In this thesis we study modeling and simulation approaches for multiscale biochemical systems. The thesis addresses both modeling methods and simulation strategies. In the first part, we propose modeling methods to study the behavior of the insulin secretion pathway. We first expand the single cell model proposed by Bertram et. al. to model multiple cells. Synchronization among multiple cells is observed. Then an unhealthy cell model is proposed to study the insulin secretion failure caused by weakening of mitochondria function. By studying the interaction between the healthy and unhealthy cells, we find that the insulin secretion can be reinstated by increasing the glucokinase level. This new discovery sheds light on antidiabetic medication. In order to study the stochastic dynamics of the insulin secretion pathway, we first apply the hybrid method to model the discrete events in the insulin secretion pathway. Based on the hybrid model, a probability based measurement is proposed and applied to test the new antidiabetic remedy. In the second part, we focus on different simulation schemes for multiscale biochemical systems. We first propose a partitioning strategy for the hybrid method which leads to an efficient way of building stochastic cell cycle models. Then different implementation methods for the hybrid method are studied. A root finding method based on inverse interpolation is introduced to implement the hybrid method with three different ODE solvers. A detailed discussion of the performance of these three ODE solvers is presented. Last, we propose a new strategy to automatically detect stiffness and identify species that cause stiffness for the Tau-Leaping method, as well as two stiffness reduction methods. The efficiency is demonstrated by applying this new strategy on a stiff decaying dimerization model and a heat shock protein regulation model. / Ph. D.

The 2010-2011 Canterbury, New Zealand, Earthquake Sequence (CES) resulted in 185 fatalities and approximately $NZ40 billion in damage, much of which was due to liquefaction and related phenomena. As a result, an extensive soil improvement field testing program was initiated and Rammed Aggregate Piers� (RAP) were shown to be a feasible method to mitigate the risk from liquefaction during future events. To better design and more fully assess the efficacy of reinforcement techniques against liquefaction, pre- and post-treatment in-situ test data are compiled, to include results from cone penetration tests (CPT), direct-push crosshole tests, and vibroseis (T-Rex) shaking tests. The data are used to evaluate the capabilities of numerical tools to predict the liquefaction response of unimproved and improved sites. A finite difference (FD) numerical model is developed in a FLAC platform and a coupled analysis using the Finn model with Byrne (1991) formulation is conducted. The FD model calibrated for top-down shakings similar to the vibroseis tests succeeded in qualitatively reproducing the general observed behavior without quantitatively matching the in-situ values for shear strains and excess pore pressure ratios. The introduction of the RAP elements to the FD model reduced the shear strain, but slightly overestimated that reduction. Considering more advanced constitutive models that better simulate the complexity of the soil behavior under dynamic loading would likely increase the accuracy of the predicted response. / MS / During earthquakes, a significant loss of strength in soil can occur. This phenomenon, known as liquefaction, can have a devastating impact on the area affected. The 2010-2011 Canterbury, New Zealand, Earthquake Sequence (CES) resulted in 185 fatalities and approximately $NZ40 billion in damage, much of which was due to liquefaction and related phenomena. Consequently, the New Zealand Earthquake Commission implemented a field testing program in order to investigate the efficiency of ground improvement techniques in reducing soil liquefaction potential. One of the tested techniques was Rammed Aggregate Piers™ (RAP) and was shown to be a feasible method in mitigating the risk from liquefaction during future events. The focus of this study is to develop a numerical model capable of predicting the liquefaction response of unimproved and RAP-improved sites. Pre- and post-treatment test data are therefore compiled and used to calibrate the model. The numerical model calibrated for shakings similar to the on-site tests succeeded in qualitatively, but not quantitatively, reproducing the behavior observed in the field. The introduction of the RAP elements to the model revealed an improvement against liquefaction hazard; however, the improvement was overestimated compared to the field results. Considering more advanced numerical features that better simulate the complexity of the soil behavior under dynamic loading would likely increase the accuracy of the predicted response.

京都大学 / 新制・論文博士 / 博士(工学) / 乙第13618号 / 論工博第4215号 / (主査)教授 渦岡 良介, 教授 肥後 陽介, 准教授 上田 恭平, 教授 安原 英明 / 学位規則第4条第2項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Yes / In this study, the evolution process of the swallow-tailed flip bucket water nappe entering into the plunge pool is simulated by using the standard 𝑘-𝜀 turbulence model and the volume of fluid method. The effects of the upstream opening width ratio and downstream bucket angle on the flow pattern, the unit discharge distribution and the impact pressure distribution are studied. Based on the numerical results, the inner and outer jet trajectories are proposed by using the data. Results show that the longitudinal stretching length decreases with the increase of the upstream opening width ratio, and increases with the increase of the downstream bucket angle. The water nappe enters the plunge pool in a long strip shape. Thus, the unit discharge distribution of water nappe entry is consistent with the pressure distribution at the plunge pool bottom. The upstream opening width ratio and downstream bucket angle should be chosen as their intermediate values in order to have a uniform discharge distribution and to reduce the pressure peak at the plunge pool floor, which is effectively to avoid instability and destruction of plunge pool floor. / National Science Fund for Distinguished Young Scholars (No. 51625901) and National Nature Science Foundation of China (No: 51579165).

Thesis (PhD (Civil Engineering))--Stellenbosch University, 2008. / The velocity, density and turbulence profiles of a horizontal, saline gravity current were measured experimentally. Stable stratfication damped the turbulence and prevented the gravity current from becoming self-similar. The velocity and density prfiles were measured simultaneously and non-intrusively with particle image velocimetry scalar (PIV-S) technology. The application of the PIV-S technology had to be extended in order to measure the continuously stratified gravity current. Measurement of the Reynolds fluxes and Reynolds stresses revealed the anisotropic turbulent transport of mass and momentum within the gravity current body. These measurements also allowed the interaction between turbulence and stratification to be studied. The measured profiles were used to evaluate the accuracy of a gravity current model which did not assume self-similarity. The gravity current model was based on a Reynolds-averaged Navier-Stokes (RANS) multispecies mixture model. The Reynolds flux and Reynolds stress profiles did not show self-similarity with increasing downstream distance. Comparison of the vertical and horizontal Reynolds fluxes showed that gravity strongly damped the vertical flux. At a downstream location, where the bulk Richardson number was supercritical, the shear production profile had a positive inner (near bed) peak and a positive outer peak, while the buoyancy production pro le had a negative outer peak. Further downstream, where the bulk Richardson number was near-critical, the outer shear and buoyancy production peaks disappeared, due to the continuous damping of the turbulence intensities by the stable stratification. However, near bed shearing allowed the inner shear production peak to remain. Sensitivity analyses of different turbulence models for the gravity current model showed that the standard k -e turbulence model, as well as the Renormalization Group theory (RNG) k -e turbulence model, generally underpredicted the mean streamwise velocity profile and overpredicted the excess density pro le. The flux-gradient hypothesis, used to provide closure for the Reynolds uxes, modelled the vertical Reynolds ux reasonably, but not the horizontal flux. This did not compromise the results, since the horizontal gravity current had the characteristics of a boundary-layer ow, where the horizontal flux does not contribute significantly to the flow structure. It was shown that the gravity current model, implementing the standard k -e turbulence model with a constant turbulent Schmidt number of ot = 1;3, produced profiles which were within 10% - 20% of the measured profiles.

High-resolution physical and biogeochemical field data in central Lake Erie during the summers of 2008-2009 along with a three-dimensional numerical model were used to investigate the dynamics of basin scale waves and sediment resuspension mechanisms. In Chapter 2, the modal response of the Poincaré waves in the lake is assessed. The vertical mode-one Poincaré wave was found to be mostly dominant during the seasonal stratified period. The horizontal modal structure was also investigated in a sensitivity analysis, using the numerical model forced with real and idealized wind events. In Chapter 3, dynamics of bottom mixed layer (BML), primarily forced in the outer layer by surface seiches and Poincaré waves is studied for two 10-days representative intervals of weak and strong stratification. Shear velocity was calculated by least square fitting the well-known law-of-the-wall equation to observed near-bed velocity in a region of constant shear stress. Height of the BML is computed using water density (from water temperature) and compared with heights of logarithmic layer approximated using the law-of-the-wall equation and its modified form with buoyancy length scale term. Published equations for estimating BML heights are evaluated and modified for the lake. In Chapter 4, we investigate physical processes leading to sediment resuspension in the lake including surface waves (periods of 4-8s), up/downwelling events (periods of 3-4 day), and high frequency internal waves (periods of 5-45min). Temporal changes in near-bottom sediment resuspension are illustrated using changes in acoustic backscatter signals from current profilers and time series of turbidity measurements to identify the mechanism responsible for sediment resuspension. Resuspension is parameterized as a function of the critical velocity ~0.25ms-1 and from surface waves using linear wave theory. Finally, based on the critical velocity and sediment grain size analysis (from in-site field data), critical shear stress and Shields parameter are calculated and compared with previous observations in Lake Erie and in other locations suggesting a modified Shields diagram for silty bed materials. / Thesis (Ph.D, Civil Engineering) -- Queen's University, 2012-12-19 20:54:15.832

Among sources of renewable energy, development of tidal energy has traditionally been plagued by relatively high costs and limited availability of sites with sufficiently high tidal amplitudes or flow velocities. However, many recent technology developments and improvements, both in design (e.g. dynamic tidal power, tidal lagoons) and turbine technology (e.g. new axial turbines, crossflow turbines), showed that the economic and environmental costs may be brought down to competitive levels comparing to other conventional energy sources. It has long been identified that the Bay of Fundy is one of the world’s premier locations for the development of tidal power generating systems, since it has some of the world’s largest tidal ranges. Consequently, several proposals have been made in the recent years to find economical ways to harness the power of tides. Presently, there is considerable interest in installing tidal lagoons in the Bay of Fundy. The lagoon concept involves temporarily storing seawater behind an impoundment dike and generating power by gradually releasing the impounded seawater through conventional low-head hydroelectric turbines. A tidal lagoon will inherently modify the tides and tidal currents regime in the vicinity of the lagoon, and possibly induce effects that may be felt throughout the entire Bay of Fundy. The nature of these hydrodynamic impacts will likely depend on the size of the tidal lagoon, its location, and its method of operation. Any changes in the tidal hydrodynamics caused by a tidal lagoon may also impact on the transport of sediments throughout the region and upset ecosystems that are well adapted to existing conditions. The scale and character of the potential hydrodynamic impacts due to tidal lagoons operating in the Bay of Fundy have not been previously investigated. The present study endeavours to investigate these potential impacts to help the development of sustainable, science-based policies for the management and development of clean energy for future generations. After outlining fundamental aspects of tidal power projects taken in consideration in the Bay of Fundy, an analysis of present knowledge on tidal lagoons was conducted in order to provide a focus for subsequent investigations. Hydrodynamic modeling was used to quantify any of the potential hydrodynamic changes induced in the Bay of Fundy due to the presence of tidal lagoons. In the last part of the thesis, new relationships were derived in order to describe the amount of energy removed from tidal lagoons associated with its hydrodynamic impacts.

No description available.

Reflux condensation occurs in a vertical tube when there is an upward core flow of vapour (or gas-vapour mixture) and a downward flow of the liquid film. The understanding of this condensation configuration is crucial in the design of reflux condensers and in loss-of-coolant safety analyses in nuclear power plant steam generators. A range of modelling approaches exists for co-current film condensation from gas-vapour mixtures in parallel-plate channels and tubes. These methods are based on marching from the inlet down the tube and do not apply to the reflux condensation. In this research, however, a two-dimensional two-phase model was developed that solves the steady, full elliptic governing equations in both the film and the gas-vapour core flow on a non-orthogonal mesh that dynamically adapts to the phase interface. Gas-vapour shear and heat and mass transfer at the interface were accounted for fundamentally. This modelling is a big step ahead of current capabilities by removing the limitations of previous reflux condensation models which inherently cannot account for the detailed local balances of shear, mass, and heat transfer at the phase interface. The model was developed and applied for co-current and counter-current flows in vertical parallel-plate channels, followed by vertical tubes. In each stage, the model results were compared against the available experimental and numerical data for validation purposes. A wide range of boundary conditions and geometries have been studied to examine the details of co-current and counter-current condensation phenomena. Velocity, temperature, pressure, and gas mass fraction profiles along with the axial variation of various parameters such as local Nusselt number, film thickness, interface and centre-line temperature and gas mass fraction are presented in parametric studies. / February 2017

To model clouds in the mesoscale a 3D nonhydrostatic numerical model - GESIMA - was used, with a new cloud scheme which includes a quasispectral treatment of 6 different bulk water species ( water vapor, cloud water, rain, ice, snow, graupel) . lt allows to predict the distribution parameters since the number concentration and the mass mixing ratio were prognosed. So it is possible to vary the average particle masses ( diameters) in time which gives more realistic results. According to measurements two different distribution functions (log-normal for rain and cloud water and Marshall-Palmer for solid water classes) were used to describe the different water species. The cloud model is tested in a simulation of a mesoscale snowfall event over the southern Baltic Sea. / Für die mesoskalige Simulation von Wolken wurde ein nichthydrostatisches numerisches 3D-Modell - GESIMA - benutzt, in dem ein neuer Wolkenmodul mit quasispektraler Behandlung 6 verschiedener Wolkenteilchenklassen (Wasserdampf, Wolkenwasser, Regen, Eis, Schnee, Graupel) implementiert wurde. Es erlaubt die Vorhersage der Verteilungsparameter, da sowohl die Teilchenzahlkonzentration als auch das Massenmischungsverhältnis prognostiziert werden. Damit ist es möglich auch die mittlere Masse (Durchmesser) einer Teilchensorte zeitlich zu variieren, was zu realistischeren Resultaten führt. In Übereinstimmung mit Messungen wurden 2 verschiedene Verteilungsfunktionen zur Beschreibung für die verschiedenen Teilchenklassen (log-normal für Wolkenwasser und Regen und Marshall-Palmer für Schnee und Graupel) benutzt. Das Wolkenmodell wurde in einer Simulation eines mesoskaligen Schneefallereignisses über der südwestlichen Ostsee getestet.