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At least 109 records · Page 6

A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws

Theoretical analysis of signaling pathways can provide a substantial amount of insight into their function. One particular area of research considers signaling pathways capable of assuming two or more stable states given the same amount of signaling ligand. This phenomenon of bistability can give rise to switch-like behavior, a mechanism that governs cellular decision making. Investigation of whether or not a signaling pathway can confer bistability and switch-like behavior, without knowledge of specific kinetic rate constant values, is a mathematically challenging problem. Recently a technique based on optimization has been introduced, which is capable of finding example parameter values that confer switch-like behavior for a given pathway. Although this approach has made it possible to analyze moderately sized pathways, it is limited to reaction networks that presume a uniterminal structure. It is this limited structure we address by developing a general technique that applies to any mass action reaction network with conservation laws. In this paper we developed a generalized method for detecting switch-like bistable behavior in any mass action reaction network with conservation laws. The method involves (1) construction of a constrained optimization problem using the determinant of the Jacobian of the underlying rate equations, (2) minimization of the objective function to search for conditions resulting in a zero eigenvalue, (3) computation of a confidence level that describes if the global minimum has been found and (4) evaluation of optimization values, using either numerical continuation or directly simulating the ODE system, to verify that a bistability region exists. The generalized method has been tested on three motifs known to be capable of bistability. We have developed a variation of an optimization-based method for the discovery of bistability, which is not limited to uniterminal chemical reaction networks. Successful completion of the method provides an S-shaped bifurcation diagram, which indicates that the network acts as a bistable switch for the given optimization parameters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanical loading prediction through accelerometry data during walking and running

ABSTRACT Currently, there is no way to assess mechanical loading variables such as peak ground reaction forces (pGRF) and peak loading rate (pLR) in clinical settings. The purpose of this study was to develop accelerometry‐based equations to predict both pGRF and pLR during walking and running. One hundred and thirty one subjects (79 females; 76.9 ± 19.6 kg) walked and ran at different speeds (2–14 km·h −1 ) on a force plate–instrumented treadmill while wearing accelerometers at their ankle, lower back and hip. Regression equations were developed to predict pGRF and pLR from accelerometry data. Leave‐one‐out cross‐validation was used to calculate prediction accuracy and Bland–Altman plots. Our pGRF prediction equation was compared with a reference equation previously published. Body mass and peak acceleration were included for pGRF prediction and body mass and peak acceleration rate for pLR prediction. All pGRF equation coefficients of determination were above 0.96, and a good agreement between actual and predicted pGRF was observed, with a mean absolute percent error (MAPE) below 7.3%. Accuracy indices from our equations were better than previously developed equations. All pLR prediction equations presented a lower accuracy compared to those developed to predict pGRF. Walking and running pGRF can be predicted with high accuracy by accelerometry‐based equations, representing an easy way to determine mechanical loading in free‐living conditions. The pLR prediction equations yielded a somewhat lower prediction accuracy compared with the pGRF equations.

Veras, Lucas↗

Probing the antiknock effect of anisole through an ignition, speciation and modeling study of its blends with isooctane

In order to unravel the reaction pathways relevant to anisole co-oxidation within a fuel blend, a detailed study of isooctane/anisole blends was performed with the ULille RCM. Ignition delays as well as mole fraction profiles were measured during a two-stage ignition delay using sampling and GC techniques. These results are used to validate a kinetic model developed from ab initio calculations for the most relevant rate constants which included H-atom abstraction reactions from anisole, and reactions on the potential energy surfaces of methoxyphenyl + O 2 and anisyl + O 2 . Pressure dependent rate constants were computed for the methoxyphenyl + O 2 and anisyl + O 2 reactive systems using master equation code analysis. The new kinetic model shows good agreement with the experimental data. Dual brute-force sensitivity analysis was performed, on both first- and second-stages of ignition, allowing the identification of the most important reactions in the prediction of both ignition delays. It was observed that while pure anisole does not show NTC behavior, a 60/40 isooctane/anisole blend displays such behavior, as well as two-stage ignition. This suggests anisole addition may not be as beneficial to knock resistance as expected from its high octane number. The kinetic modeling results demonstrate the importance of H-abstraction reactions both from the methoxy group and from the aryl ring in ortho-position and the addition of the resultant radicals to O2, mostly leading to the formation of polar or non-aromatic products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Concepts Relevant for the Kinetic Analysis of Reversible Reaction Systems

The net rate of a reversible chemical reaction is the difference between unidirectional rates of traversal along forward and reverse reaction paths. In a multistep reaction sequence, the forward and reverse trajectories, in general, are not the microscopic reverse of one another; rather, each unidirectional route is comprised of distinct rate-controlling steps, intermediates, and transition states. Consequently, traditional descriptors of rate (e.g., reaction orders) do not reflect intrinsic kinetic information but instead conflate unidirectional contributions determined by (i) the microscopic occurrence of forward/reverse reactions (i.e., unidirectional kinetics) and (ii) the reversibility of reaction (i.e., nonequilibrium thermodynamics). This review aims to provide a comprehensive resource of analytical and conceptual tools which deconvolute the contributions of reaction kinetics and thermodynamics to disambiguate unidirectional reaction trajectories and precisely identify rate- and reversibility-controlling molecular species and steps in reversible reaction systems. The extrication of mechanistic and kinetic information from bidirectional reactions is accomplished through equation-based formalisms (e.g., De Donder relations) grounded in principles of thermodynamics and interpreted in the context of theories of chemical kinetics developed in the past 25 years. Here, the aggregate of mathematical formalisms detailed herein is general to thermochemical and electrochemical reactions and encapsulates a diverse body of scientific literature encompassing chemical physics, thermodynamics, chemical kinetics, catalysis, and kinetic modeling.

42 ENGINEERING↗

Modelling the ejection of primary aerosols during the fast pyrolysis of biomass anisotropic particles

A model for the fast pyrolysis of anisotropic biomass particles is presented which considers bubbling dynamics within the liquid intermediate phase (metaplast) and aerosol ejection from this phase. The model employs the population balance equation and the method of moments to estimate the production rate and resultant size distribution of aerosol ejections, incorporating a detailed CRECK reaction mechanism, and considers the effect of anisotropic biomass microstructure on the intraparticle transport of mass and energy. Here, this study investigates the impact of particle size, heating rate (heat transfer coefficient), and lignocellulosic composition on aerosol ejection. The model predicts that, at high heating rates (convective heat transfer coefficient of 359 W/m 2 .K), aerosols can contribute over 20% to the heavy fraction yield in bio-oil for small particles (1 mm diameter, 4 mm length). The model can predict aerosol size distribution and surface area, indicating an average size of 20 μm for bubbles and 5 μm for aerosols during increased bubble production and aerosol ejection rates. These findings are consistent with prior experimental results and provide essential information for future modeling of extra-particle reactions of the aerosols as they progress through the reactor.

09 BIOMASS FUELS↗

High-accuracy first-principles-based rate coefficients for the reaction of OH and CH 3 OOH

Here, the ˙OH-initiated oxidation of methyl hydroperoxide, which plays an important role in the atmospheric chemistry of methane, was theoretically characterized using high-accuracy composite amHEAT-345(Q) coupled-cluster calculations followed by a two-dimensional E,J resolved master equation analysis. The reaction is found to proceed through two distinct hydrogen-bonded pre-reactive complexes leading to two product channels, in accord with the experimental observations: (i) ˙OH + CH 3 OOH → CH 3 OO˙ + H 2 O with a yield of 0.8 ± 0.1, and (ii) ˙OH + CH 3 OOH → HCHO + ˙OH + H 2 O with a yield of 0.2 ± 0.1. The calculated reaction enthalpies are within 0.2 kcal mol -1 of the benchmark ATcT values. Overall thermal rate coefficients obtained from first principles are found to be in the low-pressure limit at atmospheric pressure; the total rate coefficient can be expressed over the T = 200–450 K range as k(T) = 5.0 × 10 -12 × T -0.152 × exp(287/T) cm 3 s -1 , strongly supporting the experimental results of Vaghjiani and Ravishankara, with which this expression agrees within ca. 15%. The current results show that (i) is the principal reaction channel and support the view that, due to its inherently fast transformations, CH 3 OOH is an important redistribution species for HO x ˙ radicals in the Earth's atmosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Combining DPG in space with DPG time-marching scheme for the transient advection–reaction equation

In this article, we present a general methodology to combine the Discontinuous Petrov–Galerkin (DPG) method in space and time in the context of methods of lines for transient advection–reaction problems. We first introduce a semidiscretization in space with a DPG method redefining the ideas of optimal testing and practicality of the method in this context. Then, we apply the recently developed DPG-based time-marching scheme, which is of exponential-type, to the resulting system of Ordinary Differential Equations (ODEs). Further, we also discuss how to efficiently compute the action of the exponential of the matrix coming from the space semidiscretization without assembling the full matrix. Finally, we verify the proposed method for 1D+time advection–reaction problems showing optimal convergence rates for smooth solutions and more stable results for linear conservation laws comparing to the classical exponential integrators.

42 ENGINEERING↗

Combining DPG in space with DPG time-marching scheme for the transient advection-reaction equation

In this article, we present a general methodology to combine the Discontinuous PetrovGalerkin (DPG) method in space and time in the context of methods of lines for transient advection-reaction problems. We first introduce a semidiscretization in space with a DPG method redefining the ideas of optimal testing and practicality of the method in this context. Then, we apply the recently developed DPG-based time-marching scheme, which is of exponential-type, to the resulting system of Ordinary Differential Equations (ODEs). We also discuss how to efficiently compute the action of the exponential of the matrix coming from the space semidiscretization without assembling the full matrix. Finally, we verify the proposed method for 1D+time advection-reaction problems showing optimal convergence rates for smooth solutions and more stable results for linear conservation laws comparing to the classical exponential integrators.

97 MATHEMATICS AND COMPUTING↗

Learning heterogeneous reaction kinetics from X-ray videos pixel by pixel

Reaction rates at spatially heterogeneous, unstable interfaces are notoriously difficult to quantify, yet are essential in engineering many chemical systems, such as batteries and electrocatalysts. Experimental characterizations of such materials by operando microscopy produce rich image datasets, but data-driven methods to learn physics from these images are still lacking because of the complex coupling of reaction kinetics, surface chemistry and phase separation. Here we show that heterogeneous reaction kinetics can be learned from in situ scanning transmission X-ray microscopy (STXM) images of carbon-coated lithium iron phosphate (LFP) nanoparticles. Combining a large dataset of STXM images with a thermodynamically consistent electrochemical phase-field model, partial differential equation (PDE)-constrained optimization and uncertainty quantification, we extract the free-energy landscape and reaction kinetics and verify their consistency with theoretical models. We also simultaneously learn the spatial heterogeneity of the reaction rate, which closely matches the carbon-coating thickness profiles obtained through Auger electron microscopy (AEM). Across 180,000 image pixels, the mean discrepancy with the learned model is remarkably small (<7%) and comparable with experimental noise. Our results open the possibility of learning nonequilibrium material properties beyond the reach of traditional experimental methods and offer a new non-destructive technique for characterizing and optimizing heterogeneous reactive surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A combined experimental and modelling study of granite hydrothermal alteration

Geochemical reactions can induce significant changes of rock reservoir porosity and permeability via mineral dissolution and precipitation processes, affecting the long-term fluid behaviour within various geological systems. Here, the understanding and quantification of these reactions rely on field and experimental studies and on the predictions of reactive transport models. The present study was aimed at assessing the extent to which current geochemical models integrating available mineral dissolution/precipitation rate equations can reproduce the experimental data obtained from 4 to 17-day long hydrothermal alteration experiments of a muscovite-biotite granite and, thus, help provide an accurate description of the evolution of geothermal systems within granitic reservoirs. The experiments were conducted at a constant temperature of 180 °C and over an aqueous fluid pH range of 2 to 8.5, using both mixed-flow and static batch reactors. Modelled major element (K, Al, Si, Ca, and Mg) concentrations were generally in satisfactory agreement with the corresponding measured elemental fluxes – the differences between modelled and experimental values were generally within a factor of 5 – and the predicted identity and mass of formed secondary phases were consistent with the microscopic observations of the reacted solids. However, larger differences between measured and modelled element concentrations were observed when significant amounts of secondary phases formed, notably at pH 2 to 3, and for longer-term batch experiments. Much of this concentration difference stems from the underestimation of the amounts of Al-phases formed at acid to near-neutral pH. Although an idealized rock composition was considered, the observed mismatch between model calculations and experimental data can be attributed to inadequate mineral precipitation reaction rates and a poor description of reactive surface areas in existing geochemical modelling codes. More accurate quantification of precipitation kinetics, including nucleation and growth, and improved descriptions of the temporal change of mineral surface area would enhance the predictive capabilities of reactive transport models and benefit, particularly, the efforts aimed at increasing the sustainability of EGS reservoirs.

58 GEOSCIENCES↗

Dehydroxylation kinetics of kaolinite and montmorillonite examined using isoconversional methods

The use of calcined clays as supplementary cementitious materials (SCMs) in concrete is a promising strategy towards decarbonizing the cement and concrete industry. This is especially relevant considering the ever-increasing demand for concrete. Comprehensive understanding of the kinetics of calcination is essential towards maximizing the potential reactivity of clay minerals while ensuring energy efficiency. In this study, the kinetics of the dehydroxylation of kaolinite and montmorillonite are investigated under non-isothermal conditions at constant heating rate. Activation energies ( E a ) are determined via Friedman differential and advanced Vyazovkin incremental methods over the isoconversional range; these are devoid of computational approximations, thus allowing kinetic analysis without assuming a specific reaction model. Kinetic equations—in the differential form as well as a combination of differential and integral forms are compared against the experimentally determined reaction models to identify the most probable dehydroxylation mechanism for kaolinite and montmorillonite. A reaction order mechanism is established for dehydroxylation of kaolinite, while montmorillonite is noted to undergo dehydroxylation via a single-step reversible diffusion-controlled process. Kinetic triplet—comprising activation energy, reaction model and pre-exponential factor—is used to predict isothermal calcination conditions, which is further verified using analytical techniques. Heat release rates of clay-portlandite blends from isothermal calorimetry are used within a thermodynamic framework to quantify reactivity of the calcined clays. Here, the study demonstrates a general approach based on isoconversional methods to predict calcination conditions for different clays that can be used in efficient and optimized production of blended cements or SCMs.

36 MATERIALS SCIENCE↗

Learning heterogeneous reaction kinetics from X-ray movies pixel-by-pixel

Reaction rates at spatially heterogeneous, unstable interfaces are notoriously difficult to quantify, yet are essential in engineering many chemical systems, such as batteries 1 and electrocatalysts 2. Experimental characterizations of such materials by operando microscopy produce rich image datasets 3–6, but data-driven methods to learn physics from these images are still lacking because of the complex coupling of reaction kinetics, surface chemistry and phase separation 7. Here we show that heterogeneous reaction kinetics can be learned from in situ scanning transmission X-ray microscopy (STXM) images of carbon-coated lithium iron phosphate (LFP) nanoparticles. Combining a large dataset of STXM images with a thermodynamically consistent electrochemical phase-field model, partial differential equation (PDE)-constrained optimization and uncertainty quantification, we extract the free-energy landscape and reaction kinetics and verify their consistency with theoretical models. We also simultaneously learn the spatial heterogeneity of the reaction rate, which closely matches the carbon-coating thickness profiles obtained through Auger electron microscopy (AEM). Across 180,000 image pixels, the mean discrepancy with the learned model is remarkably small (<7%) and comparable with experimental noise. Our results open the possibility of learning nonequilibrium material properties beyond the reach of traditional experimental methods and offer a new non-destructive technique for characterizing and optimizing heterogeneous reactive surfaces.

Chueh, William↗

Diffusion-limited hydrolysis in polymeric materials

Polymer degradation under aggressive environmental stressors often develops heterogeneities due to diffusion-limited reaction phenomena. This is well established for diffusion-limited oxidation (DLO), which is known to occur for most polymeric materials at elevated temperatures but has been less summarized for the conditions of diffusion-limited hydrolysis (DLH). Here, an overview of hydrolysis for several materials and a computational model, analogous to the underlying equations for DLO, able to define this diffusion-reaction system is presented. A systematic study of the influence of various parameters, such as water diffusivity, reaction rate and order, and a more in-depth focus on residual isocyanate hydrolysis in a polymeric methylene diphenyl diisocyanate (pMDI) based polyurethane (PU) foam is given. For this system, we present experimental data for model ‘input’ parameters and discuss predictions for different conditions. We conceptually compare the behavior of diffusion-limited oxidation to that of diffusion-limited hydrolysis (DLH). With the mathematical framework and key material properties presented herein, any DLH phenomena following Fickian diffusion behavior can be understood, modeled, and predicted.

36 MATERIALS SCIENCE↗

A Unified Workflow for Sensitivity-Based Kinetic Analysis in Microkinetic Models

Degrees of rate control (DRC), apparent activation energies, and apparent reaction orders are established local sensitivity diagnostics for interpreting microkinetic models, but applying them routinely to large mechanisms often requires substantial reaction-specific bookkeeping, perturbation design, and postprocessing. Here, in this study, we present a unified derivative-based workflow that evaluates these quantities from a single compiled reaction-network model and target-rate definition. For any user-provided microkinetic model, the workflow compiles the mechanism into stoichiometrically consistent mass-action rate equations, solves the surface dynamics, and uses automatic differentiation to compute sensitivities with respect to rate constants, temperature, and gas partial pressures. By combining their calculations in the same framework, the workflow clearly demonstrates the relationships between different DRCs and the apparent activation energy. Using existing examples of propylene partial oxidation and methane oxidation on Pd(100), we verify expected transient redistribution of rate control, distinguish net Campbell DRCs from one-sided directional sensitivities, and show how apparent activation energy can be reconstructed either from one-sided DRCs or from state-based DRCs while critical mechanistic insights are obtained consistently. In the methane oxidation case, a pathway-subset test further illustrates how a simplified mechanism preserves key kinetic signatures of a full model, showing the potential of our user-friendly tool for model construction beyond kinetic analysis.

36 MATERIALS SCIENCE↗

Recent progress on the APOLLO3 calculation scheme for the FLUOLE2 experiment

Studies of the neutron fluence on reactor pressure vessel and the correlated reactor lifetime issues require very good knowledge of the neutron source distribution in the reactor core and especially in the peripheral region. The FLUOLE2 experiment offers an appropriate starting configuration to investigate the possibility of using the APOLLO3 deterministic code with a two-step calculation scheme. It enables us to calculate a pin-by-pin neutron source distribution in the core, then to carry out the neutron propagation from the core to neutron detectors. In this paper, we focus on a calculation scheme dedicated to the determination of core neutron source distribution using APOLLO3 with the SHEM281 energy mesh, a Method of Characteristics (MOC) to solve the transport equation for the lattice computation step and a 20-groups 3D computation using the MINARET SN solver of APOLLO3. Reactivity and pin-by-pin reaction rate results have been analyzed. Results obtained with both lattice and core computations show a good agreement with those produced through a reference calculation using the TRIPOLI-4 Monte Carlo transport code. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Effect of lot microstructure variations on detonation performance of the triaminotrinitrobenzene (TATB)-Based insensitive high explosive PBX 9502

PBX 9502 is an important insensitive high explosive due to its combination of safety properties and detonation performance. It is a polymer-bonded formulation consisting of 95 wt.% 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) as the high explosive crystal, bound with Kel F-800 (FK-800), a co-polymer of chlorotrifluoroethylene and vinylidene-fluoride. Two different types are used, one known as virgin that uses only pristine manufactured TATB, and a second known as recycled that has 50 wt.% of its TATB reclaimed from machining scraps of previously pressed virgin PBX 9502. Recycled lots have a higher percentage of fine particles compared to virgin lots, due to the fracturing and damage sustained by TATB crystals during pressing. We examine the influence that this TATB microstructure difference between virgin and recycled PBX 9502 has on detonation performance properties. New rate-stick geometry diameter effect, detonation front shape and cylinder expansion test data are obtained for two previously uncharacterized virgin lots and one recycled lot of PBX 9502. This is combined with previously published data for one virgin and one recycled lot for evaluation purposes. Detonation shock dynamics model calibrations are conducted on each of the five lots to provide an assessment of the detonation timing characteristics of virgin versus recycled PBX 9502 lots. For two of the virgin lots, detonations propagate slower in the rate-stick geometry than those in the two recycled lots. However, the other virgin lot tested has propagation rates comparable to that of the recycled lots for larger diameter rate-sticks. The latter result, though, is shown to be geometry dependent and depends on the range of detonation curvatures accessed in different geometries. New copper-confined, cylinder expansion tests are conducted on each of the three virgin and two recycled lots to obtain detonation product Jones-Wilkins-Lee equations of state, enabling an assessment of the metal push capabilities for each of the five lots. We find that the metal push capabilities, characterized by the evolution of the heat of detonation with volume, are similar between the virgin and recycled lots. Thus, changes in microstructure between different PBX 9502 lots seemingly affect the rate of reaction, but not the overall energy content.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spiers Memorial Lecture: Theory of unimolecular reactions

One hundred years ago, at an earlier Faraday Discussion meeting, Lindemann presented a mechanism that provides the foundation for contemplating the pressure dependence of unimolecular reactions. Since that time, our ability to model and predict the kinetics of such reactions has grown in leaps and bounds through the synergy of ever more sophisticated experimental studies with increasingly high level theoretical analyses. Herein, this review begins with a brief historical overview of the progress from the Lindemann mechanism to the master equation, which now provides the cornerstone for most theoretical analyses. The current status of ab initio transition state theory based implementations of the master equation is then reviewed, beginning with a discussion of the energy resolved chemical conversion rates, followed by a review of the pressure dependence of the thermal kinetics. The latter discussion focusses on the collisional energy and angular momentum transfer rates as well as the complexities of non-thermal effects and of multiple-well multiple-channel reactions. The synergy with recent state-of-the-art experiments is used to motivate these discussions. Attempts to automate the calculations are also briefly reviewed. Throughout the discussion, we provide our perspective on current understanding and continuing challenges and opportunities. One key challenge relates to the coupling of sequences of reactions, which frequently leads to deviations from the classic presumption of thermal reactants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Finite flame thickness effects on Kolmogorov-Petrovsky-Piskunov turbulent burning velocities

KPP (Kolmogorov-Petrovsky-Piskunov) solutions of the reaction-diffusion equation have application in various physical phenomena occurring in biology, ecology, and reacting flows. In particular, these solutions are commonly used in turbulent combustion to scale turbulent burning velocities. Subject to certain conditions on reaction rate profile through the flame brush and turbulent diffusivity, this theory relates the turbulent burning velocity to the derivative of the reaction rate ($\tilde{ω}$) at the leading edge of the flame brush ($d\tilde{ω}$/$d\tilde{c}$ | $\tilde{c} =$0 ). Such waves are often referred to as “pulled fronts.” However, turbulent flames never actually satisfy the KPP conditions for a pulled front, as the turbulent flame brush, parametrized here by the thickness δ t , consists of an ensemble of laminar flamelets of thickness δ, where ε=δ/δ t $\ll$ 1 is very small, but nonzero, and $d\tilde{ω}$ /$d\tilde{c}$ tends to zero at the brush leading edge for high activation energy, combustion-type kinetics. Here, this paper analyzes these effects on KPP wave solutions, parametrized by ε=δ/δ t and Zeldovich number Ze focusing on whether turbulent flames retain their pulled front character and what the correction to the KPP wave speed is. Variational solutions of the reaction-diffusion equation show that the solution can be expanded in powers of 1/|ln⁡ε|. Both numerical and asymptotic results are presented, showing that the wave still exhibits pulled front solutions but with significant corrections to the KPP result. The leading order correction is of the form |ln⁡ε| –2 and independent of Ze. Higher order corrections are function of both ε and Ze. However, the dominant factor influencing the wave speed correction is due to the finite ε, with Ze exhibiting a weaker effect.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗