Application Of Chemical Kinetics Research Articles

Developing a predictive model for low-temperature Laval nozzles with applications in chemical kinetics

Laval nozzles are used in the CRESU (“Cinétique de Réaction en Écoulement Supersonique Uniforme”) method to generate a collimated low temperature (5–200 K), low pressure (30–500 Pa), high Mach number (1 < M < 20) supersonic jet. Laval nozzles have been designed using the Method of Characteristics (MOC) since the development of CRESU, which is an analytical method that assumes inviscid, isentropic flow, and is routinely used to design nozzle profiles for a particular gas and temperature with a uniform shock free exit. This study aims to provide a robust computational framework to overcome the limitations of the MOC while also providing recommendations on the numerical model setup required to model a low-temperature supersonic jet. It also discusses the blockage effects when using the Pitot tube method for flow characterization, the influence of inlet turbulence and reservoir size. Numerical results are validated using two different experimental apparatuses from research groups at the University of Leeds and the University of Birmingham. Finally, a MATLAB framework was developed and has been provided as an open source toolbox to allow any user to perform computational fluid dynamics on any Laval nozzle, with the ability to change nozzle geometry, operating conditions and bath gas. The toolbox has been rigorously tested against many benchmark cases, which shows that steady-state Reynolds-averaged Navier–Stokes with the k-omega-shear stress transport turbulence model can be used to accurately predict global quantities, such as average temperature in the stable region of the supersonic jet.

A projection-based analytical Jacobian framework for chemical kinetics applications

A major challenge in simulating complex combustion systems with detailed chemical kinetic models is the cost of integrating the chemical source terms, often done using stiff ODE solvers that require frequent Jacobian evaluations. Using analytically derived Jacobian matrices instead of divided-difference-based numerical Jacobian approximations can significantly reduce the associated computational cost. However, ambiguities arise in the formulation of analytical Jacobians because the chemical state of the system, or state vector, can be expressed in multiple ways, involving variables that are typically not independent from one another. In this work, the consequences of those ambiguities on practical calculations are characterized in detail, and a generalized, projection-based framework is proposed as a mitigation strategy. Performances are assessed in a series of test cases involving a variety of configurations and numerical solution approaches. Results show that with proper treatment, commonly used analytical Jacobian formulations can be considered as equivalent for practical purposes, thereby alleviating concerns that the state vector chosen to express the governing equations and corresponding analytical Jacobian may significantly impact the accuracy of the simulations.

High-accuracy extrapolated ab initio thermochemistry. IV. A modified recipe for computational efficiency.

A number of economical modifications to the high-accuracy extrapolated ab initio thermochemistry (HEAT) model chemistry are evaluated. The two resulting schemes, designated as mHEAT and mHEAT+, are designed for efficient and pragmatic evaluation of molecular energies in systems somewhat larger than can be practically studied by the unapproximated HEAT scheme. It is found that mHEAT+ produces heats of formation with nearly subchemical (±1 kJ/mol) accuracy at a substantially reduced cost relative to the full scheme. Total atomization energies calculated using the new thermochemical recipes are compared to the results of the HEAT-345(Q) model chemistry, and enthalpies of formation for the three protocols are also compared to Active Thermochemical Tables. Finally, a small selection of transition states is studied using mHEAT and mHEAT+, which illuminates some interesting features of reaction barriers and serves as an initial benchmark of the performance of these model chemistries for chemical kinetics applications.

Active subspace-based dimension reduction for chemical kinetics applications with epistemic uncertainty

We focus on an efficient approach for quantification of uncertainty in complex chemical reaction networks with a large number of uncertain parameters and input conditions. Parameter dimension reduction is accomplished by computing an active subspace that predominantly captures the variability in the quantity of interest (QoI). In the present work, we compute the active subspace for a H2/O2 mechanism that involves 19 chemical reactions, using an efficient iterative strategy. The active subspace is first computed for a 19-parameter problem wherein only the uncertainty in the pre-exponents of the individual reaction rates is considered. This is followed by the analysis of a 36-dimensional case wherein the activation energies and initial conditions are also considered uncertain. In both cases, a 1-dimensional active subspace is observed to capture the uncertainty in the QoI, which indicates enormous potential for efficient statistical analysis of complex chemical systems. In addition, we explore links between active subspaces and global sensitivity analysis, and exploit these links for identification of key contributors to the variability in the model response.

SimKinet: A free educational tool based on an electrical analogy to solve chemical kinetic equations.

In this article we introduce the software SimKinet, a free tool specifically designed to solve systems of differential equations without any programming skill. The underlying method is the so-called Network Simulation Method, which designs and solves an electrical network equivalent to the mathematical problem. SimKinet is versatile, fast, presenting a real user-friendly interface, and can be employed for both educational and researching purposes. It is particularly useful in the first courses of different scientific degrees, mainly Chemistry and Physics, especially when facing non-analytic or complex-dynamics problems. Moreover, SimKinet would help students to understand fundamental concepts, being an opportunity to improve instruction in Chemistry, Mathematics, Physics and other Sciences courses, with no need of advanced knowledge in differential equations. The potency of SimKinet is demonstrated via two applications in chemical kinetics: the photochemical destruction of stratospheric ozone and the chaotic dynamics of the peroxidase-oxidase reaction.

Kinetic Approach to Determine 3-Amino Methyl Hexanoic Acid in Pharmaceutical Formulations

A simple and sensitive colorimetric spectrophotometric method based on application of chemical kinetics was produced and developed for the quantitative determination of 3-amino methyl hexanoic acid (pregabalin) in bulk and pharmaceutical preparations. Ninhydrin, a chromogenic agent was reacted with pregabalin at 70 °C and the absorbance was measured at 575 nm and kinetic correlation was evaluated between absorbance and time. The initial-rate, rate-constant and fixed-time (80 min) methods were employed for the estimation of pregabalin in the range of 10-30ug mL-1 which showed good correlation >0.9990 in all three cases with LOQ values ranging from 1.2-1.5 mL-1and LOD values ranging from 0.76-0.95 mL-1. Method validation was carried out using ICH recommendations and the variables were evaluated and optimized. The newly developed method has useful applications to determine pregabalin in pharmaceutical formulation with good recovery (98.38 to 102.12 %t) and precision (RSD < 1.4 %). Standard free energy changes and association constant were found to be 1.212 X 103 and -4.747, respectively, as determined by the Benesi-Hildebrand equation. Keywords: Colorimetric determination, pregabalin, ninhydrin, charge transfer complex.

Teaching the biological relevance of chemical kinetics using cold-blooded animal biology

Author(s): Ramachandran, Roshini | Abstract: This lesson plan was created to support non-chemistry major students in making connections between chemical kinetics and biological systems. Chemical kinetics is often viewed by students as an abstract topic, and one that is limited only to chemical reactions that occur in a laboratory. The subtopics of chemical kinetics can be challenging for students to apply in a different context, and students often learn the topic as remote tidbits of knowledge without a clear indication of its application. The lesson involves an activity utilizing real-life case studies with biological applications of chemical kinetics to enhance student understanding and improve interest and engagement in the topic. The case studies detail the immobilization of cold-blooded animals at very low temperatures and enlightens students about the unfortunate situation that iguanas and sea turtles faced as consequences of a particularly cold spell in in Florida during winter 2018. This activity allows students to view chemical kinetics in a new light and to brainstorm on methods to solve such problems faced in real-life.

Chemical Kinetics of Radiolabelling Reactions

The application of chemical kinetics is one of the most powerful and versatile tools for investigating reaction mechanisms in complex mixtures. Kinetic studies are commonplace in traditional synthetic chemistry but are seldom used in radiopharmaceutical sciences. When deriving standard reaction rate laws, the focus is normally placed on calculating the chemical concentration of different species over time. In radiopharmaceutical synthesis, the desired product is one of the radioactive components of the mixture. Reaction conditions are optimised to obtain the radioactive product in the highest activity yield. When short-lived radionuclides are used, radioactive decay during the reaction window means that the maximum activity yield does not necessarily coincide with the chemical or decay-corrected radiochemical yields. To account for this difference in the kinetic models, it is shown how standard integrated rate laws can be modified to incorporate the contribution from radioactive decay. An example is then presented to show how radiochemical kinetics can be used to model complex systems, like [18 F]FDG radiosynthesis, that involve parallel or competing reactions at the different chemical scales of the radionuclide and substrate. Increased knowledge of reaction rates, and a more wide-spread application of radiochemical kinetics, can facilitate the development of new radiolabelling reactions. Accurate identification of maximum activity yields using kinetic models also has the potential to improve the optimisation and radiochemical efficiency of all current and future radiopharmaceutical syntheses.

GPU-accelerated atmospheric chemical kinetics in the ECHAM/MESSy (EMAC) Earth system model (version 2.52)

Abstract. This paper presents an application of GPU accelerators in Earth system modeling. We focus on atmospheric chemical kinetics, one of the most computationally intensive tasks in climate–chemistry model simulations. We developed a software package that automatically generates CUDA kernels to numerically integrate atmospheric chemical kinetics in the global climate model ECHAM/MESSy Atmospheric Chemistry (EMAC), used to study climate change and air quality scenarios. A source-to-source compiler outputs a CUDA-compatible kernel by parsing the FORTRAN code generated by the Kinetic PreProcessor (KPP) general analysis tool. All Rosenbrock methods that are available in the KPP numerical library are supported.Performance evaluation, using Fermi and Pascal CUDA-enabled GPU accelerators, shows achieved speed-ups of 4. 5 × and 20. 4 × , respectively, of the kernel execution time. A node-to-node real-world production performance comparison shows a 1. 75 × speed-up over the non-accelerated application using the KPP three-stage Rosenbrock solver. We provide a detailed description of the code optimizations used to improve the performance including memory optimizations, control code simplification, and reduction of idle time. The accuracy and correctness of the accelerated implementation are evaluated by comparing to the CPU-only code of the application. The median relative difference is found to be less than 0.000000001 % when comparing the output of the accelerated kernel the CPU-only code.The approach followed, including the computational workload division, and the developed GPU solver code can potentially be used as the basis for hardware acceleration of numerous geoscientific models that rely on KPP for atmospheric chemical kinetics applications.

Chemical Kinetics for the Microbial Safety of Foods Treated with High Pressure Processing or Hurdles

The application of chemical kinetics is well known in food engineering, such as the use of Arrhenius plots and D- and z-values to characterize linear microbial inactivation kinetics by thermal processing. The emergence and growing commercialization of nonthermal processing technologies in the past decade provided impetus for the development of nonlinear models to describe nonlinear inactivation kinetics of foodborne microbes. One such model, the enhanced quasi-chemical kinetics (EQCK) model, postulates a mechanistic sequence of reaction steps and uses a chemical kinetics approach to developing a system of rate equations (ordinary differential equations) that provide the mathematical basis for describing an array of complex nonlinear dynamics exhibited by microbes in foods. Specifically, the EQCK model characterizes continuous growth–death–tailing dynamics (or subsets thereof) for pathogens such as Staphylococcus aureus, Listeria monocytogenes, or Escherichia coli in various food matrices (bread, turkey, ham, cheese) controlled by “hurdles” (water activity, pH, temperature, antimicrobials). The EQCK model is also used with high pressure processing (HPP), to characterize nonlinear inactivation kinetics for E. coli (inactivation plots show lag times), baro-resistant L. monocytogenes (inactivation plots show slight lag times and protracted tailing), and Bacillus amyloliquefaciens spores (inactivation plots show protracted tailing; HPP also induces spore activation and spore germination). We invoke further chemical kinetics principles by applying transition-state theory (TST) to the HPP inactivation of L. monocytogenes and develop novel dimensionless secondary models for temperature and pressure (TST temperature and TST pressure) to estimate kinetics parameters (activation energy E a and activation volume ∆V ‡), thereby offering new insights into the inactivation mechanisms of pathogenic organisms by HPP.

An Overview on Recent Trends in Catalysis

Copyright: © 2014 Shehadi IA. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The vast majority of chemical and biological activities and processes involve catalytic steps. Catalysis (homogeneous or heterogeneous) play an important role for chemicals manufacturing, utilizing of energy resources, energy conversion systems, devices and environmental control system, biological activities and drug discovery and design. However, the most important issues in any catalytic process are the activity and the selectivity of the catalysts by which processes are performed. In order to understand and control how a catalysts function, one must understand the energy profile through which the catalytic processes must go through. The energy content and transfer of any catalytic processes is easily understood by applying the principles of thermodynamics which provides an insight whether the process is attainable or not. Therefore, thermodynamics is used to describe the macroscopic behavior of chemical systems through understanding the properties of atoms and molecules. The area of thermodynamics is fully established and all laws that govern the energy flow and transfer are developed. Alternatively, the routes and the rate of the chemical processes happening are not yet fully comprehended. Hence, the application of chemical kinetics to understand catalytic activity and selectivity is still under investigation. Moreover, tremendous amounts of scientific discoveries are continually being achieved and more are to be revealed in the years to come. Even though a unifying principle has been identified in the area of chemical kinetics and compiled, but none are faultless. Each principle has its own defects and limitations. Understanding the mechanistic behavior of chemical systems in general and catalysis in particular, lead to significant discoveries in current scientific research. These days, scientists can study, monitor and characterize fast and ultra-fast reactions using laser pulses involved in numerous techniques. One of the most prominent areas of catalytic research these days is to understand the electronic and ionic transfer in biological systems. Functional ion channels in particular are the focus of many recent catalytic research works directed to understand gating, closing and filtering mechanism of the channel. In order to understand the basic channel mechanics, researchers have focused upon questions surrounding the functioning, selectivity, and gating mechanisms of ion channels. Another attractive area for research is to study electron transfer in proteins and enzymes in order to understand functions and properties. Such areas have boomed after the discovery of the genomic code of many living organisms which led to the discovery of thousands of proteins and enzymes of unknown functions and structures. However, recent advances in biophysics especially in X-ray crystallography, high-resolution electron microscopy and molecular biology have helped shed light on some of the issues in scientific quests.

OS3-1 KUCRS - Detailed Kinetic Mechanism Generator for Versatile Fuel Components and Mixtures(OS3 Application of chemical kinetics to combustion modeling,Organized Session Papers)

OS3-1 KUCRS - Detailed Kinetic Mechanism Generator for Versatile Fuel Components and Mixtures(OS3 Application of chemical kinetics to combustion modeling,Organized Session Papers)

OS3-7 Numerical Analysis of Effect of Intermediate Species Diffusion on Low Temperature Oxidation Process in a Homogeneous n-Heptane Mixture(OS3 Application of chemical kinetics to combustion modeling,Organized Session Papers)

OS3-7 Numerical Analysis of Effect of Intermediate Species Diffusion on Low Temperature Oxidation Process in a Homogeneous n-Heptane Mixture(OS3 Application of chemical kinetics to combustion modeling,Organized Session Papers)

OS3-5 Comparison of PRF and Toluene/n-heptane Mixture in the Mechanism of Compression Ignition Using Transient Species Measurements and Simplified Model Analysis(OS3 Application of chemical kinetics to combustion modeling,Organized Session Papers)

OS3-5 Comparison of PRF and Toluene/n-heptane Mixture in the Mechanism of Compression Ignition Using Transient Species Measurements and Simplified Model Analysis(OS3 Application of chemical kinetics to combustion modeling,Organized Session Papers)

OS3-4 Correlations Between Ignition Delay Times and Research Octane Number of Alkanes(OS3 Application of chemical kinetics to combustion modeling,Organized Session Papers)

OS3-4 Correlations Between Ignition Delay Times and Research Octane Number of Alkanes(OS3 Application of chemical kinetics to combustion modeling,Organized Session Papers)

OS3-3 Chemical Kinetics Study on Effect of Pressure on Hydrocarbon Ignition Process(OS3 Application of chemical kinetics to combustion modeling,Organized Session Papers)

OS3-3 Chemical Kinetics Study on Effect of Pressure on Hydrocarbon Ignition Process(OS3 Application of chemical kinetics to combustion modeling,Organized Session Papers)

Nonisothermal Analysis of Solution Kinetics by Spreadsheet Simulation

A fast and generally applicable alternative solution to the problem of determining the useful shelf life of medicinal solutions is described. It illustrates the power and convenience of the combination of numerical simulation and nonlinear least squares with a practical pharmaceutical application of chemical kinetics and thermodynamics, validated by comparison with literature data.

Chemical kinetics and diffusion approach: the history of the Klein–Kramers equation

In this essay, the first statistical and stochastic treatments of chemical dynamics are analyzed and discussed, in particular the diffusive description of chemical reactions. The first part of the paper introduces the historical and methodological basis of the theories about stochastic processes and diffusion as well as their lesser-known applications in chemical kinetics, which were advanced by Jens Anton Christiansen (1888–1969). In the second, part we will focus our attention on the early works of Oskar Benjamin Klein (1894–1977) and Hendrik Anton Kramers (1894–1952) on electrolytes and the latter’s more mature work, which completes and gives a firm theoretical background to Christiansen’s description.

Detailed balance in multiple-well chemical reactions

Chemical reactions that involve multiple, interconnected potential wells are of paramount importance in applications of chemical kinetics, particularly combustion and atmospheric chemistry. The only accurate way of determining phenomenological rate constants theoretically for this type of reaction is from the solution of a time-dependent, multiple-well master equation. In this Perspective we address the issue of whether or not (and to what extent) detailed balance is satisfied by rate constants obtained from such solutions. In addressing this issue we discuss a number of related topics, including necessary and sufficient conditions for a system of first-order rate equations to evolve to chemical equilibrium and the relationship between detailed balance and Wegscheider conditions. The assumption of a "near-Boltzmann" distribution in the wells sheds considerable light on the issue at hand. We discuss this approximation in some detail and suggest a quantitative measure of "near-Boltzmann". It is extremely unlikely that the rate constants of interest satisfy detailed balance exactly (there is no reason to believe that they do). However, the discrepancies are expected to be vanishingly small, as observed in practice.

Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics

In cell biology, cell signaling pathway problems are often tackled with deterministic temporal models, well mixed stochastic simulators, and/or hybrid methods. But, in fact, three dimensional stochastic spatial modeling of reactions happening inside the cell is needed in order to fully understand these cell signaling pathways. This is because noise effects, low molecular concentrations, and spatial heterogeneity can all affect the cellular dynamics. However, there are ways in which important effects can be accounted without going to the extent of using highly resolved spatial simulators (such as single-particle software), hence reducing the overall computation time significantly. We present a new coarse grained modified version of the next subvolume method that allows the user to consider both diffusion and reaction events in relatively long simulation time spans as compared with the original method and other commonly used fully stochastic computational methods. Benchmarking of the simulation algorithm was performed through comparison with the next subvolume method and well mixed models (MATLAB), as well as stochastic particle reaction and transport simulations (CHEMCELL, Sandia National Laboratories). Additionally, we construct a model based on a set of chemical reactions in the epidermal growth factor receptor pathway. For this particular application and a bistable chemical system example, we analyze and outline the advantages of our presented binomial tau-leap spatial stochastic simulation algorithm, in terms of efficiency and accuracy, in scenarios of both molecular homogeneity and heterogeneity.