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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 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
NASA NTRS2014

X-Ray Absorption near Edge Structure Spectroscopic Study of Hayabusa Category 3 Carbonaceous Particles

Analyses with a scanning transmission x-ray microscope (STXM) using x-ray absorption near edge structure (XANES) spectroscopy were applied for the molecular characterization of two kinds of carbonaceous particles of unknown origin, termed category 3, which were collected from the Hayabusa spacecraft sample catcher. Carbon-XANES spectra of the category 3 particles displayed typical spectral patterns of heterogeneous organic macromolecules; peaks corresponding to aromatic/olefinic carbon, heterocyclic nitrogen and/or nitrile, and carboxyl carbon were all detected. Nitrogen-XANES spectra of the particles showed the presence of N-functional groups such as imine, nitrile, aromatic nitrogen, amide, pyrrole, and amine. An oxygen-XANES spectrum of one of the particles showed a ketone group. Differences in carbon- and nitrogen-XANES spectra of the category 3 particles before and after transmission electron microscopic (TEM) observations were observed, which demonstrates that the carbonaceous materials are electron beam sensitive. Calcium-XANES spectroscopy and elemental contrast mapping identified a calcium carbonate grain from one of the category 3 particles. No fluorine-containing molecular species were detected in fluorine-XANES spectra of the particles. The organic macromolecular features of the category 3 particles were distinct from commercial and/or biological ‘fresh (non-degraded)’ polymers, but the category 3 molecular features could possibly reflect degradation of contaminant polymer materials or polymer materials used on the Hayabusa spacecraft. However, an extraterrestrial origin for these materials cannot currently be ruled out.

Asteroides↗
NASA NTRS2018

Organic Matter Preserved in 3-Billion-Year-Old Mudstones at Gale Crater, Mars

Establishing the presence and state of organic matter, including its possible biosignatures, in martian materials has been an elusive quest, despite limited reports of the existence of organic matter on Mars. We report the in situ detection of organic matter preserved in lacustrine mudstones at the base of the ~3.5-billion-year-old Murray formation at Pahrump Hills, Gale crater, by the Sample Analysis at Mars instrument suite onboard the Curiosity rover. Diverse pyrolysis products, including thiophenic, aromatic, and aliphatic compounds released at high temperatures (500° to 820°C), were directly detected by evolved gas analysis. Thiophenes were also observed by gas chromatography–mass spectrometry. Their presence suggests that sulfurization aided organic matter preservation. At least 50 nanomoles of organic carbon persists, probably as macromolecules containing 5% carbon as organic sulfur molecules.

Eigenbrode, Jennifer L.↗
NASA NTRSDate not supplied

Sample Processing Instrumentation to Enable Lab-like Analysis of Lipids, Hydrocarbons, and Kerogen in situ

Introduction: Over the last decade, our team based out of NASA Ames Research Center has made advances in fluidic technologies to enable laboratory-grade processes in space environments. More recently, we have designed and developed two instruments that utilize sample processing steps to extract and purify organic molecules that are key targets in the search for life. The first instrument targets soluble lipids and hydrocarbons that have been preserved in soil or rock material for millions to billions of years called ExCALiBR (Extractor for Chemical Analysis of Lipid Biomarkers in Regolith). The second instrument called KAMELOT (Kerogen and Macromolecule Extractor Liberating Organics Thermolytically) targets kerogen or insoluble macromolecular material that reside in the residue left behind after solvent extraction. Together, these instruments can be coupled to existing flight sample acquisition and analytical instrumentation (e.g., mass spectrometers) to achieve our overall science goal of identifying molecular patterns and features that are diagnostic of how the organic matter was synthesized, either through biological or non-biological processes.

Mary Beth Wilhelm↗
NASA NTRS2024

Independent Scientific Review of Biological Assumptions and Planned Ultraviolet Treatment for Mars Sample Return Backward Planetary Protection

The Backward Planetary Protection Study Team (“the Study Team”), assembled by the Office of the Chief Scientist (OCS) at the request of the Office of Planetary Protection (OPP), has conducted numerous detailed discussions on the potential use of an active ultraviolet (UV) approach for minimizing or eliminating biological contamination of the exterior of the planned Orbiting Sample container (OS) of the Mars Sample Return (MSR) mission. This review of the backward planetary protection (BPP) considerations for the MSR mission focused on two key parameters that are opportunities for further process development to support implementation of planetary protection practices in meeting mission requirements. These parameters include: 1) Sub-cellular biological assumptions – should Mars missions consider self-replicating organisms only or do they need to consider non-self-replicating entities without a cellular organization such as viruses, prions, etc. and macromolecules capable of genetic information transfer, as well? 2) UV biocidal impact – what is the UV fluence in the Mars atmosphere and its associated potential biocidal credit? The assembled subject matter experts (SMEs) in the Study Team are listed in Appendix A, with a brief description of each member’s relevant expertise.

Mamta Patel Nagaraja↗
NASA NTRS2024

Two mechanisms for the spontaneous emergence, execution, and reprogramming of chemical logic circuits

A key question in origin-of-life research is how primitive life or life-like systems obtained reusable and reprogrammable machinery of processing information to respond to various environmental and internal stimuli. One strategy to approach this question is to view living systems as universal chemical computers. This approach focuses upon uncovering how reusable and reprogrammable chemical NOT, AND, and OR logic gates could appear under prebiotically possible scenarios where simple chemicals and second- or lower-order reactions are more frequent than macromolecules and higher-order reactions. In this article, we theoretically model two generic mechanisms of forming Boolean gates based on geochemically plausible reaction systems that could have preceded complex biopolymers. The mechanisms exploit simple bistable autocatalytic systems to encode binary variables and use heterogeneous dilution rates to differentially activate or deactivate autocatalysis in different reactors. We found that NOT, AND, and OR gates, as well as more complex logic circuits, can spontaneously arise from connected, well-mixed flow reactors based on (i) catalysis by a heterodimer between mutually inhibitory autocatalysts or (ii) selectively permeable tunnels connecting reactors. Our results suggest that simple machinery can support the prebiotic emergence of complex chemical logic circuits and provide new guides for experimentally actualizing chemical computation.

Zhen Peng↗
DOE OSTI2020

Multiphase Reacting Flow Simulations and Optimization of Commercial-Scale Aerobic Bioreactors

Aerobic bioreactors are widely used in the synthesis of value-added products in pharmaceutical and biotechnology industries, wherein microbial bioreactions aid in the conversion of sugars to macromolecules. These reactors are also being actively investigated as a cost-effective pathway for the production of low-value commodities such as biofuels and animal feed. Reactor scale-up is one of the important challenges when designing these systems. Gas and liquid phase transport, mass-transfer, and mixing physics at large length scales can significantly affect microbial conversion rates, particularly when the microbial reaction requires a narrow set of conditions. These phenomena are difficult to study in small-scale bench-top reactors that are typically well-mixed. Predictive computational fluid dynamics (CFD) based simulations can therefore aid in the design and optimization of these reactors. This work presents multiphase Euler-Euler CFD simulations of commercial-scale (~ 500 m3) aerobic bioreactors. Our mathematical model treats the gas and liquid as interpenetrating phases. This approach reduces the computational complexity of tracking individual gas bubbles that are several orders of magnitude smaller than reactor dimensions. We solve the Reynolds averaged Navier-Stokes (RANS) multiphase equations that account for phase and chemical species transport, interphase mass and momentum transfer and uses a phenomenological model for oxygen uptake by microbes. We use a customized solver derived from open-source CFD toolbox, OpenFOAM, to perform these simulations, which has been validated against small-scale reactors in our previous work. This work examines the performance of three different reactor designs, viz. bubble column reactor, airlift reactor with an internal draft tube, and a stirred-tank reactor with Rushton impellers. Reactor oxygen mass-transfer coefficient, gas hold-up, and oxygen distribution are critically analyzed among reactors, and sensitivity studies pertaining to gas flow rates and reactor geometry will be presented.

09 BIOMASS FUELS↗
DOE OSTI2021

Coupled Microbial-Conversion and Computational-Fluid-Dynamics (CFD) Models for Butanediol Production in Micro-Aerated Reactors

Microbial conversion of substrates to macromolecules has been widely used in the synthesis of value-added products in pharmaceutical and biotechnology industries. These bioreactions are also being investigated in the production of low-value commodities such as biofuels [1]. Gas-liquid mass-transfer and transport-reaction coupling are important challenges when designing and scaling up these reactor systems. Experiments in wellmixed small-scale reactors have enabled characterization of microbial reactivity, while their coupling with macroscale transport remains relatively unexplored. In this work, we use a coupled metabolic-CFD model to study the action of a genetically engineered microbe Zymomonas mobilis [2] on sugars to produce 2,3-Butanediol (BDO). BDO is an important hydrocarbon intermediate that can be catalytically upgraded to several fuels and chemicals [3]. An important aspect to this particular microbial conversion is the need for micro-aerated environments as opposed to traditional aerobic fermentation. Slight variations in oxygen concentration can result in competing reaction pathways that disable BDO production. Hence, gas-liquid mass transfer and transport need to be optimized in large-scale reactors to maximize BDO production, for which CFD is a valuable tool. The aerobic-fermentation CFD model previously developed by the authors [5] for simulating bubble-column and airlift reactors at scale was used in this study. The Reynolds-averaged mass, momentum and energy transport equations for interpenetrating gas and liquid phase are solved in this model along with the transport and interphase mass transfer of oxygen. Our previous work used a phenomenological model for microbial oxygen uptake that neglected microbial growth and other reaction pathways. In this work, a detailed metabolic model enabled prediction of product formation and inhibition pathways. In order to manage computational cost, we used a subcycling technique [6] that takes advantage of the clear separation in transport (~ 200 sec) and reaction (~ 2-3 hours) timescales. The CFD model is first solved to steady state, after which the metabolic model is advanced at every cell in the computational domain using the local oxygen concentration. The CFD model is then run to achieve a new steady state that provides a new oxygen distribution for the metabolic model. This process, where reaction and fluid updates are interleaved together, is iterated until reactants are completely exhausted. This work will examine the performance of different reactor designs such as bubble column and airlift reactors at scale (250-500 m3). Oxygen mass-transfer coefficient and distribution are critically analyzed among reactors, and optimization studies pertaining to aeration is presented. Furthermore, it has been observed in experiments that high BDO production may be achieved by manipulating the aerobic environment over the course of reaction, such that oxygen concentration is high during the growth phase, and very low as sugar is depleted. This characteristic will be addressed by our simulations for which a timedependent scheduling strategy for aeration is presented that maximizes BDO production. [1] Humbird, D., Davis, R., and McMillan, J., Aeration costs in stirred-tank and bubble column bioreactors, Biochemical Engineering Journal, 127, 161—166, 2017 [2] Yang, S., Mohagheghi, A., Franden, M. A., Chou, Y.-C., Chen, X., Dowe, N., Himmel, M. E., and Zhang, M., Metabolic engineering of zymomonas mobilis for 2, 3-butanediol production from lignocellulosic biomass sugars. Biotechnology for biofuels, 9(1):189, 2016 [3] Kim, S. J., Sim, H. J., Kim, J. W., Lee, Y. G., Park, Y. C., and Seo, J. H., Enhanced production of 2,3-butanediol from xylose by combinatorial engineering of xylose metabolic pathway and cofactor regeneration in pyruvate decarboxylase-deficient Saccharomyces cerevisiae. Bioresource Technology, 245:1551–1557, 2017 [4] Weller, H., Tabor, G., Jasak, H. and Fureby, C., A tensorial approach to computational continuum mechanics using object-oriented techniques, Computers in physics, 12, 6, 620--631, 1998

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

Study on Emulsification/Demulsification Behavior and Mechanism of Produced Liquid from Polymer Flooding on Alaska North Slope

Heavy oil reservoirs on Alaska North Slope (ANS) are unconsolidated and contain abundant clay minerals, where the first-ever field pilot is currently implemented to validate the use of polymer floods for heavy oil enhanced oil recovery (EOR). The polymer molecules and/or fine clay particles carried with the produced liquid could potentially affect the oil/water separation, which is one of the major concerns for field operators. This dissertation aims to investigate the emulsification behavior of produced liquid, understand the emulsifying mechanism, and seek an adaptive and cost-effective method to treat the produced liquid from polymer flooding. Emulsions were prepared by mechanically mixing the actual heavy oil and the produced water from the pilot site, of which the stability was investigated by bottle test method or multiple light scattering method. Drop size distribution and interfacial properties were measured via microscope and pendant drop technique to probe the stability mechanism further. Results showed that oil-continuous or water-continuous emulsion could be generated depending on the water cut, clay types, clay concentration, and polymer concentration. In the crude oil/water system, the increasing water cut triggered the phase inversion of oil-continuous emulsion to water-continuous emulsion, resulting in faster separation and lower emulsion stability. Whereas, clay particles, no matter added to the oil or water phase, resulted in an unfavorable phase inversion from the loose water-continuous emulsion to the tight oil-continuous emulsion as clay concentration increased. For all four types of clay except Ca-montmorillonite, clay particles added to water led to an earlier phase inversion and higher emulsion stability than that added to the oil. The dual function of polymer on emulsion stability was observed. On the one hand, both sheared and unsheared polymer tended to convert the oil-continuous emulsion formed in either crude oil/water system or complex crude oil/water/clay particle system to the water-continuous emulsion, acting as a weak demulsifier to accelerate the oil/water separation. On the other hand, the addition of polymer to the water-continuous emulsion could result in enhanced emulsion stability, which is primarily attributed to the increased viscosity of the continuous phase and the decreased drop size of the dispersed oil phase. Particularly, the sheared polymer had a weaker ability to stabilize the o/w emulsion than the unsheared polymer due to the lower viscosity of the sheared polymer solution resulting from the breakdown of the polymer macromolecules. As for the chemical demulsification tests, the performance of demulsifiers showed a complex dependency upon the water cut, the shearing intensity, demulsifier type and dosage, and the polymer concentration. A compound emulsion breaker, E12+E18, exhibited the most satisfactory demulsification performance despite the varied test conditions. For severe water-continuous emulsions that might require a multi-fold dosage of demulsifier, a less expensive electrolyte, KCl, was proposed to be used in combination with demulsifier E12+E18 to improve the demulsification performance. In the proposed demulsifier formula, the effectiveness of the commercial demulsifier relied on its destructive effect on the interfacial film, while the efficacy of KCl was mainly dependent on its viscosity reduction effect on the continuous phase. This dissertation illustrates that intermediate layer elimination and water clarification are the major challenges for produced liquid treatment from polymer flooding. It also provides practical and theoretical guidance in advance for the demulsification strategy of the produced liquid from the ongoing first-ever polymer flooding pilot on ANS.

Chang, Hongli↗
DOE OSTI2020

Study of an Unrefined Humate Solution as a Possible Attenuation-based Remedy for Uranium Contamination in Acidic Groundwater - 20351

The Savannah River Site (SRS), joined the environmental cleanup program in 1981 after the Cold War, and was designated as a hazardous waste management facility. About 1.8 billion gallons of acid wastes were disposed into the F/H Area Seepage Basin that included many radionuclides and dissolved metals, resulting in highly contaminated groundwater plumes with pH of 3 - 5.5. The acidity of the plumes contributes to the mobility of several constituents of concern (COC) such as H-3, U-238, I-129, and Sr-90 for the F-Area plume and H-3, Sr-90 and mercury for the H-Area plume. An active treatment (pump-and-treat and re-injection) system was constructed and put in place in 1997 to address the removal of metals and radionuclides from the contaminated groundwater. As remediation projects advanced, active treatments were transitioned to more passive or enhanced-passive approaches such as the subsurface barrier with base injection system, which has been controlling the mobility of contaminants. However, new and more efficient attenuation-based remedies are always sought. Several studies have proposed that humic substances can be used to remediate sites contaminated with heavy metals by creating a permeable reactive barrier. Humic substances (HS) are major components of soil organic matter. HS are polyfunctional organic macromolecules formed by the chemo-microbiological decomposition of biomass or dead organic matter. These substances are usually divided into three main fractions: humin (insoluble at all pH values), humic acid (soluble at pH greater than 3.5), and fulvic acid (soluble at all pH values). Humic substances are major components of the soil at SRS and, in addition, are also helpful in the removal process of uranium. This research focuses on uranium (VI), which is a key contaminant of concern in the F-Area groundwater plume. The interaction of uranium with sediment in the presence or absence of humic substances involves complex mechanisms that are not yet well understood. The interaction of U(VI) with humic substances can affect the adsorption of U on sediment, altering its mobility in the subsurface. The objective of this study is to study the mobility of uranium in the presence of humic acid and to determine if sediments amended by humic acid can enhance the sorption of heavy metals onto sediments. In this research, experiments were conducted using background (clean) F-Area aquifer sediments to understand and predict uranium mobility. A blended material, humate, containing both humic and fulvic acids and a chemically modified humate (KW15 modified humic or mod-HA) was studied as a possible amendment for uranium remediation in SRS groundwater. Batch experiments were conducted in triplicates using 20 ml of aqueous suspension in DI water containing SRS sediment and mod-HA and studied the effect of pH, kinetics of humate sorption onto SRS sediment and also studied the sorption of uranium onto mod-HA amended SRS sediment. Results indicate that mod-HA amended sediment increases uranium removal significantly. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Large-scale atomistic model construction of subbituminous and bituminous coals for solvent extraction simulations with reactive molecular dynamics

Large-scale atomistic models for complex polycyclic aromatic hydrocarbon systems help understand the chemical properties and behaviors of complex feedstocks such as coal or petroleum. However, the development and utilization of large-scale models remain limited due to the difficulty in achieving the varied structural characteristics necessary to capture stochastic nature of these feedstocks. Here we demonstrate a systematic workflow to construct stochastic molecular systems from a broad analytical suite: high-resolution transmission electron microscopy (HRTEM), carbon-13 nuclear magnetic resonance spectroscopy ( 13 C NMR), laser desorption ionization mass spectroscopy (LDI-MS), and elemental analysis. We present a model construction and analysis utility of a new Python-based module. We selected one subbituminous and three high-volatile bituminous coals to construct large-scale models (~40,000 atoms). The constructed models were utilized to examine the affinity for solvent extraction (naphthalene or tetralin) and the effect of structural properties (e.g., aromatic cluster size, functional groups, and cross-linking) in reactive molecular dynamics simulations. Complex chemical reactions were monitored with bond order transitions, intermediates formation, and mass distributions. Reactive molecular dynamics simulations suggest a plausible chemical extraction process and products for the complex fossil feedstocks. The results indicated that radical formations with bond breaking of bridging oxygens and carbons were required at high temperatures to facilitate hydrogeneration and extraction of gas molecules from radical-free molecules. We observed that aliphatic chains of tetralin were easily decomposed and combined with radicals to form small size of molecules with aryl bonding, mainly increasing molecules in the 500–1000 Da, while naphthalene had little impact on chemical extraction process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Non-linear enhancement of ultrafast X-ray diffraction through transient resonances

Diffraction-before-destruction imaging with ultrashort X-ray pulses can visualize non-equilibrium processes, such as chemical reactions, with sub-femtosecond precision in the native environment. Here, a nanospecimen diffracts a single X-ray flash before it disintegrates. The sample structure can be reconstructed from the coherent diffraction image (CDI). State-of-the-art X-ray snapshots lack high spatial resolution because of weak diffraction signal. Bleaching effects from photo-ionization significantly restrain image brightness scaling. We find that non-linear transient ion resonances can overcome this barrier if X-ray laser pulses are shorter than in most experiments. We compared snapshots from individual ≈ 100 nm Xe nanoparticles as a function of pulse duration and incoming X-ray fluence. Our experimental results and Monte Carlo simulations suggest that transient resonances can increase ionic scattering cross sections significantly beyond literature values. This provides a novel avenue towards substantial improvement of the spatial resolution in CDI in combination with sub-femtosecond temporal precision at the nanoscale.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

PolyDODT: a macrocyclic elastomer with unusual properties

The effect of reaction conditions on the structure of poly(3,6-dioxa-1,8-octanedithiol) (polyDODT) made by Reversible Radical Recombination Polymerization (R3P) using triethylamine (TEA), H 2 O 2 and air was investigated. 800 MHz (1 and 2D) NMR was used to investigate the polymer structures. Sensitivity analysis provided direct evidence for high purity cyclic polyDODT up to M n ~ 100 000 g mol –1 . Here, comparative analysis by High Resolution Multidetector Size Exclusion Chromatography (SEC) using integrated data showed that the cycles had lower viscosity and were more compact (both for R g and R h ) than linear samples of similar molecular weight. However, differential data revealed unusual behavior. While lower molecular weight cyclic polymers eluted later and had lower intrinsic viscosity than their linear counterparts at the same molecular weight, at higher molecular weights the polymers showed strange behavior: both the diffusion coefficient measured by Quasielastic Light Scattering (QELS) and Mark–Houwink–Sakurada plots of intrinsic viscosity for linear and cyclic polyDODT were found to converge. R3P, an aqueous based “green” method is capable of producing polymers at the 10–100 g scale in the lab, which will allow more detailed studies of this new class of biodegradable elastomers so further experimentation can be performed to elucidate the reasons for the unusual findings.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Thermodynamics of calcium binding to heparin: Implications of solvation and water structuring for polysaccharide biofunctions

Heparan sulfates are found in all animal tissues and have essential roles in living systems. This family of biomacromolecules modulates binding to calcium ions (Ca 2+ ) in low free energy reactions that influence biochemical processes from cell signaling and anticoagulant efficacy to biomineralization. Despite their ubiquity, the thermodynamic basis for how heparans and similarly functionalized biomolecules regulate Ca 2+ interactions is not yet established. Using heparosan (Control) and heparins with different positions of sulfate groups, we quantify how SO 3 − and COO − content and SO 3 − position modulate Ca 2+ binding by isothermal titration calorimetry. The free energy of all heparin-Ca2+ interactions (ΔG rxn ) is dominated by entropic contributions due to favorable water release from polar, hydrophilic groups. Heparin with both sulfate esters (O-SO 3 − ) and sulfamides (N-SO 3 − ) has the strongest binding to Ca 2+ compared to heparosan and to heparin with only O-SO 3 − groups (~3X). By linking Ca 2+ binding thermodynamics to measurements of the interfacial energy for calcite (CaCO 3 ) crystallization onto polysaccharides, we show molecule-specific differences in nucleation rate can be explained by differences in water structuring during Ca 2+ interactions. A large entropic term (-TΔS rxn ) upon Ca 2+ –polysaccharide binding correlates with high interfacial energy to CaCO 3 nucleation. Combining our measurements with literature values indicates many Ca 2+ –polysaccharide interactions have a shared thermodynamic signature. The resulting enthalpy–entropy compensation relationship suggests these interactions are generally dominated by water restructuring involving few conformational changes, distinct from Ca 2+ –protein binding. Our findings quantify the thermodynamic origins of heparin-specific interactions with Ca 2+ and demonstrate the contributions of solvation and functional group position during biomacromolecule-mediated ion regulation.

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

BioXTAS RAW 2 : new developments for a free open-source program for small-angle scattering data reduction and analysis

BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI ; updated automated Guinier fitting and D max finding algorithms; automated series ( e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares ( REGALS ); creation of electron-density reconstructions using electron density via solution scattering ( DENSS ); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management

3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression—factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Modeling Functional Organic Chemistry in Arctic Rivers: An Idealized Siberian System

Rivers of the Arctic will become ever more important for the global climate, since they carry a majority of continental dissolved organic carbon flux into the rapidly changing polar ocean. Aqueous organics comprise a wide array of functional groups, several of which are likely to impact coastal and open water biophysical properties. Light attenuation, interfacial films, aerosol formation, gas release and momentum exchange can all be cited. We performed Lagrangian kinetic modeling for the evolution of riverine organic chemistry as the molecules in question make their way from the highlands to Arctic outlets. Classes as diverse as the proteins, sugars, lipids, re-condensates, humics, bio-tracers and small volatiles are all included. Our reduced framework constitutes an idealized northward flow driving a major hydrological discharge rate and primarily representing the Russian Lena. Mountainous, high solute and tundra sources are all simulated, and they meet up at several points between soil and delta process reactors. Turnover rates are parameterized beginning with extrapolated coastal values imposed along a limited tributary network, with connections between different terrestrial sub-ecologies. Temporal variation of our total dissolved matter most closely resembles the observations when we focus on the restricted removal and low initial carbon loads, suggesting relatively slow transformation along the water course. Thus, channel combinations and mixing must play a dominant role. Nevertheless, microbial and photochemical losses help determine the final concentrations for most species. Chemical evolution is distinct for the various functionalities, with special contributions from pre- and post-reactivity in soil and delta waters. Several functions are combined linearly to represent the collective chromophoric dissolved matter, characterized here by its absorption. Tributaries carry the signature of lignin phenols to segregate tundra versus taiga sources, and special attention is paid to the early then marine behaviors of low molecular weight volatiles. Heteropolycondensates comprise the largest percentage of reactive carbon in our simulations due to recombination/accumulation, and they tend to be preeminent at the mouth. Outlet concentrations of individual structures such as amino acids and absorbers lie above threshold values for biophysical influence, on the monolayer and light attenuation. The extent of coastal spreading is examined through targeted regional box modeling, relying on salinity and color for calibration. In some cases, plumes reach the scale of peripheral arctic seas, and amplification is expected during upcoming decades. Conclusions are mapped from the Lena to other boreal discharges, and future research questions are outlined regarding the bonding type versus mass release as permafrost degrades. Dynamic aqueous organic coupling is recommended for polar system models, from headwaters to coastal diluent.

54 ENVIRONMENTAL SCIENCES↗