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1
Whiley, G. S. "Dynamics of adsorbed polymers." Thesis, University of Cambridge, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.382705.
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Huang, S. N. "Dynamics of interacting galaxies." Thesis, University of Manchester, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.378332.
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Zang, Chen. "Ultrafast Spectroscopic Study of Protein Conformation Dynamics and Hydration Dynamics." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1299481658.
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Giboudot, Yoel. "Study of beam dynamics in NS-FFAG EMMA with dynamical map." Thesis, Brunel University, 2011. http://bura.brunel.ac.uk/handle/2438/5947.
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Dynamical maps for magnetic components are fundamental to studies of beam dynamics in accelerators. However, it is usually not possible to write down maps in closed form for anything other than simplified models of standard accelerator magnets. In the work presented here, the magnetic field is expressed in analytical form obtained from fitting Fourier series to a 3D numerical solution of Maxwell’s equations. Dynamical maps are computed for a particle moving through this field by applying a second order (with the paraxial approximation) explicit symplectic integrator. These techniques are used to study the beam dynamics in the first non-scaling FFAG ever built, EMMA, especially challenging regarding the validity of the paraxial approximation for the large excursion of particle trajectories. The EMMA lattice has four degrees of freedom (strength and transverse position of each of the two quadrupoles in each periodic cell). Dynamical maps, computed for a set of lattice configurations, may be efficiently used to predict the dynamics in any lattice configuration. We interpolate the coefficients of the generating function for the given configuration, ensuring the symplecticity of the solution. An optimisation routine uses this tool to look for a lattice defined by four constraints on the time of flight at different beam energies. This provides a way to determine the tuning of the lattice required to produce a desired variation of time of flight with energy, which is one of the key characteristics for beam acceleration in EMMA. These tools are then benchmarked against data from the recent EMMA commissioning.
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Petchenko, Arkady. "Numerical study of flame dynamics." Doctoral thesis, Umeå : Institute of Physics, Umeå Univ, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1313.
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Harper, David. "The dynamics of the outer satellites of Saturn." Thesis, University of Liverpool, 1987. http://livrepository.liverpool.ac.uk/10393/.
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The satellite system of Saturn has been the subject of much research in celestial mechanics since the foundation of this branch of astronomy in its classical form by Laplace in the late 18th century. It has been described as a "solar system in miniature" by virtue of the range of types of behaviour which characterise the satellite orbits. Within a single system we have A very dominant satellite (Titan) which is unaffected by periodic perturbations of a planetary type by its neighbours, and whose motion features only secular perturbations and small periodic solar perturbations. Two pairs of satellites (Mimas - Tethys and Enceladus - Dione) whose mean motions are very nearly in the ratio 2:1, causing (among other things) significant librations in the mean longitude of the satellites concerned. A satellite of rather low mass (Hyperion) whose motion is entirely characterised by a close 3:4 resonance with the dominant satellite in the system. The theory of the motion of Hyperion is a problem of such great complexity that Newcomb placed it second only to the lunar theory. A satellite (Iapetus) whose theory is dominated by large periodic solar perturbations due to the great distance at which it orbits Saturn. Moreover, the position of the orbit plane of this satellite is governed by long-period perturbations of roughly equal size acting in two widely-separated planes. This means that the secular theory of the node and inclination of Iapetus is of particular interest. This diversity of behaviour might at first appear daunting, but each satellite (even Titan) only affects its closest neighbours. Most of the satellites are very small and their perturbing effect is only noticeable when it is amplified by a near-resonance. Thus Tethys perturbs Mimas but not Enceladus or Dione, despite the fact that the latter two are its closest neighbours. We may treat the inner satellites (Mimas, Enceladus, Tethys and Dione) as a self-contained system, and likewise the outer satellites, Rhea, Titan, Hyperion and Iapetus. It is the outer satellite system, and in particular the subset consisting of Titan, Hyperion and Iapetus, that is the subject of this thesis. We choose not to include Rhea as an object for direct study, though we shall always be mindful of its perturbations upon the other three satellites. We begin in chapter 2 with a revision of Sinclair's (1974) theory of the motion of Iapetus in the light of later critical work by Rapaport (1978) and Sinclair and Taylor (1985). Both papers note that Sinclair's theory requires improvement and Rapaport investigates a near-resonance with Titan which affects the mean longitude of Iapetus. During the course of our revision, we find that the principal omissions from Sinclair's theory arise from solar perturbations in the node and inclination. These perturbations have periods of up to 29 years and affect the observed position of the satellite as seen from Earth by as much as 0.14 arc-seconds. We also find that Rapaport overestimates the significance of the Titan quasi-resonance perturbations by a factor of 3, and we present an improved theory of the motion of Iapetus which includes the additional solar and Titan perturbations. The theory is compared with Sinclair and Taylor's (1985) integration of the motion of the outer satellites to obtain a quantitative estimate of the precision of the theory. Chapter 3 contains a study of the secular motion of the orbit plane of a satellite acted upon by several perturbing forces in different fixed planes. We find that the concept of a Laplacian plane may easily be extended to any number of perturbing forces up to fourth order in the inclinations. We use auxiliary parameters p = sin i sin Ω and q = sin i cos Ω to represent the position of the orbit plane of the perturbed satellite in an arbitrary fixed reference frame and we show that the pole of the orbit describes an ellipse about a point which is the pole of the Laplacian plane of the orbit. This method is applied to the particular case of Iapetus, which is subject to significant perturbations by Titan and the Sun, and smaller perturbations due to the oblateness of Saturn. The orbit of Iapetus is shown to maintain an almost constant inclination of 7° to its Laplacian plane, upon which it precesses with a period of 3000 years. We fit this model to observed values of the node and inclination of the orbit of Iapetus and we determine the mass of Titan as a result of the fitting process. Chapters 4 and 5 are concerned with the problem of modelling the motion of Titan, Hyperion and Iapetus by numerical integration. This approach has been used by Sinclair and Taylor with some success. They fitted an integration to photographic (astrometric) observations over the period 1967 to 1982 and determined values for the initial position and velocity components of each of the satellites plus the J2 form-factor and the mass of Saturn and the mass of Titan. In this thesis we attempt to fit a similar integration to visual (micrometric) observations made during the period 1874 to 1947. Chapter 4 gives an account of the preparation of the raw data for comparison with any dynamical model. This preparation includes the reduction of the various timescales to Universal Time and Ephemeris Time, the calculation of the topocentric position vector of Saturn at the instant of each observation, and an analysis of the effects of stellar aberration and atmospheric refraction upon position angle and separation measures. In addition, we develop the partial derivatives of position angle and separation observations with respect to the Saturnicentric rectangular coordinates of the satellite(s) involved. Chapter 5 contains a description of the numerical integration method and the procedure employed in fitting the integration to the observations. It also contains an account of the results of a number of trial iterations in which we attempt to determine the parameters of the satellite system. In particular, values are obtained for the J2 form-factor of Saturn and the mass of Titan.
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Cao, Jing. "Molecular dynamics study of polymer melts." Thesis, University of Reading, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.553653.
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In this thesis we investigated three different aspects of polymer dynamics using molecular dynamics simulations: orientation relaxation in equilibrium, shear flows and possible ways of coarse-graining. In the first part, we studied the orientation relaxation function of monodisperse and bidisperse melts of linear polymers. A universal time- dependent coupling parameter was derived to build the bridge between the monodisperse and bidisperse melts, which facilitates application of the theory of mono disperse melts to polydisperse samples. In the second part, non-equilibrium molecular dynamics simulations were used to investigate start-up shear of polymer melts. Shear stress, first and second normal stresses were measured in both transient and steady states. A possible shear banding was observed in mildly entangled system, which is in contradiction with experimental observation. We also tried to map our simulation results to PI experimental results according to the same number of entanglements and a qualitative agreement was obtained. In the last part, a systematic method was developed to derive the effective interaction forces between polymer chains in the melts. If we apply the pair-wise interaction obtained from vacuum to the melts, a reasonable agreement between the original MD simulations and the coarse- grained simulations can be achieved. However, if many-body effects were introduced, the agreement became worse.
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Mitra, Aditee. "Zooplankton growth dynamics : a modelling study." Thesis, Open University, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.434264.
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Walsh, Tiffany Raquel. "A theoretical study of cluster dynamics." Thesis, University of Cambridge, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624880.
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Ericson, Tristan Martin. "Experimental Study of Planetary Gear Dynamics." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1354212365.
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Champneys, Alan R. "The nonlinear dynamics of articulated pipes conveying fluid." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302850.
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Leung, Shun Cheong. "The mechanical characteristics of cemented sand : particulate scale study /." View abstract or full-text, 2005. http://library.ust.hk/cgi/db/thesis.pl?CIVL%202005%20LEUNGS.
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D'Eath, F. "Basking dynamics and thermoregulation in the lizard Lacerta vivipara." Thesis, University of Bristol, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.379552.
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Simon, Jean-Marc, Ole-Erich Haas, Signe Kjelstrup, and Ramstad Astrid Lund. "Dynamical behaviour of H 2 molecules on graphite surface: a molecular dynamics study." Diffusion fundamentals 6 (2007) 37, S. 1-2, 2007. https://ul.qucosa.de/id/qucosa%3A14214.
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Corradini, Daniele. "Computational study of resting state network dynamics." Bachelor's thesis, Alma Mater Studiorum - Università di Bologna, 2017. http://amslaurea.unibo.it/14524/.
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Lo scopo di questa tesi è quello di mostrare, attraverso una simulazione con il software The Virtual Brain, le più importanti proprietà della dinamica cerebrale durante il resting state, ovvero quando non si è coinvolti in nessun compito preciso e non si è sottoposti a nessuno stimolo particolare. Si comincia con lo spiegare cos’è il resting state attraverso una breve revisione storica della sua scoperta, quindi si passano in rassegna alcuni metodi sperimentali utilizzati nell’analisi dell’attività cerebrale, per poi evidenziare la differenza tra connettività strutturale e funzionale. In seguito, si riassumono brevemente i concetti dei sistemi dinamici, teoria indispensabile per capire un sistema complesso come il cervello. Nel capitolo successivo, attraverso un approccio ‘bottom-up’, si illustrano sotto il profilo biologico le principali strutture del sistema nervoso, dal neurone alla corteccia cerebrale. Tutto ciò viene spiegato anche dal punto di vista dei sistemi dinamici, illustrando il pionieristico modello di Hodgkin-Huxley e poi il concetto di dinamica di popolazione. Dopo questa prima parte preliminare si entra nel dettaglio della simulazione. Prima di tutto si danno maggiori informazioni sul software The Virtual Brain, si definisce il modello di network del resting state utilizzato nella simulazione e si descrive il ‘connettoma’ adoperato. Successivamente vengono mostrati i risultati dell’analisi svolta sui dati ricavati, dai quali si mostra come la criticità e il rumore svolgano un ruolo chiave nell'emergenza di questa attività di fondo del cervello. Questi risultati vengono poi confrontati con le più importanti e recenti ricerche in questo ambito, le quali confermano i risultati del nostro lavoro. Infine, si riportano brevemente le conseguenze che porterebbe in campo medico e clinico una piena comprensione del fenomeno del resting state e la possibilità di virtualizzare l’attività cerebrale.
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Nguyen, Kim Trong. "Molecular dynamics study of the wurtzite structure." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq22368.pdf.
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Lion, Thomas. "Osmosis : a molecular dynamics computer simulation study." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/7877.
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Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modi cation to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modi cation on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures.
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Mondol, Dilip Kumar. "A study on population dynamics in Bangladesh." Thesis, Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43224040.
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Oh, Sang Jin. "A study of the foundry industry dynamics/." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/59145.
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Thesis (S.M.)--Massachusetts Institute of Technology, Sloan School of Management, 2010.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 76-79).
In the process of industrial evolution, it is a general tendency that companies which specialize in a specific value chain have emerged. These companies should construct a business eco-system based on their own platform to compete successfully with vertically integrated companies and other specialized companies. They continue to sustain their competitive advantage only when they share their ability to create value with other eco-system partners. The thesis analyzes the dynamics of the foundry industry. Through the top-down approach (how the semiconductor industry trends have influenced the foundry industry), the foundry market size is expected to grow continuously as the semiconductor industry becomes more horizontal due to exponential increase in IC manufacturing/design cost and focusing strategy on design or manufacturing capabilities. In addition, the bottom-up approach (how companies in the foundry industry compete with each other) indicated that previous key success factors such as time to market, economies of scale and learning curve effect are not necessary conditions any more in this industry. Rather, the success of a foundry company is mainly driven by successful management of eco-system partners based on leading process platform. However, sustainability of platform leadership in the foundry industry can always be threaten by continuous innovation in a technology driven industry, hold-up problem with eco-system partners and change of regulations. These factors are expected to make the foundry industry extremely dynamic despite first mover advantages.
by Sang Jin Oh.
S.M.
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Monk, Joshua D. "Study of Nanowires Using Molecular Dynamics Simulations." Diss., Virginia Tech, 2007. http://hdl.handle.net/10919/29615.
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In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by observing grain sizes over time for temperatures from 800K to 1450K and we discovered grain growth to be linearly time-dependant, contrary to coarse grained materials with square root dependence. Strain induced grain growth studies consisted of straining the nanostructures in tension at a strain rate of 3.3 x 10^8 s^-1. Grain boundary movement was recorded to quantify grain boundary velocities and grain growth. It was shown that during deformation, there is interplay between dislocation-mediated plasticity and grain boundary accommodation of plasticity through grain boundary sliding. To further understand the effect of stress on nanocrystalline materials we performed tensile tests at different strain rates, varying from 2.22 x 10^7 s^-1 to 1.33 x 10^9 s^-1 for a 5 nm grain size nc-Ni nanowire with a 5 nm radius. The activation volume was given as ~2b^3, where b is the Burgerâ s vector and is consistent with a grain boundary dominate deformation mechanism. We expanded our research to 10 nm grain size nc-Ni nanowires with radii from 5 nm to 18 nm. Each wire was deformed 15% in tension or compression at a strain rate of 3.3 x 10^8 s^-1. Asymmetry was observed for all radii, in which larger radii produced higher flow stresses for compression and small radii yielded higher flow stresses in tension. A cross over in the tension-compression asymmetry is found to occur at a radius of ~9 nm. A change in the dominate deformation mechanism in combination with the ease of grain boundary sliding contributes to the phenomena of the asymmetry. In the final chapter we focus on the energetic stability of multi-twinned Ag nanorods at the nanoscale. We used a combination of molecular statics and dynamics to find the local minimum energies for the multi-twinned nanorods and the non-twinned â bulkâ materials and concluded that the stability of multi-twinned nanorods is highly influenced by the size of the sample and the existence of the ends. Using an analytical model we found the excess energy of the nanorods with ends and determined the critical aspect ratio below which five-twinned nanorods are stable.Ph. D.
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Del, Donno Andrew Mark. "Experimental Study of Multi-Mesh Gear Dynamics." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1229474343.
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Guo, Yichao. "Analytical Study On Compound Planetary Gear Dynamics." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1312289370.
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Chen, Long-Qing 1962. "Molecular dynamics study of ionic grain boundaries." Thesis, Massachusetts Institute of Technology, 1990. https://hdl.handle.net/1721.1/128799.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 1990.Includes bibliographical references (leaves 240-244).
by Long-Qing Chen.
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 1990.
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Moon, Chang Man. "Molecular dynamics study of phase transition phenomena." Thesis, University of Edinburgh, 2000. http://hdl.handle.net/1842/12675.
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This computer simulation study carried out by classical the molecular dynamics technique (MD) investigates structural phase transitions of various atomic and molecular condensed matter systems. Particularly, our attention is focused on the signals for their observation. Classical nucleation theory is briefly reviewed in relation to the present study. An overall review is made on the methodology of the MD simulation technique such as the integration of the equations of motion, the rotational motion of molecules which is dealt with the four-component quaternion, and other various techniques involved with the simulation of atomic clusters, the simulation of bulk molecular systems using periodic boundary conditions, and isobaric molecular dynamics. There are also reviews on measurements of thermodynamic quantities which are monitored during the simulation including the pressure, the kinetic energy, and the potential energy as well as their corrections due to the spherical cutoff. In addition, various analysis techniques for the observation of the signals of structural phase transitions are discussed. All the potential functions used in this study are of the pairwise additive atom-atom Lennard-Jones interaction for both the atomic and the molecular systems. A small cluster of a binary mixture of krypton and argon atoms is studied by triggered breathing motions to investigate anharmonic motion which involves the structural phase transitions. A small cluster of krypton atoms is also simulated and discussed in detail concerning the very first moment of nucleation in relation to five-fold symmetric structures. In simulations of sulphurhexafluoride molecule systems, artifacts of finite size and periodic boundary conditions are investigated. Freezing the system by MD is investigated since it is known to supercool in computer simulations. Furthermore, accelerating the nucleation process by various methods such as shear flow, accelerated layer, inclusion of defect molecules, and pressure fluctuations is investigated.
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Brace, Garry Richard. "The design of an instructional model to transform students' alternate framework of dynamics." Thesis, University of British Columbia, 1988. http://hdl.handle.net/2429/28582.
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This study concerns the design and implementation of an instructional model that was intended to explicate students' alternate conceptions of dynamics and transform them into a conceptual set which more closely approximates Newtonian conceptions of dynamics. The design of this instructional model has employed Frame Theory as the basis for the development of an analytical clue structure that was used to describe students' alternate conceptions of dynamics and track any changes to these conceptions as the lesson sequence progressed. In addition, this instructional model has attempted to utilize discordant event demonstrations as the catalyst required to initiate transformations of the alternate conceptions of dynamics held by students.
Data for this study have been collected within an operational science classroom by video taping a series of lessons that dealt with the dynamics of linear acceleration and deceleration, and uniform motion. These data were subsequently reduced to lesson transcripts which were then analyzed, using the clue structure, for student conceptual data. These data were then reconstructed into conceptual frames that represented individual and collective student interpretations of force/motion events both before and after the demonstration of the discordant events. 'Before and after' comparisons were then made of these frames in order to determine if any conceptual transformation had occurred.
Results from this study have indicated that a majority of students that took an active role in these classes explained the motion of objects, both before and after instruction, using a 'motion implies a force' set of conceptions. This study also found that the explication and representation of student conceptions of dynamics could be successfully accomplished by using the analytical clue structure to reconstruct transcript data into student interpretational frames of motion. Comparisons of the interpretational frames that students were employing before the demonstration of specific, discordant events with those frames that were being employed after these events indicated that use of discordant events to initiate conceptual transformation was only minimally successful.Education, Faculty of
Curriculum and Pedagogy (EDCP), Department of
Graduate
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Fried, Jeremy. "Numerical Simulation of Viscous Flow: A Study of Molecular Dynamics and Computational Fluid Dynamics." Thesis, Virginia Tech, 2007. http://hdl.handle.net/10919/34661.
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Molecular dynamics (MD) and computational fluid dynamics (CFD) allowresearchers to study fluid dynamics from two very different standpoints. From a microscopic standpoint, molecular dynamics uses Newton's second law of motion to simulate the interatomic behavior of individual atoms, using statistical mechanics as a tool for analysis. In contrast, CFD describes the motion of a fluid from a macroscopic level using the transport of mass, momentum, and energy of a system as a model.
This thesis investigates both MD and CFD as a viable means of studying viscous flow on a nanometer scale. Specifically, we investigate a pressure-driven Poiseuille flow. The results of the MD simulations are processed using software we created to measure velocity, density, and pressure. The CFD simulations are run on numerical software that implements the MacCormack method for the Navier-Stokes equations. Additionally, the CFD simulations incorporate a local definition of viscosity, which is usually uncharacteristic of this simulation method. Based on the results of the simulations, we point out similarities and differences in the obtained steady-state solutions.Master of Science
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Bennett, C. L. "The spectroscopy and predissociation dynamics of low Rydberg states of ammonia." Thesis, University of Bristol, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.380199.
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Keady, John David. "The dynamics of dementia : a modified grounded theory study." Thesis, Bangor University, 1999. https://research.bangor.ac.uk/portal/en/theses/the-dynamics-of-dementia--a-modified-grounded-theory-study(88bebabb-f361-40f3-8bf1-3a19f49c4a77).html.
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This thesis explores the experience of dementia as recounted by family carers and people with the early experience of dementia. Between October, 1992 and May, 1996 sixty four semi-structured interviews were conducted with family carers of people with dementia using a modified grounded theory approach. Constant comparative analysis of the data led to the emergence of a five stage integrated scheme to explain their experiences, namely: Recognising the Need (1); Taking it On (2); Working Through It (3); Reaching the End (4); and A New Beginning (5), with critical junctures attached to each stage which either locked the carer in, or moved the carer through, the model. A second phase of data collection comprised eleven interviews with ten people with the early experience of dementia and their family carers. Analysis of these data resulted in the emergence of the stage of Keeping it Hidden with its supporting strategies: Closing Down; Regrouping; and Covering your Tracks which help to explain how people with early dementia manage their changing cognitive abilities. Following a theoretical integration of the two phases of data collection the process of 'working' emerged in three forms, i.e. Working Apart; Working Together; and Working Alone to explain movement between the above two models. Transcending the data, the study also generated the linking scheme of Maintaining Involvement to help explain the dynamics of dementia. The 'fit and grab' of this linking scheme was subjected to preliminary empirical scrutiny via a third series of interviews with six carers of people with dementia. It is suggested that the grounded theory emerging from this study helps to explain the shared experience of dementia, while also having implications for policy and practice which are briefly explored in the concluding chapter, together with some of the methodological implications and limitations of the study.
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Liu, Li Ph D. Massachusetts Institute of Technology. "Study of slow dynamics in supercooled water by molecular dynamics and quasi-elastic neutron scattering." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/34440.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Nuclear Engineering, 2005.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
CDROM contains thesis in .pdf format; appendix B (MD simulation code: SPC/E Potential) and appendix C (Programs to fit QENS data by RCM) in .doc format; and a readme file in .txt format.
Includes bibliographical references (leaves 101-108).
The slow dynamics of supercooled water is studied by modelling the spectrum of test particle fluctuations: intermediate scattering function (ISF). The theoretical models are compared with experimental measurements by quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulation results. The dynamics of supercooled water can be decoupled into a product of translational and rotational dynamics. While the translational dynamics is modelled well by a product of a ISF representing short time in-cage vibrations and long time cage relaxation processes, the rotational dynamics is an aspect we shall study in this thesis. We introduce a model for the first, second and third order rotational correlation functions, which are required for the computation of the rotational intermediate scattering function corresponding to the incoherent QENS spectra from supercooled water. The model is tested against MD data generated from an extended-simple-point-charge (SPC/E) model of water and is found to be satisfactory. The analysis can be used as a practical method for extracting rotational relaxation parameters from QENS spectra measured at large Q from supercooled bulk water or interfacial water in porous materials.
(cont.) By confining water in nano-pores of silica glass, we can bypass the crystallization and study the pressure effect on the dynamical behavior in deeply supercooled state using incoherent QENS technique. we investigated the dynamics of water confined in nanoporous alumino-silicate matrices, from ambient temperature to the deeply supercooled state. We collected data on three instruments, with widely different resolutions, the Fermi chopper (FCS), the disk chopper (DCS) and the backscattering (HFBS) spectrometers at the NIST Center for Neutron Research (NIST NCNR). The confining systems were lab synthesized nanoporous glasses MCM-41-S and MCM-48-S. Inside the pores of these matrices the freezing process of water is retarded so that freezing occurs at a temperature about 50 K less than in bulk water. Thus, with the combined use of different instruments and nano-pore confinement, we were able to study the system over a wide temperature range, 160-325 K, with different energy resolutions. The data from all the three spectrometers were analyzed using a single consistent expression based on the relaxing cage model (RCM) for the translational and rotational dynamics.
(cont.) A remarkable slowing down of the translational and rotational relaxation times has been observed. The behavior of shear viscosity j7 or equivalently the structural relaxation time T of a supercooled liquid as it approaches the glass transition temperature is called 'fragile' if it exhibits non-Arrhenius character, such as that described by the Vogel-Fulcher-Tammann (VFT) law; otherwise, with q and obeying Arrhenius law, it is called 'strong'. The fragile behavior is typical to ionic and van der Waals systems. In contrast, a liquid being strong reflects that its structural makeup, to a large extent by strong (commonly covalent) bonds forming a network structure. Bulk water is considered as a fragile liquid at room temperature but for supercooled water, a 'fragile-to-strong' (F-S) transition at around 228 K has been proposed to occur at around 228 K, based on a thermodynamic argument. The F-S transition in a molecular liquid like water may be interpreted as a variant of kinetic glass transition predicted by the ideal Mode-Coupling Theory (MCT), where the real structural arrest transition is avoided by an activated hoping mechanism below the transition. Experiments at DCS and HFBS for water in MCM-41-S with 14 A pore diameter were also done under selective pressures, from ambient to 2400 bar.
(cont.) We observe a clear evidence of a cusp-like F-S dynamic transition at pressures lower than 1600 bar. Here we show that the transition temperature decreases steadily with an increasing pressure, until it intersects the homogeneous nucleation temperature line of bulk water at a pressure of 1600 bar. Above this pressure, it is no longer possible to discern the characteristic feature of the F-S transition. The discussion part of this thesis concludes that the high-temperature liquid corresponds to the high-density liquid (HDL) of which the hydrogen bond network is not fully developed to conform a locally tetrahedral coordination, while the low-temperature liquid corresponds to the low-density liquid (LDL) of which the more open, locally 4-coordinated, ice-like hydrogen bond network is fully developed. Identification of the end point of F-S transition with a possible second critical point is also discussed.
by Li Liu.
Ph.D.
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Edenhammar, Clara. "The dynamics of the case method: A comparative study." Thesis, Högskolan i Halmstad, Akademin för ekonomi, teknik och naturvetenskap, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:hh:diva-32997.
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Hockey, Athol James Temlett. "A pilot study of secondary teachers' understanding of population dynamics." Thesis, Rhodes University, 1996. http://hdl.handle.net/10962/d1003586.
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Population dynamics is a South African secondary school biology syllabus topic which deals specifically with ecology or concepts within the realm of ecology. It is currently taught in a way which largely emphasises the teaching and learning of facts and concepts, often out of any context to which students can relate. While it is important to convey scientific concepts, it is just as important to address social and political issues regarding overpopulation and the environment. This research involved the administration of a questionnaire to Std 10 biology teachers in the Department of Education and Training (DET), which sought to obtain information about various aspects of teachers' teaching of population dynamics. These included their feelings toward the teaching of the specific sections of the population dynamics syllabus, and their knowledge and views of environmental issues and human population expansion. The findings of the research suggest that population dynamics is an important topic for students to learn about. The traditional teacher-centred approach to teaching is used by the teachers in the research sample. The sections considered by the teachers to be most important for learning were also considered the most interesting and the easiest to teach. The majority of the teachers in the research sample recognised that human population growth is a global and local problem and that South Africa cannot sustain its present population growth. The teachers in the sample show a diversity of opinions about sustainable development, and have a limited understanding of the links between population, poverty and consumption. Important information gained from the research will be significant in the development of a teaching and learning module on population dynamics that reflects the aims and purpose of environmental education.
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Ries, Jonas. "Advanced Fluorescence Correlation Techniques to Study Membrane Dynamics." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2008. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1219846317196-73420.
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Fluorescence Correlation Spectroscopy (FCS) is a powerful tool to measure important physical quantities such as concentrations, diffusion coefficients, diffusion modes or binding parameters, both in solution and in membranes. However, it can suffer from severe artifacts, especially in non-ideal systems. Here we develop several novel implementations of FCS which overcome these limitations and facilitate accurate and quantitative determination of dynamic parameters in membranes. Two-focus FCS with camera-detection allows for accurate and calibration-free determination of diffusion coefficients. Confocal FCS using a laser scanning microscope provides an unprecedented positioning accuracy which enabled us to study, for the first time with FCS, dynamics in bacterial membranes. Scanning FCS with a scan path perpendicular to the membrane plane allows to correct for instabilities permitting long measurement times necessary to study slow diffusion. It can easily be extended to measure calibration-free diffusion coefficients with two-focus scanning FCS and to quantify binding with dual color scanning FCS. Spectral crosstalk can be avoided effectively by using alternating excitation. Using this method we were able to perform measurements in systems previously not accessible with FCS, such as yeast cell membranes or membranes of living zebrafish embryos. Line-scan FCS with a scan path in the membrane plane uses the parallel acquisition along the line to increase the statistical accuracy and decrease the measurement times. Knowledge of the scan speed serves as an internal calibration, enabling accurate diffusion and concentration measurements within seconds, hardly affected by photobleaching. Both realizations of scanning FCS can be easily implemented with commercial laser scanning microscopes. Often, a fluorescence background around the membrane cannot be avoided. The high surface selectivity needed in this case can be achieved efficiently by using a novel objective for FCS, the supercritical angle objective, which produces a very flat and laterally confined detection volume. Another technique with similar surface selectivity is FCS with total internal reflection excitation (TIRFCS). Due to the lack of a correct model, the accurate analysis of TIR-FCS data was previously not possible. In this work we develop such a model, enabling quantitative measurements of membrane dynamics with TIR-FCS. The novel FCS techniques developed here will have a high impact on the use of FCS to address key questions in biological systems, previously inaccessible by other methodsFluoreszenz-Korrelations-Spektroskopie (FCS) ist eine mächtige Methode, um wichtige physikalische Parameter wie Konzentrationen, Diffusionskoeffizienten, Diffusionsarten oder Bindungsparameter in Lösung und in Modell- oder Zellmembranen zu bestimmen. In nichtidealen Systemen ist FCS fehleranfällig. In dieser Arbeit entwickeln wir mehrere neuartige Realisierungen von FCS, welche diese Fehlerquellen umgehen und die genaue und quantitative Messung dynamischer Parameter in Membranen ermöglichen. Zwei-Fokus FCS mit Kamera-Detektion erlaubt eine genaue und kalibrationsfreie Messung von Diffusionskoeffizienten. Konfokale FCS mit einem Laserscanningmikroskop besitzt eine bislang unerreichte Positionsgenauigkeit, welche uns erstmals dynamische Messungen in Bakterienmembranen mit FCS ermöglichte. Scanning FCS mit einem Scanweg senkrecht zur Membran ermöglicht eine Korrektur von Instabilitäten und damit lange Messzeiten, die zur Bestimmung langsamer Diffusionskoeffizienten notwendig sind. Eine Erweiterung zur kalibrationsfreien Messung von Diffusionskoeffizienten mit Zwei-Fokus Scanning FCS und von Bindungsparametern mit Zwei-Farben Scanning FCS ist einfach. Mit diesen Methoden konnten wir in Systemen messen, die bislang FCS nicht zugänglich waren, so in Hefezellmembranen oder in Membranen lebender Zebrafischembryonen. Line-scan FCS besitzt einen Scanweg parallel zur Membran. Die parallele Messung entlang der ganzen Linie führt zu einer deutlichen Verbesserung der Statistik und damit zu kurzen Messzeiten. Die Kenntnis der Scangeschwindigkeit dient einer internen Kalibration und erlaubt eine akkurate Bestimmung von Diffusionskoeffizienten und Konzentrationen innerhalb weniger Sekunden, kaum beeinflusst vom Bleichen von Fluorophoren. Beide Arten von Scanning FCS können mit einem kommerziellen Laserscanningmikroskop realisiert werden. Häufig kann bei FCS Messungen ein fluoreszierender Hintergrund nicht vermieden werden. Hier ist eine hohe Oberflächenselektivitiät nötig, welche effizient mit einem neuartigen Objektiv erreicht werden kann. Dieses Supercritical Angle-Objektiv erzeugt ein sehr flaches und lateral begrenztes Detektionsvolumen. Eine weitere Methode mit einer ähnlich guten Oberflächenselektivität ist FCS mit Anregung über totale interne Reflektion (TIR-FCS). Bislang war eine quantitative Analyse der TIR-FCS Daten kaum möglich, da keine ausreichend genaue theoretische Beschreibung existierte. In dieser Arbeit entwickeln wir ein akkurates Modell, welches quantitative Messungen mit TIR-FCS erlaubt. Die hier entwickelten neuartgien FCS-Techniken ermöglichen die Untersuchung biologischer Fragestellungen, welche bislang keiner anderen Methode zugänglich sind
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Sanchez, Jose Luis Hernandez. "A Study of Dynamics of Coupled Nonlinear Circuits." Diss., Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/6984.
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We consider a type of forced "Van Der Pol" oscillator where the forced function is periodic and oscillatory around the t-axis. This problem derived from an electrical model. The important issues here is that this circuits presents the spiking phenomena over a one time period and it has important applications in signal processing and digital communication. The three most important problems that we addressed here in this thesis are to compute the number of spikes a solution completes in one time period (it can be used to transform the analog signal into digital information), how the dynamics of the number of spikes change with respect to the parameters amplitude (k) and frequency (w), and when the coupled circuits synchronize (i.e., the driver and the respond are on synchronous). Sophisticated mathematical and numerical analysis has been developed that enable us to give a complete study of the problems above described.
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Govind, Niranjan. "Theoretical study of models for driven interface dynamics." Thesis, McGill University, 1992. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=56667.
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In this dissertation, we review the physics associated with surfaces and interfaces in equilibrium and non-equilibrium. Our emphasis will be on interfaces that are driven far away from equilibrium with special interest in the phenomenon of kinetic roughening. Models which describe non-equilibrium interfaces will be introduced and analyzed using techniques such as the Renormalization Group, Monte Carlo simulations, and direct integration of the equation of motion. Different interface relaxation mechanisms will be discussed with a focus on surface diffusion, which is believed to be the dominant effect in Molecular Beam Epitaxy. These interface growth models generate self-affine structures with various correlations satisfying a dynamic scaling law. We compute the scaling exponents and functions. Finally, we study the effect of quenched impurities on the dynamics of a driven interface with a conservation law. The impurity effect leads to anomalous scaling exponents and qualitatively changes the interface dynamics. Our results are summarized in two articles to be published: Refs. (Govind and Guo, 1992; Govind, Guo and Grant, 1992).
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Bazzanini, Federico. "Polymer-liquid crystal interface: a molecular dynamics study." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2013. http://amslaurea.unibo.it/5757/.
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Liquid crystals (LCs) are an interesting class of soft condensed matter systems characterized by an unusual combination of fluidity and long-range order, mainly known for their applications in displays (LCDs). However, the interest in LC continues to grow pushed by their application in new technologies in medicine, optical imaging, micro and nano technologies etc. In LCDs uniaxial alignment of LCs is mainly achieved by a rubbing process. During this treatment, the surfaces of polymer coated display substrates are rubbed in one direction by a rotating cylinder covered with a rubbing cloth. Basically, LC alignment involves two possible aligning directions: uniaxial planar (homogeneous) and vertical (homeotropic) to the display substrate. An interesting unresolved question concerning LCs regards the origin of their alignment on rubbed surfaces, and in particular on the polymeric ones used in the display industry. Most studies have shown that LCs on the surface of the rubbed polymer film layer are lying parallel to the rubbing direction. In these systems, micrometric grooves are generated on the film surface along the rubbing direction and also the polymer chains are stretched in this direction. Both the parallel aligned microgrooves and the polymer chains at the film surface may play a role in the LC alignment and it is not easy to quantify the effect of each contribution. The work described in this thesis is an attempt to find new microscopic evidences on the origin of LC alignment on polymeric surfaces through molecular dynamics (MD) simulations, which allow the investigation of the phenomenon with atomic detail. The importance of the arrangement of the polymeric chains in LCs alignment was studied by performing MD simulations of a thin film of a typical nematic LC, 4-cyano-4’-pentylbiphenyl (5CB), in contact with two different polymers: poly(methyl methacrylate)(PMMA) and polystyrene (PS).
At least four factors are believed to influence the LC alignment:
1. the interactions of LCs with the backbone vinyl chains;
2. the interactions of LCs with the oriented side groups;
3. the anisotropic interactions of LCs with nanometric grooves;
4. the presence of static surface charges.
Here we exclude the effect of microgrooves and of static surface charges from our virtual experiment, by using flat and neutral polymer surfaces, with the aim of isolating the chemical driving factors influencing the alignment of LC phases on polymeric surfaces.
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Law, Chi-kin. "A study on population dynamics in Hong Kong." Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B31355316.
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López, Asamar Abraham. "Study of the conformational dynamics of prolyl oligopeptidase." Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/301430.
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Prolyl oligopeptidase (POP) is an 81-KDa bidomain enzyme which hydrolyses short proline-containing peptides. This enzyme is involved in mnemonic and cognitive processes, and the dysregulation of POP activity is related to mental diseases. Probably, POP modulates the phosphoinositide signalling pathway through protein-protein interactions (PPI). Hence, the development of POP inhibitors is an area of great interest for the treatment of cognitive deficits associated with mental and neurodegenerative diseases. Recently, it has been found that the administration of POP inhibitors increases the clearance of a-synuclein aggregates in vivo, indicating that POP can be related to some extend with the pathogenic conditions of Parkinson’s disease (PD). Probably, this increase in the a-synuclein catabolism might be a consequence of a direct interaction between the two proteins. For this reason, POP inhibitors might be drug candidates for the preventive treatment of PD.
Although the X-ray structure of POP is well studied, it is not clear which are the conformational fluctuations responsible for the circulation of substrates and products during the catalytic cycle. Several studies suggest that loops surrounding the active site are involved in a gating mechanism, while others postulate that interdomain separation might expose the active site. Moreover, such conformational transitions might be essential for the recognition events of POP. The elucidation of the conformational landscape of POP is a challenging task due to the high molecular weight of the enzyme.
In this PhD thesis we have used a combination of robust biophysical tools (in particular, NMR and SAXS) together with molecular dynamics simulations (MD) in order to decipher the conformational dynamics of POP in solution. In addition, POP was also analysed by ion mobility mass spectrometry, an emerging biophysical tool in structural biology. Finally, we performed preliminary studies of the interaction between POP and a-synuclein by NMR.
The results obtained in this PhD thesis demonstrated that POP exists in solution in a slow conformational exchange between open and closed conformations. The conformational transitions involved the periodic separation of the two domains in a hinge-type motion. Relaxation dispersion experiments showed that this long range conformational transition was better described by several independent motions of different amplitudes, stressing the highly dynamic behaviour of POP. Moreover, the analysis of SAXS data complemented by MD simulations found that the interdomain separation caused the inactive arrangement of the active site. This suggests that the separation between domains might be critical for substrate recruitment and product release. Of interest, inhibitors caused the total displacement of this equilibrium towards the stabilized closed conformation, therefore quenching dynamics and the catalytic activity.
The study of the interaction between POP and a-synuclein by NMR disclosed that both proteins might be involved in a weak and transient interaction. Of interest, this interaction showed more affinity in the case of POP bound to inhibitors. In this case, interaction specially affected a broad segment of the C-terminal region of a-synuclein. This result suggested that the recognition between the two proteins depends on the conformational state of POP. Therefore, modulating the conformational landscape of POP by inhibitors might control this interaction.
In summary, the results obtained in this PhD thesis demonstrated that POP undergo slow exchange between open and closed conformations in solution, and found that inhibitors have deep effects in the native conformational landscape of POP. Of interest, these conformational transitions might be essential for regulating the PPI necessary for the biological function of POP. Hence, the in vivo effects of POP inhibitors might result as a consequence of the alterations in the recognition events of POP.La prolil oligopeptidasa (POP) es un enzim de 81 KDa que hidrolitza pèptids curts amb contingut en prolina. La POP actua en el sistema nerviós central mitjançant interaccions proteïna-proteïna (IPP), i la seva funció biològica està relacionada amb la memòria i els processos cognitius. Per aquesta raó, els inhibidors de la POP són compostos d’interès terapèutic per al tractament dels dèficits cognitius. Recentment, s’ha descobert que els inhibidors de la POP poden prevenir la patogènesis de la malaltia de Pàrkinson, probablement a través d’una interacció directa entre la POP i l’a-sinucleïna (la principal proteïna causant dels processos neurodegeneratius de la malaltia de Parkinson). Tot i que l’estructura cristal·logràfica de la POP està ben definida, no es sap quines són les transicions conformacionals que permeten completar el cicle catalític de la POP. Probablement, aquesta riquesa conformacional també té un paper rellevant en el control de les IPP. Malauradament, l’estudi conformacional complet de la POP és tot un repte degut al seu elevat pes molecular. En aquesta tesis doctoral s’ha emprat una combinació de tècniques biofísiques avançades (en concret, la resonància magnètica nuclear, la dispersió de raigs X de baix angle, i l’espectrometria de masses de mobilitat iònica) conjuntament amb simulacions de dinàmica molecular, per tal d’analitzar la dinàmica conformacional de la POP en solució. A més, s’ha estudiat la possible interacció entre la POP i l’a-sinucleïna mitjançant experiments de RMN. Els resultats obtinguts en aquesta tesi doctoral han demostrat que la POP es troba en solució en un equilibri conformacional lent entre conformacions obertes i tancades, originades a partir de la separació entre dos dominis. Els inhibidors de la POP causen una gran estabilització de la conformació tancada, amb la qual cosa l’equilibri dinàmic es desplaça totalment cap a aquesta conformació. A més, es va poder detectar una interacció dèbil i transitòria entre la POP i l’a-sinucleïna, que esdevenia especialment afavorida en la presència d’inhibidors. Així, els nostres resultats suggereixen que la diversitat conformacional de la POP es necessària per a la seva funció, i que els inhibidors poden desencadenar la seva funció biològica desplaçant l’equilibri conformacional.
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Whittaker, A. "A numerical study of the dynamics of subduction." Thesis, Durham University, 1988. http://etheses.dur.ac.uk/6337/.
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The mechanics and dynamics of subduction have been studied using 2-D finite element analysis. Two finite element formulations have been employed; one formulation for Newtonian viscous flow and one formulation for linear elasticity and viscoelasticity. Quadratic isoparametric quadrilateral and triangular elements are used for both formulations. Models of flow in the mantle driven by oblique subduction produce an asymmetric depression of the surface above the slab. The width and depth of this depression are dependent on the value of the viscosity of the lower mantle, the length and mechanical strength of the slab. Analysis of the flow patterns suggests that the viscosity contrast at the 670 km sesmic discontinuity is likely to be of the order x 10. The stress regime at an island arc margin with a subducting slab dipping at 45 has been modelled using an elastic-viscoelastic rheology. The body forces of the slab produce an asymmetric depression of the surface above the slab which generates horizontal deviatoric compression in the plates. Unlocking the thrust zone between the subducting and overriding plates eliminates the shear stress in the fault plane resulting in regional horizontal tension in both plates, uplift of the leading edge of the overriding plate and depression of the subducting plate. The regional tension is interpreted as the source of the plate driving forces of slab pull and trench suction. Local horizontal compression in the arc-forearc region produced by the surface depression exceeds the regional tension and this may be the source of lateral variation in stress that is ob- served across the strike of convergent margins. It may also be the source of backarc compression for low angle slabs at Chilean type margins. Depression of the surface provides partial compensation of the slab body forces. Thus the downdip force is reduced and the resulting stress regime in the slab is controlled by the isostatic upthrust at the trench and the viscosity contrast at 670 km depth. A low pressure zone above and high pressure zone below the slab may act against the body forces which rotate the slab towards vertical subduction. Anomalous pressures in the mantle are created and sustained by continuous subduction and rollback, and may behave in a self-regulating mechanism. A low viscosity zone in the mantle wedge above the slab leads to the development of double seismic zones as suggested by Sleep (1979).
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Mitchell, Jonathan Stewart. "A molecular dynamics study of supercoiled DNA minicircles." Thesis, University of Leeds, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.535666.
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Norberto, de Souza Osmar. "Intrinsic curvature of DNA : a molecular dynamics study." Thesis, Birkbeck (University of London), 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.361080.
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DNA intrinsic curvature is, at present, one of the major topics of research concerning DNA conformation and dynamics because of its implications in phenomena of great biological relevance including transcription activation and chromatin packaging. DNA sequences containing runs of adenines residues (A-tracts) are of central importance to this phenomenon since the length of the A-tracts and their phasing with the helix screw significantly alter the curvature profile of DNA. X-ray crystallography of DNA single crystals has provided a wealth of information about the local, short range conformational features of general-sequence and also A-tractcontaining DNA oligomers but it lacks the same strength in the analysis of long range conformational features of DNA. On the other hand, gel-electrophoresis analysis of DNA has not only uncovered the macroscopic curvature of DNA but it also provides most of the available data on DNA intrinsic curvature. However, gel electrophoresis can not identify features of DNA structure at the nucleotide or atomic level. This work is an attempt of bridging the gap between such techniques by using the method of molecular dynamics (MD) simulations. MD simulations were performed on 5 A-tract-containing dodecamers, 3 of which have available crystal structures, and on a 51 base-pair DNA fragment from the kinetoplast DNA of Leishmania tarentolae. The results shows that A-tracts can be strongly curved, contrary to what is expected from X-ray analysis of DNA single crystals. The detailed analysis of the MD trajectories also shows that DNA curves towards the major groove. An explanation which demonstrate the consistence between major groove curvature and uncurving of DNA upon binding of the antibiotic distamycin is provided. Furthermore, regions of hyperflexibility or junctions between A-tracts and general-sequence DNA are identified and shown to modulate DNA intrinsic curvature. The flexibility pattern of the sugar rings can provide an alternative explanation for the cleavage pattern of A-tract-containing DNA by the hydroxyl radical. An attempt to predict the curvature of other A-tract-containing DNA sequences is also presented. It is shown that, in order to realistically represent the curvature of A-tract-containing DNA, the intrinsic structure of individual A-tracts must be preserved and not averaged as in the Wedge model. Finally, some computer experiments are suggested in order to refine our knowledge of DNA conformation and dynamics using MD simulations before such technique can be routinely used in the investigation of phenomena of biological and medicinal relevance.
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Law, Chi-kin, and 羅智健. "A study on population dynamics in Hong Kong." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B31355316.
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Adhikari, Subhasis, and Frank Cichos. "Single molecule study of heterogeneous dynamics in polymers." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-182224.
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Evteev, Alexander V., Elena V. Levchenko, Irina V. Belova, and Graeme E. Murch. "Molecular dynamics study of carbon diffusion in cementite." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-193325.
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Bhattrai, Gopendra R. "An empirical study of software design balance dynamics." Virtual Press, 1995. http://liblink.bsu.edu/uhtbin/catkey/958786.
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The Design Metrics Research Team in the Computer Science Department at Ball State University has been engaged in developing and validating quality design metrics since 1987. Since then a number of design metrics have been developed and validated. One of the design metrics developed by the research team is design balance (DB). This thesis is an attempt to validate the metric DB. In this thesis, results of the analysis of five systems are presented. The main objective of this research is to examine if DB can be used to evaluate the complexity of a software design and hence the quality of the resulting software. Two of the five systems analyzed were student projects and the remaining three were from industry. The five systems analyzed were written in different languages, had different sizes and exhibited different error rates.Department of Computer Science
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Hernández, José Luis Sánchez. "A study of dynamics of coupled nonlinear circuits." Available online, Georgia Institute of Technology, 2005, 2004. http://etd.gatech.edu/theses/available/etd-12192004-194550/unrestricted/sanchez%5Fjose%5Fl%5F200505%5Fphd.pdf.
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Thesis (Ph. D.)--Mathematics, Georgia Institute of Technology, 2005.Feodor Vainstein, Committee Member ; Dieci Luca, Committee Member ; Yi Yingfei, Committee Member ; Wang Yang, Committee Member ; Shui-Nee, Chow, Committee Chair. Vita. Includes bibliographical references.
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Boleininger, Max. "Gaussian tight binding study of ultrafast electron dynamics." Thesis, Imperial College London, 2017. http://hdl.handle.net/10044/1/54667.
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Computer simulations are invaluable for the study of ultrafast phenomena, as it is not possible to directly access the electronic and nuclear dynamics in experiments. We present an efficient method for simulating the time-dependent coupled electron-ion dynamics within the Ehrenfest picture in molecules under the influence of time-dependent electric fields, based on an extension of the density-functional tight binding model. We consider self-consistency in a self-multipole-consistent framework, expanding the electron density in terms of radial Gaussian and angular real cubic harmonic functions. This enables the efficient computation of the electrostatic interaction energy while retaining a physical description of charge transfer and ionic polarisation. We show that this Gaussian tight binding method produces molecular polarisabilities, time-dependent dipole moments, and electron densities in strong agreement with density-functional theory, but at a small fraction of the cost. This efficiency enables high-throughput ultrafast studies on molecules, which we demonstrate on the example of transient core-spectroscopy on polythiophene fragments.
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Gerwin, Howard R. (Howard Ross) 1964. "A system dynamics study of technology strategy implementation." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/88325.
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David, Michael (Michael Steven). "A study of the dynamics of shotcrete formwork." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/60764.
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Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2010.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 41).
This study models and analyzes the dynamic behavior of shotcrete formwork during standard application procedure. Based on standard shotcrete application, a program was developed to simulate shotcrete application and the dynamic behavior of shotcrete formwork. This study shows that the random behavior standard shotcrete application have minimal impact on the maximum values of displacement and acceleration of a shotcrete formwork system, which justifies the significance of the simulations based on the precision of the results obtained. Standard design parameters were varied in order to determine their impact on the behavior of a formwork system, and determine which parameters had the greatest ability to control the displacement and acceleration of formwork during shotcrete application.
by Michael David.
M.Eng.
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Ferrara, Joseph. "A Study of Nonlinear Dynamics in Mathematical Biology." UNF Digital Commons, 2013. http://digitalcommons.unf.edu/etd/448.
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We first discuss some fundamental results such as equilibria, linearization, and stability of nonlinear dynamical systems arising in mathematical modeling. Next we study the dynamics in planar systems such as limit cycles, the Poincaré-Bendixson theorem, and some of its useful consequences. We then study the interaction between two and three different cell populations, and perform stability and bifurcation analysis on the systems. We also analyze the impact of immunotherapy on the tumor cell population numerically.
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Kiselev, Vladimir. "Computational study of electrostatic contribution to membrane dynamics." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5751.
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Electrostatics plays a crucial role in the membrane biology. Negatively charged lipids (such as PS, PA and PIP2) are subject to redistribution under the action of electrostatic forces during various signalling events. Membrane recruitment of multiple signalling proteins (such as MARCKS or Src kinase) is often maintained by positively charged polybasic domains (PD). Even though adsorption of these proteins to the cellular membrane has been extensively investigated, very little is known about how electrostatic interactions contribute to their membrane lateral dynamics. This thesis presents an investigation of the contribution of electrostatic interactions to the membrane lateral dynamics by means of novel computational tools. First, I developed a dynamic Monte-Carlo automaton that faithfully simulates lateral diffusion of the adsorbed positively charged PD of a peripheral membrane protein, as well as the dynamics of mono- (PS, PA) and polyvalent (PIP2) anionic lipids within the bilayer. This model allowed to investigate the major characteristics of protein-membrane diffusion on the uniform membrane. In agreement with earlier results, the simulations revealed the following microscopic phenomena: 1) Electrostatic lipid demixing in the vicinity of the PD; 2) PD interacts with PIP2 stronger than with monovalent lipids. On the spatially heterogeneous membrane the automaton predicted a directional drift of the PD, which was validated by a simple mean-field analytical model. The predicted phenomenon could potentially play a major role in membrane domain formation. To test this hypothesis and to investigate the membrane dynamics on larger scales I developed a continuous model, which was based on the results of the automaton simulations. The results of the continuous model and the Monte-Carlo simulations were shown to be in quantitative agreement. The continuous model allows one to simulate the electrostatic membrane dynamics on micrometer scales and can be used to describe various biologically important processes, such as endocytic cup initiation.