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A Closer Look at Chemical Kinetics
This book proposes a closer look at chemical kinetics, which in this specific case, should be understood as a more detailed study of the connections of this discipline with other branches of chemistry and, even more, with other areas of science and technology. The first part which includes two chapters explores theoretical developments where the connections of chemical kinetics with mathematical modeling of scientific and industrial problems are clearly illustrated. The second part of the volume is devoted to experimental chemical kinetics, where specific reactions are studied in Chapters Three to Six. In all these chapters, kinetic studies allow the authors to propose mechanisms consistent with the experimental results obtained. In the third part of the book which includes the following two chapters different types of catalytic processes are studied, particularly those related to electrocatalysis, photocatalysis, and surface phenomena. The fourth part of this volume presents a work related to nanotechnology and its catalytic applications. The fifth and last part of this volume exemplifies the link between chemical kinetics and industrial processes, particularly in metallurgy.
eBook
Advanced prediction of combustion phasing in methane homogeneous engines via in-cylinder ion current profiling and a novel ionic kinetics framework
This study presents a reduced ionic chemical kinetics mechanism for predicting combustion phasing in methane-fueled homogeneous charge compression ignition (HCCI) engines. Starting from the detailed GRI-Mech 3.0 mechanism, a reduced scheme with 22 species and 48 reactions was developed. Ionic reactions were then added, forming a comprehensive mechanism with 27 species and 54 reactions. The mechanism was integrated into a multi-zone combustion model and validated against experimental data from a CFR engine under four operating conditions. Results show that the mechanism accurately predicts the start of combustion (SOC), with a maximum error below 0.09%. In-cylinder pressure and temperature profiles closely match experimental data. The model also captures the behavior of key radicals and ions, including H₃O⁺, OH⁻, and O₂⁻. Exhaust emissions such as CO and CO₂ are predicted with relative errors under 12%, while UHC predictions show moderate discrepancies. Notably, electrons are fully consumed during combustion, while some ions remain in the exhaust. The proposed mechanism offers a reliable and computationally efficient tool for combustion diagnostics and control, with potential applications in low-temperature and fuel-flexible engine technologies.
Journal Article
Molecular kinetics in condensed phases
A guide to the theoretical and computational toolkits for the modern study of molecular kinetics in condensed phases
Molecular Kinetics in Condensed Phases: Theory, Simulation and Analysis puts the focus on the theory, algorithms, simulations methods and analysis of molecular kinetics in condensed phases. The authors – noted experts on the topic – offer a detailed and thorough description of modern theories and simulation methods to model molecular events. They highlight the rigorous stochastic modelling of molecular processes and the use of mathematical models to reproduce experimental observations, such as rate coefficients, mean first passage times and transition path times.
The book's exploration of simulations examines atomically detailed modelling of molecules in action and the connections of these simulations to theory and experiment. The authors also explore the applications that range from simple intuitive examples of one- and two-dimensional systems to complex solvated macromolecules. This important book:
* Offers an introduction to the topic that combines theory, simulation and analysis
* Presents a guide written by authors that are well-known and highly regarded leaders in their fields
* Contains detailed examples and explanation of how to conduct computer simulations of kinetics. A detailed study of a two-dimensional system and of a solvated peptide are discussed.
* Discusses modern developments in the field and explains their connection to the more traditional concepts in chemical dynamics
Written for students and academic researchers in the fields of chemical kinetics, chemistry, computational statistical mechanics, biophysics and computational biology, Molecular Kinetics in Condensed Phases is the authoritative guide to the theoretical and computational toolkits for the study of molecular kinetics in condensed phases.
eBook
Dynamics and kinetics in structural biology: the example of DNA photolyase
All biochemical reactions directly involve structural changes that may occur over a very wide range of timescales from femtoseconds to seconds. Understanding the mechanism of action thus requires determination of both the static structures of the macromolecule involved and short-lived intermediates between reactant and product. This requires either freeze-trapping of intermediates, for example by cryo-electron microscopy, or direct determination of structures in active systems at near-physiological temperature by time-resolved X-ray crystallography. Storage ring X-ray sources effectively cover the time range down to around 100 ps that reveal tertiary and quaternary structural changes in proteins. The briefer pulses emitted by hard X-ray free electron laser sources extend that range to femtoseconds, which covers critical chemical reactions such as electron transfer, isomerization, breaking of covalent bonds, and ultrafast structural changes in light-sensitive protein chromophores and their protein environment. These reactions are exemplified by the time-resolved X-ray studies by two groups of the FAD-based DNA repair enzyme, DNA photolyase, over the time range from 1 ps to 100 μs.
Journal Article
A hybrid tau-leap for simulating chemical kinetics with applications to parameter estimation
We consider the problem of efficiently simulating stochastic models of chemical kinetics. The Gillespie stochastic simulation algorithm (SSA) is often used to simulate these models; however, in many scenarios of interest, the computational cost quickly becomes prohibitive. This is further exacerbated in the Bayesian inference context when estimating parameters of chemical models, as the intractability of the likelihood requires multiple simulations of the underlying system. To deal with issues of computational complexity in this paper, we propose a novel hybrid τ-leap algorithm for simulating well-mixed chemical systems. In particular, the algorithm uses τ-leap when appropriate (high population densities), and SSA when necessary (low population densities, when discrete effects become non-negligible). In the intermediate regime, a combination of the two methods, which uses the properties of the underlying Poisson formulation, is employed. As illustrated through a number of numerical experiments, the hybrid τ offers significant computational savings when compared with SSA without, however, sacrificing the overall accuracy. This feature is particularly welcomed in the Bayesian inference context, as it allows for parameter estimation of stochastic chemical kinetics at reduced computational cost.
Journal Article
A Stochastic Simulator of Birth–Death Master Equations with Application to Phylodynamics
In this article, we present a versatile new software tool for the simulation and analysis of stochastic models of population phylodynamics and chemical kinetics. Models are specified via an expressive and human-readable XML format and can be used as the basis for generating either single population histories or large ensembles of such histories. Importantly, phylogenetic trees or networks can be generated alongside the histories they correspond to, enabling investigations into the interplay between genealogies and population dynamics. Summary statistics such as means and variances can be recorded in place of the full ensemble, allowing for a reduction in the amount of memory used—an important consideration for models including large numbers of individual subpopulations or demes. In the case of population size histories, the resulting simulation output is written to disk in the flexible JSON format, which is easily read into numerical analysis environments such as R for visualization or further processing. Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships.
Journal Article
Response Surface Modeling for COD Removal in Electroplating Effluent Using Sacrificial Electrodes by Electro Fenton Process: Optimization and Analysis
The effluent produced by the electroplating industry contains hazardous and toxic chemicals that pose a threat to living organisms and ecosystems. Consequently, it is essential to employ advanced treatment technologies to remove the toxicants from the wastewater. Over the past two decades, the concept of Electro Fenton has been developed and demonstrated as an effective method for significantly alleviating pollutants in wastewater, making it a promising solution for treating wastewater. In the present investigation, the efficiency of the Electro Fenton (EF) process in removing Chemical oxygen demand (COD) from electroplating wastewater using stainless steel as the sacrificial electrode was examined. The influence of various operating parameters, including pH, hydrogen peroxide concentration, reaction time, and Fe2+ concentration, was investigated with the help of Box-Behnken design (BDD) in Response surface methodology (RSM). Notably, EF treatability studies demonstrated that optimal conditions of pH 2, Fe2+ concentration of 0.005M, H2O2 concentration of 0.5M, and RPM of 450 resulted in more than 75% COD removal. Hence, the sacrificial electrodes can be effective in removing COD from the wastewater.
Journal Article