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1

Christophorov, L. N. "Indirect Evidences of Conformational Regulation in Protein Reactions: How Much Can Be Learnt?" Ukrainian Journal of Physics 57, no. 7 (2012): 746. http://dx.doi.org/10.15407/ujpe57.7.746.

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Almost all reactions of proteins manifest deviations from the simple behaviour prescribed by standard (bio)chemical kinetics. This is caused by the extraordinary structural lability of protein macromolecules which is often not less important for the reaction efficiency than the properties of the active center. Unveiling the mechanisms of structural regulation encounters serious difficulties because of their hidden character, as either modern experiments or computational methods still fall short of monitoring simultaneously the reaction events and concomitant conformational changes, so that one
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2

König, Matthias. "cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK." F1000Research 5 (July 18, 2016): 1736. http://dx.doi.org/10.12688/f1000research.9211.1.

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Kinetic data of biochemical reactions are essential for the creation of kinetic models of biochemical networks. One of the main resources of such information is SABIO-RK, a curated database for kinetic data of biochemical reactions and their related information. Despite the importance for computational modelling there has been no simple solution to visualize the kinetic data from SABIO-RK. In this work, I present cy3sabiork, an app for querying and visualization of kinetic data from SABIO-RK in Cytoscape. The kinetic information is accessible via a combination of graph structure and annotation
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3

Shishanov, Mikhail V., Ilya D. Tsvetkov, Dmitry V. Yashunin, et al. "KINETICS OF ANILINE-FORMALDEHYDE INTERACTION UNDER CONDITIONS OF HOMOGENEOUS CATALYSIS." ChemChemTech 67, no. 11 (2024): 55–62. https://doi.org/10.6060/ivkkt.20246711.7030.

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The work is devoted to the kinetic modeling of reactions for the production of 4,4-diaminodiphenylmethane (MDA) in the presence of a catalyst. FASHION is a solid substance from colorless to pale yellow in color with a faint odor. It is used on an industrial scale mainly for the manufacture of polyurethanes, which have many applications, for example, insulating materials in mail containers. MDA is also used for the manufacture of coating materials, adhesives, spandex fibers, dyes, and rubber. This product belongs to the categories of medium and low-tonnage industries, which determines its impor
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Menshutina, Natalia V., Igor V. Lebedev, Evgeniy A. Lebedev, Ratmir R. Dashkin, Mikhail V. Shishanov, and Maxim L. Burdeyniy. "STUDY AND MODELING 4,4'-DIAMINODIPHENYLMETHANE SYNTHESIS." IZVESTIYA VYSSHIKH UCHEBNYKH ZAVEDENII KHIMIYA KHIMICHESKAYA TEKHNOLOGIYA 64, no. 4 (2021): 100–103. http://dx.doi.org/10.6060/ivkkt.20216404.6314.

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The presented work is devoted to reactions of obtaining 4,4´-diaminodiphenylmethane in the presence of a catalyst. The work describes the importance of studying 4,4´-diaminodiphenylmethane obtaining process and possibility of cellular automata approach in modelling chemical reactions. Cellular automata model which allows to predict the kinetic curves of the studied 4,4´-diaminodiphenylmethane-obtaining reaction. Model reflects two processes that are observed in the system under study - the movement of reagents under the stirring and the reaction in the presence of a catalyst. The suggested mod
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Menshutina, Natalia, Igor Lebedev, Evgeniy Lebedev, et al. "Complex Modelling and Design of Catalytic Reactors Using Multiscale Approach—Part 2: Catalytic Reactions Modelling with Cellular Automata Approach." Computation 8, no. 4 (2020): 87. http://dx.doi.org/10.3390/computation8040087.

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The presented work is devoted to reactions of obtaining 4,4’-Diaminodiphenylmethane (MDA) in the presence of a catalyst model. The work describes the importance of studying the MDA obtaining process and the possibility of the cellular automata (CA) approach in the modelling of chemical reactions. The work suggests a CA-model that makes it possible to predict the kinetic curves of the studied MDA-obtaining reaction. The developed model was used to carry out computational experiments under the following different conditions—aniline:formaldehyde:catalyst ratios, stirrer speed, and reaction temper
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6

Ke, Wei, Guang-Jin Chen, and Daoyi Chen. "Methane–propane hydrate formation and memory effect study with a reaction kinetics model." Progress in Reaction Kinetics and Mechanism 45 (January 2020): 146867832090162. http://dx.doi.org/10.1177/1468678320901622.

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Although natural gas hydrates and hydrate exploration have been extensively studied for decades, the reaction kinetics and nucleation mechanism of hydrate formation is not fully understood. In its early stage, gas hydrate formation can be assumed to be an autocatalytic kinetic reaction with nucleation and initial growth. In this work, a reaction kinetics model has been established to form structure II methane–propane hydrate in an isochoric reactor. The computational model consists of six pseudo-elementary reactions for three dynamic processes: (1) gas dissolution into the bulk liquid, (2) a s
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7

Rosero Chicaíza, David Camilo, and Bibian A. Hoyos. "Reaction kinetic parameters for a distributed model of transport and reaction in Pd/Rh/CeZrO three-way catalytic converters." DYNA 86, no. 210 (2019): 216–23. http://dx.doi.org/10.15446/dyna.v86n210.78596.

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This paper presents a two-dimensional distributed model for the transport and reaction of combustion gases in channels of three-way catalytic converters, considering a detailed reaction kinetics with 16 chemical reactions in palladium and rhodium catalysts, and taking into account diffusive effects within the coating, to obtain a new set of reaction kinetic parameters that do not depend on the thickness of the coating. The model was solved using a finite volume method with a first order upwind scheme and simulations were conducted using computational fluid dynamics. The model with the new dist
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8

Yen, Shih-Wei, Wei-Hsin Chen, Jo-Shu Chang, Chun-Fong Eng, Salman Raza Naqvi, and Pau Loke Show. "Torrefaction Thermogravimetric Analysis and Kinetics of Sorghum Distilled Residue for Sustainable Fuel Production." Sustainability 13, no. 8 (2021): 4246. http://dx.doi.org/10.3390/su13084246.

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This study investigated the kinetics of isothermal torrefaction of sorghum distilled residue (SDR), the main byproduct of the sorghum liquor-making process. The samples chosen were torrefied isothermally at five different temperatures under a nitrogen atmosphere in a thermogravimetric analyzer. Afterward, two different kinetic methods, the traditional model-free approach, and a two-step parallel reaction (TPR) kinetic model, were used to obtain the torrefaction kinetics of SDR. With the acquired 92–97% fit quality, which is the degree of similarity between calculated and real torrefaction curv
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9

Huang, Sijia, Kangmin Kim, Grant M. Musgrave, et al. "Determining Michael acceptor reactivity from kinetic, mechanistic, and computational analysis for the base-catalyzed thiol-Michael reaction." Polymer Chemistry 12, no. 25 (2021): 3619–28. http://dx.doi.org/10.1039/d1py00363a.

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10

Varela, J. A., S. A. Vázquez, and E. Martínez-Núñez. "An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis." Chemical Science 8, no. 5 (2017): 3843–51. http://dx.doi.org/10.1039/c7sc00549k.

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A novel computational method based on a procedure combining accelerated direct dynamics with an efficient geometry-based post-processing algorithm is proposed for use in discovering reaction mechanisms and solving the kinetics of transition metal-catalyzed reactions.
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11

Park, Jongmin, Hyo Seok Kim, Won Bo Lee, and Myung-June Park. "Trends and Outlook of Computational Chemistry and Microkinetic Modeling for Catalytic Synthesis of Methanol and DME." Catalysts 10, no. 6 (2020): 655. http://dx.doi.org/10.3390/catal10060655.

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The first-principle modeling of heterogeneous catalysts is a revolutionarily approach, as the electronic structure of a catalyst is closely related to its reactivity on the surface with reactant molecules. In the past, detailed reaction mechanisms could not be understood, however, computational chemistry has made it possible to analyze a specific elementary reaction of a reaction system. Microkinetic modeling is a powerful tool for investigating elementary reactions and reaction mechanisms for kinetics. Using a microkinetic model, the dominant pathways and rate-determining steps can be elucida
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Gajewska, Magdalena, and Katarzyna Skrzypiec. "Kinetics of nitrogen removal processes in constructed wetlands." E3S Web of Conferences 26 (2018): 00001. http://dx.doi.org/10.1051/e3sconf/20182600001.

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The aim of this paper is to present a state-of-the-art review of the kinetics of nitrogen removal in constructed wetlands. Biological processes of nitrogen removal from wastewater can be described using equations and kinetic models. Hence, these kinetic models which have been developed and evaluated allow for predicting the removal of nitrogen in treatment wetlands. One of the most important, first order removal model, which is still applied, was analysed and its rate coefficients and factors were compared. This study also demonstrates the validity of Monod and multiple Monod kinetics, commonl
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13

Shibata, Masao Suzuki, Yu Chen, Alexandra Zagalskaya, et al. "Impact of Double Layer on Electrochemical Kinetics via Bottom up Multiscale Modeling Approach." ECS Meeting Abstracts MA2024-02, no. 61 (2024): 4090. https://doi.org/10.1149/ma2024-02614090mtgabs.

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Electric double layers (EDLs) play a fundamental role in various electrochemical processes such as colloidal dispersions, surface charging, and charge-transfer reactions. Increasingly, the role of EDLs on reaction kinetics is being studied[1], revealing their importance in predicting the intrinsic and electrolyte-dependent kinetics of electrochemical reactions. Despite the extensive history of EDL modeling, there remain challenges in predicting the impact of EDL structure on reaction kinetics. The characteristic length of EDL for non-dilute solutions (typically 10 – 100 nanometers) exceeds the
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14

Saraee, Hossein S., Kevin J. Hughes, and Mohamed Pourkashanian. "Construction of a Small-Sized Simplified Chemical Kinetics Model for the Simulation of n-Propylcyclohexane Combustion Properties." Energies 17, no. 5 (2024): 1103. http://dx.doi.org/10.3390/en17051103.

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The development of a compact mechanism has made a great contribution to work on the combustion of hydrocarbon species and facilitates the investigations on chemical kinetics and computational fluid dynamics (CFD) studies. N-propylcyclohexane (NPCH) is one of the important components for jet, diesel, and gasoline fuels which needs a reliable compact reaction kinetics mechanism. This study aims to investigate the construction of a well-validated mechanism for NPCH with a simplified chemical kinetics model that delivers a good prediction ability for the key combustion parameters in a wide range o
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15

Ilyin, Daniil V., William A. Goddard, Julius J. Oppenheim, and Tao Cheng. "First-principles–based reaction kinetics from reactive molecular dynamics simulations: Application to hydrogen peroxide decomposition." Proceedings of the National Academy of Sciences 116, no. 37 (2018): 18202–8. http://dx.doi.org/10.1073/pnas.1701383115.

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This paper presents our vision of how to use in silico approaches to extract the reaction mechanisms and kinetic parameters for complex condensed-phase chemical processes that underlie important technologies ranging from combustion to chemical vapor deposition. The goal is to provide an analytic description of the detailed evolution of a complex chemical system from reactants through various intermediates to products, so that one could optimize the efficiency of the reactive processes to produce the desired products and avoid unwanted side products. We could start with quantum mechanics (QM) t
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16

Lording, William J., Alan D. Payne, Tory N. Cayzer, Michael S. Sherburn, and Michael N. Paddon-Row. "A Combined Computational–Experimental Study of the Kinetics of Intramolecular Diels–Alder Reactions in a Series of 1,3,8-Nonatrienes." Australian Journal of Chemistry 68, no. 2 (2015): 230. http://dx.doi.org/10.1071/ch14430.

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Activation enthalpies for a series of five 1,3,8-nonatriene intramolecular Diels–Alder (IMDA) reactions involving substrates 1–5 have been determined experimentally and Singleton’s natural abundance method has been employed to determine kinetic isotope effects in the IMDA reaction of fumarate 3. The activation enthalpies for the IMDA reactions of the systems possessing a –CH2OCH2– diene/dienophile tether are significantly smaller than their counterparts possessing the –CH2OC(=O)– tether. The experimental activation enthalpies have been used to benchmark computed values from four model chemistr
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17

Dias Vicentini, Eduardo, Ana P. de Lima Batista, and Antonio G. Sampaio de Oliveira-Filho. "Computational mechanistic investigation of the Fe + CO2 → FeO + CO reaction." Physical Chemistry Chemical Physics 22, no. 29 (2020): 16943–48. http://dx.doi.org/10.1039/d0cp00479k.

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18

Yu, Chunkan, Felipe Minuzzi, and Ulrich Maas. "Numerical Simulation of Turbulent Flames based on a Hybrid RANS/Transported-PDF Method and REDIM Method." Eurasian Chemico-Technological Journal 20, no. 1 (2018): 23. http://dx.doi.org/10.18321/ectj705.

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A hybrid RANS/Transported-PDF model for the simulation of turbulent reacting flows based on automatically reduced mechanisms for the chemical kinetics (reaction-diffusion manifold, REDIM) is presented in this work. For modelling of turbulent reacting flows, chemistry is a key problem and affects largely the accuracy. The PDF method has been widely used since the chemical source term is in a closed form, without any modelling. Despite of this advantage of PDF method, detailed chemical kinetics is not desired due to its heavy computational effort. From this aspect, the detailed chemical kinetics
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19

Wacławek, Stanisław. "Do We Still Need a Laboratory to Study Advanced Oxidation Processes? A Review of the Modelling of Radical Reactions used for Water Treatment." Ecological Chemistry and Engineering S 28, no. 1 (2021): 11–28. http://dx.doi.org/10.2478/eces-2021-0002.

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Abstract Environmental pollution due to humankind’s often irresponsible actions has become a serious concern in the last few decades. Numerous contaminants are anthropogenically produced and are being transformed in ecological systems, which creates pollutants with unknown chemical properties and toxicity. Such chemical pathways are usually examined in the laboratory, where hours are often needed to perform proper kinetic experiments and analytical procedures. Due to increased computing power, it becomes easier to use quantum chemistry computation approaches (QCC) for predicting reaction pathw
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20

Raymond, K. W., and Y. Pocker. "Bistability and the ordered bimolecular mechanism." Biochemistry and Cell Biology 69, no. 9 (1991): 661–64. http://dx.doi.org/10.1139/o91-098.

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An equation describing the instantaneous velocity of an ordered bimolecular enzymatic reaction that exhibits inhibition by substrate and product was derived. Using kinetic constant values for horse liver alcohol dehydrogenase, the velocity expression was applied to an open-reaction system. The calculated steady-state surfaces displayed regions of bistability, which further substantiates the link between substrate inhibition and multiple steady states. This general computational approach may be applied to any system that can be described by an instantaneous velocity equation.Key words: bistabil
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21

Li, Han-Jung, Hui-Lung Chen, Jee-Gong Chang, Hsin-Tsung Chen, Shiuan-Yau Wu, and Shin-Pon Ju. "Computational Study on Reaction Mechanisms and Kinetics of Diazocarbene Radical Reaction with NO." Journal of Physical Chemistry A 114, no. 18 (2010): 5894–901. http://dx.doi.org/10.1021/jp1008016.

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22

Kočí, V., M. Keppert, and R. Černý. "Reaction kinetics of basaltic elements in cementitious matrices: theoretical considerations." Journal of Physics: Conference Series 2628, no. 1 (2023): 012011. http://dx.doi.org/10.1088/1742-6596/2628/1/012011.

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Abstract Basalt fibers, the frequently mentioned alternative to those made of steel, possess very good mechanical properties and temperature resistance. The alkaline environment of cement matrix makes it vulnerable due to partial fiber decomposition by the effects of OH- ions. This paper aims at computational modelling of such reactions in order to approximate the course of degradation or to predict it lately. The isothermal reaction models are discussed to reveal their strong/weak points by means of fundamental reaction mechanisms analysis. The shape factor and diffusion-based deceleration of
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23

Venier, Cesar M., Erick Torres, Gastón G. Fouga, Rosa A. Rodriguez, Germán Mazza, and Andres Reyes Urrutia. "Computational Modeling of Biomass Fast Pyrolysis in Fluidized Beds with Eulerian Multifluid Approach." Fluids 9, no. 12 (2024): 301. https://doi.org/10.3390/fluids9120301.

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This study investigated the fast pyrolysis of biomass in fluidized-bed reactors using computational fluid dynamics (CFD) with an Eulerian multifluid approach. A detailed analysis was conducted on the influence of various modeling parameters, including hydrodynamic models, heat transfer correlations, and chemical kinetics, on the product yield. The simulation framework integrated 2D and 3D geometrical setups, with numerical experiments performed using OpenFOAM v11 and ANSYS Fluent v18.1 for cross-validation. While yield predictions exhibited limited sensitivity to drag and thermal models (with
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Yang, Shu, San Kiang, Parham Farzan, and Marianthi Ierapetritou. "Optimization of Reaction Selectivity Using CFD-Based Compartmental Modeling and Surrogate-Based Optimization." Processes 7, no. 1 (2018): 9. http://dx.doi.org/10.3390/pr7010009.

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Mixing is considered as a critical process parameter (CPP) during process development due to its significant influence on reaction selectivity and process safety. Nevertheless, mixing issues are difficult to identify and solve owing to their complexity and dependence on knowledge of kinetics and hydrodynamics. In this paper, we proposed an optimization methodology using Computational Fluid Dynamics (CFD) based compartmental modelling to improve mixing and reaction selectivity. More importantly, we have demonstrated that through the implementation of surrogate-based optimization, the proposed m
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25

Akanni, Olatokunbo O., Hisham A. Nasr-El-Din, and Deepak Gusain. "A Computational Navier-Stokes Fluid-Dynamics-Simulation Study of Wormhole Propagation in Carbonate-Matrix Acidizing and Analysis of Factors Influencing the Dissolution Process." SPE Journal 22, no. 06 (2017): 2049–66. http://dx.doi.org/10.2118/187962-pa.

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Summary This study demonstrates the application of an alternative numerical-simulation approach to effectively describe the flow field in a two-scale carbonate-matrix-acidizing model. The modified model accurately captures the dissolution regimes that occur during carbonate-matrix acidizing. Sensitivity tests were performed on the model to compare the output with experimental observations and previous two-scale models in the literature. A nonlinear reaction-kinetics model for alternative acidizing fluids is also introduced. In this work, the fluid-field flow is described by the Navier-Stokes m
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26

Moghazy, Yasmen M., Nagwa MM Hamada, Magda F. Fathalla, Yasser R. Elmarassi, Ezzat A. Hamed, and Mohamed A. El-Atawy. "Understanding the reaction mechanism of the regioselective piperidinolysis of aryl 1-(2,4-dinitronaphthyl) ethers in DMSO: Kinetic and DFT studies." Progress in Reaction Kinetics and Mechanism 46 (January 2021): 146867832110274. http://dx.doi.org/10.1177/14686783211027446.

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Reactions of aryl 1-(2,4-dinitronaphthyl) ethers with piperidine in dimethyl sulfoxide at 25oC resulted in substitution of the aryloxy group at the ipso carbon atom. The reaction was measured spectrophotochemically and the kinetic studies suggested that the titled reaction is accurately third order. The mechanism is began by fast nucleophilic attack of piperidine on C1 to form zwitterion intermediate (I) followed by deprotonation of zwitterion intermediate (I) to the Meisenheimer ion (II) in a slow step, that is, SB catalysis. The regular variation of activation parameters suggested that the r
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27

Poley, Isabela M., and Leandro S. Oliveira. "CFD Modeling and Simulation of Transesterification Reactions of Vegetable Oils with an Alcohol in Baffled Stirred Tank Reactors." Applied Mechanics and Materials 390 (August 2013): 86–90. http://dx.doi.org/10.4028/www.scientific.net/amm.390.86.

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Alcohol and triglycerides do not form a single phase mixture and thus there is a poor surface contact between them causing transesterification to proceed relatively slow. Introduction of stirring improves the surface contact and consequently the reaction rates and biodiesel yields. Thus, in industrial processes, transesterification is usually carried out in stirred tank reactors. Investigating how this type of reactor works is necessary for successful design, operation and optimization. Experimental methods for investigating flow-fields and chemical reactions are expensive and time demanding a
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28

Nissen, Anna, Zhouyuan Zhu, Anthony Kovscek, Louis Castanier, and Margot Gerritsen. "Upscaling Kinetics for Field-Scale In-Situ-Combustion Simulation." SPE Reservoir Evaluation & Engineering 18, no. 02 (2015): 158–70. http://dx.doi.org/10.2118/174093-pa.

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Summary We demonstrate the effectiveness of a non-Arrhenius kinetic upscaling approach for in-situ-combustion processes, first discussed by Kovscek et al. (2013). Arrhenius reaction terms are replaced with equivalent source terms that are determined by a work flow integrating both laboratory experiments and high-fidelity numerical simulations. The new formulation alleviates both stiffness and grid dependencies of the traditional Arrhenius approach. Consequently, the computational efficiency and robustness of simulations are improved significantly. In this paper, we thoroughly investigate the p
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29

Cerri, G., V. Michelassi, S. Monacchia, and S. Pica. "Kinetic combustion neural modelling integrated into computational fluid dynamics." Proceedings of the Institution of Mechanical Engineers, Part A: Journal of Power and Energy 217, no. 2 (2003): 185–92. http://dx.doi.org/10.1243/09576500360611218.

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The attempt to replace traditional chemical kinetics model calculations with new ones based on neural networks (NNs) has been successfully carried out. The paper deals with the methodology that has been followed to replace traditional model calculations with neural models (NMs) for methane/air combustion. The reacting flowfield has been described with account taken of the detailed chemical reaction mechanism. Convective and turbulent diffusive transport of species has been taken into consideration by means of a well-known finite volume computational fluid dynamics (CFD) code. Two versions of s
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30

Berkemeier, Thomas, Matteo Krüger, Aryeh Feinberg, Marcel Müller, Ulrich Pöschl, and Ulrich K. Krieger. "Accelerating models for multiphase chemical kinetics through machine learning with polynomial chaos expansion and neural networks." Geoscientific Model Development 16, no. 7 (2023): 2037–54. http://dx.doi.org/10.5194/gmd-16-2037-2023.

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Abstract. The heterogeneous chemistry of atmospheric aerosols involves multiphase chemical kinetics that can be described by kinetic multi-layer models (KMs) that explicitly resolve mass transport and chemical reactions. However, KMs are computationally too expensive to be used as sub-modules in large-scale atmospheric models, and the computational costs also limit their utility in inverse-modeling approaches commonly used to infer aerosol kinetic parameters from laboratory studies. In this study, we show how machine learning methods can generate inexpensive surrogate models for the kinetic mu
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31

Simka, H., M. Hierlemann, M. Utz, and K. F. Jensen. "Computational Chemistry Predictions of Kinetics and Major Reaction Pathways for Germane Gas‐Phase Reactions." Journal of The Electrochemical Society 143, no. 8 (1996): 2646–54. http://dx.doi.org/10.1149/1.1837063.

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Huang, Xue Zheng, and Hai Ling Chen. "Development of the Simulation Software on the Complex Reaction Kinetics." Advanced Materials Research 634-638 (January 2013): 7–10. http://dx.doi.org/10.4028/www.scientific.net/amr.634-638.7.

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The design idea and design flow of the simulation software on the complex reaction kinetics are introduced in this article. Firstly, the total framework of the software was determined by the goal and function of the software; Secondly, the manuscript was written, the multimedia material was made and the computational programs were designed, the examples of making multimedia material by Photoshop and Flash are introduced, moreover, the thinking and method of program is introduced; Finally, The material such as text, images, sounds, animation is integrated by Authorware. The simulation software
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Benjamin, Ilan. "Chemical Reaction Dynamics at Liquid Interfaces: A Computational Approach." Progress in Reaction Kinetics and Mechanism 27, no. 2 (2002): 87–126. http://dx.doi.org/10.3184/007967402103165360.

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Recent advances in experimental and theoretical studies of liquid interfaces provide remarkable evidence for the unique properties of these systems. In this review we examine how these properties affect the thermodynamics and kinetics of chemical reactions which take place at the liquid/vapor interface and at the liquid/liquid interface. We demonstrate how the rapidly varying density and viscosity, the marked changes in polarity and the surface roughness manifest themselves in isomerization, electron transfer and photodissociation reactions.
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Xue, Jingwen, Fangfang Ma, Jonas Elm, Jingwen Chen, and Hong-Bin Xie. "Atmospheric oxidation mechanism and kinetics of indole initiated by ●OH and ●Cl: a computational study." Atmospheric Chemistry and Physics 22, no. 17 (2022): 11543–55. http://dx.doi.org/10.5194/acp-22-11543-2022.

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Abstract. The atmospheric chemistry of organic nitrogen compounds (ONCs) is of great importance for understanding the formation of carcinogenic nitrosamines, and ONC oxidation products might influence atmospheric aerosol particle formation and growth. Indole is a polyfunctional heterocyclic secondary amine with a global emission quantity almost equivalent to that of trimethylamine, the amine with the highest atmospheric emission. However, the atmospheric chemistry of indole remains unclear. Herein, the reactions of indole with ⚫OH and ⚫Cl, and subsequent reactions of resulting indole radicals
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Lakin, Matthew R., Simon Youssef, Luca Cardelli, and Andrew Phillips. "Abstractions for DNA circuit design." Journal of The Royal Society Interface 9, no. 68 (2011): 470–86. http://dx.doi.org/10.1098/rsif.2011.0343.

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DNA strand displacement techniques have been used to implement a broad range of information processing devices, from logic gates, to chemical reaction networks, to architectures for universal computation. Strand displacement techniques enable computational devices to be implemented in DNA without the need for additional components, allowing computation to be programmed solely in terms of nucleotide sequences. A major challenge in the design of strand displacement devices has been to enable rapid analysis of high-level designs while also supporting detailed simulations that include known forms
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Ai, Jiali, Chi Zhai, and Wei Sun. "Study on the Formation of Complex Chemical Waveforms by Different Computational Methods." Processes 8, no. 4 (2020): 393. http://dx.doi.org/10.3390/pr8040393.

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Chemical wave is a special phenomenon that presents periodic patterns in space-time domain, and the Belousov–Zhabotinsky (B-Z) reaction is the first well-known reaction-diffusion system that exhibits organized patterns out of a homogeneous environment. In this paper, the B-Z reaction kinetics is described by the Oregonator model, and formation and evolution of chemical waves are simulated based on this model. Two different simulation methods, partial differential equations (PDEs) and cellular automata (CA) are implemented to simulate the formation of chemical waveform patterns, i.e., target wa
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Gaidamauskaitė, E., and R. Baronas. "A Comparison of Finite Difference Schemes for Computational Modelling of Biosensors." Nonlinear Analysis: Modelling and Control 12, no. 3 (2007): 359–69. http://dx.doi.org/10.15388/na.2007.12.3.14697.

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This paper presents a one-dimensional-in-space mathematical model of an amperometric biosensor. The model is based on the reaction-diffusion equations containing a non-linear term related to Michaelis-Menten kinetics of the enzymatic reactions. The stated problem is solved numerically by applying the finite difference method. Several types of finite difference schemes are used. The numerical results for the schemes and couple mathematical software packages are compared and verified against known analytical solutions. Calculation results are compared in terms of the precision and computation ti
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38

SHIH, ANGELA, CALINA CIOBANU, and FU-MING TAO. "THEORETICAL MECHANISMS AND KINETICS FOR THE REACTION OF DIMETHYL SULFIDE AND OZONE IN WATER VAPOR." Journal of Theoretical and Computational Chemistry 04, no. 04 (2005): 1101–17. http://dx.doi.org/10.1142/s0219633605001982.

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The reaction mechanisms and kinetics for DMS + O 3 ⇒ DMSO + O 2 in water vapor are studied using density functional theory. A series of reaction pathways are determined with molecular clusters containing the reacting species and up to three water molecules. The results show that the energy barrier, defined as the energy difference between the reactant complex and the transition state, decreases progressively as each water molecule is added to the reacting system. A decreasing energy barrier is attributed to favorable electrostatic interactions between the reacting species and water at the tran
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39

Eikerling, Michael, and Xinwei Zhu. "(Keynote) Deciphering Electrocatalytic Reactions with Theory and Computation: The Case of CO2 Reduction." ECS Meeting Abstracts MA2022-01, no. 49 (2022): 2076. http://dx.doi.org/10.1149/ma2022-01492076mtgabs.

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The interfacial region between metal surface and aqueous electrolyte is of central importance for electrochemical reactions. The need to understand the properties of this electrochemical double layer (EDL) region drives extensive research.1,2 A foremost goal of research in electrocatalysis is the development of a theoretical-computational framework. The fundamental task for such a framework is to unravel the complex interplay of electronic structure effects of the catalyst material, potential-induced variations of the chemisorption state, local reaction conditions on the electrolyte side, and
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40

Baiano, Carmen, Jacopo Lupi, Nicola Tasinato, Cristina Puzzarini, and Vincenzo Barone. "The Role of State-of-the-Art Quantum-Chemical Calculations in Astrochemistry: Formation Route and Spectroscopy of Ethanimine as a Paradigmatic Case." Molecules 25, no. 12 (2020): 2873. http://dx.doi.org/10.3390/molecules25122873.

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The gas-phase formation and spectroscopic characteristics of ethanimine have been re-investigated as a paradigmatic case illustrating the accuracy of state-of-the-art quantum-chemical (QC) methodologies in the field of astrochemistry. According to our computations, the reaction between the amidogen, NH, and ethyl, C2H5, radicals is very fast, close to the gas-kinetics limit. Although the main reaction channel under conditions typical of the interstellar medium leads to methanimine and the methyl radical, the predicted amount of the two E,Z stereoisomers of ethanimine is around 10%. State-of-th
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41

Zhang, Yunju, Bing He, and Yuxi Sun. "Computational study on the mechanisms and kinetics of the CH2CCl + O2 reaction." Canadian Journal of Chemistry 98, no. 8 (2020): 395–402. http://dx.doi.org/10.1139/cjc-2019-0293.

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The potential energy surface for the CH2CCl + O2 reaction has been investigated by using the CCSD(T)/cc-pVTZ//B3LYP/6-311++G(d,p) method. Two type reaction mechanisms have been located. The H-abstraction of CH2CCl by O2 generates CHCCl + HO2 surmounting a 20.86 kcal/mol barrier. The addition between O2 and CH2CCl proceeds to an intermediate CH2CClO2 (IM1t and IM1c) without a barrier, which can further dissociate or isomerize to various products with the complicated processes. The temperature and pressure dependence rate constants for the CH2CCl + O2 reaction were computed by means of multi-cha
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42

Xu, Z. F., and M. C. Lin. "Kinetics and mechanism for the CH2O + NO2 reaction: A computational study." International Journal of Chemical Kinetics 35, no. 5 (2003): 184–90. http://dx.doi.org/10.1002/kin.10115.

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43

Thota, Srinivasarao, C. Balarama Krishna, and Thulasi Bikku. "AN ITERATIVE ALGORITHM FOR OPTIMIZING REACTION KINETICS AND THERMODYNAMIC EQUILIBRIA: APPLICATIONS IN CHEMICAL SYSTEMS." RASAYAN Journal of Chemistry 18, no. 03 (2025): 1347–53. https://doi.org/10.31788/rjc.2025.1839247.

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his article presents a novel repetitive procedure to work out non-linear equations commonly encountered in chemical systems, such as reaction kinetics and thermodynamic equilibria. The algorithm combines exponential decay and derivative-based adjustments to iteratively refine solutions, making it highly effective for optimizing reaction rates and determining equilibrium concentrations in complex chemical reactions. We demonstrate the algorithm's applicability in solving reaction rate optimization problems and chemical equilibrium equations, where traditional analytical solutions are often impr
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44

Gallego-Villada, Luis A., Wander Y. Perez-Sena, Julián E. Sánchez-Velandia, et al. "Synthesis of dihydrocarvone over dendritic ZSM-5 Zeolite: A comprehensive study of experimental, kinetics, and computational insights." Chemical Engineering Journal 498 (June 7, 2024): 155377. https://doi.org/10.1016/j.cej.2024.155377.

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This study explores the isomerization of limonene-1,2-epoxide (LE) from kinetic and mechanistic viewpoints, using a dendritic ZSM-5 zeolite (d-ZSM-5) as a highly selective catalyst for the formation of dihydrocarvone (DHC) in the form of diastereoisomers (<em>cis</em>&nbsp;+&nbsp;<em>trans</em>). Ethyl acetate, a green solvent, was used at mild reaction temperatures (50&ndash;&ndash;&ndash;70&nbsp;&deg;C). DHC, which can also be extracted from caraway oil, is widely used as an intermediate for epoxylactone production and as a constituent in flavors and perfumes. Kinetic modeling of LE isomeriz
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He, Bo, Wan Sheng Nie, Song Jiang Feng, and Guo Qiang Li. "A Modified Implicit Iterative Difference Algorithm for Stiff Chemical Kinetic Equations in Complex Combustion System." Advanced Materials Research 295-297 (July 2011): 2333–40. http://dx.doi.org/10.4028/www.scientific.net/amr.295-297.2333.

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The splitting-operator method has been widely used in the numerical simulation of complex combustion system with its high computation efficiency. The main difficult encountered in the method is how to integrate the stiff chemical kinetics ordinary differential equation (ODE) efficiently and accurately in each grid node of flow field. Although several ODE software packages such as LSODE and VODE have very predominant performance in integrating stiff and non-stiff case, it couldn’t ensure the positivity of mass fraction in integrating stiff chemical kinetic ODE. A detail liquid rocket hypergolic
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Stack, Andrew G., and Paul R. C. Kent. "Geochemical reaction mechanism discovery from molecular simulation." Environmental Chemistry 12, no. 1 (2015): 20. http://dx.doi.org/10.1071/en14045.

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Environmental context Computational simulations are providing an increasingly useful way to isolate specific geochemical and environmental reactions and to test how important they are to the overall rate. In this review, we summarise a few ways that one can simulate a reaction and discuss each technique’s overall strengths and weaknesses. Selected case studies illustrate how these techniques have helped to improve our understanding for geochemical and environmental problems. Abstract Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile and ro
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47

Planas, Ferran, Michael J. McLeish, and Fahmi Himo. "Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis." Beilstein Journal of Organic Chemistry 15 (January 16, 2019): 145–59. http://dx.doi.org/10.3762/bjoc.15.15.

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Thiamin diphosphate (ThDP)-dependent enzymes constitute a large class of enzymes that catalyze a diverse range of reactions. Many are involved in stereospecific carbon–carbon bond formation and, consequently, have found increasing interest and utility as chiral catalysts in various biocatalytic applications. All ThDP-catalyzed reactions require the reaction of the ThDP ylide (the activated state of the cofactor) with the substrate. Given that the cofactor can adopt up to seven states on an enzyme, identifying the factors affecting the stability of the pre-reactant states is important for the o
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48

Boteju, Welathantrige Thilini Niranga, Akhil Abraham, Sathish Ponnurangam, and Venkataraman Thangadurai. "Effective Lithium Polysulfides Anchoring on Vanadium Disulfide Facets for Lithium-Sulfur Batteries – A Computational Study." ECS Meeting Abstracts MA2024-01, no. 5 (2024): 742. http://dx.doi.org/10.1149/ma2024-015742mtgabs.

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The commercialization of Li-S batteries is hindered by the shuttle effects of lithium polysulfides (LiPS) and the sluggish reaction kinetics. Hence, effectively trapping and promoting the conversion rates of LiPSs is of prime importance1. However, the fundamental kinetics of the electrocatalytic charging and discharging of Li-S batteries and the underlying mechanism have not been sufficiently explored yet.2 Therefore, by taking the 2D transition metal sulfide, VS2 as a model, we conducted a systematic investigation using density functional theory to study the ability of dominant exposed crysta
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49

Makul, Natt. "Towards Computational CO2 Capture and Storage Models." Global Environmental Engineers 8 (December 25, 2021): 55–69. http://dx.doi.org/10.15377/2410-3624.2021.08.5.

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This review is aimed to increase knowledge on computational CO2 capture and storage models that are gradually evolving in the design and development to act as more effective carbon capture agents with acceptable toxicity and costs and complementary adjuncts to experiments for comprehending amino-CO2 reaction mechanisms. Also, the review discussed experimental research of degradation reactions of aqueous organic amines, measurements, kinetics and forecasts of amine pKₐ values and amine-CO2 equilibria. Also, the researcher comprehensively discussed the computational simulation of mechanisms of c
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Hafeez, Sumbul, Vikas Khatri, Hemant K. Kashyap, and Leena Nebhani. "Computational and experimental approach to evaluate the effect of initiator concentration, solvents, and enes on the TEMPO driven thiol–ene reaction." New Journal of Chemistry 44, no. 43 (2020): 18625–32. http://dx.doi.org/10.1039/d0nj02882g.

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The fundamental mechanism and reaction kinetics of the TEMPO initiated thiol–ene reaction between benzyl mercaptan and variable enes in the presence of varying initiator concentration and varying solvents has been studied experimentally and computationally.
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