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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Superconducting Radio Frequency Resonators for Quantum Computing: A Short Review

Superconducting radiofrequency (SRF) technology is being used not only in discovery science programs and basic research but also for several applications that benefit society more directly. The advantage of superconducting resonators over those made of normal-conducting metal is their ability to store electromagnetic energy with much lower dissipation. The high-quality factor and longer dissipation time provided by these superconducting resonators can deliver superior performance. Currently, the quantum processing architecture uses resonators and interconnecting circuits operating in the microwave regime with superconducting strip-line technology and low noise electronic devices for switching and communication. The performance of these devices can be enhanced by embedding them in 3D SRF cavity resonators to prolong the coherence time, which improves the utility of the device by reducing error rates and allowing more manipulations (calculations) before the quantum state decays. Here, we present a short review of current microwave technology used in quantum computers and progress towards the 3D resonators to enhance thecoherence time.

Dhakal, Pashupati↗
DOE OSTI2021

Visualization and modeling of inhibition of IL-1β and TNF-α mRNA transcription at the single-cell level

Abstract IL-1β and TNF-α are canonical immune response mediators that play key regulatory roles in a wide range of inflammatory responses to both chronic and acute conditions. Here we employ an automated microscopy platform for the analysis of messenger RNA (mRNA) expression of IL-1β and TNF-α at the single-cell level. The amount of IL-1β and TNF-α mRNA expressed in a human monocytic leukemia cell line (THP-1) is visualized and counted using single-molecule fluorescent in-situ hybridization (smFISH) following exposure of the cells to lipopolysaccharide (LPS), an outer-membrane component of Gram-negative bacteria. We show that the small molecule inhibitors MG132 (a 26S proteasome inhibitor used to block NF-κB signaling) and U0126 (a MAPK Kinase inhibitor used to block CCAAT-enhancer-binding proteins C/EBP) successfully block IL-1β and TNF-α mRNA expression. Based upon this single-cell mRNA expression data, we screened 36 different mathematical models of gene expression, and found two similar models that capture the effects by which the drugs U0126 and MG132 affect the rates at which the genes transition into highly activated states. When their parameters were informed by the action of each drug independently, both models were able to predict the effects of the combined drug treatment. From our data and models, we postulate that IL-1β is activated by both NF-κB and C/EBP, while TNF-α is predominantly activated by NF-κB. Our combined single-cell experimental and modeling efforts show the interconnection between these two genes and demonstrates how the single-cell responses, including the distribution shapes, mean expression, and kinetics of gene expression, change with inhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Frequency-bin photonic quantum information

Discrete frequency modes, or bins, present a blend of opportunities and challenges for photonic quantum information processing. Frequency-bin-encoded photons are readily generated by integrated quantum light sources, naturally high-dimensional, stable in optical fiber, and massively parallelizable in a single spatial mode. Yet quantum operations on frequency-bin states require coherent and controllable multifrequency interference, making them significantly more challenging to manipulate than more traditional spatial degrees of freedom. In this mini-review, we describe recent developments that have transformed these challenges and propelled frequency bins forward. Focusing on sources, manipulation schemes, and detection approaches, we introduce the basics of frequency-bin encoding, summarize the state of the art, and speculate on the field’s next phases. Given the combined progress in integrated photonics, high-fidelity quantum gates, and proof-of-principle demonstrations, frequency-bin quantum information is poised to emerge from the lab and leave its mark on practical quantum information processing—particularly in networking where frequency bins offer unique tools for multiplexing, interconnects, and high-dimensional communications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Leakless end-to-end transport of small molecules through micron-length DNA nanochannels

Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. We design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Geochemistry in support of LANL's national and energy security missions [Slides]

Geochemistery is a field of science that uses chemistry to explain processes occurring within geological systems. It can encompass interconnected fields of geology, hydrology, biology, and atmospheric science as they relate to natural processes in the environment. Geochemistry can play an important role in mission-critical LANL research areas of science of signatures and complex natural and engineered systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a high-throughput application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a thermophile. We applied DAP-seq to >90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum. Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA- and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike towards a desired phenotype.

09 BIOMASS FUELS↗
DOE OSTI2020

SAM Plug-in Development (Phase I Final Report)

The DOE Office of Nuclear Energy (NE) has created an extensive set of advanced modeling and simulation tools for nuclear engineering analysis. The advanced capabilities of these newer analysis codes require more in-depth training, skills, and knowledge in order to effectively utilize them for the design, analysis, and licensing of advanced nuclear systems and experiments. A high learning curve for inexperienced users may deter organizations from incorporating these tools into their internal processes. This project involved development of a plug-in to the Symbolic Nuclear Analysis Package (SNAP) for the System Analysis Module (SAM) tool. SAM is an advanced system analysis tool for reactor transient analyses being developed at Argonne National Laboratory under the U.S. DOE Office of Nuclear Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. SAM utilizes an object-oriented application framework (MOOSE), and its underlying meshing and finite-element library (libMesh) and linear and non-linear solvers (PETSc), to leverage modern advanced software environments and numerical methods. SNAP provides a highly flexible framework for creating, modifying and documenting input for engineering analysis codes such as SAM as well as extensive functionality for submitting, monitoring, and interacting with the codes through an intuitive graphical user interface (GUI). The common user interface provided by SNAP minimizes the learning curve for engineers starting with a new analysis code and provides an intuitive framework for transitioning between different analysis codes. SNAP provides a powerful but intuitive interface to facilitate access to advanced modeling and simulation tools for inexperienced users. Unlike many “form based” GUI’s, SNAP maps each engineering code’s component input to an internal database which manages all component input parameters along with component interconnections. This level of abstraction permits SNAP to support several advanced capabilities such as renodalization, model validation and consistency checks, embedded documentation, model notebook generation, data ownership and reviewer tracking, and variable assignment for inputs to name a few. SNAP includes a built-in Python interpreter and is interfaced to several commercial and open source packages including CPython, MATLAB/OCTAVE, Microsoft Office, Open Office, and SANDIA’s DAKOTA package which provides Uncertainty Quantification analysis through the SNAP plug-ins. Phase I of this project involved development a fully functional basic SAM plug-in to SNAP. This plug-in provides the ability to import existing models, graphically construct, edit and submit models using SNAP’s extensive functionality.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to > 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum . Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Background Information on the Protection Requirements in IEEE Std 1547-2018

As the DER penetration level has risen significantly in recent times, parameter settings and configuration of installed DERs are having direct impact on local electric distribution utilities as well as bulk power systems during normal and abnormal grid conditions. On the other hand, all grid-connected DERs in the United States of America must conform to the interconnection requirements prescribed in the IEEE Std 1547-2018. Because of these reasons, it is crucial to understand the expected DER performance during abnormal grid conditions considering the requirements of the IEEE Std 1547-2018. The aim of this document is twofold: (1) to summarize requirements in IEEE Std 1547-2018 having direct implications in distribution network protection, and (2) to provide the reader with knowledge and information that will be required for users to apply the requirements specified. Since the focus of this document is on distribution network protection in the presence of DERs, it is assumed that the readers have basic understanding of distribution network protection as well as working principles of DERs. This document starts with a brief introduction on protection systems for distribution network followed by a discussion on the impact of DER on the protection systems. Current practices to provide network protection in the presence of DER is briefly discussed. The document then explores the DER performance requirements in IEEE Std. 1547-2018; especially on those related to distribution network protection. Section 6.1 in IEEE Std. 1547-2018 provides an overview of capabilities and control requirements for DER under abnormal operating conditions. This section also introduces abnormal operating performance categories I, II, III. The DER response to various types of faults and grid conditions such as short-circuit faults and open phase conditions are discussed in section 6.2 in the standard while requirements for coordination with the Area EPS reclosing scheme are provided in section 6.3. Section 6.4 in the IEEE Std 1547-2018 specifies requirements for mandatory voltage tripping and ride-through requirements during low and high voltage disturbances and section 6.5 specifies similar requirements for low and high frequency disturbances. IEEE Std. 1547 requires that the conformance of the DERs to IEEE Std 1547-2018 requirements should be verified in accordance with IEEE Std. 1547. 1. There are several parameters and settings of DERs that need to be properly selected for reliable operation during abnormal grid condition while applying the requirements of IEEE Std 1547-2018. Key decisions for proper selections of parameter and settings are: 1. Determination of required DER abnormal operating performance category, 2. Determination of DER response (shall trip) to abnormal voltages and 3. Determination of DER response (shall trip) to abnormal frequency.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Robust highly durable solid oxide fuel cell cathodes – Improved materials compatibility & self-regulating surface chemistry

Solid oxide fuel cells (SOFCs) are electrochemical conversion devices that directly transform hydrogen or hydrocarbon fuels to electricity, with energy efficiencies as high as 90%, coupled with reduced emissions. Several factors, however, remain to be addressed when considering scale-up of SOFC technology, including the need to overcome decreased performance due to sluggish rates of the oxygen reduction reaction (ORR) at the cathode under reduced temperatures and susceptibility to degradation in performance from surface poisoning e.g. from chromia, while limiting the use of critical raw materials (lanthanides and transition metals) present in high performing mixed ionic electronic conducting electrodes like (La,Sr)CoO 3 (LSC). In this project we explored the key descriptors for determining ORR activity in SOFC electrodes and tried to recover performance degradation by applying them to SOFC electrodes. In order to do this, we first selected a model mixed ionic electronic conducting (MIEC) oxide, Pr-doped CeO 2 (Pr 0.1 Ce 0.9 O 2-δ , PCO), which is a chemically stable fluorite and free of inherent poison sources (e.g. Sr segregation in LSC) that potentially react with external impurities such as Cr-species vaporized from the interconnect. The three approaches originally planned in this project are as follows: 1) evaluation of scavenger exsolution characteristics, 2) study of scavengers gettering efficacy following Cr and Si poisoning and 3) integration of new compositions into porous electrodes. Among them, exceptional progress has been made in 2) and 3), especially understanding the role of surface infiltrants in impacting electrode performance and degradation of PCO materials. We found that the Smith acidity scale for binary oxides serves as a powerful descriptor for tuning and predicting the oxygen exchange kinetics on MIEC PCO surfaces. As a result, with infiltration with binary oxides, ranging from strongly basic (Li 2 O) to strongly acidic (SiO 2 ) onto the surface of porous PCO, it was possible to systematically vary the chemical surface exchange coefficient (k chem ) by 6 orders of magnitude! L i2 O increased k chem by nearly 1,000 times over that of pristine PCO, while SiO 2 decreased k chem by nearly the same factor. Strikingly, although the pre-exponential of k chem scales linearly with the acidity of the infiltrated binary oxide, there is nearly no change in the activation energy. With this insight, we attributed the origin of these dramatic changes in k chem values to the systematic increase and decrease in the surface electron density induced by infiltrated binary oxides. More interestingly, although both Cr 2 O 3 and SiO 2 were determined to be acidic by Smith, suggesting that this feature could likely be the primary reason that these compounds serve to poison the ORR on SOFC cathodes, the effect of poisoning could be subsequently tuned by adding multiple infiltrants and controlling their relative surface acidities. We also systematically examined the effect of serial infiltration of basic and acidic oxides. It turned out that serial infiltration of Li not only recovers approximately 20-fold degraded k chem of PCO by acidic Cr 2 O 3 but its k chem is enhanced even beyond that of the non-infiltrated PCO by more than three orders of magnitude. This was further verified with a screen-printing PCO symmetric cell in terms of the electrode performance (area-specific resistance, ASR) related to approach 3). These observations point to acidity as a key descriptor not only in tuning and predicting the ORR activity of SOFC cathodes that largely determines the overall performance of SOFC, but in mitigating and reactivating poisoned electrode performance. This work provides novel guidelines for making the electrode performance much more active and robust in SOFCs, which can further be applied to all applications requiring oxygen exchange reaction, such as electrolyzers, permeation membranes and gas sensors.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2022

Reduced diffusion and enhanced retention of multiple radionuclides from pore structure characterization of barrier materials for enhanced repository performance

Fluid flow and chemical transport in porous media are the macroscopic consequences of pore structure, which integrates geometry (e.g., pore size and surface area, pore-size distribution) and topology (e.g., pore connectivity). Low-permeability geological media whose pores are poorly interconnected will exhibit the characteristics of anomalous diffusion and sample size-dependent effective porosity, which will strongly impact long-term net diffusion and retention of radionuclides in geological repository settings involving different host rocks and barrier materials. A suite of innovative and complementary experimental approaches is utilized to study the microscopic pore structure and macroscopic fluid flow & chemical transport for a range of host rocks and barrier materials, in addition to standard clay minerals and reference rocks. With a particular focus on quantifying the presence and magnitude of “isolated” pores for a reduced effective porosity in low-permeability geomedia, the integrated methodologies for basic properties and pore structure characterization of these geomedia include X-ray diffraction, thin section petrography, grain size distribution, water immersion porosimetry after vacuum-pulling for full saturation, mercury intrusion porosimetry, nitrogen physisorption, scanning electron microscopy, X-ray computed tomography, and (ultra-)small angle neutron (X-ray) scattering. In addition, custom-designed gas diffusion, tracer recipe involving a range of anionic and cationic chemicals with subsequent analyses by laser ablation and inductively coupled plasma-mass spectrometry, along with batch sorption, column transport, and imbibition tests were conducted for coupled effects of pore structure and chemical retention/transport. From the perspectives of pore structure in conjunction with multiple and complementary approaches to examining a range of sample sizes under different observational scales, we find that the poor pore connectivity is prevalent in low-permeability media (mudstone and crystalline rock) that is related to geological processes (e.g., compaction, diagenesis and thermal maturation). For example, the deep and organic matter-rich mudstones have a much smaller effective porosity than the total porosity (as a result of poor pore connectivity) and associated diffusion coefficient, and the effective porosity & diffusion coefficients are also dependent upon the sample sizes used in the measurement. Similarly, most of the pore space in the shallow mudstone is also controlled by pore-throat diameters in the 5-50 nm range of intergranular pore types from its fine-grained nature, but with an overall good pore connectivity. However, the nm-sized pore space (physically pore-network architecture) and strong sorption capacities (chemical retention from clay minerals) of both shallow and deep mudstones lead to the synergistic retention of cationic radionuclides and their utilities as effective host rocks and barrier materials. Our unique approaches of studying how the micro-scale pore structure affect macro-scale fluid flow, diffusion & retention, and chemical transport produce improved mechanistic understanding, and realistic quantification, of diffusion and retention of typical radionuclides in a range of generic host rocks and barrier materials (clay/shale, salt, crystalline rock, and tuff), with the overall results leading to scientifically-based understanding of enhanced isolation (from both diffusion and retention) of radionuclides and improved confidence on the long-term performance of geological repository to store high-level radioactive wastes. In addition to the training of 25 undergraduates, graduates, and postdocs of UTA, the scientists (organizations) involved in performing this work (e.g., discussion, sample sharing, and operation of SANS and SAXS instruments) include Ed Matteo, Yifeng Wang, and Kristopher Kuhlman (Sandia National Laboratories), Jens Birkholzer, Liange Zheng, Tim Kneafsey, and Sharon Borglin (Lawrence Berkeley National Laboratory), Mavrik Zavarin (Lawrence Livermore National Laboratory), Yukio Tachi and Yuta Fukatsu (Japan Atomic Energy Agency), Mieke de Craen (Euridice, Belgium), Markus Bleuel (NIST), Wei-Ren Chen, Gergely Nagy, Changwoo Do, William Heller, Larry Anovitz, and Kenneth Littrell (ORNL), as well as Jan Illvsky, Ivan Kuzmenko, Ju-Sang Park and Jon Almers (ANL). Key deliverables include a total of 13 peer-reviewed journal articles (nine published and three under review), 23 presentations at scientific conferences (AAPG, AAPG Southwest Section, AGU, Asian Clay Conference, GSA, GSA South-Central Section, IHLRWM, InterPore, International Conference on Chemistry and Migration Behavior of Actinides and Fission Products in the Geosphere, International Conference on Coupled Processes in Fractured Geological Media: Observation, Modeling and Application), and academic institutions (UTA, New Mexico State University; University of Poitiers, France; University of Helsinki, Finland; Uppsala University, Sweden; Istanbul Technical University, Turkey) and other organizations (Andra, France; Posiva Oy, Finland).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Interrogating biomineralization one amino acid at a time: amplification of mutational effects in protein-aided titania morphogenesis through reaction-diffusion control

To emulate the control that biomineralizing organisms exert over reactant transport, we construct a countercurrent reaction-diffusion chamber in which an agarose hydrogel regulates the fluxes of inorganic precursor and precipitating solid-binding protein. Furthermore, we show that the morphology of the bioprecipitated titania can be changed from monolithic to interconnected particle networks and dispersed nanoparticles either by decreasing reaction time or by increasing agarose weight percentage at constant precursor and protein concentrations. More strikingly, protein variants with one or two substitutions in their metal oxide-binding domain yield unique peripheral morphologies (needles, threads, plates, and peapods) with distinct crystallography and photocatalytic activity. Our results suggest that diffusional control can magnify otherwise subtle mutational effects in biomineralizing proteins and provide a path for the green synthesis of morphologically and functionally diverse inorganic materials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Machine learning unifies flexibility and efficiency of spinodal structure generation for stochastic biomaterial design

Abstract Porous biomaterials design for bone repair is still largely limited to regular structures (e.g. rod-based lattices), due to their easy parameterization and high controllability. The capability of designing stochastic structure can redefine the boundary of our explorable structure–property space for synthesizing next-generation biomaterials. We hereby propose a convolutional neural network (CNN) approach for efficient generation and design of spinodal structure—an intriguing structure with stochastic yet interconnected, smooth, and constant pore channel conducive to bio-transport. Our CNN-based approach simultaneously possesses the tremendous flexibility of physics-based model in generating various spinodal structures (e.g. periodic, anisotropic, gradient, and arbitrarily large ones) and comparable computational efficiency to mathematical approximation model. We thus successfully design spinodal bone structures with target anisotropic elasticity via high-throughput screening, and directly generate large spinodal orthopedic implants with desired gradient porosity. This work significantly advances stochastic biomaterials development by offering an optimal solution to spinodal structure generation and design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Advances in genome-scale metabolic models of industrially important fungi

Many fungal species have been used in industrial production for biofuels and bioproducts. Developing strains with better performance in biomanufacturing requires systematic understanding of cellular metabolism. Genome-scale metabolic models (GEMs) offer a comprehensive view of interconnected pathways and a mathematical framework for downstream analysis. Recently, GEMs have been developed or updated in several industrially important fungi. Some of them incorporate enzyme constraints, enabling improved predictions of cell states and proteome allocation. In this report we provide an overview of these newly developed GEMs and computational methods that facilitate construction of enzyme-constrained GEMs and utilize flux predictions from GEMs. Furthermore, we highlight the pivotal roles of these GEMs in iterative design-build-test- learn cycles, ultimately advancing the field of fungal biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution

Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution1,2,3. However, cryo-EM studies of protein-free RNA are in their early days. The Tetrahymena thermophila group I self-splicing intron was the first ribozyme to be discovered and has been a prominent model system for the study of RNA catalysis and structure–function relationships4, but its full structure remains unknown. Here we report cryo-EM structures of the full-length Tetrahymena ribozyme in substrate-free and bound states at a resolution of 3.1 Å. Additionally, newly resolved peripheral regions form two coaxially stacked helices; these are interconnected by two kissing loop pseudoknots that wrap around the catalytic core and include two previously unforeseen (to our knowledge) tertiary interactions. The global architecture is nearly identical in both states; only the internal guide sequence and guanosine binding site undergo a large conformational change and a localized shift, respectively, upon binding of RNA substrates. These results provide a long-sought structural view of a paradigmatic RNA enzyme and signal a new era for the cryo-EM-based study of structure–function relationships in ribozymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Mapping periplasmic binding protein oligosaccharide recognition with neutron crystallography

Numerous studies have shown how periplasmic binding proteins (PBPs) bind substrates with exquisite specificity, even distinguishing between sugar epimers and anomers, or structurally similar ions. Yet, marked substrate promiscuity is also a feature encoded in some PBPs. Except for three sub-Ångström crystal structures, there are no reports of hydrogen atom positions in the remaining (> 1000) PBP structures. The previous X-ray crystal structure of the maltodextrin periplasmic-binding protein from Thermotoga maritima (tmMBP) complexed with oligosaccharide showed a large network of interconnected water molecules stretching from one end of the substrate binding pocket to the other. These water molecules are positioned to form multiple hydrogen bonds, as well as forming interactions between the protein and substrate. Here we present the neutron crystal structure of tmMBP to a resolution of 2.1 Å. This is the first neutron crystal structure from the PBP superfamily and here we unambiguously identify the nature and orientation of the hydrogen bonding and water-mediated interactions involved in stabilizing a tetrasaccharide in the binding site. More broadly, these results demonstrate the conserved intricate mechanisms that underlie substrate-specificity and affinity in PBPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

2020 State of the Science Report, Chapter 8: Encounters of Marine Animals with Marine Renewable Energy Device Mooring Systems and Subsea Cables

Many marine renewable energy (MRE) technologies, including floating or midwater wave and tidal devices, require mooring systems (i.e., mooring lines and anchors) to maintain their position within the water column or on the sea surface. In the case of some devices such as tidal kites, these lines and cables can be highly dynamic. An array of non-bottom-mounted devices may also include transmission cables within the water column interconnecting devices to one another, or to offshore substations or hubs on the seabed. The potential for these lines and cables to present hazards for marine animals that may become entangled or entrapped in them, or confused by their presence remains an issue of uncertainty. The degree to which mitigation to avoid or reduce entanglement risk might be required for future MRE installations is yet to be determined, pending greater understanding of the actual nature of the risk. In this chapter, the entanglement or entrapment of a marine animal is defined as the cause to become caught in a system without possibility of escaping. https://tethys.pnnl.gov/publications/state-of-the-science-2020-chapter-8-moorings

16 TIDAL AND WAVE POWER↗
DOE OSTI2021

Defining the Expression, Production, and Signaling Roles of Specialized Metabolites during Bacillus subtilis Differentiation

Bacterial specialized (or secondary) metabolites are structurally diverse molecules that mediate intra- and interspecies interactions by altering growth and cellular physiology and differentiation. Bacillus subtilis, a Gram-positive model bacterium commonly used to study biofilm formation and sporulation, has the capacity to produce more than 10 specialized metabolites. Some of these B. subtilis specialized metabolites have been investigated for their role in facilitating cellular differentiation, but only rarely has the behavior of multiple metabolites been simultaneously investigated. In this study, we explored the interconnectivity of differentiation (biofilm and sporulation) and specialized metabolites in B. subtilis. Specifically, we interrogated how development influences specialized metabolites and vice versa. Using the sporulation-inducing medium DSM, we found that the majority of the specialized metabolites examined are expressed and produced during biofilm formation and sporulation. Additionally, we found that six of these metabolites (surfactin, ComX, bacillibactin, bacilysin, subtilosin A, and plipastatin) are necessary signaling molecules for proper progression of B. subtilis differentiation. This study further supports the growing body of work demonstrating that specialized metabolites have essential physiological functions as cell-cell communication signals in bacteria.

59 BASIC BIOLOGICAL SCIENCES↗