Principles Of Chemical Kinetics Research Articles

A thermo-chemo-mechanically coupled peridynamics for investigating crack behavior in solids

In engineering applications, the phenomenon of cracking is often accompanied by a coupled multiphysics effect. Peridynamics (PD) is an effective approach for solving cracking problems, but currently, no general PD model accounts for the coupling of multiple physical fields. In this work, we develop a PD model of coupled deformation, heat conduction, species diffusion, and chemical reactions. First, we establish the equations for mass, linear momentum, and energy. Then we establish fully coupled constitutive laws that interpret the interactions between the various fields and formulate evolution equations that govern the flux of species and heat. These laws and equations are developed based on the inequality of energy dissipation and the principles of chemical kinetics. Species diffusion and chemical reactions are treated as separate processes to study their effects on the Helmholtz free energy density of solids and the subsequent formation and propagation of cracks. In addition, certain coupling coefficients are calibrated by equating the corresponding physical quantities in the PD model with those in continuum mechanics. Four specific cases are simulated to validate the model, including redistribution of vacancies in ceramics, hydrogen traps, and embrittlement in metals.

Competitive Chemical Reaction Kinetic Model of Nucleosome Assembly Using the Histone Variant H2A.Z and H2A In Vitro.

Nucleosomes not only serve as the basic building blocks for eukaryotic chromatin but also regulate many biological processes, such as DNA replication, repair, and recombination. To modulate gene expression in vivo, the histone variant H2A.Z can be dynamically incorporated into the nucleosome. However, the assembly dynamics of H2A.Z-containing nucleosomes remain elusive. Here, we demonstrate that our previous chemical kinetic model for nucleosome assembly can be extended to H2A.Z-containing nucleosome assembly processes. The efficiency of H2A.Z-containing nucleosome assembly, like that of canonical nucleosome assembly, was also positively correlated with the total histone octamer concentration, reaction rate constant, and reaction time. We expanded the kinetic model to represent the competitive dynamics of H2A and H2A.Z in nucleosome assembly, thus providing a novel method through which to assess the competitive ability of histones to assemble nucleosomes. Based on this model, we confirmed that histone H2A has a higher competitive ability to assemble nucleosomes in vitro than histone H2A.Z. Our competitive kinetic model and experimental results also confirmed that in vitro H2A.Z-containing nucleosome assembly is governed by chemical kinetic principles.

Plasma assisted NH3 combustion and NOx reduction technologies: Principles, challenges and prospective

Combustion is the cornerstone for generating energy in various sectors and applications. The predominance of hydrocarbons combustion causes several environmental and human health issues. The ever-increasing demand for decarbonization of combustion technologies in order to reduce or eliminate undesirable emissions has created a major challenge, putting tremendous pressure on the international research community to develop alternative fuels. Ammonia has recently been explored as a promising carbon-free fuel and a great alternative to hydrocarbon fuels to achieve zero-carbon emissions. However, despite its advantages over hydrogen, ammonia combustion has some drawbacks including low burning velocity, flame stability, and high NOx emissions. This review begins with energy and environmental issues before moving on to hydrogen and ammonia as promising potential solutions, their advantages and drawbacks, and ammonia combustion kinetics. It summarises the principles of chemical kinetics of both ammonia combustion and NOx reduction coupled with the chemistry, kinetic mechanisms and impact of plasma on ammonia combustion. The effects of plasma on ammonia combustion and NOx reduction are also discussed, with a comparison of NOx reduction mechanisms and plasma approach. Finally, the review discusses the perspectives and challenges of using plasma in ammonia combustion.

Nucleosome Assembly and Disassembly in vitro Are Governed by Chemical Kinetic Principles.

As the elementary unit of eukaryotic chromatin, nucleosomes in vivo are highly dynamic in many biological processes, such as DNA replication, repair, recombination, or transcription, to allow the necessary factors to gain access to their substrate. The dynamic mechanism of nucleosome assembly and disassembly has not been well described thus far. We proposed a chemical kinetic model of nucleosome assembly and disassembly in vitro. In the model, the efficiency of nucleosome assembly was positively correlated with the total concentration of histone octamer, reaction rate constant and reaction time. All the corollaries of the model were well verified for the Widom 601 sequence and the six artificially synthesized DNA sequences, named CS1–CS6, by using the salt dialysis method in vitro. The reaction rate constant in the model may be used as a new parameter to evaluate the nucleosome reconstitution ability with DNAs. Nucleosome disassembly experiments for the Widom 601 sequence detected by Förster resonance energy transfer (FRET) and fluorescence thermal shift (FTS) assays demonstrated that nucleosome disassembly is the inverse process of assembly and can be described as three distinct stages: opening phase of the (H2A–H2B) dimer/(H3–H4)2 tetramer interface, release phase of the H2A–H2B dimers from (H3–H4)2 tetramer/DNA and removal phase of the (H3–H4)2 tetramer from DNA. Our kinetic model of nucleosome assembly and disassembly allows to confirm that nucleosome assembly and disassembly in vitro are governed by chemical kinetic principles.

KMS platform: A complete tool for modeling chemical and biochemical reactors

Computer-based activities to study chemical kinetic principles have been widely used in engineering education for the last 60 years. These academic tools must be user-friendly for teachers and students and easy to adapt to practical cases. The Chemical and Environmental Engineering Group (GIQA) at University Rey Juan Carlos (URJC) has developed a Kinetic, Modeling and Simulation (KMS) platform for chemical and biochemical processes. The KMS platform provides different simulation applications programmed in Matlab® with a friendly interface design environment for users. In this work, we will focus on the Kinetics in Conventional Activated Sludge (KCAS) application, as part of the KMS platform. The design of kinetic models and the dynamic simulation of wastewater treatment plants are typically implemented by a variety of dedicated software, mostly developed for research and development purposes at universities, institutes or consulting companies. These programming tools have inherent weaknesses as simulators in virtual laboratories for academics, needing steep learning curves and lacking flexibility to evaluate complex problems, particularly in bachelor degrees programs that are not completely devoted to the mathematical modeling of processes. The simplicity and versatility of KCAS simulator make it very useful for students as starting educational tool to define kinetic models and to make the dynamic simulation of a conventional activated sludge reactor followed by a secondary decanter using different inlet streams or operation conditions. The students interact with the program through a friendly Graphical User Interface (GUI), and the results can be easily exported to a conventional spreadsheet in EXCEL© format files. With KCAS, the students can formulate kinetic models (potential models, diffusional models, Monod equations, etc.) to simulate the evolution from simple reaction systems, to complex biochemical models such as ASM (Activated Sludge Models) from the International Water Association (IWA). The KCAS simulator allows the students to enhance the understanding of complex interactions among the physical, chemical, and biological processes, reinforcing the acquisition of competences and learning skills in Environmental Engineering. The KCAS application was implemented as laboratory demonstration practice in subjects of different Engineering Degrees at URJC.

Rolling the Dice: Modeling First- and Second-Order Reactions via Collision Theory Simulations in an Undergraduate Laboratory

The principles of chemical kinetics comprise one of the core topics that appear throughout chemistry. Standard kinetics lessons typically cover reaction rates and relative rates, rate laws, integra...

IMPORTANCE OF SYNERGISM FOR DEGRADATION OF ELASTOMERS IN COMBINED RADIATION PLUS TEMPERATURE ENVIRONMENTS

ABSTRACTUnderstanding the importance of synergistic effects that occur in combined radiation (dose rate R) plus thermal aging (temperature T) environments has been of interest for many years. Although suggested approaches for achieving this objective are contained in two recent international publications, the validity of these approaches is questioned. A new approach is described based on chemical kinetic principles, and applied to elongation data for two elastomeric materials: a chloroprene and a chlorosulfonated polyethylene. At low temperatures and high dose rates, the chemistry from radiation-initiation totally dominates the degradation, leading to the rate constant kR in the radiation limit. This rate constant is shown to be independent of temperature as long as the dose rate at that temperature is high enough to reach radiation-limit conditions. For combined environment experiments at R + T, this result, added to the rate constant kT appropriate to the thermal limit (obtained from thermal-only exposures), leads to the combined environment rate constant expected in the absence of synergism. Comparing this result to the experimental combined environment rate constant kR+T leads to quantitative estimates of synergism across (R-T) space. Important synergistic effects are found for both materials.

A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data.

Analysis methods based on simulations and optimization have been previously developed to estimate relative translation rates from next-generation sequencing data. Translation involves molecules and chemical reactions, hence bioinformatics methods consistent with the laws of chemistry and physics are more likely to produce accurate results. Here, we derive simple equations based on chemical kinetic principles to measure the translation-initiation rate, transcriptome-wide elongation rate, and individual codon translation rates from ribosome profiling experiments. Our methods reproduce the known rates from ribosome profiles generated from detailed simulations of translation. By applying our methods to data from S. cerevisiae and mouse embryonic stem cells, we find that the extracted rates reproduce expected correlations with various molecular properties, and we also find that mouse embryonic stem cells have a global translation speed of 5.2 AA/s, in agreement with previous reports that used other approaches. Our analysis further reveals that a codon can exhibit up to 26-fold variability in its translation rate depending upon its context within a transcript. This broad distribution means that the average translation rate of a codon is not representative of the rate at which most instances of that codon are translated, and it suggests that translational regulation might be used by cells to a greater degree than previously thought.

From statistical thermodynamics to molecular kinetics: the change, the chance and the choice

A survey on the principles of chemical kinetics (the “science of change”) is presented here. This discipline plays a key role in molecular sciences, however, the debate on its foundations had been open for the 130 years since the Arrhenius equation was formulated on admittedly purely empirical grounds. The great success that this equation has had in the development of experimental research has motivated the need of clarifying its relationships with the foundations of thermodynamics on the one hand and especially with those of statistical mechanics (the “discipline of chances”) on the other. The advent of quantum mechanics in the Twenties and the scattering experiments by molecular beams in the second half of last century have validated collisional mechanisms for reactive processes, probing images of single microscopic events; molecular dynamics computational techniques have been successfully applied to interpret and predict phenomena occurring in a variety of environments: the focus here is on a key aspect, the effect of temperature on chemical reaction rates, which in cold environments show departure from Arrhenius law, so arguably from Maxwell–Boltzmann statistics. Modern developments use venerable mathematical concepts arising from “criteria for choices” dating back to Jacob Bernoulli and Euler. A formulation of recent progress is detailed in Aquilanti et al. 2017.

Computerized geochemical modeling of burial diagenesis of the Eocene turbidite reservoir elements: Urucutuca Formation, Esp\xedrito Santo Basin, southeastern Brazil passive margin

The computerized geochemical modeling, a useful tool to understand the diagenetic processes influencing the quality of hydrocarbon reservoirs, is performed by using different modules of computer codes based on the thermodynamic and chemical kinetic principles and their associated parameters. As observed in the reservoir lithofacies deposited from the marine sediment-gravity flows, a case study of diagenesis is presented here from the Espírito Santo Basin in southeastern Brazil. The study uses the Geochemist’s Workbench (GWB™), PHREEQC™ and TOUGHREACT™ computation packages. The comparison of performances of these packages demonstrates the convergence of results from the software-based geochemical modeling with the petrographic observation of dissolution, albitization, kaolinization, and the precipitation of calcite and dolomite. Moreover, with limited data points, e.g., the sedimentary petrographic data acquired from limited number of boreholes, the computer simulation establishes itself to be a powerful quantitative method estimating the degree and type of diagenetic alteration of turbidite reservoir bodies in contact with a source of saline-water influx associated with salt tectonics. Therefore, using the limited petrographic data points, the geochemical computer-simulation method can even be utilized and extrapolated for areas where similar geological context is interpreted but no borehole data are available. Hence, porosity of turbidite reservoir lithofacies can be predicted in relation to the spatial distribution of dissolution, kaolinization, and albitization of feldspars and authigenic carbonate precipitation.

Numerical simulation of rock salt dissolution in dynamic water

The dissolution process of the rock salt is actually a complicated process in fluid dynamics and chemical kinetics; therefore, the mathematical model for the solute-fluid flow during the cavern building may be established to research the change rule of the form of the cavern boundary based on the kinetic analysis of the convection–diffusion process, with integration of the basic theories of fluid mechanics and the principles of chemical kinetics. In order to research the dissolution mechanism of the rock salt under the condition of dynamic water, the method of numerical simulation has been employed to simulate and study the factors with effect on the fluid transport mechanism in solution mining cavern of the rock salt, and its dissolution in dynamic water has been simulated and researched. The result shows that the model established in this paper may well describe the dissolution process of rock salt under the condition of dynamic water, providing basic analyzing means for the research on the rock salt dissolution in dynamic water.

The Statistical Experimental Design for Chemical Reactors Modeling

The Statistical Experimental Design techniques are the most powerful tools for the chemical reactors experimental modeling. Empirical models can be formulated for representing the chemical behavior of reactors with the minimal effort in the necessary number of experimental runs, hence, minimizing the consumption of chemicals and the consumption of time due to the reduction in the number of experimental runs and increasing the certainty of the results. Four types of nonthermal plasma reactors were assayed seeking for the highest efficiency in obtaining hydrogen and ethylene. Three different geometries for AC high voltage driven reactors, and only a single geometry for a DC high voltage pulse driven reactor were studied. According to the fundamental principles of chemical kinetics and considering an analogy among the reaction rate and the applied power to the plasma reactor, the four reactors are modeled following the classical chemical reactors design to understand if the behavior of the nonthermal plasma reactors can be regarded as the chemical reactors following the flow patterns of PFR (Plug Flow Reactor) or CSTR (Continuous Stirred Tank Reactor). Dehydrogenation is a common elimination reaction that takes place in nonthermal plasmas. Owing to this characteristic, a paraffinic heavy oil with an average molecular weight corresponding to C15 was used to study the production of light olefins and hydrogen.

Kinetic study of the dehydrogenation reaction in polyacrylonitrile‐based carbon fiber precursors during thermal stabilization

AbstractThe kinetics of dehydrogenation reaction and the structural evolution in polyacrylonitrile precursor fibers during thermal stabilization in air have been studied by Fourier transform infrared spectroscopy. The results indicate that, with the progress of dehydrogenation, the absorbance of methylene groups (CH2) gradually decreases, whereas that of methine groups (CH) gradually increases. The dehydrogenation reaction in the fibers is basically completed after 20‐min stabilization above 255°C. According to the Beer–Lambert law, the values of the absorbance for both CH2 groups and the resulting CH groups have been calculated and converted into the concentration fractions of CH2 groups via the Lorentzian multipeak fitting. According to the principles of chemical kinetics, the dehydrogenation reaction has been determined as a pseudo‐second‐order reaction with an activation energy of 107.6 kJ mol−1. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013

Theoretical and experimental investigations of a downdraft biomass gasifier-spark ignition engine power system

A mathematical model which was developed to predict steady state performance of a biomass downdraft gasifier/spark ignition engine power system is described. A mathematical model of the integrated system consists of two parts: the fixed bed downdraft gasifier and spark ignition internal combustion engine models. For calculations the gasifier is split into three zones, namely drying – pyrolysis, oxidation and reduction sections. The gasifier’s mathematical model consists of three separate sub-models, each describing the processes in the corresponding zone. The process taking place in the reduction zone has been described using chemical kinetic principles in order to avoid introduction of assumptions related to achievement of the thermo-chemical equilibrium state during gasifier’s operation. The model is capable to accurately predict molar concentrations of different species in syngas (CO 2, CO, H 2O, H 2, CH 4 and N 2) and the temperature profile in the gasifier along its height. This information then can be used for sizing the reactor and material selection. The engine’s model is based on the fuel–air thermodynamic cycle for spark ignition engines and such model takes into account the composition of syngas used as fuel. The engine’s model also takes into account effects of heat losses in the cycle through the walls of the cylinders and due to the gas blow by. Finally, the influence of dissociation processes during the combustion and the residual gases remaining in the cylinders at the beginning of the compression stroke is accounted for computations of the engine’s performance. The numerical results obtained using the proposed model are in a good agreement with data produced with the use of other theoretical models and experimental data published in open literature and with experimental data obtained in these investigations. The proposed model is applicable for modelling integrated downdraft gasifier/engine biomass energy systems and can be used for more accurate adjustment of design parameters of the gasifier and the engine in order to provide the higher overall efficiency of the system.

Mathematical modeling in chemistry. Application to water quality problems

This paper deals with mathematical modeling of chemical reaction systems. For the sake of simplicity the stirred tank assumption is made which allows us to remain in the framework of ordinary differential systems. The principles of chemical kinetics are recalled and the equations for the evolution of concentration of the chemical species involved in the reactions are given. The equilibrium of reversible reactions is also characterized. Then the case where low and fast reactions coexist is specifically considered by using asymptotic techniques to obtain limit models. Numerical methods are proposed and the whole methodology is applied to water quality models.

A Microscale Approach to Chemical Kinetics in the General Chemistry Laboratory: The Potassium Iodide Hydrogen Peroxide Iodine-Clock Reaction

A microscale laboratory for teaching chemical kinetics utilizing the iodine clock reaction is described. Plastic pipets, 3 mL volume, are used to store and deliver precise drops of reagents and the reaction is run in a 24 well plastic tray using a total 60 drops of reagents. With this procedure, students determine the rate of reaction and the order of reaction as a function of iodide ion concentration or hydrogen peroxide concentration. Six reaction concentrations are run concurrently in about an hour. The students also calculate the value of the rate constant and determine the concentration of an unknown iodide ion sample. The procedure has been adopted to run at a lower temperature to determine the energy of activation. The experiment teaches the principles of chemical kinetics to first-year college students and can also be used in second-year or advanced-placement high school chemistry classes.

Shelf Life of Packaged Bakery Goods—A Review

Packaging requirements for fresh bakery goods are often minimal as many of the products are for immediate consumption. However, packaging can be an important factor in extending the shelf life of other cereal-based goods (toast, frozen products, biscuits, cakes, pastas). Some amount of the texture changes and flavor loss manifest over the shelf life of a soft-baked good can usually be minimized or delayed by effective use of packaging materials. The gains in the extension of shelf life will be application specific. It is recognized that defining the shelf life of a food is a difficult task and is an area of intense research for food product development scientists (food technologists, microbiologists, packaging experts). Proper application of chemical kinetic principles to food quality loss allows for efficiently designing appropriate shelf-life tests and maximizing the useful information that can be obtained from the resulting data. In the development of any new food product including reformulating, change of packaging, or storage/distribution condition (to penetrate into a new market), one important aspect is the knowledge of shelf life.

Modelling the ontogeny of ectotherms exhibiting indeterminate growth

Numerous growth functions exist to describe the ontogeny of animals. Such functions (e.g., von Bertalanffy's equation, thermal-unit growth coefficient) are currently applied to ectotherms even though they fail to provide analytical expressions that adapt to a wide range of fluctuating temperatures. The underlying mechanisms responsible for the ontogeny of ectotherms exhibiting indeterminate growth have not yet been summarised in terms of a simple but meaningful mathematical equation. Here, a growth function is developed, with parameters having physical or biological interpretation that accommodates indeterminate growth under fluctuating temperatures assuming the latter vary seasonally. The equation is derived as a special case of von Bertalanffy's equation providing realistic growth trajectories throughout the ontogeny of several groups of ectotherms ( R 2>0.90). The results suggest that the effect of temperature on growth trajectory supersedes that of reproduction in an environment with fluctuating temperature. Furthermore, values of the allometric weight exponent (0< b<0.75) indicate that the rules of body surface and body weight do not apply under certain circumstances. Finally, the growth function circumvents problems associated with models based on thermodynamic and chemical kinetic principles (e.g., inability to predict growth of organisms in which ontogeny exceeds 3 months) and on rule of thermal summation (e.g., reliable only in a certain range of temperature). The growth function can handle a wide range of temperature fluctuations, encompass life stages and apply to key organisms in ecology, fisheries and agriculture.

Amplified temperature dependence in ecosystems developing on the lava flows of Mauna Loa, Hawai'i

Through its effect on individual metabolism, temperature drives biologically controlled fluxes and transformations of energy and materials in ecological systems. Because primary succession involves feedbacks among multiple biological and abiotic processes, we expected it to exhibit complex dynamics and unusual temperature dependence. We present a model based on first principles of chemical kinetics to explain how biologically mediated temperature dependence of "reactant" concentrations can inflate the effective temperature dependence of such processes. We then apply this model to test the hypothesis that the temperature dependence of early primary succession is amplified due to more rapid accumulation of reactants at higher temperatures. Using previously published data from the lava flows of Mauna Loa, HI, we show that rates of vegetation and soil accumulation as well as rates of community compositional change all display amplified temperature dependence (Q(10) values of approximately 7-50, compared with typical Q(10) values of 1.5-3 for the constituent biological processes). Additionally, in young ecosystems, resource concentrations increase with temperature, resulting in inflated temperature responses of biogeochemical fluxes. Mauna Loa's developing ecosystems exemplify how temperature-driven, biologically mediated gradients in resource availability can alter the effective temperature dependence of ecological processes. This mechanistic theory should contribute to understanding the complex effects of temperature on the structure and dynamics of ecological systems in a world where regional and global temperatures are changing rapidly.

A historical and current perspective on predicting thermal cookoff behavior

Prediction of thermal explosions using chemical kinetic models dates back nearly a century. However, it has only been within the past 25 years that kinetic models and digital computers made reliable predictions possible. Two basic approaches have been used to derive chemical kinetic models for high explosives: [1] measurement of the reaction rate of small samples by mass loss (thermogravimetric analysis, TG), heat release (differential scanning calorimetry, DSC), or evolved gas analysis (mass spectrometry, infrared spectrometry, etc.) or [2] inference from larger-scale experiments measuring the critical temperature (T m, lowest T for self-initiation), the time to explosion as a function of temperature, and sometimes a few other results, such as temperature profiles. Some of the basic principles of chemical kinetics involved are outlined, and major advances in these two approaches through the years are reviewed.