Using Neural Networks to Accelerate TALYS-2.0 Nuclear Reaction Simulations
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07 ISOTOPE AND RADIATION SOURCES↗
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Quantifying Negative Effects of Carbon-Binder Networks from Electrochemical Performance of Porous Li-Ion Electrodes
Porous Li-ion electrodes contain active particles, ion transporting electrolyte, and carbon-binder networks. While macrohomogeneous models are often used to predict electrode behavior, accurate predictions remain challenging, owing to the incomplete understanding of the critical role of carbon-binder networks and how they affect the electrochemical response. The present study systematically characterizes these effects in terms of effective properties by utilizing macrohomogeneous models to analyze the measured responses for electrodes with different carbon-binder content, electrode thickness, and porosity but with identical materials. We find that the impact of the carbon-binder network is more severe than previously thought. Even for low carbon-binder content (5 %wt. dry electrode), the presence of the network decreases the reaction area and increases the ion transport resistance, negatively impacting electrode performance. These effects scale with not just porosity or active material volume but also with carbon-binder content. The findings underscore the importance of connecting all effective properties to electrode specifications in a full factorial sense to transform the electrode design paradigm.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks
Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between a network’s various chemical components. Modular elements with standardized performance could be used to rapidly construct networks with designed functions. Here we develop standardized excitable chemical regulatory elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet elements with uniform performance and minimal crosstalk. Furthermore, these elements can be combined to engineer feedforward and feedback modules whose dynamics match those predicted by a simple kinetic model. Modules can then be rationally integrated and organized into networks that produce tunable temporal pulses and act as multistate switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis
Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determine cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA) that relies on the patterns of isotope labeling of metabolites in the network. For metabolic systems, typical for plants, where all potentially labeled atoms effectively have only one source atom pool, only isotopically nonstationary MFA can provide information about intracellular fluxes. There are several global approaches that implement MFA for an entire metabolic network and estimate, at once, a steady-state flux distribution for all reactions with identifiable fluxes in the network. In contrast, local approaches deal with estimation of fluxes for a subset of reactions, with smaller data demand for flux estimation. Here we present a systematic comparative review and benchmarking of the existing local approaches for isotopically nonstationary MFA. The comparison is conducted with respect to the required data and underlying computational problems solved on a synthetic network example. Furthermore, we benchmark the performance of these approaches in estimating fluxes for a subset of reactions using data obtained from the simulation of nitrogen fluxes in the Arabidopsis thaliana core metabolism. The findings pinpoint practical aspects that need to be considered when applying local approaches for flux estimation in large-scale plant metabolic networks.
59 BASIC BIOLOGICAL SCIENCES↗
Reactive Transport Modeling of Mineral Precipitation and Carbon Trapping in Discrete Fracture Networks
In this study we use numerical experiments to analyze reactive flow and transport behavior in discrete intersecting fracture networks, focusing on (a) how reaction-induced changes in physical and chemical properties affect flow connectivity and (b) how fracture networks developed in the Earth's critical zone contribute to carbon sequestration via mineral weathering reactions. In the first part of the study, we used two-dimensional reactive flow and transport simulations to analyze the impacts of mixing in a natural discrete fracture network. We concluded that reaction-induced changes can substantially alter the flow connectivity, especially at fracture intersections. The second set of simulations considered the problem of natural weathering of fractured mafic and ultramafic rocks in the partially saturated Earth's critical zone as a function of infiltration rates, fracture permeability, and partially saturated flow parameters. As a model system, we considered an incongruent reaction network with dissolution of forsterite and precipitation of magnesite. The behavior is complex in terms of the rate-controlling processes because of the multicomponent nature of the system as shown by the grid Peclet number: the CO 2 behavior is gas diffusion-controlled in the partially saturated zone, while the rate of water flow via the Damkӧhler number controls Mg 2+ transport through the fracture network. The amounts of carbon that can be trapped are modest, but the naturally fractured domain considered here provides a useful “base case” against which various engineered solutions can be compared.
58 GEOSCIENCES↗
Understanding Adsorption and Reactions at Aqueous Oxide Interfaces with Neural Network Potential Molecular Dynamics
Chemical processes at metal oxide−water interfaces are of central importance in geochemistry, biology, and energy technologies. A better understanding of these processes would allow us to make a significant step toward optimizing and controlling them, which could in turn lead to broader impacts. Computational modeling is indispensable to accomplishing this task because complexity and disorder often make it difficult to extract atomistic information from experiments. Balancing computational cost and accuracy, simulation schemes based on efficient machine learning representations of the potential energy surface (PES) predicted by ab initio calculations have become increasingly popular over the past decade. In particular, several studies have demonstrated the ability of machine learning models to accurately reproduce the complex ab initio PESs of aqueous oxide interfaces, allowing simulations of systems and processes that are not accessible with ab initio methods. In this Account, we review our recent efforts to understand adsorption processes and reactions at aqueous oxide interfaces using deep potential molecular dynamics (DPMD), a simulation scheme employing deep neural networks (DNNs), which has proven to be quite successful in accurately describing many different systems in the condensed phase. After summarizing the DPMD methodology, we first review our work on the acid−base chemistry of oxide surfaces in contact with water, a fundamental characteristic that controls proton transfer and surface charge at the interface. We focus on the aqueous interface of rutile IrO 2 , an oxide material thus far considered the best catalyst for the oxygen evolution reaction (OER). We show that this interface is characterized by a large fraction of dissociated water and a strong Brønsted acidity of the surface sites, in good agreement with the experimentally measured value of the point of zero proton charge. In our second example, we investigate how the adsorption of organic species from ambient air or water affects the structure and wettability of the aqueous interfaces of TiO 2 , a prototypical photocatalytic material. This is a question that is relevant to understanding the UV-induced hydrophilicity of TiO 2 surfaces, a property at the basis of self-cleaning windows and related applications. Specifically focusing on formic and acetic acids, the two most common atmospheric organic acids, our simulations reveal that these acids control the wettability of TiO 2 largely through acid−base chemistry at the interface rather than chemisorption on the oxide surface, a finding that could help improve the design of self-cleaning surfaces and photocatalytic devices. Finally, we review our recent study of methanol at TiO 2 −water interfaces, a system whose interest is largely motivated by the role of methanol in enhancing photocatalytic hydrogen evolution on TiO 2 . Our simulations provide mechanistic insights into the coupled roles of the organic adsorbate and water at the TiO 2 interface, with implications for how methanol enhances the activity of H 2 evolution.
adsorption↗
Covalent Adaptable Networks: Reprocessable Cross-Linked Polymers
Thermoset polymers have desirable properties, such as excellent thermal and mechanical stability, but their covalent cross-links typically prevent repair or recycling. By enabling and controlling dynamic exchange reactions within polymer networks, their covalent bonds rearrange and allow the polymer to be reshaped. These viscoelastic polymer networks, now known as covalent adaptable networks (CANs), are an important frontier for improving plastic circularity, as well as for designing valuable stimuli-responsive materials. This Review describes the history of CANs, dating back to the early days of polymer science, and the evolution of their classification and nomenclature. A comprehensive survey of dynamic reactions and linkage chemistries is provided, as well as methods to characterize and reprocess CANs. Beyond straightforward reprocessing, many advanced applications of CANs and their composites are now emerging. Lastly, we provide perspective on how the development of new chemistries, strategies to control stimuli-responsive bond exchange and mechanical properties, and a deep understanding of exchange reactions will advance this field toward scalable, sustainable, and high-value materials.
Sun, Molly [Northwestern University, Evanston, IL ↗
Toward more mechanistic representations of biogeochemical processes in river networks: Implementation and demonstration of a multiscale model
A recently introduced multiscale model for representing the effects of small-scale hyporheic-zone biogeochemical processes is extended from the reach scale to river network scales. The model uses advection-dispersion-reaction equations for the channel network and one-dimensional advection-reaction subgrid models for the hyporheic zone. We summarize implementation in the integrated surface/subsurface hydrology modeling system Amanzi-ATS. The extension uses topologically defined meshes to represent stream/river networks and associates a hyporheic subgrid model with each channel grid cell. Biogeochemical reaction modeling capability residing in community software is accessed through an application programming interface. The implementation is verified against independent numerical solutions on a single reach. Mesh convergence studies show that commonly used semi-distributed representations can introduce significant spatial discretization error. Denitrification of farm runoff in a subbasin of the Portage River Basin in Ohio, USA is used to demonstrate the general-purpose reactive transport capability.
54 ENVIRONMENTAL SCIENCES↗
Recyclability of reversible polymer networks over a Dozen reprocessing cycles
Reversible polymer networks capable of reversible reactions along their backbone provide a promising strategy for addressing waste management challenges associated with conventional thermoset products. However, reversible polymer networks cannot be recycled infinitely. Unavoidable side reactions eventually cause significant degradation of mechanical properties or loss of recyclability. This study aims to answer a simple yet critical question on reversible polymer network systems: how many reprocessing cycles can be achieved before profound mechanical degradation or a loss of recyclability? The recyclability of Diels–Alder (DA) network samples was evaluated by repeating consistent reprocessing cycles until they were no longer reprocessable. To enhance their recyclability, the chemical structure of the maleimide precursor was tailored to mitigating side reactions by maleimide homopolymerization. Remarkably, by employing a maleimide precursor with alkyl substitutions on its phenyl group, the DA network system attained 12 reprocessing cycles using injection molding at 160 °C without significant degradation of mechanical properties. However, the 13th reprocessing cycle did not succeed. Rheological analysis revealed the accumulation of non-reversible bonds within the network structure during repeated reprocessing, despite fairly consistent mechanical properties under operating conditions. This study demonstrates that the rational design of the maleimide precursor is an effective means to enhance the reprocessability of DA networks.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Low-energy measurement of the 25 Mg (𝛼,𝑛) 28 Si reaction via neutron spectroscopy
During core helium and carbon burning in massive stars, neutrons are produced mainly by the 22 Ne (𝛼,𝑛) 25 Mg reaction. Some of these released neutrons are captured by heavy seed nuclei from previous nucleosynthesis events, resulting in the slow production of many of the elements between masses 60 ≤ 𝐴 ≤ 90 via the weak 𝑠 process. Determining the overall neutron flux available in this environment is one of the main challenges in modeling its contributions to heavy element production. Not only must the reaction rate be well defined for the primary neutron source, but the rates of neutron poison and recycling reactions must also be well determined. One critical reaction in the simulation network is 25 Mg (𝛼,𝑛) 28 Si. This reaction, together with 25 Mg (𝑛,𝛾) 26 Mg and 25 Mg (𝛼,𝛾) 29 Si, determine how 25 Mg nuclei affect the available neutron flux. Past attempts to measure the 25 Mg (𝛼,𝑛) 28 Si cross section using neutron moderator counters have been greatly hindered by lower-𝑍 background reactions. Here, in the present work, neutron spectroscopy with deuterated liquid scintillator detectors has been used. The experimental spectra have been analyzed by applying spectrum unfolding techniques to achieve improved background discrimination for the 25 Mg (𝛼,𝑛) 28 Si reaction at low energies, down to 𝐸 𝛼 = 1.75 MeV. The separation of the different background contributions gives further insight into the results of previous moderator counter measurements and the measurements lead to a revised and more reliable determination of the reaction rate.
hydrostatic stellar nucleosynthesis↗
Tomographic 3D Analysis of Reduction Displacement Reaction with Associated Formation of a Conductive Network in High Energy Primary Batteries
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99 GENERAL AND MISCELLANEOUS↗
Fe-single-atom catalyst nanocages linked by bacterial cellulose-derived carbon nanofiber aerogel for Li-S batteries
Li-S battery (LSB) is promising for achieving high capacity. Still, its development is hindered by the complex redox process with sluggish kinetics and particularly the resulting lithium polysulfides (LiPS) shuttle effects. Single-atom catalysts (SACs), with their maximized atom utilization, could effectively chemisorb soluble LiPSs and expedite the sulfide conversion reaction kinetics. Here we report incorporating Fe single metal atom catalyst (Fe-SAC) in the sulfur cathode design and its electrocatalytic effects. Fe-doped ZIF-8 nanocages were introduced into a cheap biomass bacteria cellulose. A pyrolysis process converted them into an aerogel structure with Fe-SAC-functionalized N-doped carbon nanocages linked by a carbon nanofiber network (FeSA-NC@CBC), which was applied as a scaffold to fabricate freestanding and binder-free sulfur cathodes. He we conducted electrochemical measurements to reveal Fe-SAC functions including lowering energy barriers for S 8 reduction to liquid-phase LiPSs and further to solid-phase Li 2 S 2 /Li 2 S and accelerating Li 2 S 2 /Li 2 S nucleation and deposition, as corroborated by our theoretical calculation results. Benefiting from the synergistic effects of highly active Fe-SAC and three-dimensional conductive network, the sulfide reaction kinetics is improved, which can diminish LiPS shuttle effects and therefore improve LBS rate performance and cycling stability. Accordingly, the fabricated FeSA-NC@CBC composite cathode delivers an excellent rate capability at 2C with a reversible capacity of 840 mAh/g and a long-term cyclic stability of 800 mAh/g at 1C after 500 cycles.
25 ENERGY STORAGE↗
The advanced evolution of massive stars
The nuclear rates for reactions involving 12 C and 16 O are key to computing the energy release and nucleosynthesis evolution of massive stars during their advanced burning phases. Ultimately, these burning rates shape the stellar structure and evolution and influence the nature of the compact objects produced at the end of the stellar life. We explore the implications of new nuclear reaction rates from both experimental and theoretical studies for 12 C(α, γ) 16 O, 12 C+ 12 C, 12 C+ 16 O, and 16 O+ 16 O reactions for massive stars. Our goal is to investigate how the chemical structure and nucleosynthesis evolve from the He-exhaustion stage to the O-burning phase and how these processes influence the ultimate stellar fate. We computed rotating and non-rotating models for stars of different masses at solar metallicity. We used the stellar evolution code GENEC, which includes a large network of nuclear reactions and isotopes involved in advanced phases, as well as updated rates for 12 C(α,γ) 16 O. For the three fusion reactions involving 12 C and 16 O, we considered new rates following a data-driven fusion suppression scenario (hereafter HIN(RES)) and new theoretical rates obtained with time-dependent Hartree-Fock (TDHF) calculations. The updated 12 C(α, γ) 16 O rates mainly impact the chemical structure evolution changing the 12 C/ 16 O ratio at He-exhaustion and have little effect on the CO core mass. This variation in the 12 C/ 16 O ratio is in some cases critical for predicting the final fate of the model, which is very sensitive to 12 C abundance, and in particular the 20 M ⊙ remnant may change from a black hole to a neutron star. The He-burning (C-burning) lifetime is also decreased (increased) by about −2% (+15%). The combined new rates for 12 C+ 12 C and 16 O+ 16 O fusion reactions according to the HIN(RES) model lead to shorter C- and O-burning lifetimes by ≈ − 10%, and −50%, respectively, and shift the ignition conditions to higher temperatures and densities. In contrast, the theoretical TDHF rates primarily affect C-burning, increasing its duration by about 30% and lowering the ignition temperature. These changes modify the chemical structure of the core, the size and duration of C-burning shells, and hence their compactness. They also impact the central and shell nucleosynthesis (by ±1 dex and by factors of ±2–10, respectively), while 12 C+ 16 O reaction rates variations remain the least important.
abundances↗
Quantitative principles of microbial metabolism shared across scales
Metabolism is the complex network of chemical reactions occurring within every cell and organism, maintaining life, mediating ecosystem processes and affecting Earth’s climate. Experiments and models of microbial metabolism often focus on one specific scale, overlooking the connectivity between molecules, cells and ecosystems. Here we highlight quantitative metabolic principles that exhibit commonalities across scales, which we argue could help to achieve an integrated perspective on microbial life. Mass, electron and energy balance provide quantitative constraints on their flow within metabolic networks, organisms and ecosystems, shaping how each responds to its environment. The mechanisms underlying these flows, such as enzyme–substrate interactions, often involve encounter and handling stages that are represented by equations similar to those for cells and resources, or predators and prey. Here we propose that these formal similarities reflect shared principles and discuss how their investigation through experiments and models may contribute to a common language for studying microbial metabolism across scales.
59 BASIC BIOLOGICAL SCIENCES↗
An automated workflow that generates atom mappings for large‐scale metabolic models and its application to Arabidopsis thaliana
SUMMARY Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large‐scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large‐scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana . We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating 15 N isotope enrichment and identifying nitrogen (N)‐containing metabolites which show enrichment patterns that are informative for flux estimation in future 15 N‐MFA studies of A. thaliana . The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph‐theoretic structural analyses with large‐scale metabolic networks.
59 BASIC BIOLOGICAL SCIENCES↗
Space-Time Finite Element Tensor Network Approach for the Time-Dependent Convection–Diffusion–Reaction Equation with Variable Coefficients
In this paper, we present a new space-time Galerkin-like method, where we treat the discretization of spatial and temporal domains simultaneously. This method utilizes a mixed formulation of the tensor-train (TT) and quantized tensor-train (QTT) (please see Section Tensor-Train Decomposition), designed for the finite element discretization (Q1-FEM) of the time-dependent convection–diffusion–reaction (CDR) equation. We reformulate the assembly process of the finite element discretized CDR to enhance its compatibility with tensor operations and introduce a low-rank tensor structure for the finite element operators. Recognizing the banded structure inherent in the finite element framework’s discrete operators, we further exploit the QTT format of the CDR to achieve greater speed and compression. Additionally, we present a comprehensive approach for integrating variable coefficients of CDR into the global discrete operators within the TT/QTT framework. The effectiveness of the proposed method, in terms of memory efficiency and computational complexity, is demonstrated through a series of numerical experiments, including a semi-linear example.
convection–diffusion–reaction equation↗
Hydrotreatment of Nylon 66 and Amide Model Compounds Over Sulfided NiMo Catalysts
Molybdenum sulfide-based catalysts, such as nickel–molybdenum on alumina (NiMoS x /Al 2 O 3 ), are widely used in hydrotreating and have potential for catalyzing waste plastic conversion via hydrogenolysis, yet their performance, such as reaction kinetics and network, for amide-rich polymer feeds is poorly defined. Here we combine Nylon 66 with the amide model compound, N,N-dibutylhexanediamide (DBDAD), to quantify hydrodeoxygenation (HDO) and hydrodenitrogenation (HDN) chemistry in a stirred batch reactor (53 bar H 2 , 280–320°C). DBDAD conversion is near-linear with time, indicating strong adsorption of the substrates on the active sites. Time-resolved product identification indicates parallel C─O first-cleavagedeoxygenation (DO) and C─N first-cleavagedenitrogenation (DN) sequences proceeding through amine and diol intermediates, respectively, to C 4 ─C 6 alkanes. Increasing temperature shifts selectivity toward DN, decreasing the initial r(DO)/r(DN) from 1.38 (280°C) to 0.69 (320°C), with an apparent activation energy of 173 kJ mol −1 for DBDAD conversion. At 300°C, nylon 66 converts faster than DBDAD, producing a complex mixture of oxygen- and nitrogen-containing species and an initial rate ratio r(DO)/r(DN) of 1.6. No heteroaromatic nitrogen products are detected by the method used. These results provide reaction pathways and product signatures relevant to hydro-processing catalysts exposed to polyamide-derived streams.
Nylon 66↗