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1
Steele, Aaron J. "Collective behavior in chemical systems." Morgantown, W. Va. : [West Virginia University Libraries], 2007. https://eidr.wvu.edu/etd/documentdata.eTD?documentid=5386.
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Thesis (Ph. D.)--West Virginia University, 2007.Title from document title page. Document formatted into pages; contains vii, 126 p. : ill. (some col.) + video files. Includes supplementary video files in a zip file. Includes abstract. Includes bibliographical references.
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Degrand, Elisabeth. "Evolving Chemical Reaction Networks." Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-257491.
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One goal of synthetic biology is to implement useful functions with biochemical reactions, either by reprogramming living cells or programming artificial vesicles. In this perspective, we consider Chemical Reaction Networks (CRNs) as a programming language. Recent work has shown that continuous CRNs with their dynamics described by ordinary differential equations are Turing complete. That means that any function over the reals that is computable by a Turing machine in arbitrary precision, can be computed by a CRN over a finite set of molecular species. The proof uses an algorithm which, given a computable function presented as the solution of a PIVP (PolynomialInitial Values Problem), generates a finite CRN to implement it. In the generated CRNs, the molecular concentrations play the role of information carriers, similarly to proteins in cells. In this Master’s Thesis, we investigate an approach based on an evolutionary algorithm to build a continuous CRN that approximates a real function given a finite set of the values of the function. The idea is to use a two-level parallel genetic algorithm. A first algorithm is used to evolve the structure of the network, while the other one enables us to optimize the parameters of the CRNs at each step. We compare the CRNs generated by our method on different functions. The CRNs found by evolution often give good results with quite unexpected solutions.Ett mål med syntetisk biologi är att genomföra användbara funktioner med biokemiska reaktioner, antingen genom omprogrammering av levande celler eller programmering av artificiella vesiklar. I detta perspektiv anser vi Chemical Reaction Networks (CRNs) som ett programmeringsspråk. Det senaste arbetet har visat att kontinuerliga CRNs med dynamik som beskrivs av vanliga differentialekvationer är Turingkompletta. Det betyder att en funktion över de realla talen som kan beräknas av en Turing-maskin i godtycklig precision, kan beräknas av en CRN över en ändlig uppsättning molekylära arter. Beviset använder en algoritm som, givet en beräkningsbar funktion som presenteras som lösningen av ett PIVP (Polynomial Initial Values Problem), genererar en ändlig CRN för att implementera den. I de genererade CRN:erna spelar molekylkoncentrationerna rollen som informationsbärare, på samma sätt som proteiner i celler. I detta examensarbete undersöker vi ett tillvägagångssätt baserat på en evolutionär algoritm för att bygga en kontinuerlig CRN som approximerar en verklig funktion med en ändlig uppsättning av värden för funktionen. Tanken är att använda parallell genetisk algoritm i två nivåer. En första algoritm används för att utveckla nätets struktur, medan den andra möjliggör att optimera parametrarna för CRN:erna vid varje steg. Vi jämför de CRN som genereras av vår metod på olika funktioner. De CRN som hittas av evolutionen ger ofta bra resultat med ganska oväntade lösningar.
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Knight, Daniel William. "Reactor behavior and its relation to chemical reaction network structure." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1438274630.
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Du, Yimian. "Bifurcation analysis in chemical reaction network." Thesis, Imperial College London, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.511282.
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Hayes, Michael Y. "Theoretical studies of chemical reaction dynamics." Connect to online resource, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3273678.
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Ritchie, Grant A. D. "Laser studies of chemical reaction dynamics." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325785.
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English, Philip J. "Automated discovery of chemical reaction networks." Thesis, University of Newcastle Upon Tyne, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.500929.
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The identification of models of chemical reaction networks is of importance in the safe, economic and environmentally sensitive development of chemical products. Qualitative models of a network of interactions are used in the design of drugs and other therapies. Quantitative models of the behaviour of reaction networks are the foundation of the science of reaction engineering (e.g. see Levenspiel, 1999); allowing the use of simulation software in the rapid development of commercial scale production processes. This work extends the existing methods reported by Burnham et al. (2006); adopting the global basis fonction method first applied to this problem by Crampin et al. (2004a).
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Domijan, Mirela. "Mathematical aspects of chemical reaction networks." Thesis, University of Warwick, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.495019.
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Chemical and biological processes present a challenge when it comes to modelling and analysis. The models usually have to take into account many chemicals and complex interactions and in turn, they are often described by large ODE systems with complicated nonlinear terms. If there is a lack of quantitative information about the chemical interactions, there will also be parameter uncertainty in the systems. Such systems present a challenge to analyse. In response, an increasing consensus calls for emphasis on the underlying chemical reaction network structure and the use of network information to predict possible system dynamics.
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Xu, Jin, and 徐进. "A study of chemical reaction optimization." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B48199242.
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Complex optimization problems are prevalent in various fields of science and
engineering. However, many of them belong to a category of problems called NP-
hard (nondeterministic polynomial-time hard). On the other hand, due to the
powerful capability in solving a myriad of complex optimization problems, metaheuristic
approaches have attracted great attention in recent decades. Chemical
Reaction Optimization (CRO) is a recently developed metaheuristic mimicking
the interactions of molecules in a chemical reaction. With the flexible structure
and excellent characteristics, CRO can explore the solution space efficiently to
identify the optimal or near optimal solution(s) within an acceptable time. Our
research not only designs different versions of CRO and applies them to tackle
various NP-hard optimization problems, but also investigates theoretical aspects
of CRO in terms of convergence and finite time behavior.
We first focus on the problem of task scheduling in grid computing, which
involves seeking the most efficient strategy for allocating tasks to resources. In
addition to Makespan and Flowtime, we also take reliability of resource into
account, and task scheduling is formulated as an optimization problem with three
objective functions. Then, four different kinds of CRO are designed to solve this
problem. Simulation results show that the CRO methods generally perform better
than existing methods and performance improvement is especially significant in
large-scale applications.
Secondly, we study stock portfolio selection, which pertains to deciding how to
allocate investments to a number of stocks. Here we adopt the classical Markowitz
mean-variance model and consider an additional cardinality constraint. Thus,
the stock portfolio optimization becomes a mixed-integer quadratic programming
problem. To solve it, we propose a new version of CRO named Super Molecule-based
CRO (S-CRO). Computational experiments suggest that S-CRO is superior
to canonical CRO in solving this problem.
Thirdly, we apply CRO to the short adjacent repeats identification problem
(SARIP), which involves detecting the short adjacent repeats shared by multiple
DNA sequences. After proving that SARIP is NP-hard, we test CRO with both
synthetic and real data, and compare its performance with BASARD, which is
the previous best algorithm for this problem. Simulation results show that CRO
performs much better than BASARD in terms of computational time and finding
the optimal solution.
We also propose a parallel version of CRO (named PCRO) with a synchronous
communication scheme. To test its efficiency, we employ PCRO to solve the
Quadratic Assignment Problem (QAP), which is a classical combinatorial optimization
problem. Simulation results show that compared with canonical sequential
CRO, PCRO can reduce the computational time as well as improve the
quality of the solution for instances of QAP with large sizes.
Finally, we perform theoretical analysis on the convergence and finite time
behavior of CRO for combinatorial optimization problems. We explore CRO
convergence from two aspects, namely, the elementary reactions and the total
system energy. Furthermore, we also investigate the finite time behavior of CRO
in respect of convergence rate and first hitting time.published_or_final_version
Electrical and Electronic Engineering
Doctoral
Doctor of Philosophy
10
Galagali, Nikhil. "Bayesian inference of chemical reaction networks." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104253.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2016.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 189-198).
The development of chemical reaction models aids system design and optimization, along with fundamental understanding, in areas including combustion, catalysis, electrochemistry, and biology. A systematic approach to building reaction network models uses available data not only to estimate unknown parameters, but to also learn the model structure. Bayesian inference provides a natural approach for this data-driven construction of models. Traditional Bayesian model inference methodology is based on evaluating a multidimensional integral for each model. This approach is often infeasible for reaction network inference, as the number of plausible models can be very large. An alternative approach based on model-space sampling can enable large-scale network inference, but its efficient implementation presents many challenges. In this thesis, we present new computational methods that make large-scale nonlinear network inference tractable. Firstly, we exploit the network-based interactions of species to design improved "between-model" proposals for Markov chain Monte Carlo (MCMC). We then introduce a sensitivity-based determination of move types which, when combined with the network-aware proposals, yields further sampling efficiency. These algorithms are tested on example problems with up to 1000 plausible models. We find that our new algorithms yield significant gains in sampling performance, with almost two orders of magnitude reduction in the variance of posterior estimates. We also show that by casting network inference as a fixed-dimensional problem with point-mass priors, we can adapt existing adaptive MCMC methods for network inference. We apply this novel framework to the inference of reaction models for catalytic reforming of methane from a set of ~/~ 32000 possible models and real experimental data. We find that the use of adaptive MCMC makes large-scale inference of reaction networks feasible without the often extensive manual tuning that is required with conventional approaches. Finally, we present an approximation-based method that allows sampling over very large model spaces whose exploration remains prohibitively expensive with ex-act sampling methods. We run an MCMC algorithm over model indicators and for each visited model approximate the model evidence via Laplace's method. Limited and sparse available data tend to produce multi-modal posteriors over the model indicators. To perform inference in this setting, we develop a population-based approximate model inference MCMC algorithm. Numerical tests on problems with around 109 models demonstrate the superiority of our population-based algorithm over single-chain MCMC approaches.
by Nikhil Galagali.
Ph. D.
11
Mashino, Michio. "Photoinduced Chemical Reaction of Halogenated Hydrocarbons." 京都大学 (Kyoto University), 2004. http://hdl.handle.net/2433/147629.
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Rowe, Stephen Michael. "The use of reaction inhibition techniques for control of runaway polymerisation reactions." Thesis, London South Bank University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.336802.
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Zwahlen, Andreas G. "Reaction and deactivation kinetics of isobutane, using a concentration-controlled internal-recycle reactor /." Title page, contents and summary only, 1989. http://web4.library.adelaide.edu.au/theses/09PH/09phz971.pdf.
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Serbetcioglu, Serpil. "Mass transfer and catalytic reaction in a three-phase monolith reactor." Thesis, University of Bath, 1993. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.332665.
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Holder, Grant Newton. "Redox reactivity of mononuclear and binuclear rhenium complexes." Diss., Georgia Institute of Technology, 1988. http://hdl.handle.net/1853/30392.
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Gao, Connie W. (Connie Wu). "Automatic reaction mechanism generation :." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104205.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2016.Cataloged from PDF version of thesis.
Includes bibliographical references.
Growing awareness of climate change and the risks associated with our society's dependence on fossil fuels has motivated global initiatives to develop economically viable, renewable energy sources. However, the transportation sector remains a major hurdle. Although electric vehicles are becoming more mainstream, the transportation sector is expected to continue relying heavily on combustion engines, particularly in the freight and airline industries. Therefore, research efforts to develop cleaner combustion must continue. This includes the development of more efficient combustion engines, identification of compatible alternative fuels, and the streamlining of existing petroleum resources. These dynamic systems have complex chemistry and are often difficult and expensive to probe experimentally, making detailed chemical kinetic modeling an attractive option for simulating and predicting macroscopic observables such as ignition delay or CO₂ concentrations. This thesis presents several methods and applications towards high fidelity predictive modeling using Reaction Mechanism Generator (RMG), an open source software package which automatically constructs kinetic mechanisms. Several sources contribute to model error during automatic mechanism generation, including incomplete or incorrect handling of chemistry, poor estimation of thermodynamic and kinetics parameters, and uncertainty propagation. First, an overview of RMG is presented along with algorithmic changes for handling incomplete or incorrect chemistry. Completeness of chemistry is often limited by CPU speed and memory in the combinational problem of generating reactions for large molecules. A method for filtering reactions is presented for efficiently and accurately building models for larger systems. An extensible species representation was also implemented based on chemical graph theory, allowing chemistry to be extended to lone pairs, charges, and variable valencies. Several chemistries are explored in this thesis through modeling three combustion related processes. Ketone and cyclic ether chemistry are explored in the study of diisoproyl ketone and cineole, biofuel candidates produced by fungi in the decomposition of cellulosic biomass. Detailed kinetic modeling in conjunction with engine experiments and metabolic engineering form a collaborative feedback loop that efficiently screens biofuel candidates for use in novel engine technologies. Next, the challenge of modeling constrained cyclic geometries is tackled in generating a combustion model of JP-10, a synthetic jet fuel used in propulsion technologies. The model is validated against experimental and literature data and succeeds in capturing key product distributions, including aromatic compounds, which are precursors to polyaromatic hydrocarbons (PAHs) and soot. Finally, oil-to-gas cracking processes under geological conditions are studied through modeling the low temperature pyrolysis of the heavy oil analog phenyldodecane in the presence of diethyldisulfide. This system is used to gather mechanistic insight on the observation that sulfur-rich kerogens have accelerated oil-to-gas decomposition, a topic relevant to petroleum reservoir modeling. The model shows that free radical timescales matter in low temperature systems where alkylaromatics are relatively stable. Local and global uncertainty propagation methods are used to analyze error in automatically generated kinetic models. A framework for local uncertainty analysis was implemented using Cantera as a backend. Global uncertainty analysis was implemented using adaptive Smolyak pscudospcctral approximations to efficiently compute and construct polynomial chaos expansions (PCE) to approximate the dependence of outputs on a subset of uncertain inputs. Both local and global methods provide similar qualitative insights towards identifying the most influential input parameters in a model. The analysis shows that correlated uncertainties based on kinetics rate rules and group additivity estimates of thermochemistry drastically reduce a model's degrees of freedom and can have a large impact on model outputs. These results highlight the necessity of uncertainty analysis in the mechanism generation workflow. This thesis demonstrates that predictive chemical kinetics can aid in the mechanistic understanding of complex chemical processes and contributes new methods for refining and building high fidelity models in the automatic mechanism generation workflow. These contributions are available to the kinetics community through the RMG software package.
by Connie W. Gao.
Ph. D.
17
Lekakou, Constantina. "Simulation of flow, reaction and heat transfer in reaction injection moulding." Thesis, Imperial College London, 1987. http://hdl.handle.net/10044/1/47048.
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Akintoye, Ayodele. "Continuous chromatographic biochemical reaction-separation." Thesis, Aston University, 1989. http://publications.aston.ac.uk/9739/.
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Combined bioreaction separation studies have been carried out for the first time on a moving port semi-continuous counter-current chromatographic reactor-separator (SCCR-S1) consisting of twelve 5.4cm id x 75cm long columns packed with calcium charged cross-linked polystyrene resin (KORELA V07C). The inversion of sucrose to glucose and fructose in the presence of the enzyme invertase and the biochemIcal synthesis of dextran and fructose from sucrose in the presence of the enzyme dextransucrase were investigated. A dilute stream of the appropriate enzyme in deionised water was used as the eluent stream. The effect of switch time, feed concentration, enzyme activity, eluent rate and enzyme to feed concentration ratio on the combined bioreaction-separation were investigated. For the invertase reaction, at 20.77% w/v sucrose feed concentrations complete conversions were achieved. The enzyme usage was 34% of the theoretical enzyme amount needed to convert an equivalent amount of sucrose over the same time period when using a conventional fermenter. The fructose rich (FRP) and glucose rich (GRP) product purities obtained were over 90%. By operating at 35% w/v sucrose feed concentration and employing the product splitting and recycling techniques, the total concentration and purity of the GRP increased from 32% w/v to 4.6% and from 92.3% to 95% respectively. The FRP concentration also increased from 1.82% w/v to 2.88% w/v. A mathematical model was developed for the combined reaction-separation and used to simulate the continuous inversion of sucrose and product separation using the SCCR-S1. In the biosynthesis of dextran studies, 52% conversion of a 2% w/v sucrose concentration feed was achieved. An average dextran molecular weight of 4 millIon was obtained in the dextran rich (DRP) product stream. The enzyme dextransucrase was purifed successfully using centrifugation and ultrafiltration techniques.
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Adhikari, Sudip. "Accelerating the Computation of Chemical Reaction Kinetics for Modeling Turbulent Reacting Flows." University of Akron / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=akron1510259399348102.
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Al-Ibadi, Muhsen Abood Muhsen. "Quantum chemical studies of organometallic reaction mechanisms." Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.547444.
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Dunning, Greg. "Bimolecular chemical reaction dynamics : a phase comparison." Thesis, University of Bristol, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.682187.
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Studies of the dynamics of chemical reactions reveal a great deal about their mechanisms and the forces that control the chemistry. However, most of these studies have been performed on isolated reactions in the gas-phase, either experimentally or using computational methods. This thesis presents experimental results for the dynamics of both gas and liquid phase reactions. The results are compared in an attempt to understand the effects a solvent has on the course of a chemical reaction. The gas phase experiments focussed on the reactions of Cl atoms with alkenes, in an extension of previous gas-phase dynamical studies of Cl + alkane reactions. The velocity map imaging (VMI) technique was applied to observe the state resolved scattering distributions of the HCI product of the Cl + propene, isobutene and 2,3-dimethyl but-2-ene reactions. The experimental results were compared to trajectory simulations and it is shown that reactions can proceed by direct hydrogen absh·action or an addition-elimination mechanism. The Cl + 2,3-dimethyl but-2-ene reaction has previously been studied in solution and comparison with the gas-phase results presented here provides direct and quantitative evidence about the influence of the solvent on energy release in a reactive system. Solution phase studies involved the reactions of F-atoms with the organic solvents CD2Cb, CD3CN and CH3CN. Computational and experimental studies of the reactions of F+ H2 and F + CH4, and their deuterated isotopologues, have been at the forefront of advances in understanding the classical and quantum mechanical contributions to a chemical reaction. The 266-nm photolysis ofXeF2 was used as a source of fluorine atoms in solution and required characterisation of the photodissociation dynamics on picosecond timescales. The reactions of F-atoms with CD3CN and CD2Cb solvent were studied with the use of time-resolved infra-red (TRIR) and time-resolved ultraviolet-visible (TRUV-Vis) spectroscopy. Efficient energy flow into the vibrational motion of the DF product competes with dissipation of the energy to the solvent bath within a few picoseconds, and bimolecular reaction rate coefficients, DF vibrational level branching ratios and vibrational cooling rates of DF extracted. Results are also presented for the reaction of CN radicals with acetone in chloroform solution. The HCN and 2-oxy-propyl products of the reaction were probed with TRIR spectroscopy, and much of the excess energy of this exothermic reaction is deposited in vibrational modes of both products. Coupling of these vibrational modes to the solvent bath then thermalizes the product on timescales of tens or hundreds of picoseconds. The results from this thesis are combined with previous studies of reactions in the gas and liquid phases to provide a picture of how the solvent can alter the potential energy surface of a reaction. Possible roles of solvent-solute complexes, solvent caging, solvent restructuring to accommodate reactions, and friction associated with the fluxional motion of the solvent bath are discussed
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Manta, Bianca. "Quantum Chemical Studies of Enzymatic Reaction Mechanisms." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-141321.
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Computer modeling of enzymes is a valuable complement to experiments. Quantum chemical studies of enzymatic reactions can provide a detailed description of the reaction mechanism and elucidate the roles of various residues in the active site. Different reaction pathways can be analyzed, and their feasibility be established based on calculated energy barriers. In the present thesis, density functional theory has been used to study the active sites and reaction mechanisms of three different enzymes, cytosine deaminase (CDA) from Escherichia coli, ω-transaminase from Chromobacterium violaceum (Cv-ωTA) and dinitrogenase reductase-activating glycohydrolase (DraG) from Rhodospirillum rubrum. The cluster approach has been employed to design models of the active sites based on available crystal structures. The geometries and energies of transition states and intermediates along various reaction pathways have been calculated, and used to construct the energy graphs of the reactions. In the study of CDA (Paper I), two different tautomers of a histidine residue were considered. The obtained reaction mechanism was found to support the main features of the previously proposed mechanism. The sequence of the events was established, and the residues needed for the proton transfer steps were elucidated. In the study of Cv-ωTA (Paper II and Paper III), two active site models were employed to study the conversion of two different substrates, a hydrophobic amine and an amino acid. Differences and similarities in the reaction mechanisms of the two substrates were established, and the role of an arginine residue in the dual substrate recognition was confirmed. In the study of DraG (Paper IV), two different substrate-binding modes and two different protonation states of an aspartate residue were considered. The coordination of the first-shell ligands and the substrate to the two manganese ions in the active site was characterized, and a possible proton donor in the first step of the proposed reaction mechanism was identified.At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.
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Poole, Anthony John. "Reaction-diffusion structures in nonlinear chemical kinetics." Thesis, University of Leeds, 1998. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.712528.
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Heard, Dwayne Ellis. "Laser studies of chemical kinetics." Thesis, University of Oxford, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.258025.
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Lamb, David R. "New reaction systems for environmentally conscious chemical processes." Diss., Georgia Institute of Technology, 1998. http://hdl.handle.net/1853/30075.
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Vaidyaraman, Sundar. "Kinetics of the bosch reaction." Thesis, Georgia Institute of Technology, 1992. http://hdl.handle.net/1853/10277.
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Saleh, Nail Asad. "Dynamical solvent effect in 1-(9-anthryl)-3-(4-dimethylaniline) propane charge transfer reactions /." free to MU campus, to others for purchase, 2002. http://wwwlib.umi.com/cr/mo/fullcit?p3060138.
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Nadeau, Patrice. "Study of the mixing with chemical reaction in a cross flow impinging jet aerosol reactor." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape3/PQDD_0029/NQ64625.pdf.
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Abou-Chahine, Fawzi. "Chemical reaction dynamics in solution in chlorinated solvents." Thesis, University of Bristol, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.617705.
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This thesis investigates chemical reaction dynamics in solution in chlorinated solvents on ultrafast timescales. Ultraviolet (UV) photolysis of the chlorinated solvents at 266 nm produces Cl atoms, which react with 2,3-dimethylbut-2-cne (DMB). Experimental studies of this reaction address the question of how the energetic pathways and fundamental mechanisms of an isolated (i.e. gas phase) reaction change when it is occurs in the more condensed phase of a liquid environment. The data analysis and proposed reactive pathways are informed by the comparable reactions of Cl with propene in the gas phase and Cl with n-pentane in the condensed phase. A key observation is that - 15 - 30 % the Hel product of the reaction of Cl atoms with DMB is formed vibrationally hot (in v= I). This deduction is reinforced by separate measurements of the lifetime of vibrationally excited HCl in neat solvents, determined using infra-red (lR) pump and IR probe spectroscopy. These studies prompted a more complete study of the consequences of UV photoexcitation of the chlorinated solvents, and extensions to photochemical behaviour of solutions of 1,5- hexadiene (Hex) in CC14 and CDC13. Strong transient absorption bands centred around 330 nm and 500 nm were observed following 266-nm excitation of CC14, and a kinetic analysis supports assignment of these bands to CI-CC14 complexes and an isomeric form of the solvent, CI-CICC12, respectively. Similar assignments are made in the case of CD Ch. The loss of CI-CCI4 complexes, and thus the rates of decay of the transient absorption features, is accelerated upon addition of Hex to CCI4, because of reaction of Cl-CC14 with the Hex solute. Transient IR spectra obtained [or solutions of Hex in CCI4 and in CDCI) show evidence for formation of Hex cations following 2-phoLon excitation of the solvent. The assignments of the IR bands to the cations, instead of a range of other possible transient intermediates, are supported by computational calculations, at the B3L YP/6-31 G/2df,p level of theory.
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Collepardo-Guevara, Rosana. "Chemical reaction rates from ring polymer molecular dynamics." Thesis, University of Oxford, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.504307.
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Burnham, Samantha Claire. "Towards the automated determination of chemical reaction networks." Thesis, University of Newcastle Upon Tyne, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.445585.
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Hii, Charles Jun Khiong. "Elucidation of chemical reaction networks through genetic algorithm." Thesis, University of Newcastle upon Tyne, 2017. http://hdl.handle.net/10443/3647.
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Obtaining chemical reaction network experimentally is a time consuming and expensive method. It requires a lot of specialised equipment and expertise in order to achieve concrete results. Using data mining method on available quantitative information such as concentration data of chemical species can help build the chemical reaction network faster, cheaper and with less expertise. The aim of this work is to design an automated system to determine the chemical reaction network (CRN) from the concentration data of participating chemical species in an isothermal chemical batch reactor. Evolutionary algorithm ability to evolve optimum results for a non-linear problem is chosen as the method to go forward. Genetic algorithm’s simplicity is modified such that it can be used to model the CRN with just integers. The developed automated system has shown it can elucidate the CRN of two fictitious CRNs requiring only a few a priori information such as initial chemical species concentration and molecular weight of chemical species. Robustness of the automated system is tested multiple times with different level of noise in system and introduction of unmeasured chemical species and uninvolved chemical species. The automated system is also tested against an experimental data from the reaction of trimethyl orthoacetate and allyl alcohol which had shown mixed results. This had prompted for the inclusion of NSGA-II algorithm in the automated system to increase its ability to discover multiple reactions. At the end of the work, a final form of the automated system is presented which can process datasets from different initial conditions and different operating temperature which shows a good performance in elucidating the CRNs. It is concluded that automated system is susceptible to ‘overfitting’ where it designs its CRN structure to fit the measured chemical species but with enough variation in the data, it had shown it is capable of elucidating the true CRN even in the presence of unmeasured chemical species, noise and unrelated chemical species.
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McKeogh, Brendan James. "Chemical Changes in Hydrothermal Carbon with Reaction Time." Digital WPI, 2017. https://digitalcommons.wpi.edu/etd-theses/1029.
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"The increasing global demands for materials and energy directly contributes to the devastating ecological, toxicological, and climate consequences currently observed. Biomass-derived energy and materials offers a sustainable option to meeting current needs and developing novel materials. Hydrothermal carbonization is a promising green platform to valorize biomass by forming Hydrochar, a carbon solid. Hydrothermal carbonization converts biomass using liquid phase water at elevated temperatures (180-350 °C), forming organic intermediates, which dehydrate and polymerize to form the solid material on time scales of several hours. Hydrochar shows promise for a wide variety of applications, including aqueous heavy-metal adsorption. The complexity of the hydrochar prevents reliable characterization, hindering a full understanding of how to optimize the material. The focus of this study was to develop spectroscopic methods better understand the material as it changes with reaction time (ex-situ). This study developed IR and Raman Spectroscopy and Mass Spectrometry (MS) methods. Hydrochars were prepared from glucose (a model for biomass) and were prepared at different reaction times between 3 and 24 hours to understand the formation of the material and how it matures under process conditions (180 °C, autogenous pressure). IR and MS identified hydroxyl and ketone functionalities and aliphatic, furanic, and aromatic moieties, and both techniques indicated decreasing hydroxyl and furan content and increasing methyl and aromatic content. The Raman spectra were consistent with aldehyde-functionalized 1- and 2-ring arenes and aldehyde-functionalized furans, and indicated increasing 2-ring arene content relative to 1-ring arenes. MS showed a significant increase in the aromatic to furan ratio, and MS confirmed the increase in 2-ring arenes relative to 1-ring arenes seen in the Raman. These spectroscopic methods are in good agreement and will allow for greater chemical information in the hydrochar, which will inform the link between material modification under process conditions and application performance."
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Ji, Haixia. "Uniqueness of Equilibria for Complex Chemical Reaction Networks." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1307122057.
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Bassolino, Giovanni. "Tuning ultrafast chemical reaction dynamics in photoactive proteins." Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:42c19c5c-c6df-48e9-bb1c-8a7098eca8b4.
Full textAbstract:
This dissertation investigates the origins of tunable and efficient photochemistry in three different photoactive proteins, bacteriorhodopsin (BR), rhodopsin (RHO) and green fluorescent protein (GFP). In all cases, significant differences exist between the photoreactivity of model chromophores in solution and in the protein environment, in terms of excited state lifetime and efficiency of the primary photochemical process (opsin proteins) or the type of reaction (excited state proton transfer versus C=C double bond photoisomerisation for GFP). The work presented here investigates for each case to what extent the protein environment is necessary to alter the photochemistry of model chromophores in solution. For GFP and BR steric and electrostatic interactions between the protein pocket and the chromophore are shown to be likely responsible for shaping the excited state surface along which the photoreactions take place. For RHO it is suggested, contrary to current belief, that selection of a reactive ground state conformer might be the main effect generating the observed differences between solution and protein environment. The solution photochemistry of structurally modified retinal protonated Schiff bases, taken as model chromophores for the opsin proteins, is studied with continuous wave irradiation experiments and ultrafast transient spectroscopies. Surprisingly large differences are observed for the isomerisation reaction depending on the starting configuration (trans or cis) of the photoactive double bond. The current model for BR based on the tuning of the excited state barrier encountered along the isomerisation coordinate is expanded to include the changes in selectivity, speed and efficiency observed for a series of all-trans derivatives. For 11-cis, the photoisomerisation in solution is proposed to take place along a barrierless isomerisation coordinate, in contrast with the models currently available in literature. It is suggested that the protein might be discriminating between ground state conformers rather than significantly changing the topography of the reaction coordinate. For GFP, excited state Raman spectra are recorded for the wild-type protein, two mutants and a model chromophore in solution. It is suggested that the high frequency vibrational modes observed in the excited state spectra of the proteins but not of the model chromophore in DMSO are a sign of a tighter chromophore environment that inhibits the photoisomerisation reaction occurring in solution.
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Orr-Ewing, Andrew John. "Laser studies of reaction dynamics." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302888.
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Morgan, Meirion. "Reaction problems in stochastic chemistry." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301256.
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Mamtani, Kuldeep. "Carbon-based Materials for Oxygen Reduction Reaction (ORR) and Oxygen Evolution Reaction (OER) in Acidic Media." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu149376896628355.
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Chung, Lung Wa. "Computational studies of the reaction mechanisms and stereochemistry of metal-mediated organic reactions /." View abstract or full-text, 2006. http://library.ust.hk/cgi/db/thesis.pl?CHEM%202006%20CHUNG.
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Holmes, R. "Reaction kinetics of oil coke particles." Thesis, University of Portsmouth, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.376048.
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Byrne, C. S. C. "The modelling of a reaction and reactor for the electrochemical production of geraniol and nerol." Thesis, University of Newcastle Upon Tyne, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.371252.
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Reding, Derek James. "Shock induced chemical reactions in energetic structural materials." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28174.
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Thesis (M. S.)--Aerospace Engineering, Georgia Institute of Technology, 2009.Committee Chair: Hanagud, Sathya; Committee Member: Kardomateas, George; Committee Member: McDowell, David; Committee Member: Ruzzene, Massimo; Committee Member: Thadhani, Naresh.
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Karaman, Mustafa. "Chemical Vapor Deposition Of Boron Carbide." Phd thesis, METU, 2007. http://etd.lib.metu.edu.tr/upload/3/12608778/index.pdf.
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Boron carbide was produced on tungsten substrate in a dual impinging-jet CVD reactor from a gas mixture of BCl3, CH4, and H2. The experimental setup was designed to minimise the effect of mass transfer on reaction kinetics, which, together with the on-line analysis of the reactor effluent by FTIR,
allowed a detailed kinetic investigation possible.
The phase and morphology studies of the products were made by XPS, XRD,micro hardness and SEM methods. XPS analysis showed the existence of chemical states attributed to the boron carbide phase, together with the existence of oxy-boron carbide species. SEM pictures revealed the formation
of 5-fold icosahedral boron carbide crystals up to 30 micron sizes for the samples produced at 1300oC. Microhardness tests showed change of boron carbide hardness with the temperature of tungsten substrate. The hardness
values (Vickers Hardness) observed were between 3850 kg/mm2 and 4750 kg/mm2 corresponding to substrate temperatures of 1100 and 1300 C, respectively.
The FTIR analysis of the reaction products proved the formation of reaction intermediate BHCl2, which is proposed to occur mainly in the gaseous boundary layer next to the substrate surface. The experimental parameters are
the temperature of the substrate, and the molar fractions of methane and borontrichloride at the reactor inlet. The effects of those parameters on the reaction rates, conversions and selectivities were analysed and such analyses were used in mechanism determination studies. An Arrhenius type of a rate
expression was obtained for rate of formation of boron carbide with an energy of activation 56.1 kjoule/mol and the exponents of methane and boron trichloride in the reaction rate expression were 0.64 and 0.34, respectively, implying complexity of reaction. In all of the experiments conducted, the rate of formation of boron carbide was less than that of dichloroborane.
Among a large number of reaction mechanisms proposed only the ones considering the molecular adsorption of boron trichloride on the substrate surface and formation of dichloroborane in the gaseous phase gave reasonable
fits to the experimental data. Multiple non-linear regression analysis was carried out to predict the deposition rate of boron carbide as well as formation rate of dichloroborane simultaneously.
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Nguyen, Nhat Khuong. "Liquid marbles as chemical microreactors." Thesis, Griffith University, 2022. http://hdl.handle.net/10072/419767.
Full textAbstract:
The miniaturisation of chemical and biological systems has become a research focus since the last century. Compared to conventional bulk reactors, microreactors have numerous advantages such as larger surface-area-to-volume ratio, higher heat and mass transfer rates as well as the reduction in energy demand and waste generation. Miniaturisation also improves control over reaction parameters and enhances reaction safety especially if hazardous substances are involved.
The need for miniaturised reaction systems has led to the development of various microreactor platforms such as droplet-based microreactors. However, these platforms possess inherent drawbacks such as rapid evaporation and difficulty in handling a minute amount of liquid that have limited their implementation in practical applications. Liquid marbles are droplets covered with hydrophobic particles and present a platform that can potentially overcome the weaknesses of bare droplets. The coating layers completely isolate the interior liquids from the surrounding environment, thus conveniently encapsulating the reactions. Great efforts have been made over the past decade to demonstrate the feasibility of liquid marble-based microreactors for chemical and biological applications. Nevertheless, the inability to monitor reactions and the lack of an effective mixing method remains the main obstacles that can significantly hinder the potential of liquid marble-based microreactors. In order to benefit from the full potential of liquid marbles as universal microreactors, it is necessary to develop effective methods to enhance the mixing and monitoring abilities in liquid marbles. My Ph.D research focuses on developing methods to enhance the ability to monitor reaction and to improve mixing process in liquid marble-based platform.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Eng & Built Env
Science, Environment, Engineering and Technology
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Chinnick, S. J. "Computer based elucidation of reaction mechanisms." Thesis, University of Leeds, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.380303.
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Wilkinson, Sam K. "Reaction kinetics in formulated industrial catalysts." Thesis, University of Birmingham, 2014. http://etheses.bham.ac.uk//id/eprint/5113/.
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In heterogeneous catalysis, a fundamental understanding of the necessary physico-chemical requirements for a catalyst formulation is essential to its success. Understanding of reaction kinetics via modelling can demonstrate how catalysts work, providing functional information around surface active sites and reaction mechanism. This tool, combined with well-designed laboratory experiments to test a catalyst under steady and/or non-steady state conditions, can provide insight into the links between catalyst formulation and reaction performance. The aim of this project is to develop novel strategies and methods in these areas utilising a range of Johnson Matthey catalysts and reaction systems. This thesis places significant focus on obtaining mechanistically and statistically sound kinetic models with reliable model parameter estimates. Methods for this are developed using a batch liquid phase hydrogenation system using a Pt/TiO2 catalyst. Subsequently, non-steady state analysis of catalyst formulations has been explored. This includes the initial transient behaviour of a fresh vanadium phosphorus oxide selective oxidation catalyst under reaction conditions which allowed understanding of the evolution of distinct active site populations on the catalyst surface. A subsequent study of copper-based methanol synthesis catalysts explored the impact of gas phase conditions on the catalyst state. A mixture of steady-state testing and transient response experiments (i.e. via an imposed change in gas phase conditions over the catalyst) provided new insights into the evolution of active site populations and populations of surface species on the catalyst surface. Overall, the reaction kinetics studies demonstrated across this thesis demonstrate not only a series of methods to understand catalyst behaviour in depth but also to understand the key functional requirements for an effective industrial catalyst.
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Mitarai, Satoshi. "A Lagrangian study of chemical reaction in isotropic turbulence /." Thesis, Connect to this title online; UW restricted, 2004. http://hdl.handle.net/1773/7050.
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Volarath, Patra. "Application of Term-Rewriting Grammar in Chemical Reaction Prediction." Digital Archive @ GSU, 2008. http://digitalarchive.gsu.edu/chemistry_diss/21.
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Synthesis planning is a critical process in chemical design. A number of computer programs have been developed to assist the chemists with this procedure. Most of the programs utilize combinations of computational approaches. These have been successfully applied to a number of the synthesis predictions. However, they require numerous rules to screen for potential targets, as well as to keep the system from reaching the combinatorial explosion. This results in the advanced algorithms becoming more complex and parameter-sensitive. This can be problematic, particularly in the cases in which a large number of the compounds are to be handled, because it can not only result in a lengthy computational time, but also cause some of the highly potential targets to be missed. We developed a simpler approach for the reaction prediction using a term-rewriting grammar. The term-rewriting strategy is used to directly assign reactions to the compounds. This greatly reduces the number of rules that are usually required for these steps, and, hence, facilitates the prediction performance, while maintaining the prediction accuracy. In this dissertation, the designs of the developed algorithms and their results are first being presented, followed by a discussion of the approach’s application in the chemical design in the final chapter.
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Parker, Duncan J. "Uncovering features of chemical reaction networks in complex systems." Thesis, University of Southampton, 2018. https://eprints.soton.ac.uk/422229/.
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This thesis introduces a comprehensive atlas of behaviour in the iron-catalysed Belousov-Zhabotinsky reaction across a wide parameter space, under both stirred and unstirred conditions, encompassing variations in the concentrations of sulfuric acid, malonic acid and sodium bromate. All stirred reactions were monitored by UV-vis spectroscopy enabling the definition of concentration-dependent transitions in behaviour including those to chaotic oscillation. A programme was generated to quantify spirals observed in the unstirred reaction. This expanded on the work of Müller et al. by increasing the length of time that such spirals had been monitored. There was good agreement between their experimental results and those set out in this thesis, which shows the transition from normal spiral wave behaviour to a final steady state. The work on spiral waves also includes the first use of a statistical image-based method for identifying changes in chemical wave behaviour with time. Attempts were made at producing a model for the iron-catalysed Belousov-Zhabotinsky reaction using a swarm intelligence algorithm having identified key reactions involved in modifying the reaction behaviour based upon the Marburg-Budapest-Missoula model. A further comparison between this model for the cerium-catalysed reaction and the chemical component of the Kyoto Encyclopaedia of Genes and Genomes database demonstrated that study of such small scale systems is applicable to a larger scale biochemical network.
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Losey, Matthew W. "Novel multiphase chemical reaction systems enabled by microfabrication technology." Thesis, Massachusetts Institute of Technology, 2001. http://hdl.handle.net/1721.1/8634.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2001.Includes bibliographical references (p. 237-251).
Advances in MEMS (micro-electromechanical systems) have enabled some of the "Lab-on-a-Chip" technologies and microfluidics that are pervasive in many of the current developments in analytical chemistry and molecular biology. Coinciding with this effort in micro-analytics has been research in chemical process miniaturization -- reducing the characteristic length scale of the unit operation to improve heat and mass transfer, and ultimately process performance. My research has involved the design and fabrication of novel chemical reaction systems using MEMS and microfabrication methods (photolithography, deep-reactive-ion etching, thin-film growth and deposition, and multiple wafer bonding). Miniature chemical systems provide the opportunity for distributed, on-demand manufacturing, which would eliminate the hazards of transportation and storage of toxic or hazardous chemical intermediates. Reactions that are particularly suitable for miniaturized chemical systems are those that are fast and involve toxic intermediates: the controlled synthesis of phosgene is such a reaction and has been demonstrated in a microfabricated packed bed reactor. Owing to the high surface-to-volume ratios, micro chemical systems also have the potential to make improvements in process performance through enhanced heat and mass transfer.
(cont.) Heterogeneously catalyzed gas-liquid reactions have been performed in the microfabricated reactors and have been shown to have mass transfer coefficients several orders of magnitude larger than their industrial-scale counterparts. Multiphase reactions are often hindered by mass-transfer limitations owing to the difficulty in transporting the gaseous reactant through the liquid to the catalytic surface. The microchemical device has been designed to increase the interfacial gas-liquid contacting area by promoting dispersion and preventing coalescence. Microfabrication allows the design of reactors with complicated fluidic distribution networks, staggered arrays of microstructural features to promote mixing, and the integration of sensing and temperature control. Other uses of microfabrication include the incorporation of porous silicon as a high surface area catalyst support. In all, performing multiphase chemistry on a chip has been demonstrated to have inherent advantages, particularly for those fast reactions that can benefit from improved mixing and mass transfer.
by Matthew W. Losey.
Ph.D.