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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Earliest Traces of Life as a Window on Life's Origins

Life is the outcome of a complex network of chemical reactions and mo-lecular interactions that emerged on Earth once primitive chemical automata could self-assemble in such a way that enabled them to self-reproduce and evolve. Yet exactly how, where and when life first appeared on our planet remains unknown. Various lines of evidence from fossilized traces of early life preserved in the geological record provide fundamental, albeit often rudimentary, insight into early life. The oldest fossils record the nature of life more than half a billion years after it emerged on Earth and suggest that considerable metabolic diversity had already evolved by this time. Microfossils, microbial mats, stromatolites and organic and inorganic geochemical signatures have been interpreted as compelling evidence for Archean biodiversity. In spite of the chemical enigmas of the earliest life and its limited record, characterization of the various classes of biosignatures indicative of life in its geological context provides guidance as to the earliest co-evolution of the geosphere and biosphere.

Cavalazzi, Barbara↗
DOE OSTI2021

Unnatural biosynthesis by an engineered microorganism with heterologously expressed natural enzymes and an artificial metalloenzyme

Synthetic biology enables microbial hosts to produce complex molecules from organisms that are rare or difficult to cultivate, but the structures of these molecules are limited to those formed by reactions of natural enzymes. The integration of artificial metalloenzymes (ArMs) that catalyse unnatural reactions into metabolic networks could broaden the cache of molecules produced biosynthetically. Here, in this work, we report an engineered microbial cell expressing a heterologous biosynthetic pathway, containing both natural enzymes and ArMs, that produces an unnatural product with high diastereoselectivity. We engineered Escherichia coli with a heterologous terpene biosynthetic pathway and an ArM containing an iridium–porphyrin complex that was transported into the cell with a heterologous transport system. We improved the diastereoselectivity and product titre of the unnatural product by evolving the ArM and selecting the appropriate gene induction and cultivation conditions. This work shows that synthetic biology and synthetic chemistry can produce, by combining natural and artificial enzymes in whole cells, molecules that were previously inaccessible to nature.

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

Variational deep learning of equilibrium transition path ensembles

Here, we present a time-dependent variational method to learn the mechanisms of equilibrium reactive processes and efficiently evaluate their rates within a transition path ensemble. This approach builds off of the variational path sampling methodology by approximating the time-dependent commitment probability within a neural network ansatz. The reaction mechanisms inferred through this approach are elucidated by a novel decomposition of the rate in terms of the components of a stochastic path action conditioned on a transition. This decomposition affords an ability to resolve the typical contribution of each reactive mode and their couplings to the rare event. The associated rate evaluation is variational and systematically improvable through the development of a cumulant expansion. We demonstrate this method in both over- and under-damped stochastic equations of motion, in low-dimensional model systems, and in the isomerization of a solvated alanine dipeptide. In all examples, we find that we can obtain quantitatively accurate estimates of the rates of the reactive events with minimal trajectory statistics and gain unique insights into transitions through the analysis of their commitment probability.

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

Magnetic resonance insights into the heterogeneous, fractal-like kinetics of chemically recyclable polymers

Moving toward a circular plastics economy is a vital aspect of global resource management. Chemical recycling of plastics ensures that high-value monomers can be recovered from depolymerized plastic waste, thus enabling circular manufacturing. However, to increase chemical recycling throughput in materials recovery facilities, the present understanding of polymer transport, diffusion, swelling, and heterogeneous deconstruction kinetics must be systematized to allow industrial-scale process design, spanning molecular to macroscopic regimes. To develop a framework for designing depolymerization processes, we examined acidolysis of circular polydiketoenamine elastomers. We used magnetic resonance to monitor spatially resolved observables in situ and then evaluated these data with a fractal method that treats nonlinear depolymerization kinetics. This approach delineated the roles played by network architecture and reaction medium on depolymerization outcomes, yielding parameters that facilitate comparisons between bulk processes. These streamlined methods to investigate polymer hydrolysis kinetics portend a general strategy for implementing chemical recycling on an industrial scale.

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

Results of time-of-flight transmission measurements for 142 Ce at a 50 m station of GELINA

Transmission measurements have been performed at the time-of-flight facility GELINA to provide data for a new evaluation of neutron resonance parameters for 142 Ce. The measurements were carried out at a 50 m transmission station using a Li-glass scintillator with the accelerator operating at 400 Hz. This report provides the experimental details required to deliver the data to the EXFOR data library, maintained by the International Network of Nuclear Reaction Data Centres (NRDC). The experimental conditions and data reduction procedures are described. In addition, the full covariance information based on the AGS concept is given such that resonance parameters together with their covariances can be derived in a least-squares adjustment to the data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Biosystems Design to Accelerate C 3 -to-CAM Progression

Global demand for food and bioenergy production has increased rapidly, while the area of arable land has been declining for decades due to damage caused by erosion, pollution, sea level rise, urban development, soil salinization, and water scarcity driven by global climate change. In order to overcome this conflict, there is an urgent need to adapt conventional agriculture to water-limited and hotter conditions with plant crop systems that display higher water-use efficiency (WUE). Crassulacean acid metabolism (CAM) species have substantially higher WUE than species performing C 3 or C 4 photosynthesis. CAM plants are derived from C 3 photosynthesis ancestors. However, it is extremely unlikely that the C 3 or C 4 crop plants would evolve rapidly into CAM photosynthesis without human intervention. Currently, there is growing interest in improving WUE through transferring CAM into C 3 crops. However, engineering a major metabolic plant pathway, like CAM, is challenging and requires a comprehensive deep understanding of the enzymatic reactions and regulatory networks in both C 3 and CAM photosynthesis, as well as overcoming physiometabolic limitations such as diurnal stomatal regulation. Recent advances in CAM evolutionary genomics research, genome editing, and synthetic biology have increased the likelihood of successful acceleration of C 3 -to-CAM progression. Here, we first summarize the systems biology-level understanding of the molecular processes in the CAM pathway. Then, we review the principles of CAM engineering in an evolutionary context. Lastly, we discuss the technical approaches to accelerate the C 3 -to-CAM transition in plants using synthetic biology toolboxes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design

Enzyme substrate promiscuity has significant implications for metabolic engineering. The ability to predict the space of possible enzymatic side reactions is crucial for elucidating underground metabolic networks in microorganisms, as well as harnessing novel biosynthetic capabilities of enzymes to produce desired chemicals. Reaction rule-based cheminformatics platforms have been implemented to computationally enumerate possible promiscuous reactions, relying on existing knowledge of enzymatic transformations to inform novel reactions. However, past versions of curated reaction rules have been limited by a lack of comprehensiveness in representing all possible transformations, as well as the need to prune rules to enhance computational efficiency in pathway expansion. To this end, we curated a set of 1224 most generalized reaction rules, automatically abstracted from atom-mapped MetaCyc reactions and verified to uniquely cover all common enzymatic transformations. Additionally, we developed a framework to systematically identify and correct redundancies and errors in the curation process, resulting in a minimal, yet comprehensive, rule set. These reaction rules were capable of reproducing more than 85% of all reactions in the KEGG and BRENDA databases, for which a large fraction of reactions is not present in MetaCyc. Our rules exceed all previously published rule sets for which reproduction was possible in this coverage analysis, which allows for the exploration of a larger space of known enzymatic transformations. By leveraging the entire knowledge of possible metabolic reactions through generalized enzymatic reaction rules, we are able to better utilize underground metabolic pathways and accelerate novel biosynthetic pathway design to enable bioproduction towards a wider range of new molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Catalytic Resonance Theory: Forecasting the Flow of Programmable Catalytic Loops

Chemical transformations on catalyst surfaces occur through series and parallel reaction pathways. These complex networks and their behavior can be most simply evaluated through a three-species surface reaction loop (A* to B* to C* to A*) that is internal to the overall chemical reaction. Application of an oscillating dynamic catalyst to this reactive loop has been shown to exhibit one of three types of behavior: (1) a positive net flux of molecules about the loop in the clockwise direction, (2) a negative net flux of molecules about the loop in the counterclockwise direction, or (3) negligible flux of molecules about the loop at the limit cycle of reaction. Three-species surface loops were simulated with microkinetic modeling to assess the reaction loop behavior resulting from a catalytic surface oscillating between two or more catalyst surface energy states. Selected input parameters for the simulations spanned an 11-dimensional parameter space using 127 688 different parameter combinations. Their converged limit cycle solutions were analyzed for their loop turnover frequencies, the majority of which were found to be approximately zero. Classification and regression machine learning models were trained to predict the sign and magnitude of the loop turnover frequency and successfully performed above accessible baselines. Notably, the classification models exhibited a baseline weighted F1 score of 0.49, whereas trained models achieved weighted F1 scores of 0.94 and 0.96 when trained on the parameters used to define the simulations and derived rate constants, respectively. The trained models successfully predicted catalytic loop behavior, and interpretation of these models revealed all input parameters to be important for the prediction and performance of each model.

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

Viscosity-Controlled Thiol–Ene Reaction and Its Impact on Mechanical Response of Dynamic Networks

The impact of curing conditions on the final properties of thioester-thiol-based dynamic polymer networks was systematically investigated. Despite identical monomer and cross-linker compositions, networks synthesized in the absence of solvent exhibited significantly higher shear moduli and longer relaxation times compared to those cured in solvent. These differences arise from viscosity-controlled photoinitiated thiol–ene reactions, where reduced chain mobility under solvent-free conditions suppresses termination between two polymer radicals, leading to higher reaction conversion. Fourier Transform Infrared (FTIR) spectroscopy and solid-state NMR (ssNMR) spectroscopy confirmed a greater degree of “click” reaction completion in higher viscosity environments. Control experiments revealed that prolonged radical lifetimes and suppressed termination reactions under solvent-free curing conditions contribute to these variations. Here, this study highlights the crucial role of processing conditions in determining cross-link density and, consequently, the dynamic mechanical behavior of polymer networks. It demonstrates that, beyond polymer chemistry, dynamic cross-linker design, and phase separation, curing conditions serve as a key design parameter for tailoring material performance to specific applications.

polymers↗
DOE OSTI2024

Developing a Redox Network for Coastal Saltmarsh Systems in the PFLOTRAN Reaction Model

Coastal ecosystems have been largely ignored in Earth system models but are important zones for carbon and nutrient processing. Interactions between water, microbes, soil, sediments, and vegetation are important for mechanistic representation of coastal processes and ecosystem function. To investigate the role of these feedbacks, we used a reactive transport model (PFLOTRAN) that has the capability to be connected to the Energy Exascale Earth System Model (E3SM). PFLOTRAN was used to incorporate redox reactions and track chemical species important for coastal ecosystems as well as define simple representations of vegetation dynamics. Here our goal was to incorporate oxygen flux, salinity, pH, sulfur cycling, and methane production along with plant-mediated transport of gases and tidal flux. Using porewater profile and incubation data for model calibration and evaluation, we were able to create depth-resolved biogeochemical soil profiles for saltmarsh habitat and use this updated representation to simulate direct and indirect effects of elevated CO 2 and temperature on subsurface biogeochemical cycling. We found that simply changing the partial pressure of CO 2 or increasing temperature in the model did not fully reproduce observed changes in the porewater profile, but the inclusion of plant or microbial responses to CO 2 and temperature manipulations was more accurate in representing porewater concentrations. This indicates the importance of characterizing tightly coupled vegetation-subsurface processes for developing predictive understanding and the need for measurement of plant-soil interactions on the same time scale to understand how hotspots or moments are generated.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Learning the factors controlling mineral dissolution in three-dimensional fracture networks: applications in geologic carbon sequestration

We perform a set of high-fidelity simulations of geochemical reactions within three-dimensional discrete fracture networks (DFN) and use various machine learning techniques to determine the primary factors controlling mineral dissolution. The DFN are partially filled with quartz that gradually dissolves until quasi-steady state conditions are reached. At this point, we measure the quartz remaining in each fracture within the domain as our primary quantity of interest. We observe that a primary sub-network of fractures exists, where the quartz has been fully dissolved out. This reduction in resistance to flow leads to increased flow channelization and reduced solute travel times. However, depending on the DFN topology and the rate of dissolution, we observe substantial variability in the volume of quartz remaining within fractures outside of the primary subnetwork. This variability indicates an interplay between the fracture network structure and geochemical reactions. We characterize the features controlling these processes by developing a machine learning framework to extract their relevant impact. Specifically, we use a combination of high-fidelity simulations with a graph-based approach to study geochemical reactive transport in a complex fracture network to determine the key features that control dissolution. We consider topological, geometric and hydrological features of the fracture network to predict the remaining quartz in quasi-steady state. We found that the dissolution reaction rate constant of quartz and the distance to the primary sub-network in the fracture network are the two most important features controlling the amount of quartz remaining. This study is a first step towards characterizing the parameters that control carbon mineralization using an approach with integrates computational physics and machine learning.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Chemical reaction enhanced graph learning for molecule representation

Abstract Motivation Molecular representation learning (MRL) models molecules with low-dimensional vectors to support biological and chemical applications. Current methods primarily rely on intrinsic molecular information to learn molecular representations, but they often overlook effectively integrating domain knowledge into MRL. Results In this article, we develop a reaction-enhanced graph learning (RXGL) framework for MRL, utilizing chemical reactions as domain knowledge. RXGL introduces dual graph learning modules to model molecule representation. One module employs graph convolutions on molecular graphs to capture molecule structures. The other module constructs a reaction-aware graph from chemical reactions and designs a novel graph attention network on this graph to integrate reaction-level relations into molecular modeling. To refine molecule representations, we design a reaction-based relation learning task, which considers the relations between the reactant and product sides in reactions. In addition, we introduce a cross-view contrastive task to strengthen the cooperative associations between molecular and reaction-aware graph learning. Experiment results show that our RXGL achieves strong performance in various downstream tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation The code is publicly available at https://github.com/coder-ACAC/RLM.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Benzene Ring Knitting Achieved by Ambient-Temperature Dehalogenation via Mechanochemical Ullmann-Type Reductive Coupling

The current approaches capable of affording conjugated porous networks (CPNs) still rely on solution-based coupling reactions promoted by noble metal complexes or Lewis acids, on-surface polymerization conducted in ultrahigh-vacuum environment at very high temperatures (>200 °C), or mechanochemical Scholl-type reactions limited to electron-rich substrates. To develop simple and scalable approaches capable of making CPNs under neat and ambient conditions, herein, a novel and complementary method to the current oxidative Scholl coupling processes is demonstrated to afford CPNs via direct aromatic ring knitting promoted by mechanochemical Ullmann-type reactions. The key to this strategy lies in the dehalogenation of aromatic halides in the presence of Mg involving the formation of Grignard reagent intermediates. Products (Ph-CPN-1) obtained via direct C-C bond formation between 1,2,4,5-tetrabromobenzene (TBB) monomer feature high surface areas together with mesoporous architecture. The versatility of this approach is confirmed by the successful construction of various CPNs via knitting of the corresponding aromatic rings (e.g., pyrene and triphenylene), and even highly crystalline graphite product was obtained. The CPNs exhibit good electrochemical performance as the anode material in lithium-ion batteries (LIBs). Overall, this approach expands the frontiers of CPN synthesis and provides new opportunities to their scalable applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Reversible Reactions, Mesh Size, and Segmental Dynamics Control Penetrant Diffusion in Ethylene Vitrimers

The diffusion of two aromatic dyes with nearly identical sizes was measured in ethylene vitrimers with precise linker lengths and borate ester cross-links using fluorescence recovery after photobleaching (FRAP). One dye possessed a reactive hydroxyl group, while the second was inert. The reaction of the hydroxyl group with the network is slow relative to the hopping times of the dye, resulting in a large slowdown by a factor of 50 for a reactive probe molecule. A kinetic model was fit to the fluorescence intensity data to determine rate constants for the reversible reaction of the dye from the network, which confirms the role of slow reaction kinetics. A second network cross-linker was also investigated with a substituted boronic ester showing ∼10,000 times faster exchange kinetics. In this system, the two dyes show the same diffusion coefficient, as the reaction is no longer the rate-limiting step. The role of dense meshes on small and large dyes is also discussed in the context of the existing theories. Finally, these results highlight the potential of dynamic networks to control penetrant transport through synergistic effects of the mesh size, dynamic bond kinetics, and penetrant–network interactions.

confinement↗
DOE OSTI2021

Spectroscopic Signatures of MQ-Resins in Silicone Elastomers

Polysiloxane elastomers have a large application space due to their versatile cross-linking chemistry and highly tunable physical and mechanical properties. One approach for improving the mechanical integrity of commercial polysiloxane “silicone” elastomers while maintaining their optical transparency is the addition of small, silicone-resin molecules to the network. However, both the poly(dimethylsiloxane) (PDMS) network and the silicone-resin particles have an amorphous structure and complex chemistry, which makes the characterization of their structural properties and segmental network dynamics difficult. Here, we report the synthesis and characterization of a series of model silicone networks modified with a specific class of silicone-resin known as MQ-resin using Raman and advanced nuclear magnetic resonance (NMR) spectroscopy methods. Raman spectroscopy was successfully used to quantify the contribution of the MQ-resin to the network, to determine the type of MQ-resin present in the network, and to investigate the completeness of the network cross-linking reaction. Furthermore, solid-state and 1H double-quantum (DQ) NMR spectroscopies were used not only as a detection method for the MQ-resins but also to quantify changes in the segmental dynamics of the network as a function of MQ-resin concentration. The combination of Raman and NMR spectroscopies describes a series of samples where the MQ-resin particles and PDMS chains maintain their independent segmental dynamics up to high concentrations of MQ-resins (40–50% MQ), where the physical properties of the resin dominate the physical properties of the overall network. The results from our spectroscopic analyses are consistent with the results from macroscopic characterization techniques such as solvent uptake and mechanical testing. The spectroscopic insights into the structure–property relationships of PDMS-MQ composites presented in this study are a valuable tool not only for the synthesis and reverse engineering of future generations of commercial silicone elastomers but also for understanding the mechanisms of aging and degradation over the material lifetime.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Toward more mechanistic representations of biogeochemical processes in stream and river networks: Implementation and demonstration of a multiscale model : Modeling Archive

This Modeling Archive supports the ORNL-SFA and IDEAS-Waterhsed publication submitted to Environmental Modeling and Software. A recently introduced multiscale model for representing the combined effect of hyporheic exchange flows and small-scale hyporheic-zone biogeochemical processes is extended from the reach scale to river network scales. The ADELS (Advection Dispersion Equation with Lagrangian Subgrid) model uses a one-dimensional advection-dispersion-reaction equation for the channel network and couples that equation at each channel location to a one-dimensional advection-reaction subgrid model representing an ensemble of streamlines that are diverted into the hyporheic zone before returning to the channel. The subgrid model is written in a computationally advantageous Lagrangian form with hyporheic age replacing the hyporheic travel distance. In the paper, we summarized implementation in the integrated surface/subsurface hydrology modeling system Advanced Terrestrial Simulator (ATS).

East Fork Poplar Creek↗
DOE OSTI2025

Highly functional microspheres facilitating Diels–Alder network formation

Introducing particles to dynamic covalent networks is a common approach to improve their performance. However, network formation can be impacted by their size and functionality. The influence can be predicted by common theories for small molecular precursors, but it is unclear whether they are applicable to precursors bearing numerous reactive groups and micrometer-scale dimensions. In this work, an experimental study was undertaken using dynamic covalent networks formed by the Diels–Alder reaction between furan and maleimide groups. The gelation behavior of the Diels–Alder networks was studied using rheometry to track their network formation at 40 °C with varying maleimide-functionalized microsphere loading. The highly functional microspheres can interact with the furan precursor, aiding in the formation of the Diels–Alder networks. A 5 wt% microsphere sample can reduce the gelation time by 23% and facilitate network formation in an unbalanced stoichiometry near the critical composition to form a percolating network.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Dependence of Linker Length and Composition on Ionic Conductivity and Lithium Deposition in Single-Ion Conducting Network Polymers

In this report, single-ion conducting electrolytes stand as promising alternatives to state-of-the-Art electrolytes in lithium batteries, although a single-ion conducting material with high Li + conductivity, stability in contact with lithium, and suitable mechanical properties has been slow to emerge. Here, we describe the synthesis of a series of single-ion conducting network polymers from the reaction of tetrakis(4-(chloromethyl)-2,3,5,6-Tetrafluorophenyl)borate with oligoethylene glycoxide linkers Li 2 O[(CH 2 CH 2 )O] n (n = 1, 2, 3, 9, and 22). Polymers with the longest linkers (n = 9 and 22; ANP-9 and ANP-10, respectively) form materials with conductivities of ~ 10 -6 S cm -1 at 100 °C. With the addition of 65 wt % propylene carbonate (PC), all the network polymers in the series exhibit high conductivities at ambient temperatures, with the n = 1 material (ANP-6) achieving a bulk ionic conductivity of 2.5 x 10 -4 S cm -1 at 25 °C. More conductive single-ion conducting gels could be prepared by using the less coordinating pentanediol dilithium salt as a linker (ANP-11; σ = 3.5 x 10 -4 S cm -1 at 25 °C), although this material exhibited a surprisingly high interfacial resistance in contact with a lithium electrode. In contrast, the gel formed with ANP-6 is notably stable in contact with metallic lithium electrodes, displays a lithium-ion transference number of unity, and boasts a wide electrochemical stability window of greater than 4.5 V. Temperature-dependent ac impedance analysis reveals that the ionic conductivity of this material-and likely the other gels in the series-matches closely to a Vogel-Tamman-Fulcher temperature model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗