexibility may strand fish, alter habitat, and create unsafe recreational conditions. We face a new challenge in facilitating the renewable energy transition—designing environmental flow requirements that protect against the impacts of flow fluctuations while allowing adequate hydropower flexibility to support a stable grid. In this paper, we discuss hydropower environmental flow requirements, operational flexibility, and electrical grid stability, their potential interactions, and opportunities to align environmental and power system needs to support healthy ecosystems, multiple water uses, and decarbonization of the electric grid.
13 HYDRO ENERGY↗
Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path
Proofreading by replicative DNA polymerases is a fundamental mechanism ensuring DNA replication fidelity. In proofreading, mis-incorporated nucleotides are excised through the 3'-5' exonuclease activity of the DNA polymerase holoenzyme. The exonuclease site is distal from the polymerization site, imposing stringent structural and kinetic requirements for efficient primer strand transfer. Yet, the molecular mechanism of this transfer is not known. Here we employ molecular simulations using recent cryo-EM structures and biochemical analyses to delineate an optimal free energy path connecting the polymerization and exonuclease states of E. coli replicative DNA polymerase Pol III. We identify structures for all intermediates, in which the transitioning primer strand is stabilized by conserved Pol III residues along the fingers, thumb and exonuclease domains. We demonstrate switching kinetics on a tens of milliseconds timescale and unveil a complete pol-to-exo switching mechanism, validated by targeted mutational experiments.
59 BASIC BIOLOGICAL SCIENCES↗
Bottom-up Assembly of Nanoporous Graphene with Emergent Electronic States
The incorporation of nanoscale pores into a sheet of graphene allows it to switch from an impermeable semimetal to a semiconducting nanosieve. Nanoporous graphenes are desirable for applications ranging from high-performance semiconductor device channels to atomically thin molecular sieve membranes, and their performance is highly dependent on the periodicity and reproducibility of pores at the atomic level. Achieving precise nanopore topologies in graphene using top-down lithographic approaches has proven to be challenging due to poor structural control at the atomic level. Alternatively, atomically precise nanometer-sized pores can be fabricated via lateral fusion of bottom-up synthesized graphene nanoribbons. This technique, however, typically requires an additional high temperature cross-coupling step following the nanoribbon formation that inherently yields poor lateral conjugation, resulting in 2D materials that are weakly connected both mechanically and electronically. Here, we demonstrate a novel bottom-up approach for forming fully conjugated nanoporous graphene through a single, mild annealing step following the initial polymer formation. We find emergent interface-localized electronic states within the bulk band gap of the graphene nanoribbon that hybridize to yield a dispersive two-dimensional low-energy band of states. We show that this low-energy band can be rationalized in terms of edge states of the constituent single-strand nanoribbons. The localization of these 2D states around pores makes this material particularly attractive for applications requiring electronically sensitive molecular sieves.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Controlled mechanochemical coupling of anti-junctions in DNA origami arrays
Abstract Allostery is a hallmark of cellular function and important in every biological system. Still, we are only starting to mimic it in the laboratory. Here, we introduce an approach to study aspects of allostery in artificial systems. We use a DNA origami domino array structure which–upon binding of trigger DNA strands–undergoes a stepwise allosteric conformational change. Using two FRET probes placed at specific positions in the DNA origami, we zoom in into single steps of this reaction cascade. Most of the steps are strongly coupled temporally and occur simultaneously. Introduction of activation energy barriers between different intermediate states alters this coupling and induces a time delay. We then apply these approaches to release a cargo DNA strand at a predefined step in the reaction cascade to demonstrate the applicability of this concept in tunable cascades of mechanochemical coupling with both spatial and temporal control.
Science & Technology - Other Topics↗
Electrolyte for Improved Durability of Dynamic Windows Based on Reversible Metal Electrodeposition
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Challenges and Solutions for Leave-One-Out Biosensor Design in the Context of a Rugged Fitness Landscape
The leave-one-out (LOO) green fluorescent protein (GFP) approach to biosensor design combines computational protein design with split protein reconstitution. LOO-GFPs reversibly fold and gain fluorescence upon encountering the target peptide, which can be redefined by computational design of the LOO site. Such an approach can be used to create reusable biosensors for the early detection of emerging biological threats. Enlightening biophysical inferences for nine LOO-GFP biosensor libraries are presented, with target sequences from dengue, influenza, or HIV, replacing beta strands 7, 8, or 11. An initially low hit rate was traced to components of the energy function, manifesting in the over-rewarding of over-tight side chain packing. Also, screening by colony picking required a low library complexity, but designing a biosensor against a peptide of at least 12 residues requires a high-complexity library. This double-bind was solved using a “piecemeal” iterative design strategy. Also, designed LOO-GFPs fluoresced in the unbound state due to unwanted dimerization, but this was solved by fusing a fully functional prototype LOO-GFP to a fiber-forming protein, Drosophila ultrabithorax, creating a biosensor fiber. One influenza hemagglutinin biosensor is characterized here in detail, showing a shifted excitation/emission spectrum, a micromolar affinity for the target peptide, and an unexpected photo-switching ability.
Chemistry↗
Enhancing the Value of Wasted and Stranded Natural Gas Resources Through Conversion Into Aromatics Using Microwaves
Natural gas flaring results in the waste of significant amounts of valuable domestic energy resources while also producing undesirable environmental impacts. Transforming natural gas into value-added chemicals via direct nonoxidative reactions presents a compelling alternative to flaring. However, traditional thermal reactor systems face challenges due to thermodynamic limitations and poor catalyst stability. Microwave-assisted reactions offer a sustainable, on-demand approach for chemical production from natural gas, suitable for compact, flexible reactor systems at the well-site that can be powered by renewable energy. This method offers a novel, non-traditional approach in catalyst activation and product selectivity compared to a conventional thermal method, potentially leading to faster rates, higher selectivities, and higher conversion efficiencies. Despite these advantages, challenges exist, such as the low microwave-sensitivity of the state-of-the-art zeolite catalyst that is highly active for the methane dehydroaromatization reaction. This presentation will discuss recent research from the National Energy Technology Laboratory concerning microwave-assisted natural gas conversion directly into aromatics. It will address the difficulties with microwave heating of traditional thermochemical catalysts, and the application of Multiphysics modeling to understand temperature and field strength in the reactor, to enhance chemical conversion. The presentation will also cover how heating aids can mitigate heating challenges and transform microwave catalysis into a quasi-thermal kinetic problem. Additionally, catalyst activation and deactivation under microwave conditions will be examined, along with the future outlook and needs for microwave enhanced catalysis applications.
catalysis↗
Hexagonal Distributed Embedded Energy Converters (HexDEECs)
Distributed Embedded Energy Converter Technologies (DEEC-Tec) is a new domain for marine renewable energy research that utilizes a conglomeration of small distributed embedded energy converters (DEECs) that, in aggregate, form larger metamaterial frameworks. These resulting DEEC-Tec metamaterials can then, in turn, be used to construct flexible ocean wave energy converters called flexWECs. DEEC-Tec enables flexWECs: (i) to be inherently broad-banded ocean wave frequency energy converters and (ii) to have an inherent lack of highly loaded rigid bodies. The DEEC-Tec domain also benefits the marine renewable energy domain by inherently availing ways that marine energy can be harvested and converted that heretofore has not yet been considered possible: real-time execution of transforming topologies (e.g., actively changing a flexWEC's shape and form) and morphologies (e.g., actively changing a flexWEC's stiffness and damping throughout its entire structure). Presented, is one specific type of DEEC, a HexDEEC, that shows promise in aiding the adoption and further development of the DEEC-Tec domain - it is a small energy transducer being developed by the United States National Renewable Energy Laboratory. The HexDEEC is a small (characteristic length approximating a centimeter) energy transducer that converts the dynamic deformations of an elastomer into electricity through a charging-discharging cycle of a capacitor whose capacitance is varied by those elastic deformations. The HexDEEC is composed of a hyperelastic hexagonal housing (nominally silicon rubber) with six electrodes on its inner faces. The upper three electrodes share the same charge while the lower three electrodes oppose the upper electrode charges. Externally, the HexDEEC has two arms extending away from the middle vertices of the hexagon. Via principles governing the relationship between electrical capacitance and electrical potential (voltage and charge), electricity is generated when the HexDEEC's arms are dynamically pulled or released under tensile loading as doing so causes the distance between the upper and lower sets of electrodes to change - varying the energy converter's overall capacitance. Analytical and numerical modeling have already been used to estimate the electrical energy produced by a HexDEEC. The cursory models approximate the HexDEEC as a parallel plate variable capacitor - simplifying from six to two opposing plates with a constant dielectric volume between those two plates. To account for the elastic HexDEEC material properties, software such as SolidWorks and STAR-CCM+ have been used to generate hyperelastic models; notably, Mooney-Rivlin based models. Individual HexDEECs have been fabricated by drawing uncured liquid silicon rubber into molds via vacuum pressure. To simplify manufacturing, HexDEEC sub-components - e.g., electrodes, wires - can be placed within those molds such that they are directly embedded into the hexagonal housing during the curing process. Furthermore, DEEC-Tec metamaterials can be created by interweaving or sequentially layering multiple HexDEEC strands together. The HexDEEC based metamaterial could then generate electricity through its gross deformations. Ultimately, HexDEECs represent a specific type of energy transducer that can be leveraged, by the DEEC-Tec domain, to create metamaterials used to construct novel flexWECs.
DEEC-Tec↗