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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Assessing models of force-dependent unbinding rates via infrequent metadynamics

Protein–ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent “bonds” being mechanically strained, and this can be integral to proper cellular function. Broadly, two classes of force dependence have been observed—slip bonds, where the unbinding rate increases, and catch bonds, where the unbinding rate decreases. Despite much theoretical work, we cannot predict for which protein–ligand pairs, pulling coordinates, and forces a particular rate dependence will appear. Here, we assess the ability of MD simulations combined with enhanced sampling techniques to probe the force dependence of unbinding rates. We show that the infrequent metadynamics technique correctly produces both catch and slip bonding kinetics for model potentials. We then apply it to the well-studied case of a buckyball in a hydrophobic cavity, which appears to exhibit an ideal slip bond. Finally, we compute the force-dependent unbinding rate of biotin–streptavidin. Here, the complex nature of the unbinding process causes the infrequent metadynamics method to begin to break down due to the presence of unbinding intermediates, despite the use of a previously optimized sampling coordinate. Allowing for this limitation, a combination of kinetic and free energy computations predicts an overall slip bond for larger forces consistent with prior experimental results although there are substantial deviations at small forces that require further investigation. Furthermore, this work demonstrates the promise of predicting force-dependent unbinding rates using enhanced sampling MD techniques while also revealing the methodological barriers that must be overcome to tackle more complex targets in the future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Hybrid combustion modeling approach for turbulent jet ignition in natural-gas pre-chamber spark-ignition engines at high EGR

Here, this study presented a hybrid modeling approach for simulating turbulent jet ignition and combustion processes in a natural-gas pre-chamber spark-ignition engine operating under exhaust gas recirculation (EGR) diluted conditions. In-depth analyses of experimental data and simulation results from previous work [Chinnathambi et al., ICEF2021-67836; Kim et al., Fuel 409: 137815, 2026] revealed two key findings: (i) the magnitude of pressure difference between the pre-chamber and main chamber ($∆P_{PC-MC}$) was positively correlated with the combustion duration from the moment of $∆P_{PC-MC}=0$ to the point of 5% mass fraction burned, with larger $∆P_{PC-MC}$ associated with longer duration; and (ii) the turbulent combustion regime in the main chamber transitioned from the broken reaction zone to the corrugated flamelet regime, with the Karlovitz number exceeding 100 immediately after turbulent hot jets were ejected from nozzles, coinciding with observed local extinction events. To accurately simulate the entire combustion process, a hybrid approach was developed under Reynolds-Averaged Navier Stokes framework, combining the G-equation model for pre-chamber combustion with the multi-zone well-stirred reactor approach and a turbulence-chemistry interaction (TCI) submodel for main chamber combustion. The TCI submodel accounted for the attenuation of reaction rates due to turbulent strain and modeled local extinction by suppressing reaction rates under certain flow and flame conditions. When applied to three EGR rate conditions toward the dilution limit, the hybrid modeling approach accurately reproduced experimental data in terms of cylinder pressure, apparent heat release rate, and the observed positive correlation, including the delayed onset of main chamber combustion—a feature not captured by existing combustion models.

computational fluid dynamics simulation↗
DOE OSTI2024

Skeletal reaction models for methane combustion

A local-sensitivity-analysis technique is employed to generate new skeletal reaction models for methane combustion from the foundational fuel chemistry model (FFCM-1). Here, the sensitivities of the thermo-chemical variables with respect to the reaction rates are computed via the forced-optimally time dependent (f-OTD) methodology. In this methodology, the large sensitivity matrix containing all local sensitivities is modeled as a product of two low-rank time-dependent matrices. The evolution equations of these matrices are derived from the governing equations of the system. The modeled sensitivities are computed for the auto-ignition of methane at atmospheric and high pressures with different sets of initial temperatures, and equivalence ratios. These sensitivities are then analyzed to rank the most important (sensitive) species. A series of skeletal models with different number of species and levels of accuracy in reproducing the FFCM-1 results are suggested. The performances of the generated models are compared against FFCM-1 in predicting the ignition delay, the laminar flame speed, and the flame extinction. The results of this comparative assessment suggest the skeletal models with 24 and more species generate the FFCM-1 results with an excellent accuracy.

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

Probabilistic and maximum entropy modeling of chemical reaction systems: Characteristics and comparisons to mass action kinetic models

We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with standard chemical potentials, we derive and compare the free energy dissipation and the entropy production rates. We express the relation between entropy production and the chemical master equation for modeling metabolism, which unifies chemical kinetics and chemical thermodynamics. Because prediction uncertainty with respect to parameter variability is frequently a concern with mass action models utilizing rate constants, we compare and contrast the maximum entropy model, which has its own set of rate parameters, to a population of standard mass action models in which the rate constants are randomly chosen. We show that a maximum entropy model is characterized by a high probability of free energy dissipation rate and likewise entropy production rate, relative to other models. We then characterize the variability of the maximum entropy model predictions with respect to uncertainties in parameters (standard free energies of formation) and with respect to ionic strengths typically found in a cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Heat of Mixing During Fast Charge/Discharge of a Li-Ion Cell: A Study on NMC523 Cathode

Predicting temperature rise accurately during fast charge/discharge of a Li-ion cell is essential to avoid thermal runaway and extend battery life. While modeling the temperature rise, it is necessary to model the heat generation correctly. Heat of mixing, one of the four main sources of heat generation in a Li-ion battery, has often been considered insignificant and therefore excluded from modeling. When included, it is modeled using the expression from a Taylor expansion approximation. In this work, we have shown the conditions when including the heat of mixing becomes important and quantified the error associated with using the Taylor expansion, especially under high charge/discharge conditions. Consequently, we carry out the calculation of the rate of enthalpy change and the heat generation rate from the most fundamental equation for the rate of the total enthalpy change without simplifying assumptions or approximations. The heat generation rate calculated doing so naturally includes irreversible, reversible and mixing heat. We then exclusively separate out the heat of mixing by subtracting the rate of enthalpy change by reaction from the rate of the total enthalpy change. Results show that the contribution of heat of mixing in the total heat generated increases with the charge/discharge rate and is as large as 23% for a 6 C discharge. This result suggests that while modeling heat generation for fast charge/discharge, it is necessary to include the heat of mixing and avoid calculating it using the Taylor expansion approximation.

25 ENERGY STORAGE↗
DOE OSTI2022

Solar Ammonia Production via Novel Two-step Thermochemical Looping of a Co 3 Mo 3 N/Co 6 Mo 6 N pair [Slides]

Ternary nitrides in the family A 3 B x N (A=Co, Ni, Fe; B=Mo; x=2,3) identified and synthesized. Experiments with Co 3 Mo 3 N in Ammonia Synthesis Reactor demonstrate cyclable NH3 production from bulk nitride under pure H 2 . Production rates were approx. constant in all the reduction steps with no evident dependence on the consumed solid-state nitrogen up to formation of 661. Material can be re-nitridized under pure N 2 (or 10% H 2 /N 2 ). Bulk N utilization per reduction step averaged between 25 – 40% of the total (2-3 hours). Rate equations and parameters extracted from data. NH 3 selectivity exceeds gas phase equilibrium at higher temperatures (in a large excess of H 2 ). Selectivity begins to decrease significantly above 650 C, N 2 production rapidly increases above 650 C seemingly due to reaction that is zero order in H 2 (thermal reduction of the nitride?). Poised to begin the systematics studies of relationships between materials and reactions.

14 SOLAR ENERGY↗
DOE OSTI2023

Polyimide dynamically compressed to decomposition pressures: Two-wave structures captured by velocimetry and modeling

We performed a series of six plate impact experiments on polyimide and modeled them using new reactant and products equations of state combined with an Arrhenius rate model. The first experiment was diagnosed with embedded electromagnetic velocity gauges through which we directly observed attenuation of the lead shock to an approximately constant state over a propagation distance of roughly 4 mm. Simulated gauge profiles were in excellent qualitative agreement with experiment and suggested a sluggish chemical reaction that did not proceed to completion. The remaining five experiments were conducted in a transmission geometry and diagnosed velocimetrically at the sample/window interface. All five of these yielded profiles with a sharp shock followed by a more gradual approach to maximum interface velocity that was “rounded” to varying degree. These profiles proved difficult to interpret unambiguously due to the convolution of the reactive wave upon first shock with reflection of the lead wave and reshock or release by the window. Comparison with thermochemical calculations strongly suggests that the point of maximum interface velocity corresponds to the equilibrium reshock or release locus. We discuss the implications of this point for the practice of impedance matching based on the reflected Hugoniot of reactive materials such as polymers. The reactant and thermochemical products equations of state are developmental SESAME tables 97710 and 97720, respectively.

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

Direct measurements for the kinetics of C–C bond fission in the high temperature decomposition of isopropanol

The thermal decomposition of isopropanol was studied experimentally and theoretically with a view to isolate and directly measure rate coefficients for the dominant radical channel in this multi-channel process. Two complementary shock tube methods, laser schlieren densitomtery and H-atom atomic resonance absorption spectroscopy, were used to obtain rate coefficents for the C–C bond fission channel. The experimental ranges span temperatures from 1200–2100 K and pressures between 30–690 torr. These are the most direct measurements of this rate coefficent in the fall-off regime of relevance to high-temperature reacting systems. Theoretical studies also performed in this work confirm that the title reaction and a molecular elimination involving dehydration were the sole unimolecular processes at high temperatures. A master equation analysis yielded k ( T, P ) for the C–C fission and these are shown to be in good agreement with the present experimental measurements. Comparisons with prior experimental and theoretical studies in the literature indicate branching ratios as well as absolute k ( T, P ) for C–C bond-fission have been under-predicted for this decomposition reaction. Consequently, results from the present studies place an increased emphasis on radical-driven secondary processes in high-temperature pyrolysis of this simplest secondary alcohol.

Kim, John H. [Univ. of Michigan, Ann Arbor, MI (Un↗
DOE OSTI2023

Mass transfer in catalytic depolymerization: External effectiveness factors and serendipitous processivity in stagnant and stirred melts

Several heterogeneous catalysts are being developed to recycle plastics. Most operate in viscous polymer melts, where external mass transfer effects could limit the supply of co-reactants to active sites. External mass transfer can also impede the diffusion of long chain products away from the catalyst after each cut. Product egress limitations could potentially confer unintentional processivity to catalyst operation, i.e. a tendency for the catalyst to repeatedly cut the same chain after an initial encounter. We formulate reaction–diffusion equations to quantify mass transfer effects on the co-reactant transport to the catalyst and the degree of serendipitous processivity. Results are developed for catalysts in stagnant or stirred melts, with simple expressions involving Damkohler, Peclet, and Sherwood numbers, i.e. dimensionless combinations of rate constants, catalyst particle size, polymer diffusivities, and shear rates (where applicable). In conclusion, we estimate the impact of these effects for a spherical core–shell catalyst.

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

Effects of non-thermal termolecular reactions on detonation development in hydrogen (H 2 )/methane (CH 4 ) - air mixtures

The binary fuel blend of H 2 /CH 4 is one of the most promising hydrogen-enriched hydrocarbon fuels in spark-ignition (SI) engines. Yet, the undesirable phenomenon of super-knock, which can severely and in-stantaneously damage an SI engine, limits its widespread adoption. Moreover, there is still a lack of con-sensus on the precise mechanism by which this phenomenon occurs i.e. via flame acceleration or spon-taneous ignition, despite numerous previous investigations. At the same time, recent studies [M. P. Burke, S. J. Klippenstein, Nat. Chem. 9 (2017) 1078 -1082, Y. Tao, A. W. Jasper, Y. Georgievskii, S. J. Klippenstein, R. Sivaramakrishnan, Proc. Combust. Inst. 38 (2021) 515-522] have demonstrated a high probability of occurrence of non-thermal reactions in premixed flames of such H 2 /CH 4 fuel blends with air due to the presence of non-trivial amounts of highly reactive radicals including H, O and OH apart from O 2 . The present study focuses on the evolution of an initial deflagration front to a detonation wave in H 2 /CH 4 - air mixtures under SI engine relevant conditions through fully resolved, constant volume 1D simulations with and without non-thermal reactivity. Non-thermal reactions were included in the macroscopic kinetics model as chemically termolecular reactions facilitated by the H + CH 3 and H + OH radical-radical recombination and the H + O 2 radical-molecule association reactions. Further, the nonthermal reactions result in a corresponding decrease in the reaction fluxes of the incipient recombination/association reactions. Therefore, an additional set of simulations were performed by applying corrections to the respective incipient recombination/association rate constants using the methodology demonstrated by Tao et al. [Y. Tao, A. W. Jasper, Y. Georgievskii, S. J. Klippenstein, R. Sivaramakrishnan, Proc. Combust. Inst. 38 (2021) 515-522]. Compared to the baseline case, the onset of spontaneous ignition in the end-gas region was observed to be delayed in the presence of non-thermal termolecular reactions. Concurrently, the developing detonation was observed to be significantly stronger. In contrast, applying corrections to the recombi-nation/association rate constants resulted in a completely different behavior. Specifically, detonation was observed to occur due to self acceleration of the primary flame in the absence of spontaneous ignition in the end-gas region. Sensitivity analysis was performed to quantify the effects of non-thermal reactions on the duration of heat release rate and thereby the mechanism of detonation formation. In addition, chemical explosive mode analysis (CEMA) was performed to identify the dominant species/reactions re-sponsible for the observed results.

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

Calculator For Radioisotope Yields, Targets, And Products

An initial number of atoms in a material (by element or by isotope), defined by ENDF library availability, is used to produce an initial reaction products (RPs). The RPs are decayed using full, analytical solutions to the Bateman equations to calculate the RP inventory at a user-specified time. Since each radioisotope's inventory is known, the proportion to the total may be shown for each isotope. The total dose rate and activity is the main objective for experimenters. Built-in information about many reactors and irradiation positions is available. Full execution and display of results takes 5-10 seconds, depending on the complexity of the input parameters.

Holschuh, ThomasV [Idaho National Laboratory (INL)↗
DOE OSTI2023

COMPUTATIONAL MODELING OF IGNITION AND PREMIXED FLAME PROPAGATION INITIATED BY A PRE-CHAMBER TURBULENT JET

Addressing the pressing need for reduced carbon emissions, Turbulent Jet Ignition (TJI) emerges as a promising technology for ultra-lean combustion, offering enhanced thermal efficiencies and minimized cyclic variability in spark-ignited engines. To facilitate rapid testing and integration of this technology, a robust computational modeling framework is crucial. This study delves into the predictive capabilities of computational models for main-chamber ignition and premixed flame propagation using a single-cycle TJI rig measured by Biswas et al. (Applied Thermal Engineering, vol 106, 2016). Employing an open-source compressible flow simulation solver with Large Eddy Simulation (LES) for turbulence modeling, the investigation integrates the conventional Laminar Finite Rate Chemistry (LFRC) model alongside the transported Probability Density Method (PDF) for turbulence-chemistry interaction. A fully-consistent Eulerian Monte-Carlo Fields (EMCF) method is utilized to approximate the transported PDF, while Interaction by Exchange with Mean is employed to close micro-mixing terms in stochastic differential equations. A reduced chemical reaction mechanism with 21 species and 84 reactions (DRM-19) is used for solving chemical kinetics, and a double Gaussian energy deposition model is used to approximate the spark ignition in the pre-chamber. An unstructured O-grid mesh with 0.3 million cells in the prechamber and 1 million cells in the main chamber is employed. Results are divided into two phases: pre-chamber initialization and full TJI simulations. Validation of the predicted pre-chamber flame propagation and the lean ignition in the main-chamber is carried out by using available experimental data. Under quiescent conditions, both the LFRC and transported PDF methods largely underestimate the flame speed and subsequent pressure growth in the pre-chamber. A linear momentum forcing technique is applied to investigate the impact of initial turbulence in the pre-chamber, demonstrating a notable influence on flame propagation. Fine-tuning of the forcing coefficient reproduces the sudden pressure growth observed in the experiment. The experimentally validated pre-chamber simulation serves as the initial condition for the full TJI simulations. It is found that the LFRC model fails to predict lean-ignition in the main-chamber, resulting in a misfiring event. Incorporation of turbulence-chemistry interaction using the transported PDF method substantially improves the prediction of the ignition event in the main-chamber, achieving fair qualitative agreement and quantitative validation of combustion parameters within ±10% of the reported experimental data. The rich simulation results consisting of a full set of statistical description of the thermo-chemical states enable us to gain deep insights into the ignition mechanisms in the main chamber, which is limited when done experimentally. A novel dual ignition phenomenon is revealed in the TJI rig for the first time. Initially, a primary ignition kernel is formed at a downstream location which eventually detaches from the main jet. As the jet momentum decreases, a secondary ignition event follows, this time at a more upstream location which eventually combines with the primary ignition kernel to form a single connected flame front. Investigation of these ignition sequences in chemical composition space reveal distinct differences between the two. The primary ignition event in the main-chamber is followed by a large concentration of active radicals from the pre-chamber jet, accelerating the chain-branching steps, characterizing what has been referred to as flame ignition. In contrast, the secondary ignition occurs in the absence of active radicals in the pre-chamber jet, hence characterized as jet ignition. Further analysis of the effect of pre-chamber jet characteristics on lean ignition in the main-chamber is conducted by setting up cases with different initial pressure ratios (por) between the two chambers, a non-dimensional parameter, ranging from 1.2 to 3.2. As the initial pressure ratio increases, jet momentum increases, with dual ignition observed in cases above por= 2.2. Case with por= 3.2 lead to misfiring. The effect of ignition sequence on global combustion characteristics of TJI is analyzed. Dual ignition events lead to non-monotonicity in combustion characteristics such as global reaction progress variable, flame penetration, and global heat release rate. In dual ignition events, although the rate of fuel consumption and global heat release rate is initially lower, the secondary ignition leads to a sudden increase in flame surface area, resulting in a sudden jump and promoting the overall performance of the TJI system.

42 ENGINEERING↗
DOE OSTI2020

Extension of OpenMC for Fixed Source Transmutation Calculations

This report documents work performed under a Strategic Partnership Project between Argonne National Laboratory (ANL) and the United Kingdom Atomic Energy Authority (UKAEA). The overall goal of this project is to extend OpenMC [1], a community-developed Monte Carlo particle transport code, to be able to perform fixed-source transmutation calculations. In fission and fusion reactors, the high flux of energetic neutrons causes materials within the reactor to “transmute,” or undergo a nuclear reaction that results in the addition/removal of neutrons and protons from the nucleus of an atom. If subjected to these reactions for long enough, the overall composition and physical properties of the material itself begin to change as a result of transmutation. Such a feature is vital for predicting the decrease in tritium production rate within a breeder blanket during the lifetime of a fusion reactor. OpenMC is capable of simulating neutron transport in fission/fusion systems, thereby allowing it to estimate the flux that causes transmutation. It is also capable of solving the transmutation equations, which determine how the composition of a material changes over time due to neutron irradiation and radioactive decay. However, solving the transmutation equations was previously only possible when the source of neutrons came from a fission system. In a fusion system, the source of neutrons is typically determined by a separate code and then given as an input to the particle transport simulation. This is known as a fixed source calculation. Through this project, we have extended OpenMC to solve the transmutation equations for a fixed source calculation. Evaluating the change in material compositions due to transmutation and its effect on physical properties is of key importance to a range of engineering analyses for fission and fusion systems. For example, in a fusion reactor, estimating the dose rate at different physical locations resulting from irradiated materials in the reactor allows designers to ensure that workers are not exposed to doses beyond applicable regulations. In order to properly dispose of irradiated materials, designers also need to estimate the radiotoxicity, which again relies on knowledge of the material composition at some future time. The specific tasks for this project that were agreed to between ANL and UKAEA were as follows: 1. Make changes and additions in the openmc.deplete and related modules in OpenMC to support transmutation calculations following a fixed source transport simulation. 2. Make necessary changes to OpenMC to model transmutation due to an arbitrary set of reactions needed for fusion applications. Use this new capability to generate a depletion chain file based on the TENDL nuclear data library. 3. Improve the openmc.deplete module in OpenMC to keep track of gases produced as a by-product of nuclear reactions during transmutation calculations. 4. Validate the new capabilities by carrying out fixed-source transmutation calculations on a suitable benchmark problem using OpenMC and a comparable Monte Carlo neutron transport code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Quantifications of growth rate and particle size of magnesium silicate hydrate cement using small‐angle X‐ray scattering

The focus of recent research on cement binders has shifted to alternatives such as magnesium silicate hydrate (M-S-H) to mitigate the environmental impact of conventional concrete production. However, a detailed understanding of the morphology and growth rate of M-S-H, which informs its applicability as a cementing agent, is lacking. These properties are important as they influence cement hydration and consequently the development of macroscopic properties. Here, in this study, the particle size distribution and growth rate of M-S-H synthesized by mixing aqueous stock solutions were analyzed using synchrotron-based small-angle X-ray scattering. The reaction solutions contained dissolved magnesium and silicon with concentrations ranging from 2 to 500 mM, corresponding to saturation indices with respect to M-S-H endmembers, M 0.75 -S-H and M 1.50 -S-H, between 5.8 and 10.3. The precipitation rates of M-S-H align with affinity-based kinetic models and can be described by the following equations: For M 0.75 -S-H: 𝑟 M 0.75 −S−H =10 −9.54±0.70 ⁢(Ω$^{0.59±0.08}_{M_{0.75}⁢\textrm{SH}}$−1), and for M 1.50 -S-H: 𝑟 M 1.50 −S−H =10 −7.56±0.37 ⁢(Ω$^{0.34±0.04}_{M_{1.50}⁢\textrm{SH}}$−1), where 𝑟 is the rate in mol/L/s, and Ω represents the saturation ratio with respect to M-S-H. Moreover, we observed that changing the [Mg]/[Si] ratio affects particle size, a trend that cannot be fully explained by changes in the saturation index alone. These insights are critical for improving the predictability and control of cementation in concrete that utilizes M-S-H-based binders.

M-S-H↗
DOE OSTI2021

On the computational solution of vector-density based continuum dislocation dynamics models: A comparison of two plastic distortion and stress update algorithms

Continuum dislocation dynamics models of mesoscale plasticity consist of dislocation transport-reaction equations coupled with crystal mechanics equations. The coupling between these two sets of equations is such that dislocation transport gives rise to the evolution of plastic distortion (strain), while the evolution of the latter fixes the stress from which the dislocation velocity field is found via a mobility law. Earlier solutions of these equations employed a staggered solution scheme for the two sets of equations in which the plastic distortion was updated via time integration of its rate, as found from Orowan's law. In this work, we show that such a direct time integration scheme can suffer from accumulation of numerical errors. We introduce an alternative scheme based on field dislocation mechanics that ensures consistency between the plastic distortion and the dislocation content in the crystal. The new scheme is based on calculating the compatible and incompatible parts of the plastic distortion separately, and the incompatible part is calculated from the current dislocation density field. Stress field and dislocation transport calculations were implemented within a finite element based discretization of the governing equations, with the crystal mechanics part solved by a conventional Galerkin method and the dislocation transport equations by the least squares method. A simple test was first performed to show the accuracy of the two schemes for updating the plastic distortion, which shows that the solution method based on field dislocation mechanics is more accurate. This method then was used to simulate an austenitic steel crystal under uniaxial loading and multiple slip conditions. By considering dislocation interactions caused by junctions, a hardening rate similar to discrete dislocation dynamics simulation results was obtained. Finally, the simulations show that dislocations exhibit some self-organized structures as the strain is increased.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Analysis of the cyanobacterial amino acid metabolism with a precise genome-scale metabolic reconstruction of Anabaena sp. UTEX 2576

Filamentous cyanobacteria such as Anabaena sp. UTEX 2576 (a.k.a., Nostoc sp. PCC 7120) are a sustainable platform for commodity and specialty chemical production. Anabaena is a model cyanobacterium adopted to study production of nitrogen-containing metabolites useful for chemical, cosmetic, and pharmaceutical industries. Therefore, a precise description of the Anabaena metabolic network is desired to analyze their amino-acid metabolism and elucidate potential applications of these cyanobacteria as host organisms for biotechnological production. Secondary metabolite production depends on the metabolic availability of amino acids. We provide new insight on the biotechnological utilization of Anabaena after predicting phycocyanobilin and amino-acid production rates, using a genome-scale metabolic model (iDN1004). This metabolic reconstruction is a highly comprehensive representation of the global metabolism of Anabaena, which also contains experimental biomass equations and constraints under photoautotrophic and photodiazotrophic growth. Modelling results ranked proteinogenic amino acids based on predicted metabolic fluxes through amino-acid producing reactions. From these, l-aspartate, glycine, l-serine, l-valine, l-alanine, l-threonine, and l-leucine were selected as the best branching points to conduct metabolic engineering, where l-aspartate, l-serine, l-valine and glycine serve as potential precursors of the secondary metabolites Schizokinen (a siderophore), Sphingosine (a ceramide), Lyngbyatoxin A (an alkaloid), and Shinorine (a sunscreen).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Reaction-induced departures from continuum Navier–Stokes turbulence

Reactive hydrodynamic turbulence is an inherently multiscale phenomenon, characterized by the separation between energy-containing, viscous, and molecular length and time scales. The separation between the viscous scale (the Kolmogorov scale) and the molecular mean free path ostensibly justifies a macroscopic description of reactive turbulence via the Navier–Stokes (NS) equations. However, here we use molecular-level simulations to demonstrate that exothermic bimolecular reactions can cause the NS description of turbulence to break down in the near-continuum regime. Sufficiently energetic heat-releasing reactive collisions strongly distort the Maxwell–Boltzmann velocity distribution function, modifying not only the macroscopic chemical rate law but the kinetic-energy-transfer processes as well. This translational nonequilibrium ultimately introduces significant departures from the NS description in the kinetic energy spectra at scales orders of magnitude larger than both the molecular mean free path and the Kolmogorov length scale. These departures prove substantial enough to meaningfully alter integrated quantities, including the overall turbulence kinetic energy itself.

molecular gas dynamics↗
DOE OSTI2023

Optimizing the electron transport chain to sustainably improve photosynthesis

Abstract Genetically improving photosynthesis is a key strategy to boosting crop production to meet the rising demand for food and fuel by a rapidly growing global population in a warming climate. Many components of the photosynthetic apparatus have been targeted for genetic modification for improving photosynthesis. Successful translation of these modifications into increased plant productivity in fluctuating environments will depend on whether the electron transport chain (ETC) can support the increased electron transport rate without risking overreduction and photodamage. At present atmospheric conditions, the ETC appears suboptimal and will likely need to be modified to support proposed photosynthetic improvements and to maintain energy balance. Here, I derive photochemical equations to quantify the transport capacity and the corresponding reduction level based on the kinetics of redox reactions along the ETC. Using these theoretical equations and measurements from diverse C3/C4 species across environments, I identify several strategies that can simultaneously increase the transport capacity and decrease the reduction level of the ETC. These strategies include increasing the abundances of reaction centers, cytochrome b6f complexes, and mobile electron carriers, improving their redox kinetics, and decreasing the fraction of secondary quinone–nonreducing photosystem II reaction centers. I also shed light on several previously unexplained experimental findings regarding the physiological impacts of the abundances of the cytochrome b6f complex and plastoquinone. The model developed, and the insights generated from it facilitate the development of sustainable photosynthetic systems for greater crop yields.

59 BASIC BIOLOGICAL SCIENCES↗