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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Superconducting disordered neural networks for neuromorphic processing with fluxons

In superconductors, magnetic fields are quantized into discrete fluxons (flux quanta Φ 0 ), made of microscopic circulating supercurrents. We introduce a multiterminal synapse network comprising a disordered array of superconducting loops with Josephson junctions. The loops can trap fluxons defining memory, while the junctions allow their movement between loops. Dynamics of fluxons through such a disordered system through a complex reconfigurable energy landscape represents brain-like spiking information flow. In this work, we experimentally demonstrate a three-loop network using YBa 2 Cu 3 O 7 –δ -based superconducting loops and Josephson junctions, which exhibit stable memory configurations of trapped flux in loops that determine the rate of flow of fluxons through synaptic connections. The memory states are, in turn, affected by the applied input signals but can also be externally configured electrically through control current/feedback terminals. These results establish a previously unexplored, biologically similar architectural approach to neuromorphic computing that is scalable while dissipating energy of atto Joules/spike.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria

To reach their final destinations, outer membrane proteins (OMPs) of gram-negative bacteria undertake an eventful journey beginning in the cytosol. Multiple molecular machines, chaperones, proteases, and other enzymes facilitate the translocation and assembly of OMPs. These helpers usually associate, often transiently, forming large protein assemblies. They are not well understood due to experimental challenges in capturing and characterizing protein-protein interactions (PPIs), especially transient ones. Using AF2Complex, we introduce a high-throughput, deep learning pipeline to identify PPIs within the Escherichia coli cell envelope and apply it to several proteins from an OMP biogenesis pathway. Among the top confident hits obtained from screening ~1500 envelope proteins, we find not only expected interactions but also unexpected ones with profound implications. Subsequently, we predict atomic structures for these protein complexes. These structures, typically of high confidence, explain experimental observations and lead to mechanistic hypotheses for how a chaperone assists a nascent, precursor OMP emerging from a translocon, how another chaperone prevents it from aggregating and docks to a β-barrel assembly port, and how a protease performs quality control. This work presents a general strategy for investigating biological pathways by using structural insights gained from deep learning-based predictions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Integrated solid-state rapid thermo-cycling system

Techniques, systems, and devices are disclosed for implementing a portable lab system for PCR testing. The portable lab system comprises a thermal cycling device including a first well and a second well to receive samples to be thermally cycled, a thermoelectric cooling (TEC) element coupled to the first well and the second well, and a controller to control operation of the TEC element. The portable lab system further includes an electronic interface including a power interface to supply power to the TEC element and the controller of the thermal cycling device to allow the TEC element to transfer energy from the first well to the second well when current flows through the TEC element in a first direction, and from the second well to the first well when current flows through the TEC element in a second direction, and a data interface to collect data from the controller.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Coordinated resource allocation to plant growth–defense tradeoffs

Summary Plant resource allocation patterns often reveal tradeoffs that favor growth (G) over defense (D), or vice versa. Ecologists most often explain G–D tradeoffs through principles of economic optimality, in which negative trait correlations are attributed to the reconciliation of fitness costs. Recently, researchers in molecular biology have developed ‘big data’ resources including multi‐omic (e.g. transcriptomic, proteomic and metabolomic) studies that describe the cellular processes controlling gene expression in model species. In this synthesis, we bridge ecological theory with discoveries in multi‐omics biology to better understand how selection has shaped the mechanisms of G–D tradeoffs. Multi‐omic studies reveal strategically coordinated patterns in resource allocation that are enabled by phytohormone crosstalk and transcriptional signal cascades. Coordinated resource allocation justifies the framework of optimality theory, while providing mechanistic insight into the feedbacks and control hubs that calibrate G–D tradeoff commitments. We use the existing literature to describe the coordinated resource allocation hypothesis (CoRAH) that accounts for balanced cellular controls during the expression of G–D tradeoffs, while sustaining stored resource pools to buffer the impacts of future stresses. The integrative mechanisms of the CoRAH unify the supply‐ and demand‐side perspectives of previous G–D tradeoff theories.

Monson, Russell K.↗
DOE OSTI2022

Curvature-controlled geometrical lensing behavior in self-propelled colloidal particle systems

In many biological systems, the curvature of the surfaces cells live on influences their collective properties. Curvature should likewise influence the behavior of active colloidal particles. We show using molecular simulation of self-propelled active particles on surfaces of Gaussian curvature (both positive and negative) how curvature sign and magnitude can alter the system's collective behavior. Curvature acts as a geometrical lens and shifts the critical density of motility-induced phase separation (MIPS) to lower values for positive curvature and higher values for negative curvature, which we explain theoretically by the nature of parallel lines in spherical and hyperbolic space. Curvature also fluidizes dense MIPS clusters due to the emergence of defect patterns disrupting the crystalline order inside the clusters. Using our findings, we engineer three confining surfaces that strategically combine regions of different curvature to produce a host of novel dynamical behaviors, including cyclic MIPS on spherocylinders, directionally biased cyclic MIPS on spherocones, and position dependent cluster fluctuations on metaballs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Nitrogen fixation and mucilage production on maize aerial roots is controlled by aerial root development and border cell functions

Exploring natural diversity for biological nitrogen fixation in maize and its progenitors is a promising approach to reducing our dependence on synthetic fertilizer and enhancing the sustainability of our cropping systems. We have shown previously that maize accessions from the Sierra Mixe can support a nitrogen-fixing community in the mucilage produced by their abundant aerial roots and obtain a significant fraction of their nitrogen from the air through these associations. In this study, we demonstrate that mucilage production depends on root cap and border cells sensing water, as observed in underground roots. The diameter of aerial roots correlates with the volume of mucilage produced and the nitrogenase activity supported by each root. Young aerial roots produce more mucilage than older ones, probably due to their root cap’s integrity and their ability to produce border cells. Transcriptome analysis on aerial roots at two different growth stages before and after mucilage production confirmed the expression of genes involved in polysaccharide synthesis and degradation. Genes related to nitrogen uptake and assimilation were up-regulated upon water exposure. Altogether, our findings suggest that in addition to the number of nodes with aerial roots reported previously, the diameter of aerial roots and abundance of border cells, polysaccharide synthesis and degradation, and nitrogen uptake are critical factors to ensure efficient nitrogen fixation in maize aerial roots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights

Abstract Bacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis , here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A dynamic kinetic model captures cell-free metabolism for improved butanol production

Cell-free systems are useful tools for prototyping metabolic pathways and optimizing the production of various bioproducts. Mechanistically-based kinetic models are uniquely suited to analyze dynamic experimental data collected from cell-free systems and provide vital qualitative insight. However, to date, dynamic kinetic models have not been applied with rigorous biological constraints or trained on adequate experimental data to the degree that they would give high confidence in predictions and broadly demonstrate the potential for widespread use of such kinetic models. In this work, we construct a large-scale dynamic model of cell-free metabolism with the goal of understanding and optimizing butanol production in a cell-free system. Using a combination of parameterization methods, the resultant model captures experimental metabolite measurements across two experimental conditions for nine metabolites at timepoints between 0 and 24 hours. Here, we present analysis of the model predictions, provide recommendations for butanol optimization, and identify the aldehyde/alcohol dehydrogenase as the primary bottleneck in butanol production. Sensitivity analysis further reveals the extent to which various parameters are constrained, and our approach for probing valid parameter ranges can be applied to other modeling efforts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms

Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. Here we find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Bayesian filtering for model predictive control of stochastic gene expression in single cells

This study describes a method for controlling the production of protein in individual cells using stochastic models of gene expression. By combining modern microscopy platforms with optogenetic gene expression, experimentalists are able to accurately apply light to individual cells, which can induce protein production. Here we use a finite state projection based stochastic model of gene expression, along with Bayesian state estimation to control protein copy numbers within individual cells. We compare this method to previous methods that use population based approaches. We also demonstrate the ability of this control strategy to ameliorate discrepancies between the predictions of a deterministic model and stochastic switching system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Light-Controlled Fermentations for Microbial Chemical and Protein Production

Microbial cell factories offer a sustainable alternative for producing chemicals and recombinant proteins from renewable feedstocks. However, overburdening a microorganism with genetic modifications can reduce host fitness and productivity. This problem can be overcome by using dynamic control: inducible expression of enzymes and pathways, typically using chemical- or nutrient-based additives, to balance cellular growth and production. Optogenetics offers a non-invasive, highly tunable, and reversible method of dynamically regulating gene expression. Here, we describe how to set up light-controlled fermentations of engineered Escherichia coli and Saccharomyces cerevisiae for the production of chemicals or recombinant proteins. We discuss how to apply light at selected times and dosages to decouple microbial growth and production for improved fermentation control and productivity, as well as the key optimization considerations for best results. Additionally, we describe how to implement light controls for lab-scale bioreactor experiments. As a result, these protocols facilitate the adoption of optogenetic controls in engineered microorganisms for improved fermentation performance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural basis for dimerization quality control

Most quality control pathways target misfolded proteins to prevent toxic aggregation and neurodegeneration 1 . Dimerization quality control further improves proteostasis by eliminating complexes of aberrant composition 2 , but how it detects incorrect subunits remains unknown. Here we provide structural insight into target selection by SCF-FBXL17, a dimerization-quality-control E3 ligase that ubiquitylates and helps to degrade inactive heterodimers of BTB proteins while sparing functional homodimers. We find that SCF-FBXL17 disrupts aberrant BTB dimers that fail to stabilize an intermolecular β-sheet around a highly divergent β-strand of the BTB domain. Furthermore, complex dissociation allows SCF-FBXL17 to wrap around a single BTB domain, resulting in robust ubiquitylation. SCF-FBXL17 therefore probes both shape and complementarity of BTB domains, a mechanism that is well suited to establish quality control of complex composition for recurrent interaction modules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Optimization of the Post-Operational Phase on Two Belgian Multi-Unit Nuclear Power Plants: the Case of the Non-Fissile Irradiated Core Items - 20156

The current legal framework in Belgium foresees the progressive phase out of nuclear power between October 2022 (Doel 3) and December 2025 (Doel 2). Upon its definitive shutdown, each unit of the Tihange and Doel sites will enter a Post-Operational Phase (POP) and be prepared for its Decontamination and Decommissioning (D and D). Prior to obtaining the D and D license, the Operator Electrabel is legally required to remove any non-fissile irradiated core items stored in the deactivation pools. The non-fissile irradiated core items consist essentially of control rods, poison rods and source thimbles as well as thimble plugs and foreign materials irradiated during operation: - Their significant content in highly radiant radionuclides (up to 6 TBq of Co-60 per kg of irradiated material) renders all existing operational waste management processes inadequate due to insufficient biological shielding; - Their high concentrations in long-lived radionuclides call for their disposal in a geological repository for which no final design nor waste acceptance criteria are expected prior to 2050. Uncertainties in the Belgian energy supply and security, however, require the Operator to be prepared for a partial nuclear phase out, where one or more units would benefit from lifetime extension while the remaining units would undergo decommissioning. The present paper aims at presenting how Electrabel, in partnership with Tractebel, addressed this challenge by maximizing the use of synergies within the respective sites as well as between both sites themselves, all the while accounting for site specificities. The most recent results and state of progress of the project will be detailed and the first lessons learned will be shared. The project has been split in multiple tasks and phased as follows: - An inventory phase aimed at mapping the contents, origin, composition and history of the non-fissile irradiated core items; - A pre-characterization phase based on neutron activation models; - A waste sorting phase aimed at separating waste forms for which an evacuation route exists from those for which such route does not exist; - A feasibility phase aimed at exploring all possible scenarios for the management of non-fissile irradiated core items and identifying the optimal feasible solution for each site; - A preparation phase (currently ongoing), developing further the optimal solution and ensuring that back-up solutions are available for any foreseeable change of context (licensing issue, modification in the nuclear phase-out program, etc.) and initiating early contacts with potential subcontractors for segmentation works and cask manufacturers, as well as the Belgian regulatory body and waste management agency. This phase also foresees the investigation of destructive and non-destructive radiological measurements to support the detailed characterization of the waste forms; - A realization phase (future work). (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

Chemically controlled pattern formation in self-oscillating elastic shells

Significance Mechanochemical processes drive various biological functions including morphogenesis and morphological changes in responsive synthetic hydrogels. By allowing reactive components to function in an elastic closed shell, autonomous chemical reactions generate microcompartments capable of expanding or contracting or induce buckled patterns. This capability can drive specific functions such as enhancing the rate of diffusion of compartmentalized chemicals or releasing cargos at specific rates. Here, we demonstrate the coupling of mechanical response to autonomous chemical reactions in elastic shells which swell and deswell to generate specific dynamic patterns and morphologies. The reverse feedback from the mechanical input triggers the chemical reaction. Our work inspires the design of responsive shells to enhance the functionality of microcompartments and nanoreactors.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Controlling colloidal crystals via morphing energy landscapes and reinforcement learning

We report a feedback control method to remove grain boundaries and produce circular shaped colloidal crystals using morphing energy landscapes and reinforcement learning–based policies. We demonstrate this approach in optical microscopy and computer simulation experiments for colloidal particles in ac electric fields. First, we discover how tunable energy landscape shapes and orientations enhance grain boundary motion and crystal morphology relaxation. Next, reinforcement learning is used to develop an optimized control policy to actuate morphing energy landscapes to produce defect-free crystals orders of magnitude faster than natural relaxation times. Morphing energy landscapes mechanistically enable rapid crystal repair via anisotropic stresses to control defect and shape relaxation without melting. This method is scalable for up to at least N = 10 3 particles with mean process times scaling as N 0.5 . Further scalability is possible by controlling parallel local energy landscapes (e.g., periodic landscapes) to generate large-scale global defect-free hierarchical structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Spatial modeling algorithms for reactions and transport in biological cells

Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate, particularly in realistic cell geometries. Here we present Spatial Modeling Algorithms for Reactions and Transport (SMART), a software package that takes in high-level user specifications about cell signaling networks and then assembles and solves the associated mathematical systems. SMART uses state-of-the-art finite element analysis, via the FEniCS Project software, to efficiently and accurately resolve cell signaling events over discretized cellular and subcellular geometries. We demonstrate its application to several different biological systems, including yes-associated protein (YAP)/PDZ-binding motif (TAZ) mechanotransduction, calcium signaling in neurons and cardiomyocytes, and ATP generation in mitochondria. Throughout, we utilize experimentally derived realistic cellular geometries represented by well-conditioned tetrahedral meshes. These scenarios demonstrate the applicability, flexibility, accuracy and efficiency of SMART across a range of temporal and spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Porin-Inspired Ionomers with sub-nm Gated Ion Channels for High Ion Conductivity and Selectivity (Final Project Report (2026))

The physiological functions of living systems heavily rely on biological ion channels, whose malfunction can lead to disease. These channels enable selective and regulated transport of water, ions, or small molecules across membranes. Analogously, ionomers used in energy conversion and storage technologies govern ion transport within membrane separators and catalyst binder layers. This DOE Office of Science Early CAREER project aimed to achieve molecular-level control over ionic conductivity and ion permselectivity by translating the functionalities of biological, gated ion channels into a novel class of ion-conducting polymers (ionomers) incorporating macrocyclic calix[4]arene-based repeat units. The overarching goal was to establish fundamental design principles and elucidate proton conduction mechanisms through strategic design of macrocyclic calix[4]arene-containing ionomers, with close relevance to energy conversion and storage devices, including proton exchange membrane fuel cells (PEMFCs). The project leveraged sub-nm-sized macrocyclic pores to facilitate exceptionally fast ion transport (beneficial to addressing sluggish ORR kinetics of PEMFC electrodes) and achieve functionalities of ionic diodes under applied electrochemical fields, beneficial for selective transport/separation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Novel Mito-Nuclear Combinations Facilitate the Global Invasion of a Major Agricultural Crop Pest

A fundamental understanding of the underlying mechanisms involved in biological invasions is crucial to developing effective risk assessment and control measures against invasive species. The fall armyworm (FAW), Spodoptera frugiperda, is a highly invasive pest that has rapidly spread from its native Americas into much of the Eastern Hemisphere, with a highly homogeneous nuclear genetic background. However, the exact mechanism behind its rapid introduction and propagation remains unclear. Here, a systematic investigation is conducted into the population dynamics of FAW in China from 2019 to 2021 and found that FAW individuals carrying “rice” mitochondria (FAW-mR) are more prevalent (>98%) than that with “corn” mitochondria (FAW-mC) at the initial stage of the invasion and in newly-occupied non-overwintering areas. Further fitness experiments show that the two hybrid-strains of FAW exhibit different adaptions in the new environment in China, and this may have been facilitated by amino acid changes in mitochondrial-encoded proteins. FAW-mR used increases energy metabolism, faster wing-beat frequencies, and lower wing loadings to drive greater flight performance and subsequent rapid colonization of new habitats. In contrast, FAW-mC individuals adapt with more relaxed mitochondria and shuttle energetics into maternal investment, observed as faster development rate and higher fecundity. The presence of two different mitochondria types within FAW has the potential to significantly expand the range of damage and enhance competitive advantage. Overall, the study describes a novel invasion mechanism displayed by the FAW population that facilitates its expansion and establishment in new environments.

60 APPLIED LIFE SCIENCES↗