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Results for “chemical reaction networks”

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DOE OSTI2026

SODAs: sparse optimization for the discovery of differential and algebraic equations

Differential-algebraic equations (DAEs) integrate ordinary differential equations (ODEs) with algebraic constraints, providing a fundamental framework for developing models of dynamical systems characterized by time-scale separation, conservation laws and physical constraints. While sparse optimization has revolutionized model development by allowing data-driven discovery of parsimonious models from a library of possible equations, existing approaches for dynamical systems assume DAEs can be reduced to ODEs by eliminating variables before model discovery. This assumption limits the applicability of such methods for DAE systems with unknown constraints and time scales. We introduce sparse optimization for differential-algebraic systems (SODAs), a data-driven method for the identification of DAEs in their explicit form. By discovering the algebraic and dynamic components sequentially without prior identification of the algebraic variables, this approach leads to a sequence of convex optimization problems. It has the advantage of discovering interpretable models that preserve the structure of the underlying physical system. To this end, SODAs improves since SODAs is singular numerical stability when handling high correlations between library terms, caused by near-perfect algebraic relationships, by iteratively refining the conditioning of the candidate library. We demonstrate the performance of our method on biological, mechanical and electrical systems, showcasing its robustness to noise in both simulated time series and real-time experimental data.

DAE↗

DOE OSTI2025

Chemo‐Mechanical Coupling in Hydrogels: Dynamics in the Diffusion‐Limited Regime

Hydrogels are characterized by substantial volume changes in response to external stimuli, making them promising candidates for developing smart materials with enhanced adaptability and responsiveness. By integrating chemical reactions, hydrogels acquire dynamic and tunable responsiveness to external stimuli through chemo‐mechanical coupling, expanding their potential in emerging applications. However, capturing their transient behavior remains challenging due to the complex interplay of chemical reactions, solvent transport, and polymer network deformation. Classical theories capture equilibrium swelling but fail to describe time‐dependent phenomena. To address this, a time‐dependent continuum model is developed that explicitly couples these processes. Volume phase transition in hydrogels with homogeneous chemical reactions is investigated, then the effects of reaction kinetics on these transitions are analyzed. The coupling of these mechanisms is further explored through a study of transient mechanical instabilities. To illustrate the impact of distinct reaction and diffusion timescales, a photo‐active gripper is studied for robotic applications. Finally, a photo‐active microswimmer that exhibits non‐reciprocal motion is proposed to highlight the solvent diffusion for locomotion at the micro‐ and nano‐ scales. The work establishes that transient dynamics of chemo‐mechanical hydrogels generate functions not accessible by steady state models and provides a predictive platform for designing adaptive materials in emerging applications.

chemo-mechanical coupling↗

NASA NTRS1995

Analysis of Gas Absorption to A Thin Liquid Film in the Presence of A Zero-Order Chemical Reaction

The paper presents a detailed theoretical analysis of the process of gas absorption to a thin liquid film adjacent to a horizontal rotating disk. The film is formed by the impingement of a controlled liquid jet at the center of the disk and subsequent radial spreading of liquid along the disk. The chemical reaction between the gas and the liquid film can be expressed as a zero-order homogeneous reaction. The process was modeled by establishing equations for the conservation of mass, momentum, and species concentration and solving them analytically. A scaling analysis was used to determine dominant transport processes. Appropriate boundary conditions were used to solve these equations to develop expressions for the local concentration of gas across the thickness of the film and distributions of film height, bulk concentration, and Sherwood number along the radius of the disk. The partial differential equation for species concentration was solved using the separation of variables technique along with the Duhamel's theorem and the final analytical solution was expressed using confluent hypergeometric functions. Tables for eigenvalues and eigenfunctions are presented for a number of reaction rate constants. A parametric study was performed using Reynolds number, Ekman number, and dimensionless reaction rate as parameters. At all radial locations, Sherwood number increased with Reynolds number (flow rate) as well as Ekman number (rate of rotation). The enhancement of mass transfer due to chemical reaction was found to be small when compared to the case of no reaction (pure absorption), but the enhancement factor was very significant when compared to pure absorption in a stagnant liquid film. The zero-order reaction processes considered in the present investigation included the absorption of oxygen in aqueous alkaline solutions of sodiumdithionite and rhodium complex catalyzed carbonylation of methanol. Present analytical results were compared to previous theoretical results for limiting conditions, and were found to have very good agreement.

S Rajagopalan↗

DOE OSTI2026

Modeling Radiolysis and Chemical Reactions during Dry Storage of Aluminum-clad Spent Nuclear Fuel

After aluminum-clad spent nuclear fuel (ASNF) is removed from the reactor, it is initially stored in spent fuel pools, which are specially designed water-filled basins that provide temporary cooling to reduce the temperature of the fuel assemblies and provide radiation shielding. ASNF continues to generate heat due to the radioactive decay of elements within the fuel, which persists for many years post-shutdown as the residual radioactive products decay into more stable elements. During the wet storage period, an oxyhydroxide layer composed of boehmite/bayerite forms on the surfaces of the aluminum cladding from exposure to water in the pools. Road-ready packaging for long-term disposition of the ASNF involves dry storage in helium backfilled DOE standard canisters (DSCs). When the ASNF is removed from water storage and dried, most of the water is removed, but some physisorbed and chemisorbed water remains in the oxyhydroxide layers. This residual water can produce hydrogen when exposed to radiation from the ASNF during dry storage. Predicting hydrogen accumulation over time in the DSCs is critical for long-term storage considerations. Previous modeling efforts have developed coupled computational fluid dynamics (CFD)-chemical models to simulate temperature, pressure, and gas phase concentrations within the DSCs. These models use the thermal field predicted by CFD as input to a radiolysis model for the gas phase and the surface oxyhydroxide layer chemistry. Given the long storage period of the DSCs and the impracticality of long-term experiments, a simulation-based approach is necessary to assess chemical evolution within the canisters. This study advances the development of a modeling framework designed to simulate the chemical evolution of spent fuel canisters. Both thermal and radiation-driven reactions are considered, with radiation kinetics quantified using G-values. Sensitivity analysis identifies key parameters influencing species composition. Reaction pathway diagrams offer insight into dominant species formation routes, enabling more effective comparisons between model predictions and experimental observations, particularly regarding the production of hydrogen. Results show that the model predicts significant hydrogen gas production with minimal oxygen generation, primarily due to hydrogen formation via boehmite pathways. These findings underscore the importance of accurately characterizing surface-bound species and radiolysis kinetics. A deeper understanding of these mechanisms is critical for evaluating the long-term safety of nuclear waste storage.

12 - MGMT OF RADIOACTIVE AND NON-RADIOACTIVE WASTE↗

DOE OSTI2025

Tree tensor network hierarchical equations of motion based on time-dependent variational principle for efficient open quantum dynamics in structured thermal environments

In this work, we introduce an efficient method, TTN-HEOM, for exactly calculating the open quantum dynamics for driven quantum systems interacting with highly structured bosonic baths by combining the tree tensor network (TTN) decomposition scheme with the bexcitonic generalization of the numerically exact hierarchical equations of motion (HEOM). The method yields a series of quantum master equations for all core tensors in the TTN that efficiently and accurately capture the open quantum dynamics for non-Markovian environments to all orders in the system–bath interaction. These master equations are constructed based on the time-dependent Dirac–Frenkel variational principle, which isolates the optimal dynamics for the core tensors given the TTN ansatz. The dynamics converges to the HEOM when increasing the rank of the core tensors, a limit in which the TTN ansatz becomes exact. We introduce TENSO, tensor equations for non-Markovian structured open systems, as a general-purpose Python code to propagate the TTN-HEOM dynamics. We implement three general propagators for the coupled master equations: two fixed-rank methods that require a constant memory footprint during the dynamics and one adaptive-rank method with a variable memory footprint controlled by the target level of computational error. We exemplify the utility of these methods by simulating a two-level system coupled to a structured bath containing one Drude–Lorentz component and eight Brownian oscillators, which is beyond what can presently be computed using the standard HEOM. Our results show that the TTN-HEOM is capable of simulating both dephasing and relaxation dynamics of driven quantum systems interacting with structured baths, even those of chemical complexity, with an affordable computational cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Photon–photon chemical thermodynamics of frequency conversion processes in highly multimode systems

Abstract Frequency generation in highly multimode nonlinear optical systems is inherently a complex process, giving rise to an exceedingly convoluted landscape of evolution dynamics. While predicting and controlling the global conversion efficiencies in such nonlinear environments has long been considered impossible, here, we formally address this challenge even in scenarios involving a very large number of spatial modes. By utilizing fundamental notions from optical statistical mechanics, we develop a universal theoretical framework that effectively treats all frequency components as chemical reactants/products, capable of undergoing optical thermodynamic reactions facilitated by a variety of multi-wave mixing effects. These photon–photon reactions are governed by conservation laws that directly determine the optical temperatures and chemical potentials of the ensued chemical equilibria for each frequency species. In this context, we develop a comprehensive stoichiometric model and formally derive an expression that relates the chemical potentials to the optical stoichiometric coefficients, in a manner akin to atomic/molecular chemical reactions. This advancement unlocks new predictive capabilities that can facilitate the optimization of frequency generation in highly multimode photonic arrangements, surpassing the limitations of conventional schemes that rely exclusively on nonlinear optical dynamics. Notably, we identify a universal regime of Rayleigh–Jeans thermalization where an optical reaction at near-zero optical temperatures can promote the complete and entropically irreversible conversion of light to the fundamental mode at a target frequency. Our theoretical results are corroborated by numerical simulations in settings where second-harmonic generation, sum-frequency generation and four-wave mixing processes can manifest.

Optics↗

DOE OSTI2026

Improved Protein Semi-Synthesis Enables Biophysical Studies of Thioamide Destabilization of β-Sheet Interactions

Abstract Thioamides are natural post-translational modifications of the peptide backbone and can be introduced synthetically to probe protein folding or functionalize peptides for translational applications. In this work, we demonstrate that thioamide-containing peptides with C-terminal thioesters can be efficiently generated using Knorr pyrazole activation and used in subsequent native chemical ligation reactions to generate thioamide-containing proteins. We compare this method to acyl azide activation and find that both routes provide similar yields. We also investigate ultrasound-mediated desulfurization of the ligation site cysteine for potential advantages over chemical radical initiators. Scaling up our syntheses allows us to study thioamide perturbations to the β-sheet region of the B1 domain of protein G (GB1) as well as β-strand interactions in amyloid fibrils of the Parkinson’s disease protein α-synuclein. In both contexts, we observe dramatic destabilization of the β-sheet networks, manifested in decreased GB1 thermal stability and altered folding and slowed aggregation of α-synuclein. These findings illustrate the impact that a single atom substitution can have on cooperative hydrogen-bonding networks and prompt future study of both systems.

Yanagawa, Evan S. K. [University of Pennsylvania ,↗

DOE OSTI2026

A multiscale packed-bed reactor model for sustainable ethylene production via chemical looping oxidative coupling of methane

The rising global warming concerns and shale gas discovery have prompted research in the direction of greenhouse gas (GHG), such as methane, reduction and conversion. Oxidative coupling of methane (OCM) offers a pathway to low carbon-intense valorization of methane while producing ethylene, a chemical regarded as central to the petrochemical industry. Even after decades of OCM discovery, researchers keep understanding the process and underlying chemical reactions in a pursuit to achieve industrial viability for OCM. Here, in general, OCM suffers from low C 2 selectivity, yield and reactor temperature runaways due to highly exothermic nature of its reactions. Computational Fluid Dynamics (CFD) tools help analyze spatial gradients within the reactor to deeply understand the diffusion of species, mass and heat transfer phenomena. Furthermore, challenges associated with scaling up such as hot spot formation and parametric sensitivity can be addressed without having to expend on costly experiments. The current paper presents a multiscale packed-bed reactor CFD model coupled with a chemical kinetic model for the chemical looping OCM. The CFD model includes two scales i.e., macroscale for catalyst bed and microscale for individual pellets. Moreover, a chemical kinetic model based on 10 gas-phase reactions is integrated with the CFD model. An additional surface reaction for the formation of gas-phase oxygen from catalyst surface is added to account for the absence of feed oxygen. The model is calibrated against experimental results. The calibrated model captures trends in CH 4 conversion, C 2 selectivity and C 2 yield within a ± 4.35 % range across a temperature range of 700-900 °C. Moreover, model fidelity is evaluated by varying key computational parameters such as mesh resolution and time step size. The model is also verified by varying the inlet methane concentration and the gas hourly space velocity (GHSV) and comparing the results with literature. A sensitivity analysis and scale-up of the current model is undergoing.

Chemical looping↗

DOE OSTI2024

Actuating Liquid Crystals Rapidly and Reversibly by Using Chemical Catalysis

Abstract Microtubules and catalytic motor proteins underlie the microscale actuation of living materials, and they have been used in reconstituted systems to harness chemical energy to drive new states of organization of soft matter (e.g., liquid crystals (LCs)). Such materials, however, are fragile and challenging to translate to technological contexts. Rapid (sub‐second) and reversible changes in the orientations of LCs at room temperature using reactions between gaseous hydrogen and oxygen that are catalyzed by Pd/Au surfaces are reported. Surface chemical analysis and computational chemistry studies confirm that dissociative adsorption of H 2 on the Pd/Au films reduces preadsorbed O and generates 1 ML of adsorbed H, driving nitrile‐containing LCs from a perpendicular to a planar orientation. Subsequent exposure to O 2 leads to oxidation of the adsorbed H, reformation of adsorbed O on the Pd/Au surface, and a return of the LC to its initial orientation. The roles of surface composition and reaction kinetics in determining the LC dynamics are described along with a proof‐of‐concept demonstration of microactuation of beads. These results provide fresh ideas for utilizing chemical energy and catalysis to reversibly actuate functional LCs on the microscale.

Chemistry↗

NASA NTRS1995

Single-Drop Reactive Extraction/Extractive Reaction with Forced Convective Diffusion and Interphase Mass Transfer

An algorithm has been developed for the forced convective diffusion-reaction problem for convection inside and outside a droplet by a recirculating flow field hydrodynamically coupled at the droplet interface with an external flow field that at infinity becomes a uniform streaming flow. The concentration field inside the droplet is likewise coupled with that outside by boundary conditions at the interface. A chemical reaction can take place either inside or outside the droplet or reactions can take place in both phases. The algorithm has been implemented and results are shown here for the case of no reaction and for the case of an external first order reaction, both for unsteady behavior. For pure interphase mass transfer, concentration isocontours, local and average Sherwood numbers, and average droplet concentrations have been obtained as a function of the physical properties and external flow field. For mass transfer enhanced by an external reaction, in addition to the above forms of results, we present the enhancement factor, with the results now also depending upon the (dimensionless) rate of reaction.

Leonid S Kleinman↗

NASA NTRS1995

Single-Drop Reactive Extraction/Extractive Reaction With Forced Convective Diffusion and Interphase Mass Transfer

An algorithm has been developed for time-dependent forced convective diffusion-reaction having convection by a recirculating flow field within the drop that is hydrodynamically coupled at the interface with a convective external flow field that at infinity becomes a uniform free-streaming flow. The concentration field inside the droplet is likewise coupled with that outside by boundary conditions at the interface. A chemical reaction can take place either inside or outside the droplet, or reactions can take place in both phases. The algorithm has been implemented, and for comparison results are shown here for the case of no reaction in either phase and for the case of an external first order reaction, both for unsteady behavior. For pure interphase mass transfer, concentration isocontours, local and average Sherwood numbers, and average droplet concentrations have been obtained as a function of the physical properties and external flow field. For mass transfer enhanced by an external reaction, in addition to the above forms of results, we present the enhancement factor, with the results now also depending upon the (dimensionless) rate of reaction.

Leonid S Kleinman↗

DOE OSTI2026

Gold Catalyzed Polymerization Reactions of Unsaturated Substrates: Towards New Functional, Recyclable, and Upcycled Aromatic Polymers (Final Report)

The overarching goal of this project lied in the translation of gold (Au) catalyzed small molecule synthetic transformations to the field of polymer science, the generation of new macromolecular structures, and the application of the materials and methodologies produced toward sustainable polymer development and chemical upcycling. Specifically, this project aimed to polymerize monomers based on unsaturated precursors and access novel polymeric materials through the extension of Au catalyzed intermolecular processes. The specific objectives of this project comprised: (1) the extension of Au-catalyzed intermolecular reactions to bifunctional monomers and the polycondensation of diverse nucleophiles; (2) to gain fundamental mechanistic insight into Au-catalyzed polymerizations; (3) the application of these reactions to the synthesis of new classes of aromatic polymers that can be readily and/or selectively deconstructed; and (4) to apply these chemistries to post-polymerization modification (PPM) of commercially relevant polyaromatic substrates, including post-industrial plastics and post-consumer waste.

36 MATERIALS SCIENCE↗

DOE OSTI1961

Laboratory Development of a Pot Calcination Process for Converting Liquid Wastes to Solids

Simulated Darex, Purex, Thorex, and TBP-25 wastes were batch-evaporated and calcined to solids. The weight of residue was decreased to ~ 8% of the original waste for Darex, to ~ 4% for Purex, to ~ 2% for Thorex, and ~ 7% for TBP-25 by calcination to 1200°C. Semicontinuous evaporation and calcination to solids at 900°C of Darex and Purex wastes gave volume reduction factors of ~ 8 and 7 to 10, respectively. The nitrate contents of the residues from batch calcination to 800°C were from ~ 0.07 to 0.5 wt % while the nitrate contents of the residues from semicontinuous calcination to 900°C were from ~ 0.1 to 0.7 wt %. Sodium, calcium, and magnesium additives to Purex waste decreased the percent of sulfate volatilized into the condensate from ~ 30% to <0.5%. Replacement of the atmosphere above the waste with nitric oxide decreased ruthenium volatility from 50 to 60% of that originally present in Purex waste to 0.5 to 3.5%. The thermal conductivities for the calcined wastes, measured in situ, were all >0.1 Btu/hr ft °F at ~ 400°F and increased almost linearly with increasing temperature to >0.3 Btu/hr ft °F at ~ 1600°F in all cases studied.

052001* -- Nuclear Fuels-- Waste Processing↗

DOE OSTI2025

From PINNs to PIKANs: recent advances in physics-informed machine learning

Physics-Informed Neural Networks (PINNs) have emerged as a key tool in Scientific Machine Learning since their introduction in 2017, enabling the efficient solution of ordinary and partial differential equations using sparse measurements. Over the past few years, significant advancements have been made in the training and optimization of PINNs, covering aspects such as network architectures, adaptive refinement, domain decomposition, and the use of adaptive weights and activation functions. A notable recent development is the Physics-Informed Kolmogorov-Arnold Networks (PIKANS), which leverage a representation model originally proposed by Kolmogorov in 1957, offering a promising alternative to traditional PINNs. In this review, we provide a comprehensive overview of the latest advancements in PINNs, focusing on improvements in network design, feature expansion, optimization techniques, uncertainty quantification, and theoretical insights. We also survey key applications across a range of fields, including biomedicine, fluid and solid mechanics, geophysics, dynamical systems, heat transfer, chemical engineering, and beyond. Lastly, we review computational frameworks and software tools developed by both academia and industry to support PINN research and applications.

Kolmogorov-Arnold networks↗

DOE OSTI2026

Nitrene generation and transfer for unnatural biosynthesis in living cells

Abstract Synthetic biology has enabled the production of natural and unnatural products from inexpensive sustainable feedstocks. Yet, the scope of available products has been limited largely to compounds accessible from nature’s chemical reactions. Evolved enzymes can catalyse reactions of unnatural substrates or reactions not found in nature but often require the addition of synthetic reagents to purified enzymes or to resting cells containing those enzymes. Here we show that chemical reactions of metabolic intermediates produced intracellularly in living cells can include intermolecular nitrene transfers. The biosynthesis of N -acetoxyanilines, in combination with the generation and transfer of N -aryl nitrene intermediates from them catalysed by a cytochrome P450, generates amino alcohols, diamines, diarylamines and aminoalkyl arenes from simple carbon feedstocks. These products—common substructures of pharmaceuticals and agrochemicals—are challenging to synthesize by standard organic chemistry and were produced from inexpensive, renewable feedstocks. Evolution of the enzymes in this pathway showed that titres can be increased by engineering and that the products can be synthesized with high enantioselectivity.

Donnell, Isaac↗

NASA NTRS1995

Extensional Flow Convecting a Reactant Undergoing a First Order Homogeneous Reaction and Diffusional Mass Transfer From a Sphere at Low to Intermediate Peclet and Damkohler Numbers

Forced convective diffusion-reaction is considered for viscous axisymmetric extensional convecting velocity in the neighborhood of a sphere. For Peclet numbers in the range 0.1 ≤ Pe ≤ 500 and for Damkohler numbers increasing with increasing Pe but in the overall range 0.02 ≤ Da ≤ 10, average and local Sherwood numbers have been computed. By introducing the eigenfunction expansion c(r,Θ) = Σ c n (r)P n (cosΘ) into the forced convective diffusion equation for the concentration of a chemical species undergoing a first order homogeneous reaction and by using properties of the Legendre functions P n (cosΘ), the variable coefficient PDE can be reduced to a system of N+1 second order ODEs for the radial functions C n (r), n=0,1,2, ... ,N. The adaptive grid algorithm of Pereyra and Lentini can be used to solve the corresponding 2(N+ 1) first order differential equations as a two-point boundary value problem on 1 ≤ r ≤ r •• . Convergence of the expansion for a specific value of N can thus be established and provides "spectral" behavior as well as the full concentration field c(r,Θ).

N Y Shah↗

DOE OSTI2027

A multi-region approach for the analysis of porous materials and gas-solid reactions using USAXS-SAXS-WAXS: application to CaO carbonation

The reaction rate of gas-solid non-catalytic reactions is typically investigated using reactant conversion data over time and ex-situ measurements of the porous solid reactant textural properties; these data enable the experimental estimation of the initial intrinsic reaction rate, whereas the evolution of the textural properties and the reaction rate over time are evaluated theoretically using reaction models. In this work, a different methodology is presented, based on: a) in-situ time-resolved USAXS-SAXS-WAXS measurements of the solid sample, and b) a multi-region modeling approach; this methodology allows for the estimation of the textural properties and the intrinsic reaction rate at any time during the reaction. Referring to a reaction in which a solid product is obtained from a solid reactant and a gaseous reactant, the porous particle is described as consisting of several distinct regions with different microstructural properties, and both a gas-solid reaction model and a SAXS model are derived and applied to the carbonation of porous CaO. The proposed reaction model highlights the role of the inaccessible reactant and accurately predicts the solid reactant conversion versus time profile. The SAXS model accurately predicts the measured linear trends of the Porod invariant and of the pre-factor of the power law scattering profile versus CaO mass fraction; in the absence of chemical reactions, the proposed equations extend classical SAXS theory to porous materials containing macropores and nonporous solid phases in addition to standard nanoscale inhomogeneous regions.

CO2 solid sorbents↗

NASA NTRS1992

Design of A CVD Reactor for the Deposition of Diamond in A Microgravity Environment

There is a growing body of theoretical and experimental evidence suggesting that the uniformity, rate, adhesion, quality, and other key properties of Chemical Vapor Deposition (CVD) diamond coatings are influenced by the gas mixing kinetics in the thermal plasma environment of the reaction chamber. The implementation of, for example, Microwave Plasma Enhanced Chemical Vapor Deposition (MPECVD) process in microgravity has, thus, been suggested. Such a diamond deposition system, which overcomes the limitations of present systems and which is distiguishable from them by the use of high pressure MPECVD and recirculation of the would be effluent hydrogen and carbon, is described. Given the key fact that there is nothing in the effluent of the MPECVD process that is truly a byproduct or 'waste', the system can, at least in principle, lend itself to being closed loop yet dynamic. The exhaust contains hydrogen and carbon species which can be recirculated to the plasma reactor, that is, since there are no unusable reaction byproducts, the effluent can be fed back to the reaction chamber with no detriment, thus allowing deployment in a microgravity environment.

M L Languell↗