An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein
Abstract not provided
Thompson, Michael C.↗
SEARCH · Engineering Papers
Results for “Substrate Specificity”
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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The structural basis for 2′−5′/3′−5′-cGAMP synthesis by cGAS
Abstract cGAS activates innate immune responses against cytosolic double-stranded DNA. Here, by determining crystal structures of cGAS at various reaction stages, we report a unifying catalytic mechanism. apo-cGAS assumes an array of inactive conformations and binds NTPs nonproductively. Dimerization-coupled double-stranded DNA-binding then affixes the active site into a rigid lock for productive metal•substrate binding. A web-like network of protein•NTP, intra-NTP, and inter-NTP interactions ensures the stepwise synthesis of 2′−5′/3′−5′-linked cGAMP while discriminating against noncognate NTPs and off-pathway intermediates. One divalent metal is sufficient for productive substrate binding, and capturing the second divalent metal is tightly coupled to nucleotide and linkage specificities, a process which manganese is preferred over magnesium by 100-fold. Additionally, we elucidate how mouse cGAS achieves more stringent NTP and linkage specificities than human cGAS. Together, our results reveal that an adaptable, yet precise lock-and-key-like mechanism underpins cGAS catalysis.
59 BASIC BIOLOGICAL SCIENCES↗
Negligible magnetic losses at low temperatures in liquid phase epitaxy grown Y 3 Fe 5 O 12 films
Yttrium iron garnet (Y 3 Fe 5 O 12 ; YIG) has a unique combination of low magnetic damping, high spin-wave conductivity, and insulating properties that make it a highly attractive material for a variety of applications in the fields of magnetics and spintronics. While the room-temperature magnetization dynamics of YIG have been extensively studied, there are limited reports correlating the low-temperature magnetization dynamics to the material structure or growth method. Here, in this study, we investigate liquid phase epitaxy grown YIG films and their magnetization dynamics at temperatures down to 10 K. We show there is a negligible increase in the ferromagnetic resonance linewidth down to 10 K, which is unique when compared with YIG films grown by other deposition methods. From the broadband ferromagnetic resonance measurements, polarized neutron reflectivity, and scanning transmission electron microscopy, we conclude that these liquid phase epitaxy grown films have negligible rare-earth impurities present, specifically the suppression of Gd diffusion from the Gd 3 Ga 5 O 12 (GGG) substrate into the Y 3 Fe 5 O 12 film, and therefore negligible magnetic losses attributed to the slow-relaxation mechanism. Overall, liquid phase epitaxy YIG films have a YIG/GGG interface that is five times sharper and have ten times lower ferromagnetic resonance linewidths below 50 K than comparable YIG films by other deposition methods. Thus, liquid phase epitaxy grown YIG films are ideal for low-temperature experiments/applications that require low magnetic losses, such as quantum transduction and manipulation via magnon coupling.
36 MATERIALS SCIENCE↗
Data and scripts associated with a manuscript modeling microbial regulation of priming effects
This data package is associated with the publication “Modeling Microbial Regulatory Feedback in Organic Matter Decomposition Identifies Copiotrophic Traits as Key Drivers of Positive Priming” published as a preprint on BioRXiv by Ahamed et al. (2026); https://doi.org/10.1101/2024.08.11.607483. The package contains MATLAB scripts and saved simulation outputs used to implement a cybernetic model of microbial regulation during complex organic matter (OM) decomposition governing priming effects. It includes models of (i) single microbial functional groups (copiotrophic or oligotrophic degraders) and (ii) binary consortia composed of degraders and non-degraders with contrasting or common growth traits. Simulation results were generated using Monte Carlo analyses, with randomized key model parameters across a range of environmental mixing fractions of complex and labile OM. The dataset was created to provide a transparent and reusable computational framework for systematically exploring how microbial growth traits, metabolic regulation, and community composition influence OM decomposition dynamics and priming effects. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes the variable definitions. This package includes: (1) annotated MATLAB code implementing the system of ordinary differential equations and cybernetic control laws; (2) saved output files containing data (e.g., biomass, substrates, enzyme levels, priming metrics); and (3) scripts for processing saved outputs and regenerating figures. Specifically, the data package contains three main MATLAB scripts: runPrimingModel.m, runPlotData.m, and runPlotSuppFigS1.m, along with this readme and supporting documentation. Users should begin with runPrimingModel.m, which contains the annotated code implementing the system of ordinary differential equations and cybernetic control laws. This script runs the Monte Carlo simulations of microbial OM decomposition and allows users to modify microbial trait definitions, adjust parameter distributions, or define new community configurations. Simulation outputs are automatically saved as .mat files in the folder named SavedData, which stores all pre-generated results included in this package. The second script, runPlotData.m, reads files from the SavedData folder and processes them to regenerate the figures presented in the manuscript. The third script, runPlotSuppFigS1.m, specifically generates Figure S1 in the Supplementary Material of the manuscript. The package also includes the aforementioned files in non-proprietary .txt format. If users intend to use them, they should first save the files in their respective .m or .mat formats prior to execution in MATLAB.
Biomass concentration↗
Efficient SABRE-SHEATH Hyperpolarization of Potent Branched-Chain-Amino-Acid Metabolic Probe [1-13C]ketoisocaproate
Efficient 13C hyperpolarization of ketoisocaproate is demonstrated in natural isotopic abundance and [1-13C]enriched forms via SABRE-SHEATH (Signal Amplification By Reversible Exchange in SHield Enables Alignment Transfer to Heteronuclei). Parahydrogen, as the source of nuclear spin order, and ketoisocaproate undergo simultaneous chemical exchange with an Ir-IMes-based hexacoordinate complex in CD3OD. SABRE-SHEATH enables spontaneous polarization transfer from parahydrogen-derived hydrides to the 13C nucleus of transiently bound ketoisocaproate. 13C polarization values of up to 18% are achieved at the 1-13C site in 1 min in the liquid state at 30 mM substrate concentration. The efficient polarization build-up becomes possible due to favorable relaxation dynamics. Specifically, the exponential build-up time constant (14.3 ± 0.6 s) is substantially lower than the corresponding polarization decay time constant (22.8 ± 1.2 s) at the optimum polarization transfer field (0.4 microtesla) and temperature (10 °C). The experiments with natural abundance ketoisocaproate revealed polarization level on the 13C-2 site of less than 1%—i.e., one order of magnitude lower than that of the 1-13C site—which is only partially due to more-efficient relaxation dynamics in sub-microtesla fields. We rationalize the overall much lower 13C-2 polarization efficiency in part by less favorable catalyst-binding dynamics of the C-2 site. Pilot SABRE experiments at pH 4.0 (acidified sample) versus pH 6.1 (unaltered sodium [1-13C]ketoisocaproate) reveal substantial modulation of SABRE-SHEATH processes by pH, warranting future systematic pH titration studies of ketoisocaproate, as well as other structurally similar ketocarboxylate motifs including pyruvate and alpha-ketoglutarate, with the overarching goal of maximizing 13C polarization levels in these potent molecular probes. Finally, we also report on the pilot post-mortem use of HP [1-13C]ketoisocaproate in a euthanized mouse, demonstrating that SABRE-hyperpolarized 13C contrast agents hold promise for future metabolic studies.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Do Flashing and Sealant Materials Need to be Exposed to Extreme Cycling?
In the U.S., over 50% of homes were built before 1980, when minimal building codes existed. The aging of building envelopes can significantly contribute to the air leakage, moisture intrusion, and durability of buildings leading to higher energy demands. Although the durability of building materials and envelope systems has been studied extensively, the durability of specific components like window-wall flashing and sealants remains underexplored. Current standards such as ASTM, NIST, and AAMA primarily focus on durability testing considering the high temperatures only and require sealant testing on anodized aluminum panels, leaving questions about performance in cold or fluctuating temperatures unanswered. Current ASTM and AAMA standards provide guidelines for durability testing but predominantly focus on exposure to higher temperature conditions. It remains unclear how exposure to cold temperatures, or cycles of both hot and cold conditions, affect the durability of these materials. Furthermore, AAMA standards mandate that flashing materials be tested on anodized aluminum panels, which may not reflect real-world applications. Therefore, this initial study aims to explore this concern through testing by constructing two window-wall interface prototypes and applying five different flashing and sealant materials to their joints. These samples were subjected to extreme temperatures, ranging from −34 ℃ (−30 °F) to 50 ℃ (122 °F), over a 28-day period (fourteen cycles of 24 hours), with daily visual inspections to document any signs of deterioration such as wrinkling, distortion, or warping. The study has two main objectives: (1) to determine whether flashing and sealant materials lose their durability and strength when exposed to varying climate conditions, specifically cold climates, and (2) to assess whether the interaction of these materials with different substrates (e.g., lumber, PVC, insulation) affects their durability and strength under varying climate conditions. The findings demonstrate how aging impacts the durability of window-wall systems interfaces, justifying future research that potentially could lead to the development of new testing protocols if significant defects are identified.
Palani, Hevar [ORNL] (ORCID:0000000220211994)↗
Investigation of test methods, material properties, and processes for solar cell encapsulants. Encapsulation task of the low-cost silicon solar array project
During this quarter, flat-plate solar collector systems were considered and six basic construction elements were identified: outer coatings, superstrates, pottants, substrates, undercoats, and adhesives. Materials surveys were then initiated to discover either generic classes or/and specific products to function as each construction element. Cost data included in the surveys permit ready evaluation of each material. Silicones, fluorocarbons, glass, and acrylic polymers have the highest inherent weatherability of materials studied to date. Only acrylics, however, combine low costs, environmental resistance, and potential processability. This class will receive particular emphasis.
Source record↗
Biomaterials for tissue engineering: summary
This article summarizes presentations and discussion at the workshop "Enabling Biomaterial Technology for Tissue Engineering," which was held during the Fifth World Biomaterials Congress in May 1996. Presentations covered the areas of material substrate architecture, barrier effects, and cellular response, including analysis of biomaterials challenges involved in producing specific tissue-engineered products.
Non-NASA Center↗
Cu(In,Ga)S2, Thin-Film Solar Cells Prepared by H2S Sulfurization of CuGa-In Precursor
Thin-film CuInS2 solar cell is the leading candidate for space power because of bandgap near the optimum value for AM0 solar radiation outside the earth's atmosphere, excellent radiation hardness, and freedom from intrinsic degradation mechanisms unlike a-Si:H cells. Ultra-lightweight thin-film solar cells deposited on flexible polyimide plastic substrates such as Kapton(trademark), Upilex(trademark), and Apical(trademark) have a potential for achieving specific power of 1000 W/kg, while the state-of-art specific power of the present day solar cells is 66 W/kg. This paper describes the preparation of Cu-rich CuIn(sub 1-x)Ga(sub x)S(sub 2) (CIGS2) thin films and solar cells by a process of sulfurization of CuGa-In precursor similar to that being used for preparation of large-compact-grain CuIn(sub 1-x)Ga(sub x)Se2 thin films and efficient solar cells at FSEC PV Materials Lab.
Dhere, Neelkanth G.↗
Genesis Solar Wind Sample Curation Documentation
Introduction: A scientist with experience as a sample science analyst, provider of flight hardware for multiple missions, and senior engineer in an ISO 2000-rated manufacturing plant has described the timeline of key participants in any PI-led sample return mission, the breadth of the organizations involved [1,2], and, of interest to this meeting, choosing the types of data to preserve and issues of future data accessibility. This work broadens that perspective by giving similar lessons from Genesis sample curation point-of-view. Curation participation regarding data gathering was part of the mission review process from the beginning. Genesis’ story illustrates outcome of several choices about types of data to record and preserve. Precision analysis of solar wind atoms captured in pure, ultraclean substrates is the driving science goal; therefore, detailed documentation was captured from all mission and curation phases and from investigator laboratories because these processes affect the final analytical results [3]. Pre-flight: Design and fabrication of the spacecraft. Like many modern small sample return missions, Genesis was a tightly managed team integrated across science, engineering and curation. Communication across the team was excellent, and, for the most part, the hands-on engineering technicians understood the impacts of “small choices” they routinely make, and the eyes-on oversight of manufacturing processes by scientists was mindful of details. The payload was designed by the Jet Propulsion Laboratory and the spacecraft by Lockheed Martin. Solar wind collectors and instruments were fabricated by multiple vendors and laboratories. The main portion of the payload was assembled at JSC. Fabrication procedures and contamination-control data (with witness coupons) were stored primarily at JSC. The original composition, dimensions and configuration of components, results of thermal testing, etc. are still needed for interpretation of analytical data. At times, these must be estimated from secondary information acquired pre-flight. Moreover, some files (e.g., original 3-D models and early Powerpoint) cannot be opened using software. Archived curation data includes 2-D drawings, material usage lists, QA documentation and analyses of consumables used during fabrication. Important chemical information still resides in archived hardware, paints and lubricants, material coupons, cleaning coupons, environmental witness plates and reference materials from manufacturing facilities. Purity and cleanliness of collector substrates. Semi-conductor vendors provided surface cleanliness data and some purity data. Purity for specific elements of interest was verified by science team members in their laboratories [4]. Curation archived procurement and shipping records, analysis reports, and non-proprietary fabrication data. A physical archive of flight collector reference materials is maintained for future use so additional data can be collected as analytical techniques improve. These are of increased value due to the hard landing upon re-entry. Cleaning and cleanliness assessments of flight hardware. Cleaning of the science canister payload was performed at JSC in a dedicated ISO 4 cleanroom using ultrapure water (UPW). The cleanliness of this UPW was monitored throughout processing. The archive for the clean lab also includes airborne particle counts, airborne molecular and inorganic contamination measurements as well as cleanroom construction material coupons and witness coupons. Hardware cleanliness was assessed by particle counts in rinse water batches. This information is recorded in batch cleaning forms and logbooks, and are, perhaps, of decreased value due to the hard landing. Post-flight: Curation-generated data. The curation handling history of each Genesis sample is documented in a typical astromaterials sample database which captures sample location, physical description and characterization data. Samples have a “shelf life”. Crucial to the preservation of samples is ongoing documentation of the sample environment, initially under curatorial control but is now a separate facility function with requires coordination. PI-generated data. Data on sample characterization and cleaning techniques continues to be generated by sample users [5]. These are often captured in LPSC abstracts, but these “engineering” results often are not publishable as stand-alone papers. We are actively looking for ways to make this information more accessible to users. Ion implants into samples have aided science return and can be shared among investigators. These (and similar) materials should be added to the curatorial collection with appropriate process and characterization data generated externally. Summary: Complete data archives for returned astromaterial samples must be broad in types and formats, and inclusive of environmental monitoring.
Genesis↗
Localised polymer networks in chiral nematic liquid crystals for high speed photonic switching
Self-assembled periodic structures based upon chiral liquid crystalline materials have significant potential in the field of photonics ranging from fast-switching optoelectronic devices to low-threshold lasers. The flexoelectro-optic effect, which is observed in chiral nematic liquid crystals (LCs) when an electric field is applied perpendicular to the helical axis, has significant potential as it exhibits analogue switching in 10–100 μs. However, the major technological barrier that prohibits the commercial realisation of this electro-optic effect is the requirement of a uniform, in-plane alignment of the helix axis between glass substrates. Here, it is shown that periodic polymer structures engineered in the nematic phase of a chiral nematic LC device using direct laser writing can result in the spontaneous formation of the necessary uniform lying helix (ULH) state. Specifically, two-photon polymerization is used in conjunction with a spatial light modulator so as to correct for aberrations introduced by the bounding glass substrates enabling the polymer structures to be fabricated directly into the device. The ULH state appears to be stable in the absence of an externally applied electric field, and the optimum contrast between the bright and dark states is obtained using polymer structures that have periodicities of the order of the device thickness.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Synthesis of MnO{sub 2}-graphene composites with enhanced supercapacitive performance via pulse electrodeposition under supergravity field
A method of pulse electrodeposition under supergravity field was proposed to synthesize MnO{sub 2}-graphene composites. Supergravity is very efficient for promoting mass transfer and decreasing concentration polarization during the electrodeposition process. The synthesis was conducted on our homemade supergravity equipment. The strength of supergravity field depended on the rotating speed of the ring electrode. 3D flower like MnO{sub 2} spheres composed of nanoflakes were acquired when the rotating speed was 3000 rpm. Graphene nanosheets play as a role of conductive substrates for MnO{sub 2} growing. The composites are evaluated as electrode materials for supercapacitors. Electrochemical results show that the maximum specific capacitance of the MnO{sub 2}-graphene composite is 595.7 F g{sup −1} at a current density of 0.5 A g{sup −1}. In addition, the composite exhibits excellent cycle stability with no capacitance attenuation after 1000 cycles. The approach provides new ideas for developing supercapacitor electrode materials with high performance. - Graphical abstract: 3D flower like MnO{sub 2} spheres composed of nanoflakes were acquired at 3000 rpm. - Highlights: • MnO{sub 2}-graphene composites were prepared by pulse electrodeposition under supergravity. • 3D flower like MnO{sub 2} spheres are anchored on the graphene nanosheets. • The MnO{sub 2}-graphene electrode exhibits a specific capacitance of 595.7 F g{sup −1}.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Substrate Recognition by a Colistin Resistance Enzyme from Moraxella catarrhalis
Lipid A phosphoethanolamine (PEtN) transferases render bacteria resistant to the last resort antibiotic colistin. The recent discoveries of pathogenic bacteria harboring plasmid-borne PEtN transferase (mcr) genes have illustrated the serious potential for wide dissemination of these resistance elements. The origin of mcr-1 is traced to Moraxella species co-occupying environmental niches with Enterobacteriaceae. Here, we describe the crystal structure of the catalytic domain of the chromosomally encoded colistin resistance PEtN transferase, ICR Mc (for intrinsic colistin resistance) of Moraxella catarrhalis. The ICR Mc structure in complex with PEtN reveals key molecular details including specific residues involved in catalysis and PEtN binding. It also demonstrates that ICRMc catalytic domain dimerization is required for substrate binding. Our structure-guided phylogenetic analysis provides sequence signatures defining potentially colistin-active representatives in this enzyme family. Combined, these results advance the molecular and mechanistic understanding of PEtN transferases and illuminate their origins.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Micro-opto-mechanical devices and systems using epitaxial lift off
The integration of high quality, single crystal thin film gallium arsenide (GaAs) and indium phosphide (InP) based photonic and electronic materials and devices with host microstructures fabricated from materials such as silicon (Si), glass, and polymers will enable the fabrication of the next generation of micro-opto-mechanical systems (MOMS) and optoelectronic integrated circuits. Thin film semiconductor devices deposited onto arbitrary host substrates and structures create hybrid (more than one material) near-monolithic integrated systems which can be interconnected electrically using standard inexpensive microfabrication techniques such as vacuum metallization and photolithography. These integrated systems take advantage of the optical and electronic properties of compound semiconductor devices while still using host substrate materials such as silicon, polysilicon, glass and polymers in the microstructures. This type of materials optimization for specific tasks creates higher performance systems than those systems which must use trade-offs in device performance to integrate all of the function in a single material system. The low weight of these thin film devices also makes them attractive for integration with micromechanical devices which may have difficulty supporting and translating the full weight of a standard device. These thin film devices and integrated systems will be attractive for applications, however, only when the development of low cost, high yield fabrication and integration techniques makes their use economically feasible. In this paper, we discuss methods for alignment, selective deposition, and interconnection of thin film epitaxial GaAs and InP based devices onto host substrates and host microstructures.
Camperi-Ginestet, C.↗
The molecular basis for recognition of 5'-NNNCC-3' PAM and its methylation state by Acidothermus cellulolyticus Cas9
Explore the source record for details and available documents.
99 GENERAL AND MISCELLANEOUS↗
Monatomic ions influence substrate permeation across bacterial microcompartment shells
Abstract Bacterial microcompartments (BMCs) are protein organelles consisting of an inner enzymatic core encased within a selectively permeable shell. BMC shells are modular, tractable architectures that can be repurposed with new interior enzymes for biomanufacturing purposes. The permeability of BMC shells is function-specific and regulated by biophysical properties of the shell subunits, especially its pores. We hypothesized that ions may interact with pore residues in a manner that influences the substrate permeation process. In vitro activity comparisons between native and broken BMCs demonstrated that increasing NaCl negatively affects permeation rates. Molecular dynamics simulations of the dominant shell protein (BMC-H) revealed that chloride ions preferentially occupy the positive pore, hindering substrate permeation, while sodium cations remain excluded. Overall, these results demonstrate that shell properties influence ion permeability and leverages the integration of experimental and computational techniques to improve our understanding of BMC shells towards their repurposing for biotechnological applications.
59 BASIC BIOLOGICAL SCIENCES↗
An evaluation of dry film lubricants and substrate materials for use on SSME gimbal bearings
Failure of the spherical bearing shaft of the Space Shuttle Main Engine (SSME) gimbal bearing assembly was encountered during Design Verification Specification testing of the full scale engine. Investigation revealed that the failure was caused by a deficiency in the lubrication system. Based upon the materials and gimbal operating conditions, a lubricant of MoS2 and graphite with a ceramic binder was the best lubricant candidate for this particular application; however, the decision to implement the change was not made without verification testing. Scaled down simulation testing was performed. Four different substrate materials and eight different dry film lubricants were subjected to tests under simulated SSME environmental and stress load conditions. The test specimens were evaluated for friction and operating life. Each test specimen was subjected to cyclic operation under load until failure. The force required to move the bearing surfaces relative to each other was monitored throughout the test, thus providing analytical data for derivation of the coefficient of friction. Results indicate that the MoS2/graphite lubricant with ceramic binder proved to be superior from the standpoint of endurance and also from the standpoint of friction reducing capabilities when applied to the titanium substrate material used on SSME. Endurance of this lubricant was approximately 16 times that of the lubricant which was being used when the SSME gimbal failed.
Harp, J. A.↗
A structural explanation for the mechanism and specificity of plant branching enzymes I and IIb
Branching enzymes (BEs) are essential in the biosynthesis of starch and glycogen and play critical roles in determining the fine structure of these polymers. The substrates of these BEs are long carbohydrate chains that interact with these enzymes via multiple binding sites on the enzyme’s surface. By controlling the branched-chain length distribution, BEs can mediate the physiological properties of starch and glycogen moieties; however, the mechanism and structural determinants of this specificity remain mysterious. In this study, we identify a large dodecaose binding surface on rice BE I (BEI) that reaches from the outside of the active site to the active site of the enzyme. Mutagenesis activity assays confirm the importance of this binding site in enzyme catalysis, from which we conclude that it is likely the acceptor chain binding site. Comparison of the structures of BE from Cyanothece and BE1 from rice allowed us to model the location of the donor-binding site. We also identified two loops that likely interact with the donor chain and whose sequences diverge between plant BE1, which tends to transfer longer chains, and BEIIb, which transfers exclusively much shorter chains. When the sequences of these loops were swapped with the BEIIb sequence, rice BE1 also became a short-chain transferring enzyme, demonstrating the key role these loops play in specificity. Taken together, these results provide a more complete picture of the structure, selectivity, and activity of BEs.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗