Rozprawy doktorskie na temat „Dissociation modeling”

ESI-MS spectra of Ni(II), Co(III), Mg(III), and Fe(II) porphyrin solutions in methanol show porphyrin monomer species with different charge states, such as [Ni(II)TPPS+H]3-, [Co(III)TPPS]3-, [Mn(III)TPPS]3-, [Mn(III)TPPS+H]2-, [Fe(II)TPPS+H]3-, and [Fe(II)TPPS+2H]2- ions. Collision-induced dissociation (CID) of these monomer species produced primarily losses of neutral SO3 and SO2. The mechanisms, in which these dissociation pathways took place, were investigated by the means of DFT calculations of the corresponding dissociation of neutral and ionized benzenesulfonate (B3-LYP/6-31+G(2d, p) level) and porphyrin monomer (B3-LYP/6-31+G(2d, p)+LANL2DZ//PM7 level). RRKM fitting of the CID breakdown curves showed that the activation energies of the reactions that experience a loss of SO2 from [Co(III)TPPS]3- and [Mn(III)TPPS]3- were similar, but of a lower magnitude than those for a loss of SO3. On the other hand, for [Ni(II)TPPS+H]3- and [Fe(II)TPPS+2H]2-, the activation energies of the reaction leading to a loss of SO2 were also similar, but this time were larger than those leading to SO3 loss. These results are consistent with a mechanism by which the SO2 loss starts with -C6H4SO3-, while the SO3 loss has to begin with -C6H4SO3H. To lose this SO3, extra energy is required for [Co(III)TPPS]3- and [Mn(III)TPPS]3- in order for them to overcome the barrier of H transfer from the porphyrin ring to -SO3-, but this is irrelevant when it comes to [Ni(II)TPPS+H]3- and [Fe(II)TPPS+2H]2- since the C6H4SO3H moiety already exists. In addition, the reaction of [Fe(II)TPPS+H]3- losing H leads to a unique dissociation mechanism.

Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2010.
Title from electronic title page (viewed Jun. 23, 2010). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry." Discipline: Chemistry; Department/School: Chemistry.

The first goal of this work is to demonstrate that using an aprotic polar solvent, such as γ- valerolactone instead of a protic polar solvent (i.e. ethanol, water), increases the yield of the esterification reaction of levulinic acid with ethanol, in presence of an acid catalyst. In fact, it is believed that an aprotic polar solvent can improve the catalytic activity of protons. The second goal is to study the influence of the variation of some parameters on the mentioned reaction. This was done by structuring the work in two sections: experimental and modelling. In the first section, two kinetic experiments were performed: one in presence of ethanol as solvent and one in presence of γ-valerolactone solvent, in order to achieve the first goal. After, different kinetic experiments were conducted, varying the process variables (i.e., temperature, catalyst concentration, molar ratio between reactants) in turn, in order to investigate their influence on the product’s yield. All experiments were performed in a batch custom reactor under isoperibolic and isobaric conditions and using γ-valerolactone as solvent. In the second section, the experimental data obtained were used in the modelling. Since the dissociation of all acids present in the esterification system was considered, an algebraic equation for the proton concentration was obtained and solved simultaneously with the differential equations (ODE) describing the molar balances. In this way, kinetic and thermodynamic parameters have been estimated.

Bulimia is often viewed as an extreme expression of eating concerns and body image disturbances that afflicts many adolescent and adult women. The cognitive strategies employed by individuals to inhibit eating and facilitate bingeing and purging are thought to include disattending internal sensations of hunger and satiety while sustaining attention on food, distorted beliefs, and interoceptive experiences (e.g., Heatherton & Baumeister, 1991). To the extent that these attentional and perceptual shifts mediate bulimic symptomatology, individuals with bulimic tendencies should exhibit certain cognitive attributes. Because hypnotizability, dissociation, and absorption have each been invoked (either directly or indirectly) as explanatory constructs for clinical and subclinical bulimia, the present study evaluated the absolute and relative effects of these factors on bulimic symptomatology in a large sample of undergraduate women (N = 309) using structural equation modeling. Following 2 assessments of hypnotic susceptibility (Harvard Group Scale of Hypnotic Susceptibility, Form A [Shor & Orne, 1962] & Group Stanford Hypnotic Susceptibility Scale, Form C [Crawford & Allen, 1982]), participants completed measures of eating disorder symptomatology (Eating Disorders Inventory-2 [Garner, 1991]; Three Factor Eating Questionnaire [Stunkard & Messick, 1985]), dissociation (Dissociative Experiences Scale [Carlson & Putnam, 1986]; Dissociation Questionnaire [Vanderlinden et al., 1993]), and absorption (Tellegen Absorption Scale [Tellegen & Atkinson, 1974]; Differential Attentional Processes Inventory [Crawford, Brown, & Moon, 1993; Grumbles & Crawford, 1981]). A final model including the latent constructs Hypnotizability, Dissociation, Absorption, and Bulimic Symptomatology provided a very good fit to the data (X 2 (58, N = 309) = 31.09, NFI = .932, CFI = .967, & RMSEA = .053). As hypothesized, dissociation was found to a have moderate effect (Standardized coefficient = .32, p < .01) on Bulimic Symptomatology when controlling for Hypnotizability and Absorption. Moreover, contrary to past research, the path between Hypnotizability and Bulimic Symptomatology and the path between Absorption and Bulimic Symptomatology were not significant. Based on these finding, we can now speak with increased confidence of a meaningful link between dissociation and the continuum of bulimic symptomatology. A pathological dissociative style appears to contribute to the development of bulimia.
Ph. D.

In the last several decades, polycyclic aromatic hydrocarbons (PAHs) have been the subject of extensive investigation due to their presumed abundance in the interstellar medium (ISM). My thesis concentrated on investigating the dissociation of ionized PAH molecules in the gas phase under similar conditions of the ISM. The twelve PAHs studied were naphthalene (NAP), anthracene (ANT), phenanthrene (PHN), cyclopenta[d,e,f] phenanthrene (CYC), pyrene (PYR), fluoranthene (FLN), perylene (PER) and coronene (COR). In addition, two dihydro PAHs were studied to examine potential intermediates in H2 catalysis, 1,2-dihydronaphthalene (DHN) and 9,10-dihydrophenanthrene (DHP), and two stabilized fragments of PAHs, acenaphthylene (ACE), fluorene-H (FLU). These ions were studied using atmospheric pressure chemical ionization (APCI) to generate the ions and the fragmentation was produced by collision-induced dissociation (CID). The CID experiments were done at different lab frame collision energies to produce breakdown curves for all fragments in each molecule. These curves were fitted by using Rice – Ramsperger-Kassel- Marcus (RRKM) theory to derive the activation energy (E0) at 0K and the entropy of activation (∆‡ S) for each reaction. The primary dissociation channel observed was H loss and this fragmentation channel was a common fragment to all PAHs molecules studied. Also, there were other fragments (CH3, C2H2, C4H2) observed in all of these molecules studied except perylene and coronene. The final step in this project was to compare these results with results derived from imaging photoelectron photoion coincidence spectroscopy (iPEPICO) reported by West and co-workers in order to determine the suitability of the APCI-CID technique for deriving reliable kinetic parameters for this class of ions.

In the first chapter we present numerical methods to describe termally activated processes and particularly the nudged elastic band method (NEB) to find minimum energy paths (MEPs) on potential energy surface (PES). In the second chapter we study a case that demonstrates by means of ab-initio calculations that steps are more reactive than plain surfaces. Water dissociation activation barrier is computed lower on stepped Pt(211) and Pt(311) surfaces respect to clean Pt(111) surface. In the third chapter we investigate water formation on Rhodium surface at high oxygen coverage with the aim to explain an interesting experiment performed at ELETTRA - Trieste. In the appendix A we make a brief discussion about density functionals and their drawbacks in correctly describing chemical reactions. In the appendix B we briefly describe a parallel work of development and code maintenance of PWSCF code of suite ESPRESSO [24] with the purpose of adding exact exchange and hybrid functionals to the code.

The objective of this study is to investigate cocrystal solubility and dissolution behavior to elucidate the factors affecting these processes in various media. Six cocrystals with xanthines (theophylline (THP), caffeine (CAF) and theobromine (THB)) were prepared and characterized by powder X-ray diffraction and thermal methods. Two cocrystals (CAFCA I and THBSA) are new solids and their crystal structures were determined by single crystal X-ray diffraction. Cocrystal solubility behavior depended on the dissolving complex solubility and its dissociation behavior in solution. Two THP cocrystals - one with acetaminophen (ACE) and one with citric acid (CA) created different degrees of free THP supersaturation in solubility and dissolution studies. High transient THP supersaturation caused almost immediate THP hydrate crystallization from THPCAH and led to non-congruent solubility behavior. Such behavior was not observed with the ACETHP because free THP supersaturation was not sufficient to induce rapid crystallization but did so over longer equilibration times. Three salicylic acid (SA) cocrystals with xanthines (THP, CAF, and THB) were prepared; two (THPSA and CAFSA) had low aqueous solubility compared to their pure components and one (THBSA) had higher solubility. Both cocrystal components in these cocrystals produced higher solubility/dissolution rates in alkaline media due to ionization. Also, at higher pH, THB precipitated from THBSA solutions because of higher THB supersaturation under alkaline conditions. Caffeine (CAF) and theophylline (THP) both form cocrystals with citric acid (CA) which is a highly water-soluble cocrystal former. Both CAFCA Form I and II solubility and dissolution behavior were studied. THPCAH exhibited non-congruent dissolution because of rapid precipitation of THP hydrate on the dissolving cocrystal surface. CAFCA exhibited congruent dissolution because it did not produce sufficient supersaturation to precipitate CAF hydrate during dissolution. CA cocrystals also have the unusual behavior of high viscosities produced in the dissolution boundary layer due to CA’s high solubility. These viscosities alter diffusion coefficients which reduce dissolution rates from that expected based purely on solubility. To further understand cocrystal dissolution, a diffusion-convection-reaction (DCR) model was developed to predict cocrystal dissolution rates in various media. This model predicted concentration profiles of all species (complex, free components and reactive species) in the diffusion layer of a rotating disk intrinsic dissolution system. Predicted dissolution rates had varying degrees of agreement with experimental data depending on the cocrystal model and the medium into which the cocrystal dissolved.

La réaction d’oxydation sélective du CO par O2 en présence d’un excès d’hydrogène (PROX) est considérée comme une étape de purification essentielle de l’H2 à utiliser dans des piles à combustible. L’objectif de cette thèse est de mieux comprendre le mécanisme de cette réaction sur des catalyseurs bimétallique s à base de Pt et Sn. Des catalyseurs modèles Pt et Pt-Sn ont été synthétisés en deux étapes : (i) formation de nanoparticules (NP) métalliques colloïdales en suspension suivi par ( ii) l’imprégnation de ces particules sur des supports. L’adsorption du CO suivit par spectroscopie FT-IR en réflexion diffuse (DRIFTS) a été utilisée pour caractériser ces solides après une réduction permettant de reformer des phases d’alliage PtSn. L’analyse DRIFTS permet de caractériser la nature des sites de Pt présents, soit dans l’alliage, soit dans des phases pures de Pt. La chaleur d’adsorption du CO sur la phase d’alliage a été mesurée par DRIFTS, pour la première fois, et apparait bien plus faible que celle sur le Pt seul. De manière surprenante, la ségrégation de l’alliage en présence de CO/H 2 à des températures inférieur es à 175°C a été mise en évidence. Des mesures in situ DRIFTS de la réaction d’oxydation préférentielle du CO (PROX) indiquent que l’alliage se transforme rapidement en Pt et SnOx de par la présence de l’O2. Aucune indication de la présence d’alliage n’a jamais pu être obtenue sous PROX, indiquant que les meilleures propriétés catalytiques associés aux phases Pt-Sn sont dues à leur habilité à générer une nouvelle phase active Pt+SnOx lors de leur ségrégation. Un modèle microcinétique du PROX sur Pt+SnOx a été développé sur la base de ceux pertinents à l’oxydation du CO et PROX sur Pt seul, permettant une modélisation satisfaisante des données. Ce travail montre l’intérêt du couplage des méthodes spectroscopiques et cinétiques pour la compréhension de la structure des catalyseurs « au travail » et des mécanismes de réactions complexes
The selective oxidation of CO in the presence of a large excess of H2 (PROX) is considered as a crucial step in the purification of H 2 to be used in low-temperature fuel cells, which are clean sources of energy. The objective of this thesis was to better understand the reaction mechanisms taking place over promising catalysts based on Pt and Sn. Model Pt-Sn catalysts were prepared by a two-step method: (i) synthesis of metallic nanoparticules (NP) in a colloidal suspension followed by (ii) the deposition of these NPs onto a support. The first step of the method enabled to produce well-controlled Pt-Sn NPs in terms of size and composition. However, the NPs were partly destroyed during the deposition step followed by calcination, due to the reoxidation of Sn. The adsorption of CO followed by diffuse reflectance spectroscopy (DRIFTS) was used to characterize the nature of these solids following a reduction, which was able to regenerate an alloyed phase. The DRIFTS analysis enabled to discriminate between Pt in an alloyed phase and Pt on monometallic surfaces. The heat of CO adsorption measured by DRIFTS appeared to be much lower than that associated with the pure Pt phase. Surprinsingly, a segregation of Pt and Sn was observed under a CO/H2 mixture below 175°C. In situ analysis by DRIFTS of the PROX reaction indicated that the Pt-Sn alloy rapidly decomposed in the presence of O2, forming an intimate mixture of Pt and SnOx. No evidence of the presence of Pt -Sn alloyed phases could be obtained under PROX conditions, suggesting that the superior catalytic activity of the Pt –Sn materials were related to the Pt+SnOx mixture. A detailed PROX microkinetic model was developed over Pt+SnOx, based on those relevant to CO oxidation and PROX over pure Pt. This work epitomises the benefits in combining in situ spectroscopic study with kinetic modelling to better understand the structure of catalysts “at work” and reaction mechanisms

The two experimental aspects of the imagining photoelectron photoion coincidence (iPEPICO) apparatus which is stationed at the VUV Beamline at the Swiss Light Source, a synchrotron source, have been used to investigate the fundamental properties of small molecules in the gas phase. The fast and slow dissociation dynamics of halogenated methanes and fluorinated ethenes have been investigated using threshold photoelectron photoion coincidence (TPEPICO) techniques. Rate constants and accurate 0 K appearance energies for the formation of subsequent daughter ions have been determined. The latter values have been used in conjunction with ab initio calculations to derive updated enthalpies of formation. The valence threshold photoelectron spectra of four fluorinated ethenes have been recorded. The spectra have been analysed using Franck–Condon simulations to model the vibrational structure, and assign the spectra, sometimes revising previous assignments. The potential energy surfaces of the ground and excited electronic states have been explored to uncover their various intriguing dissociative photodissociation mechanisms.

There is an extensive debate in the adult literature on whether recognition memory can better be explained by a single- or a dual-process account. Single-process accounts assume that a single memory strength signal underlies recognition. Dual-process accounts propose two independent processes, namely recollection (slow and associated with contextual details) and familiarity (fast and automatic). The aim of this dissertation was to advance this debate using a cognitive developmental approach. By investigating age-related changes of recognition memory across childhood as a function of theoretically motivated experimental manipulations, predictions drawn from single- and dual-process models of recognition memory were tested. We adapted the Process Dissociation Paradigm (PDP; Jacoby, 1991) to disentangle processes underlying recognition memory in 5-, 7-, and 11-year-olds and adults using a Dual-Process Signal Detection cognitive modelling approach (DPSD; Yonelinas, 1996). Experiments 1 – 6 demonstrated that 5-year-olds are able to recollect items based on perceptual details. Consistent with dual-process theory, across all age groups a response time limit decreased recollection while leaving familiarity unaffected (Chapter 2). Converging evidence consistent with dissociations during childhood was found after repeated item presentation (Chapter 3). Finally, after a thorough empirical validation of our approach, the new paradigm was used to investigate the developmental perceptual to semantic shift (Chapter 4). These findings, using a double dissociation logic, have advanced the theoretical debate on the nature of recognition memory by showing that one process is insufficient to account for the developmental and experimental findings reported here. Recollection and familiarity follow different developmental trajectories and are affected by encoding and retrieval manipulations (i.e., repetition and time limits). This provides a challenge for existing theories of recognition memory.

This research explores the links between the structure and dissociation energetics of ionized non-covalent complexes. In chapter 3, a large series of similar non-covalent complexes were probed using electrospray tandem mass spectrometry (ESI-MS/MS) and RRKM modelling in order to identify any trends in the dissociation energetics based on charge state, overall size of the complex, or size of the substrate. Ion mobility spectrometry (IMS) in conjunction with molecular mechanics/molecular dynamics (MM/MD) was used to study the conformations of these non-covalent complexes in order to determine if the same trends identified in the energetics could be corroborated independently based on structure. The system of study consisted of varying lengths of the synthetic polymer, polymethylmethacrylate (PMMA) complexed with singly or doubly protonated diaminoalkanes (DAA) of varying length. The critical energies of dissociation (E0) increased as the length of the polymer increased and was not significantly affected by the length of the singly protonated DAA substrates. The E0 of dissociation of doubly protonated complexes was strongly influenced by the length of the DAA; longer DAA substrates had greater separation of charge which decreased coulombic repulsion within the complex resulting in higher E0 values. MM/MD low energy structures of all complexes were validated with experimental IMS measurements and showed that the arrangement between the polymer and DAA were similar for different singly protonated DAAs. When doubly protonated, the length of DAA was the most important factor in determining the overall structure of the complex. In chapter 4, a direct link is shown between the observed E0 dissociation energies and the molecular conformations for eight different peptide–saccharide complexes containing either a tri-saccharide (d-(+)-raffinose and d-panose) or tetra-saccharide (stachyose and maltotetraose) with a small peptide (FLEEL and FLEEV). The E0 values were highly related to the overall conformation adopted by the non-covalent complex in the gas phase. Complexes containing peptide FLEE(L/V) with the tri-saccharide raffinose or panose had similar E0 of dissociation (∼0.64 eV) and similar conformations based on MM/MD simulations and IMS drift times. Conversely, for complexes containing a FLEE(L/V) peptide with one of the isomeric tetra-saccharides; stachyose had a E0 ∼0.08 eV greater than maltotetraose. This difference of intermolecular interaction was also reflected by the IMS drift times; maltotetraose in complex with FLEEV or FLEEL had a 5.9% and 2.3% faster IMS drift time than stachyose respectively. This indicated that the molecular arrangement between maltotetraose and the peptides was more compact than the stachyose-peptide complexes. In chapter 5, RRKM modelling of breakdown diagrams is not possible when the reactant ion signal is overlapped by other isobaric species. Trimeric, non-covalent complexes that contained two PMMA molecules and a doubly protonated DAA, [(PMMAa)(DAA+2H)(PMMAb)]+2, have m/z signals that contain multiple different complexes having the same total number of polymer repeat units but differ in the length of the each polymer. In this situation, the applicability of using the simple kinetic method to gain insight into relative binding energies was explored. The major factors which determined the suitability of the kinetic method for this system were identified as the structural arrangement of the reactant ion complex, possible reverse activation barriers, and the evaluations of Δ(ΔS‡). MM/MD simulations coupled with IMS suggests that within the reactant ion, the DAA is almost equally shared between two PMMA oligomers and that the two PMMA oligomers interact predominately with the DAA, and not with each other. MS/MS of the trimeric reactant complexes proceeds by neutral loss of one polymer and is suggested to proceed with little or no reverse activation barrier based on the low coulombic repulsion factors. The IMS drift times of [(PMMAa)(DAA+2H)]+2 complexes that were generated directly by ESI-MS or by dissociation of a trimeric, [(PMMAa)(DAA+2H)(PMMAb)]+2 complex were found to be identical. This provides some evidence that Δ(ΔS‡) ≈ Δ(ΔS) and using a statistical mechanics approach, Δ(ΔS) ≈ 0. The effective temperature (Teff) variable in the kinetic method expression was found to decrease as a function of the size of the trimeric complex, suggesting that the population distribution of the dissociating ensemble of complexes narrows as size increases. Overall, when RRKM fitting is not possible, the simple kinetic method could provide relative energetic ranking of competing dissociations reactions however the Teff term contributed to the greatest uncertainty in obtaining absolute quantities. Fitting MS/MS breakdown diagrams of non-covalent complexes with multiple dissociation channels is difficult due to the number of total fitting variables. Building from the simple kinetic method, chapter 6 shows that the relationship between the natural logarithm of competing fragment ions and reciprocal collision energy yields a branching relationship that allows for the sign of Δ(ΔS‡) and Δ(E0) between the channels to be obtained. Furthermore, the relationships between the fitting variables of RRKM modelling are empirically related to the theoretical branching relationship characteristics. This allowed for the fitting variables of all dissociation channels to be expressed as a function of a single channel so that the theoretical branching relationship matches the experimental branching relationship. Using this method, RRKM fitting of a MS/MS breakdown diagram for APCI ionized anthracene determined the E0 and ∆S‡ was 4.69 ± 0.29 eV and -3 ± 17 J K-1; 4.21 ±0.29 eV and -19 ±15 J K-1; and 4.81 ± 0.29 eV and 36 ±22 J K-1 for hydrogen loss, acetylene loss and diacetylene loss respectively. With one exception, these values are within experimental error of the iPEPICO derived energetic values. In chapter 7, MS/MS of ammoniated triacylglycerides at multiple collision energies and computational analysis are used to explain the cause of uneven dissociation rates of the FAs from different positions on the glycerol backbone. The loss of sn-1 and sn-3 FAs are found to have lower activation energies than the loss of the sn-2 position FA, however the loss of the FA from the sn-2 position is more entropically favourable. Theoretical MS/MS breakdown curves were fit to experimental values using RRKM theory to estimate the E0 of dissociation of FAs from the three glycerol positions. The E0 values for cleavage from the sn-1 and sn-3 positions were found to be approximately 1.52 eV, while that for the sn-2 position was highly dependent on the identity of the FA at that position. Computational structures and energy analysis suggest that an important step in the dissociation of [TAG+NH4]+ is the loss of ammonia. In a model system, glyceryl tributyrate, the loss of NH3 produced two distinct [TAG+H]+ product structures sitting 148 kJ and 160 kJ in energy above the ammoniated structure. The [TAG+H]+ structure that leads to the loss of the sn-1(3) is 12 kJ lower than the [TAG+H]+ structure that leads to the loss of the sn-2 FA. From this, the loss of a neutral FA that follows sits only an additional 35–48 kJ above the [TAG+H]+ structures. In Chapter 8, singly deprotonated β-cyclodextrin monomers, [(β-CD-H+]-1, and doubly deprotonated dimers, [(β-CD)2-2H+]-2, are both present following ESI-MS and have the same monoisotopic m/z. Similar to chapter 5, this makes it difficult to generate an MS/MS breakdown diagrams that can be modelled with RRKM theory. IMS was used to mobility separate [(β-CD-H+]-1 and [(β-CD)2-2H+]-2 and was followed by MS/MS of the [(β-CycD)2-2H+]-2 ion. A second problem when generating a MS/MS breakdown diagram of non-covalent complexes that contain identical components is that the fragment ions could have an identical monoisotopic m/z as the reactant ion. MS/MS of [(β-CycD)2-2H+]-2 results in two [(β-CD-H+]-1 fragments. To overcome this, breakdown diagrams were then generated by monitoring the changes in the isotopic profile. The RRKM derived E0 for dissociation of [(β-CycD)2-H+]-1 and [(β-CycD)2-2H+]-2 were 1.85 ± 0.11eV and 1.79 ± 0.09eV, respectively, corresponding to a slight decrease in complex stability due to increased charge-charge repulsion in the dianion.

L'utilisation de plasmas froids à base de gaz rares (Rg) dans des applications biomédicales ainsi que dans la propulsion spatiale est en nette évolution. Pour optimiser ces réacteurs plasmas, une compréhension fine des processus ayant lieu dans ces réacteurs est nécessaire. Ce travail de thèse a pour objectif de fournir les données manquantes dans la littérature (coefficients de transport et réaction) en passant par des données mésoscopiques (sections efficaces) obtenues à partir de données microscopiques (potentiels d'interaction) pour le xénon et krypton dans leur gaz parent. Seul des plasmas froids composés d'un seul type d'atome sont considérés. Comme le krypton et le xénon sont des gaz rares, et ont donc, à l'état de neutralité peu/pas d'interaction entre eux. Par conséquent, seules les collisions ion - atome seront considérées. Du fait des faibles énergies des ions dans le plasma froid, seul les 6 premiers états excités du couple Rg2+ seront pris en compte. Ces 6 états seront classés en deux groupes, 2P1/2 et 2P3/2. Lors de ce travail, deux potentiels d'interaction différents disponibles dans la littérature sont utilisés et comparés pour les systèmes collisionnels Kr+/Kr et Xe+/Xe dans le calcul des sections efficaces. Pour les collisions impliquant des dimères ioniques (Kr2+/Kr et Xe2+/Xe), les potentiels d'interaction sont calculés à partir du modèle DIM (Diatomics In Molecules) qui est une combinaison des potentiels atomiques d'interaction neutre - neutre et ion - neutre. Les sections efficaces, requises pour obtenir les données mésoscopiques manquantes, sont calculées à partir de trois méthodes différentes. La première méthode est la méthode quantique qui permet, par une résolution de l'équation de Schrödinger, d'obtenir de manière exacte les sections efficaces à partir des potentiels d'interaction. Cette méthode exacte, étant grande consommatrice de temps de calcul, est utilisée en tant que référence pour valider les deux autres méthodes approchées. La seconde méthode, nommée semi-classique, est basée sur la même expression que la section efficace quantique mais utilise un déphasage approché (approximation JWKB), induit par le potentiel d'interaction, entre l'onde diffusée et l'onde incidente. [...]
The use of cold plasmas based on rare gases (Rg) in biomedical applications as well as in space propulsion is clearly evolving. To optimize these plasma reactors, a fine understanding of the processes taking place in these reactors is necessary. This thesis aims to provide the missing data in the literature (transport coefficients and reaction rates) through mesoscopic data (cross-sections) obtained from microscopic data (interaction potentials) for xenon and krypton in their parent gas. Only cold plasmas composed of a single type of atom are considered. As krypton and xenon are rare gases, and so have, in the neutral state little / no interaction between them. Therefore, only ion - atom collisions will be considered. Due to the low ion energies in the cold plasma, only the first 6 excited states of the Rg2+ pair will be taken into account. These 6 states will be classified in two groups, 2P1/2 and 2P3/2. In this work, two different interaction potentials available in the literature are used and compared for the Kr+/Kr and Xe+/Xe collision systems in the calculation of cross-sections. For collisions involving ionic dimers (Kr2+/Kr and Xe2+/Xe), the interaction potentials are calculated from the DIM model (Diatomics In Molecules) which is a combination of the atomic potentials of neutral - neutral and ionic - neutral interactions. The cross-sections required to obtain the missing mesoscopic data are calculated from three different methods. The first method is the quantum method which allows, by a resolution of the Schrödinger equation, to obtain exactly the cross-sections from the interaction potentials. This exact method, which consumes a lot of computation time, is used as a reference to validate the two other approximate methods. The second method, called semi-classical, is based on the same expression as the quantum cross section but uses an approximate phase shift (JWKB approximation), induced by the interaction potential, between the scattered wave and the incident wave. [...]

Gas hydrates are crystalline solids (clathrates) in which gas molecules are encaged within lattices of hydrogen bonded water molecules. Hydrates are stable at low temperatures and high pressures; and dissociation takes place at temperatures and pressures outside the stability zone. Modeling the dissociation behavior of hydrates in porous soil media requires attention be paid to the geomechanics of hydrate dissociation. This paper addresses the issue of coupling the hydrate dissociation problem with the soil deformation problem and constructs the mathematical framework. Thermally stimulated dissociation process under undrained conditions is considered with conduction heat transfer.

By a dominant account, memory is composed of multiple storage systems, each operating according to unique principles. By an alternative account, memory is a single storage system and operates according to a single set of principles. Selective memory impairments in amnesia serve as the primary evidence for the multiple-system perspective. This thesis reports a critical appraisal of the multiple-system perspective using a combination of computational and empirical methods. In the computational analysis, I adopt the Holographic Exemplar Model, a single-system model of memory based on Hintzman’s (1986) classic MINERVA2 model. I simulate amnesia by manipulating the quality with which items are encoded in memory. In the empirical analysis, I simulate amnesia by manipulating peoples’ quality of encoding by limiting the time given to study stimuli. Simulations 1-2 and Experiments 1-2 simulate a dissociation between classification and recognition. All four analyses are consistent with the original results. Simulation 3 and Experiment 3 simulate single and double dissociations between tachistoscopic identification and recognition. The analyses were consistent with the single but not double dissociation. Simulation 4 and Experiment 4 simulate a dissociation among word-stem completion, cued recall, and recognition. Both analyses were only partially consistent with the original results, representing a failure overall. Simulation 5 and Experiment 5 derived a novel prediction from artificial grammar learning, predicting a non-dissociation between string completion and recognition. The mixed results provide some support for a single-system account of memory and opens opportunities for future work. I argue that the analysis is best considered in convergence with previous work moving toward a more integrated account of memory
February 2017

Thermochemical nonequilibrium widely exists in supersonic combustion, cold plasma and hypersonic flight. The effect can influence heat transfer, surface ablation and aerodynamic loads. One distinct feature of it is the coupling between internal energy excitation and chemical reactions, particularly the vibration-dissociation coupling. The widely used models are empirical and calibrated based on limited experimental data. Advances in theories and computational power have made the first-principle calculation of thermal nonequilibrium reaction rates by methods like quasi-classical trajectory (QCT) almost a routine today. However, the approach is limited by the uncertainties and availability of potential energy surfaces. To the best of our knowledge, there is no study of thermal nonequilibrium transport properties with this approach. Most importantly, non-trivial effort is required to process the QCT data and implement it in flow simulation methods. In this context, the first part of this work establishes the approach to compute transport properties by the QCT method and studies the influence of thermal nonequilibrium on transport properties for N₂-O molecules. The preponderance of the work is the second part, a comprehensive study of the development of a new thermal nonequilibrium reaction model based on reasonable assumptions and approximations. The new model is as convenient as empirical models. By validating against recent QCT data and experimental results, we found the new model can predict nonequilibrium characteristics of dissociation reactions with nearly the same accuracy as QCT calculations do. In general, the results show the potential of the new model to be used as the standard dissociation model for the simulation of thermochemical nonequilibrium flows.

Monitoring of the seafloor for gas hydrate dissociation around boreholes during hydrocarbon production is likely to involve seismic methods because of the strong sensitivity of P-wave velocity to gas in sediment pores. Here, based on geomechanical models, we apply commonly used rock physics modeling to predict the seismic response to gas hydrate dissociation with a focus on P-impedance and performed sensitivity tests. For a given initial gas hydrate saturation, the mode of gas hydrate distribution (cementation, frame-bearing, or pore-filling) has the strongest effect on P-impedance, followed by the mesoscopic distribution of gas bubbles (evenly distributed in pores or “patchy”), gas saturation, and pore pressure. Of these, the distribution of gas is likely to be most challenging to predict. Conceptual 2-D FD wave-propagation modeling shows that it could be possible to detect gas hydrate dissociation after a few days.

High temperature and its associated effects set the hypersonic flow regime apart from other class of flows. Viscous dissipation raises the internal energy of the high-kinetic-energy gas as it slows down in the boundary layer. For slow heat conduction into the vehicle surface, the gas temperature increases drastically, leading to real gas effects, dissociation and ionization of molecules. Due to the thickened boundary layer, strong ‘viscous interaction’ exists between the outer inviscid shock layer and the boundary layer, leading to a pressure rise compared to an inviscid case. This pressure in turn tends to make the boundary layer thinner than expected and increases the temperature gradient (for a cold wall case) and therefore the aerodynamic heating of the vehicle. High temperature near the vehicle airframe may cause surface ablation of the heat shield, releasing energy into the shock layer. Short duration flights, with a small time of flight may not experience ablation because the heat load on such vehicles may be too little, despite the high temperature in their vicinity. Energy release affects its aerothermodynamics and its performance. Effect of energy deposition (by means like plasma heat addition, electric arc discharge, chromium oxidation, etc.) on wave drag has been well documented in open literature. However, no concrete measurements exist on the aerothermodynamic effects of heat addition. Apart from ablation, flow separation may occur due to shock-boundary layer interaction (SBLI) towards the aft of a blunt nosed vehicle. Temperature in the dead air region (separated region with circulatory flow) inside the shear layer influences the performance of the vehicle and must be characterized. Apart from SBLI, another cause of intense heating is shock-shock interaction as classified by Edney. Although studies on wave drag galore, no experiments exist to characterize the temperature distribution in the separated shear layer. Characterization of these phenomena in an in-house free piston driven shock tunnel (FPST; called HST3) is the subject of this work. These studies in shock tunnels require development of a temperature measurement technique and related equipment. Most equipment tested in shock tunnels are marred by disadvantages such as single point measurement, lack of knowledge of emissivity, etc. No attempt has been made towards spatially resolved temperature characterization of the high enthalpy gas layer in shock tunnels. A non-intrusive, optical temperature measurement technique called two-colour ratio pyrometry (TCRP) was developed in the laboratory. A commercial DSLR camera was used as the pyrometer. TCRP was demonstrated in a tube furnace, by comparing the results with those obtained from other methods. The camera was then used for time integrated (and line-of-sight (LOS) integrated) temperature characterization of the shock layer at a stagnation enthalpy of 5.2 MJ/kg and Mach 10.1. Peaks over a continuous broad band, obtained from emission spectroscopy, were accounted for during temperature characterization. The stagnation region temperature was about 14% lower than that predicted by a numerical code. Time resolved temperature measurements, during the test time of 260 μs, were done by acquiring images of the flow using a high-speed camera at 20,000 fps. A numerical model was also developed in Fluent to obtain the actual stagnation plane temperature from the path length integrated value. The time resolved temperature was higher by as much as 14% from the time integrated one, whereas the actual stagnation plane temperature was only about 2.5% higher than the LOS integrated value. Next, the effect of exothermic surface ablation and heat addition, by oxidation of a thin film of chromium coated on a large angle blunt cone in air flow, was studied on the aerothermodynamics of the shock layer-by characterizing its effects on the shock layer temperature, surface heat flux and shock stand-off distance. Experiments were done at a stagnation enthalpy of 6.31 MJ/kg and Mach number of 9.73. Heat release increased the shock layer temperature (obtained from TCRP) by 173 K, convective heat flux at the model surface by 25.5% and shock stand-off distance by 17%. The effect on shock layer aerothermodynamics was more with O2 as the test gas, as it contains a larger mole fraction of oxygen than air. Numerical simulations and calculations done to simulate real gas effects and wall surface reactions predicted a Cr regression rate of 0.074 mm/sec and a total heat deposition of about 215 W/cm2. Cr being carcinogenic and possessing a high activation energy, an organic compound, Nafion was tested as its replacement and found to have more prominent effects on the shock layer aerothermodynamics. A spiked body configuration was used to study the separated flow encountered at the aft of reentry vehicles. A time integrated image of the flow over the configuration was first acquired using a DSLR camera at 5.2 MJ/kg to locate the temperature hotspots. A maximum temperature of around 2920 K was encountered, in the region enveloped by the shear layer where the flow separates and recirculates. The temperature within the dead air region is high due to conversion of kinetic energy to internal energy. The flow was found to be unsteady in the separated zone and consists of collapse and inflation. Time resolved images of the unsteady flow were taken at an enthalpy of 6.31 MJ/kg. The unsteady results also showed low temperatures inside the conical shock and extreme temperatures, as high as 3300 K in the separated region. To conclude, two important phenomena pertaining to the design of hypersonic reentry vehicles were studied, and a temperature measurement technique to study them was developed and demonstrated in the laboratory.
Defence Research and Development Organization (DRDO)

The past decade has witnessed dramatic changes in the oil and gas industry with the drilling and production extending into progressively deeper waters and higher operating pressures, therefore making it essential to gain a better understanding of the behaviour of gas hydrate at high pressure conditions. New experimental 3-phase H−LW−V (Hydrate−Liquid Water−Vapour) equilibrium data for nitrogen and H−LW−V (Hydrate−Liquid Water−Vapour) and H−LW−LHC (Hydrate−Liquid Water−Liquid Hydrocarbon) data for ethane and propane simple clathrate hydrates were generated by a reliable fixed-volume, isochoric, step-heating technique. The accuracy and reliability of the experimental measurements are demonstrated by comparing measurements with reliable literature data from different researchers. Additional experimental data up to high pressure (200 MPa when available) for CH4, C2H6, C3H8, i-C4H10, N2, Ar, Kr, Xe, H2S, O2, CO and CO2 clathrates have been gathered from literature. The Valderrama modification of the Patel-Teja (VPT) equation of state combined with non-density-dependent (NDD) mixing rules is used to model the fluid phases with previously reported binary interaction parameters. The hydrate-forming conditions are modelled by the solid solution theory of van der Waals and Platteeuw. Langmuir constants have been calculated by both Kihara potential as well as direct techniques. Model predictions are validated against independent experimental data and a good agreement between predictions and experimental data is observed, supporting the reliability of the developed model.

The present study investigated findings discussed in a review by Vickers (1985) which suggest that two types of response bias (relative caution and expectation) have dissociable effects on confidence ratings. We manipulated both biases in an attempt to replicate and expand on Vickers’ (1985) review. 32 participants completed two 1-hour sessions in which they undertook a perceptual discrimination task. One of the two biases was manipulated in each session. We found that in correct responses, expectation bias induced higher confidence ratings in responses participants were biased towards, compared to relative caution bias, p < .001. The hypothesised differential effects of the two bias manipulations on confidence ratings goes against the often-assumed unitary conception of response bias (Link, 1975). We also found that this interaction effect differed depending on the accuracy of the response, p < .001, where a flip from the findings in correct responses was found in error responses. This unexpected interaction with accuracy warrants more research. The present research advocates for the importance of confidence as a variable for the understanding and modelling of cognitive processes.

abstract: Theories of interval timing have largely focused on accounting for the aggregate properties of behavior engendered by periodic reinforcement, such as sigmoidal psychophysical functions and their scalar property. Many theories of timing also stipulate that timing and motivation are inseparable processes. Such a claim is challenged by fluctuations in and out of states of schedule control, making it unclear whether motivation directly affects states related to timing. The present paper seeks to advance our understanding of timing performance by analyzing and comparing the distribution of latencies and inter-response times (IRTs) of rats in two fixed-interval (FI) schedules of food reinforcement (FI 30-s and FI 90-s), and in two levels of food deprivation. Computational modeling revealed that each component was well described by mixture probability distributions embodying two-state Markov chains. Analysis of these models revealed that only a subset of latencies are sensitive to the periodicity of reinforcement, and pre-feeding only reduces the size of this subset. The distribution of IRTs suggests that behavior in FI schedules is organized in bouts that lengthen and ramp up in frequency with proximity to reinforcement. Pre-feeding slowed down the lengthening of bouts and increased the time between bouts. When concatenated, these models adequately reproduced sigmoidal FI response functions. These findings suggest that behavior in FI fluctuates in and out of schedule control; an account of such fluctuation suggests that timing and motivation are dissociable components of FI performance. These mixture-distribution models also provide novel insights on the motivational, associative, and timing processes expressed in FI performance, which need to be accounted for by causal theories of interval timing.
Dissertation/Thesis
Masters Thesis Psychology 2015

Droplets as precursor are extensively applied in diverse fields of science and engineering. Various contributions are provided previously towards analysis of single phase and multi-phase droplets of single and multiple components. This thesis describes modelling of multi-phase (nano fluid) droplet vaporization. The evaporation of liquid phase along with migration of dispersed particles in two-dimensional plane within droplet is detailed using the governing transport equations along with the appropriate boundary and interface conditions. The evaporation model is incorporated with aggregate kinetics to study agglomeration among nano silica particles in base water. Agglomeration model based on population balance approach is used to track down the aggregation kinetics of nano particles in the droplet. With the simulated model it is able to predict different types of final structure of the aggregates formed as observed in experimental results available in literature. High spatial resolution in terms of agglomeration dynamics is achieved using current model. Comparison based study of aggregation dynamics is done by heating droplet in convective environment as well as with radiations and using different combination of heating and physical parameters. The effect of internal flow field is also analysed with comparative study using levitation and without levitation individually. For levitation, droplet is stabilized in an acoustic standing wave. It is also attempted to study the transformation of cerium nitrate to ceria in droplets when heated under different environmental conditions. Reaction kinetics based on modified rate equation is modelled along with vaporization in aqueous cerium nitrate droplet. The thermo physical changes within the droplet along with dissociation reaction is analysed under different modes of heating. The chemical conversion of cerium nitrate to ceria during the process is predicted using Kramers' reaction velocity equation in a modified form. The model is able to explain the kinetics behind formation of ceria within droplet at low temperatures. Transformation of chemical species is observed to be influenced by temperature and configuration of the system. Reaction based model along with CFD (computational fluid dynamics) simulation within the droplet is able to determine the rate of chemical dissociation of species and predict formation of ceria within the droplet. The prediction shows good agreement with experimental data which are obtained from literature.

Droplets as precursor are extensively applied in diverse fields of science and engineering. Various contributions are provided previously towards analysis of single phase and multi-phase droplets of single and multiple components. This thesis describes modelling of multi-phase (nano fluid) droplet vaporization. The evaporation of liquid phase along with migration of dispersed particles in two-dimensional plane within droplet is detailed using the governing transport equations along with the appropriate boundary and interface conditions. The evaporation model is incorporated with aggregate kinetics to study agglomeration among nano silica particles in base water. Agglomeration model based on population balance approach is used to track down the aggregation kinetics of nano particles in the droplet. With the simulated model it is able to predict different types of final structure of the aggregates formed as observed in experimental results available in literature. High spatial resolution in terms of agglomeration dynamics is achieved using current model. Comparison based study of aggregation dynamics is done by heating droplet in convective environment as well as with radiations and using different combination of heating and physical parameters. The effect of internal flow field is also analysed with comparative study using levitation and without levitation individually. For levitation, droplet is stabilized in an acoustic standing wave. It is also attempted to study the transformation of cerium nitrate to ceria in droplets when heated under different environmental conditions. Reaction kinetics based on modified rate equation is modelled along with vaporization in aqueous cerium nitrate droplet. The thermo physical changes within the droplet along with dissociation reaction is analysed under different modes of heating. The chemical conversion of cerium nitrate to ceria during the process is predicted using Kramers' reaction velocity equation in a modified form. The model is able to explain the kinetics behind formation of ceria within droplet at low temperatures. Transformation of chemical species is observed to be influenced by temperature and configuration of the system. Reaction based model along with CFD (computational fluid dynamics) simulation within the droplet is able to determine the rate of chemical dissociation of species and predict formation of ceria within the droplet. The prediction shows good agreement with experimental data which are obtained from literature.

The goal of this study was to characterize the binding sites on the surface of wheat roots, Triticum turgidum, involved in the adsorption of protons and metals, and quantify the thermodynamic constants needed for a surface complexation model to predict metal binding. The adsorption of protons, Cd(II), Cu(II), and Ni(II) to the root surface as a function of pH and ionic strength in single metal exposure scenarios was quantitatively described using potentiometric titrations, batch metal adsorption experiments, and the least squares fitting program FITEQL. Model predictions from single metal exposures were compared to measured metal adsorption concentrations when roots were exposed to binary and ternary combinations of the metals. Proton dissociation was a function of three discrete monoprotic acid sites on the root surface with log proton dissociation constants of -4.50, -6.23, and -7.37 respectively, upon which varied ionic strength had no effect. The total proton binding capacities for the three sites were 2.58 x 10-4, 1.29 x 10-4, and 2.58 x 10-4 M, respectively. Metal complexation was best described by a two-site model having conditional stability constant log values of 3.04 and 3.30 for Cd(II), 3.21 and 3.25 for Cu(II), and 2.83 and 2.84 for Ni(II) at ionic strength 0.01M. At ionic strength 0.1 M the conditional stability constants log values were 2.37 and 3.36 for Cd(II), 3.11 and 2.56 for Cu(II), and 2.18 and 3.00 for Ni(II). When roots were exposed to binary or ternary mixtures of the metals, the two monoprotic acid single metal model did not provide ideal fits to the data indicating that adsorption in a metal mixture scenario cannot be considered additive and is dependent on the combination of metals present in the exposure environment. The experimentally determined proton dissociation constants and metal stability constants could be used in commercial geochemical speciation programs such as Visual MINTEQ to predict metal adsorption to plants.
Natural Sciences and Engineering Research Council of Canada, The Mining Association of Canada, Ontario Power Generation, Environment Canada.

This dissertation covers a series of related topics in the mathematical modelling of mass spectrometry data. The dissertation opens with a presentation of an optimal algorithm for the generation of the fine isotopic structure. We further show the applications of that algorithm to the problem of deconvoluting mixed isotopic signals, in two different ways. We also approach the problem of estimating the deep parameters of mass detectors, estimating the parameters of a function that relates the instrument-generated intensities to the numbers of ions. These solutions are applied to the problem of understanding Electron Driven reactions, whose principal aim is to induce ion fragmentation and, in that way, enhance the instrument’s identification capabilities. Finally, we show how to apply the mathematical theory of reaction kinetics to estimate the reaction rates of the electron transfer reactions.
Niniejsza rozprawa doktorska dotyczy szeregu tematyk z zakresu matematycznego modelowanie widm masowych. W pracy przedstawiam algorytm służący obliczeniom związanym z rozkładami izotopowymi cząsteczek. Algorytm ów wykorzystuję w problemie dekonwolucji mieszanek sygnałów ze znanych źródeł molekularnych, na dwa różne sposoby. Przedstawiam również sposób na wyznaczenie zależności pomiędzy zarejestrowanym sygnałem a liczbą jonów dla różnych detektorów jonów. Powyższe rozwiązania zostają również wykorzystane w celu dokładniejszego zrozumienia za- sad działania fragmentacji jonów za pomocą transferu elektronu, która znacząco poszerza możliwości identyfikacji substancji. Pokazuję również sposób na wyestymowanie parametrów tych reakcji, wykorzystując w tym celu matematyczny model kinetyki reakcji.