Calculation Of Reaction Rates Research Articles

Concentration sensing in crowded environments

Signal transduction within crowded cellular compartments is essential for the physiological function of cells. Although the accuracy with which receptors can probe the concentration of ligands has been thoroughly investigated in dilute systems, the effect of macromolecular crowding on the inference of concentration remains unclear. In this work, we develop an algorithm to simulate reversible reactions between reacting Brownian particles. Our algorithm facilitates the calculation of reaction rates and correlation times for ligand-receptor systems in the presence of macromolecular crowding. Using this method, we show that it is possible for crowding to increase the accuracy of estimated ligand concentration based on receptor occupancy. In particular, we find that crowding can enhance the effective association rates between small ligands and receptors to a degree sufficient to overcome the increased chance of rebinding due to caging by crowding molecules. For larger ligands, crowding decreases the accuracy of the receptor’s estimate primarily by decreasing the microscopic association and dissociation rates.

Photocatalytic properties of nanosized zinc ferrite and zinc chromite

A simple one-step synthesis of developed surface zinc ferrite is proposed (S BET = 453.1 m2 g−1). The formation of zinc ferrite, zinc chromite (S BET = 53.6 m2 g−1), and mixed zinc ferrite-chromite (S BET = 37.4 m2 g−1) structures is studied. The resulting materials are analysed using x-ray phase and x-ray fluorescence analysis, IR spectrometry, electron microscopy, TGA and BET method. Single-phase sample formation mechanism is proposed, which includes transition element cation chelate complex formation stage in the presence of citric acid and subsequent thermal decomposition of the complexes formed. The synthesised materials exhibited photocatalytic activity in the decomposition of an organic dye under the action of hydrogen peroxide. The highest catalytic activity is demonstrated by zinc ferrite in acidic medium; the calculated reaction rate constant is 0.010 min−1 for ZnFe2O4, 0.008 min−1 for ZnFeCrO4, 0.007 min−1 for ZnCr2O4. The results can be applied to obtain materials suitable for wastewater treatment processes at industrial enterprises where organic dyes are used in production cycles.

An integrated approach for modeling and identification of perfusion bioreactors via basis flux modes

This paper discusses the challenges associated with the reliable and optimal operation of perfusion bioreactors and presents methods for modeling and identification of perfusion bioreactors as well as the vision for their integration. After presenting a generic model of perfusion bioreactors, the paper shows how to use the concept of basis flux modes to uniquely compute reaction rates. The advantage of this concept with respect to elementary flux nodes and similar concepts in metabolic flux analysis is the reduced number of flux modes that need to be modeled. In addition, a procedure to identify the model and estimate the parameters for each reaction using Monod-type kinetics is presented. It is shown that the rational structure of these kinetic models results in optimization problems that are amenable to tractable computation of globally optimal parameter estimates. The methods are illustrated via examples with simulated or experimental data.

Exploring reactions of amines-model compounds with NH2: In relevance to nitrogen conversion chemistry in biomass

Amine-containing compounds (primary/NH2, secondary/NH and heterocyclic –NH) -are principal nitrogenated species in biomass. Amine radical (NH2) emerge as an important intermediate in the initial stages of biomass combustion and pyrolysis. A detail understanding of the nitrogen conversion chemistry necessitates acquiring accurate reaction rate constants for reactions of NH2 radicals with amine-bearing molecules. With the absence of relevant kinetic parameters, pertinent kinetic model on oxidation of surrogate biomass compounds often utilize values extracted from analogous reactions with OH and CH3 radicals. Herein, we report comprehensive kinetic parameters for H abstraction by NH2 radicals from various C/H sites in seventeen amine model compounds, comprising primary/secondary alkyl and aromatic amines. Fitted activation energies were found to linearly correlate with N–H bond dissociation enthalpies via Evans–Polanyi plots. In primary C2-C4 alkylamines and in diethylamine, abstraction from the α C–H site (gem to the amine group) largely dominates that from the NH2 group. Abstraction from NH and methyl sites in dimethylamine entails comparable importance. A vinylic CH2 group does not alter kinetics of abstraction for unsaturated amines when contrasted with primary amines. Reaction rate constants for H abstraction from heterocyclic-NH structures follow the order carbazole > indole > pyrrole, reflecting corresponding BDHs values for their N–H bonds. Updating kinetic models on combustion of small amines structures, with the newly calculated reaction rate constants, slightly improves their predictive performance toward the yields of NH2/NH3.

Acid hydrolysis-based sugarcane bagasse biorefining for levulinic acid production: Dynamic mechanistic modeling under varying operating conditions

The study on the lignocellulosic material conversion into bio-based platform chemicals, such as levulinic acid (LA), is one of the most promising routes to promote the development of advanced biorefineries. In this work, a dynamic mechanistic model is developed to simulate the LA production from lignocellulosic material. A wide operating range is used to estimate the parameters of the reaction kinetics. Because multi-parameter estimation problem is complex, a genetic algorithm-based optimization procedure is used to determine the optimum parameters values. Measurements are obtained for various reaction times (0 - 45 min) temperatures (150 – 200 °C) and acid concentration of 7.0 % w/v H2SO4. The calculated reaction rates for the state variables, concentrations of LA, glucose, 5-hydroxymethylfurfural and humins are used to construct the dynamic mechanistic model. The prediction of measured state variables was particularly accurate, as determined by the root mean square error (RMSE) and correlation coefficient (R2). Therefore, a satisfactory agreement between experimental LA yield of 57.2 mol% and computed LA yield of 56.4 mol% was achieved (at 200 °C, 7.0 % w/v H2SO4, 45 min). The proposed methodology drives the systematic development of an industrially reliable dynamic mechanistic model for LA production from sugarcane bagasse as a means to increase the LA yields in the biorefinery.

Numerical study on simplified reaction set of ground state species in CO<sub>2</sub> discharges under Martian atmospheric conditions

The exploration of Mars has attracted increasing interest in these years. The experiments and simulations show that strong electric field triggered by the dust storms in the Martian atmosphere may cause CO<sub>2</sub> discharge. Studies on this phenomenon will not only help deepen our comprehension on the evolution of Martian surface, but also provide a possibility to realize the <i>in-situ</i> oxygen generation on Mars based on plasma chemistry. In this paper, a zero-dimensional global model is used to simplify the complicated description of CO<sub>2</sub> chemical kinetics, therefore a reduced chemistry can be obtained for detailed numerical simulation in the near future. At the beginning of simplification, the graph theoretical analysis is used to pre-treat the original model by exploring the relationship between reacting species. Through the study of connectivity and the topological network, species such as O<sub>2</sub>, e, and CO prove to be important in the information transmission of the network. While gaining a clearer understanding of the chemistry model, dependence analysis will be used to investigate numerical simulation results. In this way a directed relation diagram can be obtained, where the influence between different species is quantitively explained in terms of numerical solutions. Users could keep different types of species correspondingly according to their own needs, and in this paper, some species with low activeness such as C<sub>2</sub>O, <inline-formula><tex-math id="M5">\begin{document}$ {\mathrm{O}}_{5}^{+} $\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="21-20210664_M5.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="21-20210664_M5.png"/></alternatives></inline-formula>, <inline-formula><tex-math id="M6">\begin{document}$ {\mathrm{O}}_{4}^{-} $\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="21-20210664_M6.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="21-20210664_M6.png"/></alternatives></inline-formula> and species with uncertainties such as <inline-formula><tex-math id="M7">\begin{document}$ {\mathrm{C}}_{2}{\mathrm{O}}_{2}^{+} $\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="21-20210664_M7.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="21-20210664_M7.png"/></alternatives></inline-formula>, <inline-formula><tex-math id="M8">\begin{document}$ {\mathrm{C}\mathrm{O}}_{4}^{+} $\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="21-20210664_M8.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="21-20210664_M8.png"/></alternatives></inline-formula> are removed from the original model. As for the reduction of specific reactions among species, the reaction proportion analysis based on the calculation of reaction rates is used to obtain the contribution of each reaction to the entire process of CO<sub>2</sub> discharge, through which the important reactions can be selected. Finally, a simplified chemistry model of CO<sub>2</sub> discharge based on Martian atmospheric conditions, including 16 species and 67 reactions, is established. The numerical simulations show that the trends of species densities based on the simplified chemistry model are highly consistent with those based on the original one, and considerations about the CO<sub>2</sub> conversion and the energy efficiency are also in line with expectations, which can help deepen the understanding of the essential process of CO<sub>2</sub> discharge under Martian atmospheric conditions. In addition, the quantitative results of the relationship between reactive species will lay a theoretical foundation for the accurate analysis of various products in Martian dust storm discharges and the realization of Mars <i>in-situ</i> oxygen generation technology based on plasma chemistry.

A kinetics study on hydrogen abstraction reactions of cyclopentane by hydrogen, methyl, and ethyl radicals.

Hydrogen abstraction reactions of (cyclo)alkanes by radicals play a fundamental role in both combustion and atmospheric chemistry. In this work, we select three common radicals in the pyrolysis of hydrocarbon fuels: hydrogen radical (H[combining dot above]), methyl radical (ĊH3), and ethyl radical (ĊH2CH3) to investigate the kinetics of their hydrogen abstraction reactions with cyclopentane. The rate constants over a broad temperature range of 150-3000 K are calculated by using the multi-structural variational transition state theory in the small-curvature tunneling approximation (MS-CVT/SCT), by which the multi-structural torsional (MS-T) anharmonicity of partition functions, variational effects, and corner-cutting tunneling are all included in dynamics calculations. We stress the particular importance of considering the MS-T anharmonicity in the rate constant calculation for the reaction with the ethyl radical compared to those with hydrogen and methyl radicals. The MS-T anharmonicity significantly accelerates the reaction with the ethyl radical in the whole temperature range, and in particular, it increases the rate constant by a factor of >-9 at 1000 K. We also found that the tunneling effect drastically increases the rate constants at low-temperatures by up to 3-5 orders of magnitudes. The calculated reaction rate constants have an order of .

New Thermonuclear Reaction Rate Equations for Radiative Neutron Capture

The radiative neutron capture reaction rates have been studied at very low energies which are of interest for nuclear astrophysics. The rates for many of these reactions have remained independent of temperature so far. The temperature dependence of the thermonuclear reaction rates have been explored within the statistical model. Apart from the compound nuclear contribution, the pre-equilibrium as well as the direct effects have been taken into account. The corresponding Maxwellian-averaged thermonuclear reaction rates of relevance in astrophysical plasmas at temperatures in the range from 10$^6$ K to 10$^{10}$ K have been calculated. Analytical expression as a function of $T_9$ has been provided for $^6$Li(n,$\gamma$)$^7$Li by fitting the calculated reaction rate.

High resolution measurements with miniature neutron scintillators in the SUR-100 zero power reactor

Three 1-mm3 miniature fiber-coupled scintillators have been used to perform cm-wise resolution measurements of the thermal neutron flux within experimental channels of the SUR-100 facility, a zero power thermal reactor operated by the Institute of Nuclear Technology and Energy Systems at the University of Stuttgart. The detection system is developed at the École Polytechnique Fédérale de Lausanne in collaboration with the Paul Scherrer Institut. Thermal neutrons count rates were measured along the experimental channels I and II, which cross the reactor at the center and tangentially to the core, respectively. The reactor was modelled with the Monte Carlo neutron transport code Serpent-2.1.31. The comparison of experimental and computed reaction rate distributions showed a good agreement within the core region, with discrepancies within 2σ. An unexpected discrepancy, probably caused by a geometric inconsistency in the computational model of the reactor, was observed in the reflector region of the experimental channel I, where a 20% difference (i.e. 8σ) was found between experimental and simulated results. Significant discrepancies, respectively worth 10σ and 15σ, were noticed at distance, in the lead shielding region, for both experimental channels I and II. In addition, reaction rate gradients across the 2.6 cm and 5.4 cm diameters of both channels were measured. A horizontal reaction rate gradient of (9.09 ± 0.20) % was measured within 2.4 cm across the diameter of the experimental channel II, with a difference from computed results of 2%. The absence of a vertical reaction rate gradient inside the experimental channel I was confirmed by measurements.

Calculation of Photons Reaction Rate Resulting at 120 kVp X-ray Tube Voltage and 1 mAs as Function to Digital Imaging and Communications in Medicine Pixel Numbers Using Monte Carlo N-Particle Transport and a Voxel Model of a 29-Year-Old Patient

Calculation of Photons Reaction Rate Resulting at 120 kVp X-ray Tube Voltage and 1 mAs as Function to Digital Imaging and Communications in Medicine Pixel Numbers Using Monte Carlo N-Particle Transport and a Voxel Model of a 29-Year-Old Patient

A new approach for balancing the microbial synthesis of ethyl acetate and other volatile metabolites during aerobic bioreactor cultivations.

Ethyl acetate is an organic solvent with many industrial applications, currently produced by energy‐intensive chemical processes based on fossil carbon resources. Ethyl acetate can be synthesized from renewable sugars by yeasts like Kluyveromyces marxianus in aerobic processes. However, ethyl acetate is highly volatile and thus stripped from aerated cultivation systems which complicate the quantification of the produced ester. Synthesis of volatile metabolites is commonly monitored by repeated analysis of metabolite concentrations in both the gas and liquid phase. In this study, a model‐based method for quantifying the synthesis and degradation of volatile metabolites was developed. This quantification of volatiles is solely based on repeatedly measured gas‐phase concentrations and allows calculation of reaction rates and yields in high temporal resolution. Parameters required for these calculations were determined in abiotic stripping tests. The developed method was validated for ethyl acetate, ethanol and acetaldehyde which were synthesized by K. marxianus DSM 5422 during an iron‐limited batch cultivation; it was shown that the presented method is more precise and less time‐consuming than the conventional method. The biomass‐specific synthesis rate and the yield of ethyl acetate varied over time and exhibited distinct momentary maxima of 0.50 g g‒1h‒1 and 0.38 g g‒1 at moderate iron limitation.

Multidimensional Hydrogen Tunneling in Supported Molecular Switches: The Role of Surface Interactions.

The nuclear tunneling crossover temperature (T_{c}) of hydrogen transfer reactions in supported molecular-switch architectures can lie close to room temperature. This calls for the inclusion of nuclear quantum effects (NQEs) in the calculation of reaction rates even at high temperatures. However, computations of NQEs relying on standard parametrized dimensionality-reduced models quickly become inadequate in these environments. In this Letter, we study the paradigmatic molecular switch based on porphycene molecules adsorbed on metallic surfaces with full-dimensional calculations that combine density-functional theory for the electrons with the semiclassical ring-polymer instanton approximation for the nuclei. We show that the double intramolecular hydrogen transfer (DHT) rate can be enhanced by orders of magnitude due to surface fluctuations in the deep-tunneling regime. We also explain the origin of an Arrhenius temperature dependence of the rate below T_{c} and why this dependence differs at different surfaces. We propose a simple model to rationalize the temperature dependence of DHT rates spanning diverse fcc [110] surfaces.

Kinetics of Sequential Protopectin Degradation in a Flowing Reaction Solution

The degradation mechanism of protopectin was studied using beet pulp, pomelo albedo, and sunflower calathides as examples. Experimental data were processed according to sequential irreversible reactions (PP → MG → PS) occurring in a flowing reaction solution. This approach enabled evaluation of the main kinetic parameters of the reduced equation and calculation of the reaction rate constant and activation energy of secondary phytomass protopectin degradation. The results made it possible to regulate the production of pectinic polysaccharides with given physicochemical parameters.

Calculation of Astrophysical S-factor and Thermonuclear Reaction Rates for (p,n) Medium Elements Reactions

The cross-sections of (p,n) medium elements reactions as a function of proton energies such as 45Sc(p,n)45Ti, 48Ti(p,n)48V, 51V(p,n)51Cr, 52Cr(p,n)52Mn, 55Mn(p,n)55Fe, 56Fe(p,n)56Co, 59Co(p,n)59Ni, 62Ni(p,n)62Cu, 63Cu(p,n)63Zn, and 66Zn(p,n)66Ga have been interpolated near threshold up to 10 MeV in step of 0.05 MeV using MATLAB program. Weighted averages of cross-sections have been used to calculate the astrophysical S-factor and thermonuclear reaction rates as a function of the center of mass energy, Ec.m. and T9 respectively. Polynomial expressions have been used to fit the calculated astrophysical S-factor and thermonuclear reaction rates to determine the astrophysical S-factor at various Ec.m. and thermonuclear reaction rates at various T9 from best fitting equations with minimum Chi-Square. Empirical formulae of reactions set 45Sc(p,n)45Ti, 48Ti(p,n)48V, 55Mn(p,n)55Fe, 59Co(p,n)59Ni, 66Zn(p,n)66Ga and reactions set 48Ti(p,n)48V, 51V(p,n)51Cr, 59Co(p,n)59Ni, 63Cu(p,n)63Zn, 66Zn(p,n)66Ga have been used to calculate the astrophysical S-factor as a function of Ec.m. and Z and thermonuclear reaction rates as a function of T9 and Z of target nucleus. The results have been compared with the adopted data that have been calculated from the fitting equations which have a good agreement.

An improved path-integral method for golden-rule rates.

We present a simple method for the calculation of reaction rates in the Fermi golden-rule limit, which accurately captures the effects of tunneling and zero-point energy. The method is based on a modification of the recently proposed golden-rule quantum transition state theory (GR-QTST) of Thapa, Fang, and Richardson [J. Chem. Phys. 150, 104107 (2019)]. While GR-QTST is not size consistent, leading to the possibility of unbounded errors in the rate, our modified method has no such issue and so can be reliably applied to condensed phase systems. Both methods involve path-integral sampling in a constrained ensemble; the two methods differ, however, in the choice of constraint functional. We demonstrate numerically that our modified method is as accurate as GR-QTST for the one-dimensional model considered by Thapa and co-workers. We then study a multidimensional spin-boson model, for which our method accurately predicts the true quantum rate, while GR-QTST breaks down with an increasing number of boson modes in the discretization of the spectral density. Our method is able to accurately predict reaction rates in the Marcus inverted regime without the need for the analytic continuation required by Wolynes theory.

Proceeding on the riddles of ketene pyrolysis by applying ab initio quantum chemical computational methods in a detailed kinetic modeling study

As ketene is a crucial intermediate for the high-temperature combustion of oxygenated hydrocarbons in general, an in-depth understanding of its chemistry is a fundamental requirement for the kinetic modeling of bio-based fuels. To gain a profound insight into the decomposition of ketene and subsequent reaction pathways high level ab initio methods were used. DSD-PBEP86/cc-pVTZ level of theory was applied for the geometries and frequencies, while single-point energies were determined at the CCSDT-1a level of theory extrapolated to the basis set limit. The reaction rate parameters for 38 reactions involved in the ketene chemistry including C1 to C4 species like acetylene, ethylene, propyne and allene were computed. For a total of 16 species, the thermochemistry were updated. The calculated rate parameters and the two new species cyclopropenone and 1,4-dioxo-1,3-butadiene were used to update the AramcoMech 3.0 base mechanism, which was then validated against speciation measurements during ketene pyrolysis. A reaction pathway analysis was performed to find the most prominent reactions at the investigated conditions and to discuss the simulation results. A significant improvement in the model’s prediction capability was found when applying the newly calculated reaction rate parameter and thermochemical data.

Reaction Rate of Radiative Capture of a Neutron by a 2H Nucleus

Within the framework of the modified potential cluster model with forbidden states, n2H radiative capture is considered at energies from 10 meV (0.01 eV) to 10 MeV. It is shown that on the basis of p2H-interaction potentials with small changes it is possible to correctly reproduce the available experimental data. On the basis of theoretical total cross sections, the reaction rate of n2H capture has been calculated in the temperature range from 0.01 T9 to 10 T9. The calculated reaction rate is approximated by a simple expression, which simplifies its use in other works.

Correlated energy uncertainties in reaction rate calculations

Context. Monte Carlo methods can be used to evaluate the uncertainty of a reaction rate that arises from many uncertain nuclear inputs. However, until now no attempt has been made to find the effect of correlated energy uncertainties in input resonance parameters. Aims. Our goal is to investigate the impact of correlated resonance energy uncertainties on reaction rates. Methods. Using a combination of numerical and Monte Carlo variation of resonance energies, the effect of correlations are investigated. Five reactions are considered: two fictional, illustrative cases and three reactions whose rates are of current interest. Results. The effect of correlations in resonance energies depends on the specific reaction cross section and temperatures considered. When several resonances contribute equally to a reaction rate, and when they are located on either side of the Gamow peak, correlations between their energies dilute their effect on reaction rate uncertainties. If they are both located above or below the maximum of the Gamow peak, however, correlations between their resonance energies can increase the reaction rate uncertainties. This effect can be hard to predict for complex reactions with wide and narrow resonances contributing to the reaction rate.

Reaction rate calculation of d(α, γ)6Li process at low energy in framework of effective field theory

Reaction rate of the process d(α, γ)6Li has been calculated in the framework of Effective Field Theory (EFT) at low energy. Deuteron is assumed as a dibaryon in the initial state. The reaction amplitude for the initial P-wave states of deuteron-alpha and reaction rate for sum of E1 and E2 transitions are found in the framework of EFT up to NLO. Our results are in good agreement with the recent experimental data and the other theoretical works.

A study of the oxidation behaviour of FeCrAl-ODS in air and steam environments up to 1400 °C

As a candidate accident tolerant fuel cladding material, the high temperature oxidation behaviour of an Oxygen Dispersion Strengthened (ODS) Fe–12Cr–6Al alloy has been examined in isothermal air and steam environments. While the oxidation behaviour of FeCrAl has been extensively studied, very little has been reported in the literature on FeCrAl-ODS, which is the focus of this manuscript. By conducting Thermogravimetric Analysis (TGA), oxidation experiments were performed on specimens of Fe–12Cr–6Al-ODS at temperatures up to 1400 °C in air and up to 1215 °C in high purity steam. Oxidation kinetics were evaluated by calculating reaction rate constants and activation energies. The formation of an alumina scale was correlated to kinetics results from TGA by coupling Scanning Electron Microscopy (SEM) with Energy Dispersive X-ray Spectroscopy (EDS) line scans to investigate the chemical composition of the primary oxide layer, local oxidation effects, as well as the bulk alloy material. Electron Probe Micro-Analysis (EPMA) point scans were applied to the heavily oxidized specimen to achieve an accurate composition profiling of areas of interest. Finally, thermodynamic calculations were performed to interpret the formation of the complex oxide layer. These experiments support research efforts for the development of accident tolerant fuel technologies at Nippon Nuclear Fuel Development Co., Ltd.