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1	Observation on the local structural transformation of amorphous zinc oxide during the heating process by molecular dynamics Tsai, Jen-Yu 15 August 2012 (has links) In this study, we employ molecular statics to construct the structure of amorphous zinc oxide. First, we find out the first number of higher energy structures in all local stable structures by Basin-Hopping algorithm, which are separated into different ratio of crystalline/amorphous zinc oxide structures, and then we judge the type of zinc oxide structure by radial distribution function. In addition, we use coordination number to analyse the interatomic bond length and bond angle in the structures. Furthermore, we employ molecular dynamics to increase the temperature of amorphous zinc oxide structures, and then use the distribution of coordination number, bond length and bond angle between zinc and oxygen atom to analyse the change of the local structure of amorphous zinc oxide during the heating process. radial distribution function coordination number Basin-Hopping algorithm molecular dynamics
2	Structural studies of aqueous solutions at high temperatures : critical opalescence and hydration Sullivan, Darius M. January 2000 (has links) No description available. 539.7
3	On the Oxidation of Methionine Residues during the Storage of Protein Pharmaceuticals in an Aqueous Formulation Chu, Jhih-Wei, Yin, Jin, Wang, Daniel I.C., Trout, Bernhardt L. 01 1900 (has links) This study addresses the fundamentals of an important degradation pathway of storing protein pharmaceuticals in an aqueous formulation, oxidation of methionine residues by peroxides. First, a mechanism by which methionine residues are oxidized is identified via ab initio calculations. The major difference of this new mechanism to previous ones is the role of solvent molecules in the oxidation process. Previously proposed mechanisms suggested that solvent molecules facilitate the transfer of hydrogen associated with the oxidation reaction, but the estimated activation energies and pH dependence of oxidation rates derived from this mechanism rates do not agree with experimental observations. In our proposed mechanism, however, water molecules stabilize the charge separation in the transition-state complex through specific interaction such as hydrogen bonding. This mechanism satisfies all experimental studies on the oxidation of organic sulfides by peroxides. A correct picture of instability mechanism is essential in developing stabilization strategies to design a robust formulation. Based on this mechanism, a structure/instability relationship is built to explain the oxidation rates of methionine residues in a protein molecule. Specifically, a structural property, two-shell water coordination number, is found to correlate semi-quantitatively to the rates of oxidation of methionine residues in G-CSF (granulocyte colony-stimulating factor) and hPTH (human parathoid hormone). We also show that a traditionally used structural property, solvent accessible area, can not provide such accurate correlation and that the dynamic motion of protein molecules and an explicit treatment of solvent molecules are essential to describe the rates of oxidation of methionine residues. Furthermore, the insight provided by the molecule-level understanding in developing a stabilizing formulation is discussed. / Singapore-MIT Alliance (SMA) oxidation of methionine residues protein pharmaceuticals storage two-shell water coordination number
4	Bond lengths and bond valences of ions bonded to oxygen: their variability in inorganic crystals Gagné, Olivier C. 01 August 2016 (has links) A large amount of information concerning interatomic distances in the solid state is available, but little has been done in recent times to comprehensively filter, summarize and analyze this information. Here, I examine the distribution of bond lengths for 135 ions bonded to oxygen, using 180,331 bond lengths extracted from 9367 refined crystal structures collected from the Inorganic Crystal Structure Database (ICSD). The data are used to evaluate the parameterization of the bond-length—bond-valence relation of the bond-valence model. Published bond-valence parameters for 135 cations bonded to oxygen, and the various methods used in their derivation, are evaluated. New equations to model the relation are tested and the common form of the equation is found to be satisfactory. A new method (the Generalized Reduced Gradient Method, GRG method) is used to derive new bond-valence parameters for 135 cations bonded to oxygen, leading to significant improvements in fit for many of the ions. The improved parameterization is used to gain crystal-chemical insight into the milarite structure. A literature review of 350+ published compositions is done to review the end-members of the milarite group and to identify compositions that should have been described as distinct minerals species. The a priori bond-valences are calculated for minerals of this structure, and are used to examine the controls of bond topology on site occupancy, notably by localizing the major source of strain of the structure (the B site). Examination of the compositions of all known milarite-group minerals shows that compositions with a fully occupied B site are less common than those with a vacant B site, in accord with the idea that the B site is a local region of high strain in the structure. The bond-length distributions for the ions of the alkali and alkaline-earth metal families are examined. Variations in mean bond-lengths are only partly explained by the distortion theorem of the bond-valence model. I have found that bond length also correlates with the amount of vibrational displacement of the constituent ions. The validity of some uncommon coordination numbers, e.g., [3]-coordinated Li+, [3]-coordinated Be2+, is confirmed. / October 2016 Bond length Bond valence Milarite Coordination number Alkali metal Alkaline-earth metal Structural strain Mean bond-length Bond-valence model
5	Discrete Element Modeling of Railway Ballast for Studying Railroad Tamping Operation Dama, Nilesh Madhavji 24 September 2019 (has links) The behavior of the ballast particles during their interaction with tamping tines in tamping operation is studied by developing a simulation model using the Discrete Element Model (DEM), with the aim of optimizing the railroad tamping operation. A comprehensive literature review is presented showcasing the applicability of DEM techniques in modeling ballast behavior and its feasibility in studying the fundamental mechanisms that influence the outcome of railroad tamping process is analyzed. The analysis shows that DEM is an excellent tool to study tamping operation as its important and unprecedented insights into the process, help not only to optimize the current tamping practices but also in the development of novel methods for achieving sustainable improvements in the track stability after tamping. The simulation model is developed using a commercially available DEM software called PFC3D (Particle Flow Code 3D). A detailed explanation is provided about how to set up the DEM model of railway ballast considering important parameters like selection and calibration of particle shapes, ballast mechanical properties, contact model, and parameters governing the contact force models. Tamping operation is incorporated into the simulation model using a half-track layout with a highly modular code that enables a high degree of adjustability to allow control of all process parameters for achieving optimized output. A parametric study is performed to find the best values of tine motion parameters to optimize the linear tamping efficiency and a performance comparison has been made between linear and elliptical tamping. It is found that squeeze and release velocity of the tines should be lesser for better compaction of the particles and linear tamping is better compared to elliptical tamping. / Master of Science / Railway track stability is the resistance of the tracks to deformation and is affected by the rail traffic, ballast fouling (contamination of ballast) and the changing environmental conditions. The track stability depends on the normal and frictional support provided by the ballast to the sleepers. Non-uniform ballast consolidation below the railway sleeper results in erratic wheel-rail contact forces, low traffic speeds, poor ride quality, and derailments. Thus, tamping is a railway track maintenance method done periodically on the railway tracks to ensure track stability. Tamping process involves compacting the railroad ballast underneath the sleeper. The sleeper is lifted by a desired height and then vibrating tamping tools called tines are inserted into the ballast below the sleeper to fill the void created by lifting of the sleeper and the sleeper is dropped back on to the ballast. So, it is important to understand the ballast mechanics, dynamics and ballast’s behavioral response to the tamping operation. Since, large scale experiments such as this are difficult, this operation has been simulated in a commercially available software called PFC3D using a Discrete Element Model (DEM) to represent the railway ballast. It is shown through a simulation that though spherical particles provide better computational efficiency, they cannot capture the exact ballast behavior like clumps (a collection of spherical pebbles). So using clumps to represent ballast, efforts are made to optimize the linear tamping efficiency. This is done by changing the values of parameters like tine amplitude, tine frequency, insertion velocity and squeeze velocity and finding their optimum values. Linear tamping results are compared with elliptical tamping. Thus, an optimum tamping cycle would help save money spent on the track maintenance activities. Distinct element modeling Discrete element modeling DEM railway ballast tamping contact model porosity compaction coordination number particle shape
6	Discrete Element Modeling of Railway Ballast for Studying Railroad Tamping Operation Jain, Ashish 18 January 2018 (has links) The development of Discrete Element Model (DEM) of railway ballast for the purpose of studying the behavior of ballast particles during tamping is addressed in a simulation study, with the goal of optimizing the railroad tamping operation. A comprehensive literature review of applicability of DEM techniques in modeling the behavior of railway ballast is presented and its feasibility in studying the fundamental mechanisms that influence the outcome of railroad tamping process is analyzed. A Discrete Element Model of railway ballast is also developed and implemented using a commercially available DEM package: PFC3D. Selection and calibration of ballast parameters, such as inter-particle contact force laws, ballast material properties, and selection of particle shape are represented in detail in the model. Finally, a complete tamping simulation model is constructed with high degree of adjustability to allow control of all process parameters for achieving realistic output. The analysis shows that DEM is a highly valuable tool for studying railroad tamping operation. It has the capability to provide crucial and unprecedented insights into the process, facilitating not only the optimization of current tamping practices, but also the development of novel methods for achieving sustainable improvements in track stability after tamping in the future. Different ways of modeling particle shapes have been evaluated and it has been shown that while using spheres to represent irregular ballast particles in DEM provides immense gains in computational efficiency, spheres cannot intently capture all properties of irregularly shaped particles, and therefore should not be used to model railway ballast particles. Inter-particle and wall-particle contact forces are calculated using Hertzian contact mechanics for determining ballast dynamics during tamping. The results indicate that the model is able to accurately predict properties of granular assemblies of the railway ballast in different test cases. The developed model for simulating tamping operation on a half-track layout is expected to be extended in future studies for evaluating rail track settlement and stability, optimization of tamping process, and performance of different ballast gradations. / MS / Development of a virtual simulation model for the stone bed which forms the foundation of traditional rail track structures is discussed in this study for the purpose of improving a conventional railway maintenance practice called tamping. The stone bed, called ballast, is flexible and is susceptible to undesirable deformation due to the forces from train traffic on the rail tracks over their service time. Therefore, periodic restoration of track structure is performed by tamping to maintain the operational quality of the rail tracks and reduce the risk of train accidents. This simulation model is intended to accelerate the scientific development of the current tamping practices by providing unprecedented insight into the behavior of small stones which form the bulk of the ballast and obviating the requirement for costly physical experimentation. The nuances of the mechanical behavior of ballast have been examined by a comprehensive literature review and the selection of a modeling technique called Discrete Element Modeling (DEM) has been justified for modeling of ballast owing to its suitability in capturing intricate dynamics of ballast stones. The virtual simulation model which is developed as results of this work has been found to be extremely efficient in realistically predicting the outcome of tamping process for any set of conditions of interest. This implies that quality of the rail tracks after tamping can be studied for a variety of different test cases and most optimized set of tamping parameters which results in maximum track quality can be analyzed. However, it was observed that the accuracy of the results obtained from the simulation model is dependent on the level of detail which is used to input properties of the ballast into the model. Low level of detail results in less accurate results whereas a high level of detail takes an unreasonably long time to solve. Therefore, a compromise has to be made between accuracy and solution time while programming the simulation model, and additional work is required in the future to improve the solution speed of the model. Discrete Element Modeling DEM railway ballast track settlement tamping track stability contact model particle shape ballast compaction coordination number
7	An investigation on process of seeded granulation in a continuous drum granulator using DEM Behjani, M.A., Rahmanian, Nejat, Ghani N.F.b.A., Hassanpour, A. 22 February 2017 (has links) Yes / Numerical simulation of wet granulation in a continuous granulator is carried out using Discrete Element Method (DEM) to discover the possibility of formation of seeded granules in a continuous process with the aim of reducing number of experimental trials and means of process control. Simple and scooped drum granulators are utilized to attain homogenous seeded granules in which the effects of drum rotational speed, particles surface energy, and particles size ratio are investigated. To reduce the simulation time a scale-up scheme is designed in which a dimensionless number (Cohesion number) is defined based on the work of cohesion and gravitational potential energy of the particles. Also a mathematical/numerical method along with a MATLAB code is developed by which the percentage of surface coverage of each granule is predicted precisely. The results show that use of continuous granulator is promising provided that a high level of shear is considered in the granulator design, e.g. it is observed that using baffles inside the drum granulators is essential for producing seeded granules. It is observed, moreover, that the optimum surface energy for scooped granulator with rotational speed of 50 rpm is 3 J/m2 which is close to the number predicted by Cohesion number. It is also shown that increasing the seed/fine size ratio enhances the seeded granulation both quantitatively (60% increase in seeds surface coverage) and qualitatively (more homogeneous granules). Seeded granules Drum granulator Discrete element method (DEM) Surface energy Coordination number Cohesion number Scale up method
8	Efeito da Topologia Molecular no Empacotamento Cristalino de Pirazolo[1,5-a]pirimidinas / Effect of Molecular Topology in Crystal Packing of Pyrazolo[1,5-a]pyrimidines Tier, Aniele Zolin 27 February 2013 (has links) Conselho Nacional de Desenvolvimento Científico e Tecnológico / This study shows the influence of the molecular topology of the crystal of a series of 14 pyrazolo[1,5-a]pyrimidines. The topological data were obtained from X-ray diffraction data and energy stabilization were determined by thermal analysis and chemical computations. Topological analysis carried out was Molecular Coordination Number (NCM) using the Voronoi-Dirichlet polyhedra and Hirshfeld surface. The NCM found for the majority of compounds was 14. Furthermore, it was determined contact area and the solid angle between molecules of the first coordination sphere of the cluster. Several correlations between data were performed, where it is possible highlight the correlation between the area of contact of the cluster molecules and the interaction energy and the solid angle and interaction energy were established. These correlations showed that there is a proportionality between the data, showing that the greater the contact area, the greater the interaction energy for a series of pyrazolo[1,5-a]pyrimidine studied in this thesis. As the contact area, solid angle also presents proportionality with the calculated interaction energy. Among the atom-atom contacts present on the surface of the test compounds was observed that contacts C∙∙∙H and C∙∙∙C are key to stabilize the crystals. This result corroborates the hypothesis that the contact surface between the molecules would be the driving force for the crystalline arrangement. / Este trabalho apresenta o estudo da influência da topologia molecular na organização cristalina de uma série de 14 pirazolo[1,5-a]pirimidinas. Os dados topológicos foram obtidos por difratometria de raios-X e os dados de energia de estabilização foram determinados por análises térmicas e cálculos computacionais. Dentre as análises topológicas realizadas destaca-se a determinação do Número de Coordenação Molecular (NCM) usando o Poliedro de Voronoi-Dirichlet e a Superfície de Hirshfeld. O NMC encontrado para a maioria dos compostos foi de 14. Além disso, foi determinada a área de contato, bem como o ângulo sólido entre as moléculas da primeira esfera de coordenação do cluster. Estabeleceu-se uma serie de correlações entre os dados obtidos, entre elas, destaca-se a correlação entre esta área de contato entre as moléculas do cluster e a energia de interação, bem como a correlação ângulo sólido e energia de interação. Ambas correlações mostraram que há uma proporcionalidade entre os dados, mostrando que quanto maior a área de contato, maior a energia de interação para a série de pirazolo[1,5-a]pirimidinas estudadas nesta dissertação. Assim como a área de contato, o ângulo sólido também apresenta uma proporcionalidade com a energia de interação calculada. Dentre os contatos átomo-átomo presentes na superfície dos compostos em estudo, observou-se que os contatos C∙∙∙H e C∙∙∙C são os principais para a estabilização dos cristais estudados. Este resultado corrobora com a hipótese de que a superfície de contato entre as moléculas seria a força motriz para o arranjo cristalino. Topologia molecular Pirazolo[1,5-a]pirimidinas Difratometria de raios-X Cálculos computacionais Número de coordenação molecular Poliedro de Voronoi-Dirichlet Superfície de Hirshfeld Molecular topology Pyrazolo[1,5-a]pyrimidines X-ray diffraction Computational calculations Hirshfeld surface
9	Etude expérimentale du comportement instable d'un sable silteux : application aux digues de protection. / Experimental study of the unstable behavior of silty sand : application to protection dikes. Nguyen, Kien Trung 10 April 2014 (has links) Les matériaux constitutifs des digues sont souvent des sables silteux dont le comportement mécanique peut manifester une « instabilité » à des états de contraintes situés bien avant la limite de plasticité de Mohr-Coulomb. Ce mécanisme de rupture pourrait expliquer plusieurs brèches dont l'occurrence n'a pas été attribuée aux mécanismes classiques de rupture de digues telle que l'érosion interne. L'objectif de cette thèse est de mieux comprendre, au regard de ce phénomène d'instabilité, le comportement mécanique d'un sable silteux provenant de la zone adjacente à une brèche de digue du Rhône lors de la crue de 2003, à l'aide d'essais triaxiaux.Les résultats sur le sable propre montrent que le matériau étudié est très sensible au phénomène d'instabilité. Ce dernier peut être prédit par une courbe d'instabilité reliant, au déclenchement de l'instabilité, le rapport des contraintes au paramètre d'état. L'analyse de ces résultats suggère qu'une forte contractance du matériau est la condition nécessaire pour que l'instabilité du sable lâche ait lieu et qu'une direction appropriée du vecteur d'incrément de contraintes est la condition suffisante.Les résultats sur les mélanges constitués du sable avec des fines montrent qu'un départ de fines, causé par exemple une érosion de type suffusion, favorise l'occurrence de l'instabilité dans les digues. Par ailleurs, ces résultats révèlent que l'indice des vides équivalent est un paramètre pertinent dans l'analyse du comportement du sable silteux. Le calcul de l'indice des vides équivalent nécessite la détermination du paramètre b pour lequel une nouvelle formule a été proposée. / The constitutive materials of dikes are often silty sands whose mechanical behavior can become unstable at stress states located well under the Mohr-Coulomb plasticity limit criterion. This failure mechanism could explain several dike breaches whose occurrence has not been assigned to conventional mechanisms of dike failure such as internal erosion. The objective of this thesis is to better understand, with respect to the instability phenomenon, the mechanical behavior of a silty sand which is collected in the area adjacent of a breach of the Rhone embankment dike during the flood of 2003, by means of triaxial tests.The test results obtained on clean sand show that this material is very sensitive to the instability phenomenon. The occurrence of the latter can be predicted by an instability curve relating, at the onset of instability, the stress ratio to the state parameter. The analysis of these results suggests that a strong contractiveness of the material is the necessary condition for instability of loose sand and an appropriate direction of stress increment vector is the sufficient condition.The test results obtained on mixtures of sand with fines show that a removal of fine particles caused by an erosion, such as suffusion for example, favors the occurrence of instability in the dikes. Moreover, these results indicate that the equivalent void ratio is a relevant parameter in analyzing the behavior of silty sand. The calculation of the equivalent void ratio requires the determination of the parameter b for which a new formula has been proposed. Liquéfaction Instabilité Sable silteux Teneur en fines critique Essai triaxial conventionnel Essai à q constant Courbe d'instabilité Indice des vides inter-Grains Indice des vides équivalent Tomographie Nombre de coordination. Liquefaction Instability Silty sand Threshold fine content Conventional triaxial test Drained q constant test Instability curve Intergranular void ratio Equivalent void ratio Tomography Coordination number.
10	Investigations into cyclopropanation and ethylene polymerization via salicylaldiminato copper (II) complexes Boyd, Ramon Cornell 23 January 2007 Two distinct overall research objectives are in this Masters thesis. Very little relates the two chapters apart from the ligands. The first chapter addresses diastereoselective homogeneous copper catalyzed cyclopropanation reactions. Cyclopropanation of styrene and ethyl diazoacetate (EDA) is a standard test reaction for homogeneous catalysts. Sterically bulky salicylaldimine (SAL) ligands should select for the ethyl trans-2-phenylcyclopropanecarboxylate diastereomer. Steric bulk poorly influences trans:cis ratios. Salicylaldiminine ligands do not posses the correct symmetry to affect diastereoselectivity. The SAL ligand belongs to the Cs point group in the solid state. Other ligand motifs are more effective at altering the trans:cis ratios. The second chapter addresses the general route toward successful copper(II) ethylene polymerization catalysts. Catalytic activity of the copper(II) complexes is very low. Polymer chain growth from a copper catalyst is very unlikely. Copper-carbon bonds decompose by homolytic cleavage or C-H activation. Copper-alkyls and aryls readily decompose into brown colored oils and salts with different colors. Ligand transfer to trimethylaluminum (TMA) appears to explain low yield ethylene polymerization. bulky migratory insertion mechanism coordination/insertion methodology d-block metal late transition metal phenolic ring coordination number ketimine precatalysts ketimine nitrogen bis(salicylaldiminato)copper(II) ratio cyclopropane steric bulk salicylaldiminato TMA salt trimethylaluminum aryl oil alkyl copper-aryls copper-alkyls C-H activation homolytic homolytic cleavage copper(II) polymerization ethylene cis trans symmetry diastereomer salicylaldimine SAL EDA ethyl diazoacetate styrene cyclopropanation copper diastereoselective steric protection stable CH(SiMe3)2 intermediate catalytic activity associated TMA free TMA vacant coordination site hydrolysis Lewis acid halogen anionic anionic ligand donor ligand monodentate anionic ligand aluminum(III) monodentate polymer chain polymer chain aluminum-carbon bond bulky SAL ligand open coordination site first row transition metal PE paramagnetic high molecular weight polyethylene alkylate methylaluminoxane MAO anionic ligands arylate aluminum carbon aluminum carbon bond beta-hydrogen elimination beta hydrogen elimination Aufbau reaction Aufbau neutral dialkyl aluminum aluminum-alkyl aluminum alkyl copper(0)

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