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DOE OSTI2024

Lambda-PFLOTRAN 1.0: a workflow for incorporating organic matter chemistry informed by ultra high resolution mass spectrometry into biogeochemical modeling

Abstract. Organic matter (OM) composition plays a central role in microbial respiration of dissolved organic matter and subsequent biogeochemical reactions. Here, a direct connection of organic matter chemistry and thermodynamics to reactive transport simulators has been achieved through the newly developed Lambda-PFLOTRAN workflow tool that succinctly incorporates carbon chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate organic matter degradation and the resulting biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow, executed through a Jupyter notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow and transport code PFLOTRAN. The workflow consists of the following five steps: configuration, thermodynamic (lambda) analysis, sensitivity analysis, parameter estimation, and simulation output and visualization. Two test cases are provided to demonstrate the functionality of the Lambda-PFLOTRAN workflow. The first test case uses laboratory incubation data of temporal oxygen depletion to fit lambda parameters (i.e., maximum utilization rate and microbial carrying capacity). A slightly more complex second test case fits multiple lambda formulation and soil organic matter release parameters to temporal greenhouse gas generation measured during a soil incubation. Overall, the Lambda-PFLOTRAN workflow facilitates upscaling by using molecular-scale characterization to inform biogeochemical processes occurring at larger scales.

58 GEOSCIENCES↗

DOE OSTI2022

PolyODENet: Deriving mass-action rate equations from incomplete transient kinetics data

Kinetics of a reaction network that follows mass-action rate laws can be described with a system of ordinary differential equations (ODEs) with polynomial right-hand side. However, it is challenging to derive such kinetic differential equations from transient kinetic data without knowing the reaction network, especially when the data are incomplete due to experimental limitations. We introduce a program, PolyODENet, toward this goal. Based on the machine-learning method Neural ODE, PolyODENet defines a generative model and predicts concentrations at arbitrary time. As such, it is possible to include unmeasurable intermediate species in the kinetic equations. Importantly, we have implemented various measures to apply physical constraints and chemical knowledge in the training to regularize the solution space. Here, using simple catalytic reaction models, we demonstrate that PolyODENet can predict reaction profiles of unknown species and doing so even reveal hidden parts of reaction mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

PolyODENet

Wu, Qin [Brookhaven National Lab. (BNL), Upton, NY↗

DOE OSTI2021

Transient cycling of nitrogen, organic carbon and oxygen within the free-flowing Columbia River corridor: Linking exposure time dependent biogeochemical reactions to river stage fluctuations (Final project report)

The objective of this project was to develop next-generation techniques for representing the transformations of complex reaction networks like those impacting transient river-corridors, then apply them to develop upscaling tools. The project contributed significantly to the development of Lagrangian “mass transfer particle tracking” (MTPT) tools that are the first numerical framework that explicitly separates mixing and spreading processes; a crucial distinction for accurate representations of reaction rates across scales. The MTPT approach uses an operator splitting scheme where physical transport processes are simulated using classical random walk methods and each particle is treated as a “container” that carries with it any number of chemical species. Mixing between particles is simulated using a colocation-probability based mass transfer kernel and reactions are evaluated on each particle after mixing. The method is stable, accurate, and also allows the explicit modeling of residence time distributions of the individual containers of mass. The MTPT scheme allowed us to explore several research questions related to reactive transport in river corridors and complex reaction networks. We found that it is possible to quantify the exposure time distributions (ETDs) of reactants and that this does suggest some pathways to upscaling. However, comparable approximations can be obtained using simplified (reduced dimensionality) MTPT simulations in less time with similar uncertainty, so development of extensive ETD-based methods was not productive. The major findings are that i) the MTPT schemes are robust and highly accurate across a range of arbitrarily complex reactions, ii) the methods can be efficiently parallelized and the parallel performance characteristics of MTPT are predictable, and iii) the MTPT tools allow simultaneous tracking of residence time. The development of these research tools into efficient software packages continues. The methods are already available to the community because open-source, working examples have been included with all publications.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Exploration for astromers near 132 Sn with the Canadian Penning Trap

Nuclear isomers can have significant impacts on astrophysical nucleosynthesis processes, with recent efforts demonstrating that the population of isomeric states with different half-lives may require separate treatment in reaction networks to accurately capture the differences in heating or in identifiable electromagnetic signals. Several potential so-called “astromers” in tin and antimony isotopes near doubly magic 132 Sn were identified and direct mass measurements of their ground and isomeric states were performed with the Canadian Penning Trap at Argonne National Laboratory's CARIBU facility, and their impact on astrophysical reaction rates and in reaction networks was calculated. Finally, it was found that 129⁢𝑔,𝑚 Sn , with measured mass excesses of −80593.2⁢(25) and −80557.4⁢(25) keV, respectively, and an excitation energy of 35.8(35) keV, behaves as an astromer during neutron capture in the 𝑖-process and in the 𝑟-process.

isomer decays↗

DOE OSTI2024

Integrating Tide‐Driven Wetland Soil Redox and Biogeochemical Interactions Into a Land Surface Model

Abstract Redox processes, aqueous and solid‐phase chemistry, and pH dynamics are key drivers of subsurface biogeochemical cycling and methanogenesis in terrestrial and wetland ecosystems but are typically not included in terrestrial carbon cycle models. These omissions may introduce errors when simulating systems where redox interactions and pH fluctuations are important, such as wetlands where saturation of soils can produce anoxic conditions and coastal systems where sulfate inputs from seawater can influence biogeochemistry. Integrating cycling of redox‐sensitive elements could therefore allow models to better represent key elements of carbon cycling and greenhouse gas production. We describe a model framework that couples the Energy Exascale Earth System Model (E3SM) Land Model (ELM) with PFLOTRAN biogeochemistry, allowing geochemical processes and redox interactions to be integrated with land surface model simulations. We implemented a reaction network including aerobic decomposition, fermentation, sulfate reduction, sulfide oxidation, methanogenesis, and methanotrophy as well as pH dynamics along with iron oxide and iron sulfide mineral precipitation and dissolution. We simulated biogeochemical cycling in tidal wetlands subject to either saltwater or freshwater inputs driven by tidal hydrological dynamics. In simulations with saltwater tidal inputs, sulfate reduction led to accumulation of sulfide, higher dissolved inorganic carbon concentrations, lower dissolved organic carbon concentrations, and lower methane emissions than simulations with freshwater tidal inputs. Model simulations compared well with measured porewater concentrations and surface gas emissions from coastal wetlands in the Northeastern United States. These results demonstrate how simulating geochemical reaction networks can improve land surface model simulations of subsurface biogeochemistry and carbon cycling.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

ab initio Sub-Mechanism Development for Cyclopentene Oxidation

To accurately predict low-temperature oxidation behavior, chemical kinetics mechanisms must contain complete reaction networks that include detailed consumption reactions of intermediates produced directly from hydroperoxyalkyl radicals, Q̇OOH, which undergo competing unimolecular reactions and bimolecular reactions with O2. Rates of chain-branching are governed by the flux between the two competing pathways, and inherently depend on temperature, pressure, and oxygen concentration. Neglect of consumption pathways for major oxidation intermediates leads to mechanism truncation error that is ameliorated by expanding the level of detail included in sub-mechanisms and employing ab initio methods for computing rates of elementary reactions and thermochemical properties of species involved. In the present work, an ab initio-derived sub-mechanism is developed using AutoMech to model the chemical kinetics of cyclopentene, a major product of cyclopentane oxidation. The ab initio sub-mechanism builds on a detailed mechanism developed using Reaction Mechanism Generator (RMG) for the specific purpose of determining the extent to which replacing cyclopentene-specific reactions and species with quantum chemical computations reduces model inaccuracies resulting from mechanism truncation error. In an effort to minimize interference from other reactions present during the formation of cyclopentene from cyclopentyl + O2, providing a narrower experimental scope, the model is compared against speciation measurements from jet-stirred reactor (JSR) experiments on cyclopentene oxidation. The experiments utilize vacuum ultraviolet-absorption spectroscopy and mass spectrometry for isomer-resolved speciation of intermediates at 835 Torr from 700 – 950 K. [O2]-dependent experiments were also conducted from 0.057 – 2.01 · 1018 molecules cm–3 at 825 K to examine the influence of oxygen on species profiles. Model predictions using the ab initio-revised mechanism yielded significant improvements in species profiles for both the temperature- and [O2]-dependent measurements, owing in part to increased rates of HOȮ and H2O2 production, which underscores the influence of theoretical calculations of reaction rates involving species produced from Ṙ + O2 such as cyclopentene.

AutoMech↗

DOE OSTI2025

Rate expressions and kinetic parameters for metal ferrites in relation to applications of fossil fuel conversion to hydrogen: Part 1 of 2

Here, the goal of the present work was to provide the necessary reaction emulation information to enable detailed process simulation of a chemical looping H 2 production system from fossil fuels using CaFe 2 O 4 . This specifically pertained to the necessary kinetic data, reaction model development, and model rate parameters required for reaction emulation in both reducing and oxidizing environments. A logical methodology was defined, which included discretization of the reaction network, establishing a core model for reaction emulation that could be adapted based on the system phenomena, and development of a rate parameter regression tool designed around the core model. An extensive array of data sets was acquired by which parametric regressions were performed. The work presented and tabulated a comprehensive set of rate parameters for the reduction and oxidation reactions of CaFe 2 O 4 and descendent phases of Ca 2 Fe 2 O 5 , FeO, Fe 3 O 4 , Fe, and CaO to emulate reaction behavior in a looping-based process environment. This included direct reduction using CH 4 , H 2 , and CO, and direct oxidation reactions with steam, CO 2 and O 2 . Dynamic equilibrium was quantified for reactions that could utilize H 2 O and CO 2 as soft oxidants to re-saturate lattice oxygen in the depleted structure/phases. The kinetics associated with the oxidative mechanisms with the soft oxidants were quantified and compared to those of the reducing counterparts. The analysis provided critical insight to emulate reactions for a process that seeks to use natural gas (NG) or other fossil fuels as a direct reductant for the end goal of H 2 production.

calcium ferrite oxygen carriers↗

DOE OSTI2022

Lifelike behavior of chemically oscillating mobile capsules

Inspired by the self-organization of unicellular species into multicellular organisms, we use theory and simulation to design a system of mobile, active microcapsules that produce chemicals according to a catalytic reaction network (CRN). In solution, the catalytic reactions generate a force that drives the flow of the surrounding fluid. The convective flow, in turn, transports the capsules to new chemical surroundings with each successive translation. Consequently, the chemical signal produced by a cluster of capsules is critically dependent on the proximity and spatial configuration of the neighboring capsules. If all of the capsules and chemical products involved in the CRN lie within sufficient proximity, then the system develops oscillatory behavior that drives the dynamic self-assembly of capsules into larger clusters that are capable of collective action. Finally, these simulations indicate potential chemo-mechanic mechanisms that enable single cellular units, such as ameba, to organize into multicellular life forms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Enhanced production of 60 Fe in massive stars

Massive stars are a major source of chemical elements in the cosmos, ejecting freshly produced nuclei through winds and core-collapse supernova explosions into the interstellar medium. Among the material ejected, long-lived radioisotopes, such as 60 Fe (iron) and 26 Al (aluminum), offer unique signs of active nucleosynthesis in our galaxy. There is a long-standing discrepancy between the observed 60 Fe/ 26 Al ratio by γ-ray telescopes and predictions from supernova models. This discrepancy has been attributed to uncertainties in the nuclear reaction networks producing 60 Fe, and one reaction in particular, the neutron-capture on 59 Fe. Here we present experimental results that provide a strong constraint on this reaction. We use these results to show that the production of 60 Fe in massive stars is higher than previously thought, further increasing the discrepancy between observed and predicted 60 Fe/ 26 Al ratios. The persisting discrepancy can therefore not be attributed to nuclear uncertainties, and points to issues in massive-star models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Reaction Rate Sensitivity of the Production of γ-Ray Emitting Isotopes in Core-collapse Supernovae

Radioactive isotopes produced in core-collapse supernovae (CCSNe) provide useful insights into the underlying processes driving the collapse mechanism and the origins of elemental abundances. Their study generates a confluence of major physics research, including experimental measurements of nuclear reaction rates, astrophysical modeling, and γ-ray observations. Here we identify the key nuclear reaction rates to the nucleosynthesis of observable radioactive isotopes in explosive silicon burning during CCSNe. Using the nuclear reaction network calculator SkyNet and current REACLIB reaction rates, we evolve temperature–density–time profiles of the innermost 0.45 M⊙ ejecta from the core collapse and explosion of a 12 M⊙ star. Individually varying 3403 reaction rates by factors of 100, we identify 141 reactions that cause significant differences in the isotopes of interest, namely, 43 K, 47 Ca, 44,47 Sc, 44 Ti, 48,51 Cr, 48,49 V, 52,53 Mn, 55,59 Fe, 56,57 Co, and 56,57,59 Ni. For each of these reactions, we present a novel method to extract the temperature range pertinent to the nucleosynthesis of the relevant isotope; the resulting temperatures lie within the range T = 0.47–6.15 GK. Limiting the variations to within 1σ of STARLIB reaction rate uncertainties further reduces the identified reactions to 48 key rates, which can be used to guide future experimental research. Complete results are presented in tabular form.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

The Delplot kinetic method applied to systems with adsorbates: Hydrodeoxygenation of benzofuran on a bimetallic CoPd phosphide catalyst supported on KUSY

The Delplot method provides a means of analyzing conversion and selectivity data to derive a reaction sequence and has been applied so far to gas-phase or liquid-phase species. This study analyses the applicability of the method for catalytic reactions and considers for the first time adsorbed intermediates. The method is applied to a contact time study of the hydrodeoxygenation (HDO) of benzofuran at 0.5 MPa and 350 °C over a catalyst consisting of bimetallic CoPd phosphide supported on a potassium ion-exchanged ultra-stable Y (KUSY) zeolite. Both simple and detailed reaction networks were derived. The simple networks considered only gas-phase species and were modeled by a first-order sequence of steps, whereas the detailed network took into account adsorbed intermediates and was simulated using a rake mechanism. The networks were compared using F-statistics, which accounted for the differences in the number of fitting parameters. The detailed network gave a better fit to the experimental data because it represented a more realistic description of the transformation. A suggested sequence from the Delplot method was consistent with the simple network but not with the detailed network. The lack of applicability of the Delplot analysis to the network with adsorbates was linked to overly large equilibrium constants, a determination supported by Delplot fitting for a model sequence. Further, this study indicated the inapplicability of the Delplot method in determining reaction sequences that involve adsorbed species with large equilibrium constants for formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Towards a heat- and mass-balanced kinetic model of TATB decomposition

We report TATB (1,3,5-triamino-2,4,6-trinitrobenzene) was thermally degraded by two small-scale analytical methods – simultaneous differential scanning calorimetry and thermogravimetric analysis (SDT) and a hot-stage microscope with Fourier Transform Infrared (FTIR) analysis capabilities. SDT used ramped heating, isothermal soaking, and thermal pretreatment at various conditions. The heat flow and mass loss were monitored during various treatment conditions to derive chemical decomposition kinetics and Arrhenius parameters. FTIR experiments used isothermal heating, and changes were monitored spectroscopically. Solid samples generated at specific conditions were collected from both methods and were analyzed by DMSO extraction followed by chemical speciation by optical and mass spectrometric methods. Characterization provided the following reaction insights: TATB decreases in a sigmoidal pattern in isothermally heated samples. Other soluble products gradually increase in concentration and then abruptly decline in concentration during the second exotherm, such as diamino-dinitro-benzofurazan and amino-nitro-benzodifurazan. FTIR showed gradual changes in the amino and nitro functionality, shifting positions and decreasing intensity for the first 40 min. Then the solid gradually appeared more like an amorphous C with N incorporated, similar to previous studies on thermally degraded TATB-type materials. Extracted residues (DMSO-soluble components removed) examined by FTIR showed an abrupt change in chemical composition between 40- and 45-min isothermal treatment, indicating early forming solids are different than later forming residues. A reliable mass- and energy-balanced global reaction network must include at least two autocatalytic reactions, either in parallel or series, and at least one must have an explicit initiation reaction having a low activation energy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Nuclear fission reaction simulations in compact stars

Type-Ia supernovas are powerful stellar explosions that provide important distance indicators in cosmology. Recently, we proposed a new Type-Ia supernova mechanism that involves a nuclear fission chain-reaction in an isolated white dwarf [Phys. Rev. Lett. 126, 131101 (2021)]. Here, in this work, we perform novel reaction network simulations of the actinide-rich first solids in a cooling white dwarf. The network includes neutron-capture and fission reactions on a range of U and Th isotopes with various possible values for 235 U enrichment. We find, for modest 235 U enrichments, neutron capture on 238 U and 232 Th can breed additional fissile nuclei so that a significant fraction of all U and Th nuclei may fission during the chain reaction. Finally, we compute the energy release from the fission chain reaction for various uranium enrichments; a novel result that is a necessary input for thermal diffusion simulations of carbon ignition.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Model validation and selection in metabolic flux analysis and flux balance analysis

13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both methods use metabolic reaction network models of metabolism operating at steady state so that reaction rates (fluxes) and the levels of metabolic intermediates are constrained to be invariant. They provide estimated (MFA) or predicted (FBA) values of the fluxes through the network in vivo, which cannot be measured directly. These fluxes can shed light on basic biology and have been successfully used to inform metabolic engineering strategies. Several approaches have been taken to test the reliability of estimates and predictions from constraint-based methods and to compare alternative model architectures. Despite advances in other areas of the statistical evaluation of metabolic models, such as the quantification of flux estimate uncertainty, validation and model selection methods have been underappreciated and underexplored. We review the history and state-of-the-art in constraint-based metabolic model validation and model selection. Applications and limitations of the χ 2 -test of goodness-of-fit, the most widely used quantitative validation and selection approach in 13C-MFA, are discussed, and complementary and alternative forms of validation and selection are proposed. A combined model validation and selection framework for 13C-MFA incorporating metabolite pool size information that leverages new developments in the field is presented and advocated for. Finally, we discuss how adopting robust validation and selection procedures can enhance confidence in constraint-based modeling as a whole and ultimately facilitate more widespread use of FBA in biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Automatically generated model for light alkene combustion

Light alkenes are common combustion intermediates for a variety of fuels. Therefore, understanding their oxidation and pyrolysis chemistry is key to building detailed mechanisms for heavier fuels. This work was focused on the development and evaluation of a detailed kinetic mechanism suitable for the combustion of light alkenes up to C 4 without the use of tuned parameters, instead, the parameter values come from first principles or direct measurements. The generated mechanism accurately estimates the laminar burning velocity (S u ) and ignition delay time (IDT) of light alkenes available in the literature, which represent fundamental combustion properties at a wide range of conditions. Because each parameter is thought to have a physically realistic value, not tuned to these measurements, the new model could be used as a sub-mechanism in models for other applications. The reaction network was generated with the open-source Reaction Mechanism Generator (RMG) software. Sensitivity analyses were performed under wide ranges of temperatures and pressures, allowing for the identification of the most impactful species and reactions. Based on these, a comprehensive thermochemistry database, including calculations on 550 molecules performed in this work at the CBS-QB3 level of theory, and a kinetic library, including theoretically-derived reaction rates retrieved from the literature, were built and used in the mechanism generation. The developed mechanism was compared against several existing detailed kinetic mechanisms for ethene, propene, 1-butene, 2-butene, and isobutene. Here, the newly generated model is the most accurate among the ones analyzed, in terms of fractional bias and normalized mean square error. Hence, this new model was used to analyze the chemistry of alkene combustion. Key rate coefficients were compared, to identify the cause of deviations between the models and possible areas for further improvements.

09 BIOMASS FUELS↗

DOE OSTI2020

Catalytic resonance theory: parallel reaction pathway control

Branched catalytic reaction networks with oscillating chemical pathways perfectly select for reaction products at varying frequency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Hydrogen Evolution on Restructured B-Rich WB: Metastable Surface States and Isolated Active Sites

Borides have been recently identified to be a class of earth-abundant and low-cost materials that are surprisingly active toward oxidative dehydrogenation and hydrogen evolution reaction (HER) catalysis. Here, we explain from first-principles calculations the HER activity of WB, an industrial material known for its superior physical properties and chemical inertness. We find that, compared to bulk termination, a major surface reconstruction takes place, leading to the off-stoichiometric B-rich surface termination that contains the active sites. The hydrogen adsorbate configurations are further investigated under various adsorbate coverages. Many competing configurations appear to be accessible in reaction conditions, and thus, a grand canonical ensemble is established to describe the catalytic system. A phase diagram of adsorbate coverages is constructed as a function of pH and the applied potential. A complex reaction network is presented based on the ensemble-averaged reaction rates, and the electrocatalytic activities are evaluated under different overpotentials. Here, the major contributors to the activity are found to be a few metastable surface states with a distinct electronic structure that are only accessible at high adsorbate coverages in reaction conditions. In addition, while the activity of the dominant active site is nearly the same as that on the unreconstructed WB, the B-rich formations play an important role of isolating the active sites and preventing the passivation of the surface with H 2 bubble formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗