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1
Heymes, David Verfasser], Michal [Akademischer Betreuer] [Czakon, and Werner [Akademischer Betreuer] Bernreuther. "A general subtraction scheme for next to next to leading order computations in perturbative quantum chromodynamics / David Heymes ; Michal Czakon, Werner Bernreuther." Aachen : Universitätsbibliothek der RWTH Aachen, 2015. http://d-nb.info/1128157233/34.
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Heymes, David [Verfasser], Michal [Akademischer Betreuer] Czakon, and Werner [Akademischer Betreuer] Bernreuther. "A general subtraction scheme for next to next to leading order computations in perturbative quantum chromodynamics / David Heymes ; Michal Czakon, Werner Bernreuther." Aachen : Universitätsbibliothek der RWTH Aachen, 2015. http://d-nb.info/1128157233/34.
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RATTI, CARLOALBERTO. "Topics in sym theories: * Ads/CFT & Mesonic Spectra ** Superspace & Scattering Amplitudes." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2010. http://hdl.handle.net/10281/11607.
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In this thesis two different topics in SYM theories are investigated. In the first part we use the AdS/CFT correspondence to study the problem of flavor symmetry for theories that are marginal deformations of the maximal SYM theory. In particular, we compute exactly the masses of the mesons of these theories. The results show that the mass spectrum is discrete, with a mass gap and a Zeeman-like splitting of the mass levels occurs. In the second part of the thesis, we develop a direct computational technique for scattering amplitudes in SYM theories. A combined use of background field method, superspace technologies and new pc programs makes a Feynman diagrammatic approach available. We apply this technique to compute the full two-loop MHV effective action of the maximal SYM theory. From there we move towards the extraction of the four point MHV scattering amplitude.
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Elago, David. "Robust computational methods for two-parameter singular perturbation problems." Thesis, University of the Western Cape, 2010. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_1693_1308039217.
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This thesis is concerned with singularly perturbed two-parameter problems. We study a tted nite difference method as applied on two different meshes namely a piecewise mesh (of Shishkin type) and a graded mesh (of Bakhvalov type) as well as a tted operator nite di erence method. We notice that results on Bakhvalov mesh are better than those on Shishkin mesh. However, piecewise uniform meshes provide a simpler platform for analysis and computations. Fitted operator methods are even simpler in these regards due to the ease of operating on uniform meshes. Richardson extrapolation is applied on one of the tted mesh nite di erence method (those based on Shishkin mesh) as well as on the tted operator nite di erence method in order to improve the accuracy and/or the order of convergence. This is our main contribution to this eld and in fact we have achieved very good results after extrapolation on the tted operator finitete difference method. Extensive numerical computations are carried out on to confirm the theoretical results.
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Ettenhuber, Christian. "Computational approaches for metabolic flux analysis in 13C perturbation experiments." [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=974209961.
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Lindquist, Dana Rae. "Computation of unsteady transonic flowfields using shock capturing and the linear perturbation Euler equations." Thesis, Massachusetts Institute of Technology, 1992. http://hdl.handle.net/1721.1/13090.
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Gilbert, Michael Stephen. "A Small-Perturbation Automatic-Differentiation (SPAD) Method for Evaluating Uncertainty in Computational Electromagnetics." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1354742230.
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Higgins, Erik Tracy. "Multi-Scale Localized Perturbation Method for Geophysical Fluid Flows." Thesis, Virginia Tech, 2020. http://hdl.handle.net/10919/99889.
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An alternative formulation of the governing equations of a dynamical system, called the multi-scale localized perturbation method, is introduced and derived for the purpose of solving complex geophysical flow problems. Simulation variables are decomposed into background and perturbation components, then assumptions are made about the evolution of these components within the context of an environmental flow in order to close the system. Once closed, the original governing equations become a set of one-way coupled governing equations called the "delta form" of the governing equations for short, with one equation describing the evolution of the background component and the other describing the evolution of the perturbation component. One-way interaction which arises due to non-linearity in the original differential equations appears in this second equation, allowing the background fields to influence the evolution of a perturbation. Several solution methods for this system of equations are then proposed. Advantages of the delta form include the ability to specify a complex, temporally- and spatially-varying background field separate from a perturbation introduced into the system, including those created by natural or man-made sources, which enhances visualization of the perturbation as it evolves in time and space. The delta form is also shown to be a tool which can be used to simplify simulation setup. Implementation of the delta form of the incompressible URANS equations with turbulence model and scalar transport within OpenFOAM is then documented, followed by verification cases. A stratified wake collapse case in a domain containing a background shear layer is then presented, showing how complex internal gravity wave-shear layer interactions are retained and easily observed in spite of the variable decomposition. The multi-scale localized perturbation method shows promise for geophysical flow problems, particularly multi-scale simulation involving the interaction of large-scale natural flows with small-scale flows generated by man-made structures.Master of Science
Natural flows, such as those in our oceans and atmosphere, are seen everywhere and affect human life and structures to an amazing degree. Study of these complex flows requires special care be taken to ensure that mathematical equations correctly approximate them and that computers are programmed to correctly solve these equations. This is no different for researchers and engineers interested in studying how man-made flows, such as one generated by the wake of a plane, wind turbine, cruise ship, or sewage outflow pipe, interact with natural flows found around the world. These interactions may yield complex phenomena that may not otherwise be observed in the natural flows alone. The natural and artificial flows may also mix together, rendering it difficult to study just one of them. The multi-scale localized perturbation method is devised to aid in the simulation and study of the interactions between these natural and man-made flows. Well-known equations of fluid dynamics are modified so that the natural and man-made flows are separated and tracked independently, which gives researchers a clear view of the current state of a region of air or water all while retaining most, if not all, of the complex physics which may be of interest. Once the multi-scale localized perturbation method is derived, its mathematical equations are then translated into code for OpenFOAM, an open-source software toolkit designed to simulate fluid flows. This code is then tested by running simulations to provide a sanity check and verify that the new form of the equations of fluid dynamics have been programmed correctly, then another, more complicated simulation is run to showcase the benefits of the multi-scale localized perturbation method. This simulation shows some of the complex fluid phenomena that may be seen in nature, yet through the multi-scale localized perturbation method, it is easy to view where the man-made flows end and where the natural flows begin. The complex interactions between the natural flow and the artificial flow are retained in spite of separating the flow into two parts, and setting up the simulation is simplified by this separation. Potential uses of the multi-scale localized perturbation method include multi-scale simulations, where researchers simulate natural flow over a large area of land or ocean, then use this simulation data for a second, small-scale simulation which covers an area within the large-scale simulation. An example of this would be simulating wind currents across a continent to find a potential location for a wind turbine farm, then zooming in on that location and finding the optimal spacing for wind turbines at this location while using the large-scale simulation data to provide realistic wind conditions at many different heights above the ground. Overall, the multi-scale localized perturbation method has the potential to be a powerful tool for researchers whose interest is flows in the ocean and atmosphere, and how these natural flows interact with flows created by artificial means.
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Khabir, Mohmed Hassan Mohmed. "Numerical singular perturbation approaches based on spline approximation methods for solving problems in computational finance." Thesis, University of the Western Cape, 2011. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_7416_1320395978.
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Options are a special type of derivative securities because their values are derived from the value of some underlying security. Most options can be grouped into either of the two categories: European options which can be exercised only on the expiration date, and American options which can be exercised on or before the expiration date. American options are much harder to deal with than European ones. The reason being the optimal exercise policy of these options which led to free boundary problems. Ever since the seminal work of Black and Scholes [J. Pol. Econ. 81(3) (1973), 637-659], the differential equation approach in pricing options has attracted many researchers. Recently, numerical singular perturbation techniques have been used extensively for solving many differential equation models of sciences and engineering. In this thesis, we explore some of those methods which are based on spline approximations to solve the option pricing problems. We show a systematic construction and analysis of these methods to solve some European option problems and then extend the approach to solve problems of pricing American options as well as some exotic options. Proposed methods are analyzed for stability and convergence. Thorough numerical results are presented and compared with those seen in the literature.
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PASTORE, Mariachiara. "Multireference Perturbation Theories for the accurate calculation of energy and molecular properties." Doctoral thesis, Università degli studi di Ferrara, 2009. http://hdl.handle.net/11392/2388724.
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This Ph.D. thesis deals with the development and the applications of N-Electron Valence
State Perturbation Theory (NEVPT), a novel form of Multireference Perturbation Theory
(MRPT) put forward in collaboration between the theoretical chemistry groups of the uni-
versities of Ferrara and Toulouse. A review of the NEVPT approach is presented, starting
from the original second order state–specific formulation, going through the quasidegenerate
multi–state extension and arriving at the implementations of the third order in the energy
and of the internally contracted configuration interaction, accomplished during the Ph.D. The
chief properties of NEVPT are analyzed and the test case of the C2 molecule is discussed.
An important field of applications of MRPTs is the calculation of the electronically excited
states of molecules, where the strong differential correlation effects and the possible multiref-
erence nature of the wavefunctions can be, in principle, successfully handled by a “variational
plus perturbation” scheme. Concerning the applications, the thesis is divided in two parts.
Part I concerns the calculation of electronically excited states. Different issues are addressed:
on the one hand the treatment of small aromatic molecules, Pyrrole, Furan and Thiophene,
whose description is complicated by the possible interaction with low-lying Rydberg states and
by the ionic nature of some valence states, extremely sensitive to the so-called dynamical −
polarization; on the other hand the case of a large-sized aromatic molecule, Free-Base Por-
phin, for which the crucial problem is the choice of a balanced variational space to accurately
describe the wavefunctions of the ground and of the excited states.
The second part is devoted to the description, by means of MRPT, of the Electron Transfer
(ET) process in Mixed-Valence systems. The investigation is carried out on a model spiro
− − compound, for which the ET reaction is simulated using a simplified one-mode
two-state model. The inadequacy of a standard second order MRPT approach is shown and
the application of an alternative and effective computational strategy is discussed.
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Ahlkrona, Josefin. "Computational Ice Sheet Dynamics : Error control and efficiency." Doctoral thesis, Uppsala universitet, Avdelningen för beräkningsvetenskap, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-283442.
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Ice sheets, such as the Greenland Ice Sheet or Antarctic Ice Sheet, have a fundamental impact on landscape formation, the global climate system, and on sea level rise. The slow, creeping flow of ice can be represented by a non-linear version of the Stokes equations, which treat ice as a non-Newtonian, viscous fluid. Large spatial domains combined with long time spans and complexities such as a non-linear rheology, make ice sheet simulations computationally challenging. The topic of this thesis is the efficiency and error control of large simulations, both in the sense of mathematical modelling and numerical algorithms. In the first part of the thesis, approximative models based on perturbation expansions are studied. Due to a thick boundary layer near the ice surface, some classical assumptions are inaccurate and the higher order model called the Second Order Shallow Ice Approximation (SOSIA) yields large errors. In the second part of the thesis, the Ice Sheet Coupled Approximation Level (ISCAL) method is developed and implemented into the finite element ice sheet model Elmer/Ice. The ISCAL method combines the Shallow Ice Approximation (SIA) and Shelfy Stream Approximation (SSA) with the full Stokes model, such that the Stokes equations are only solved in areas where both the SIA and SSA is inaccurate. Where and when the SIA and SSA is applicable is decided automatically and dynamically based on estimates of the modeling error. The ISCAL method provides a significant speed-up compared to the Stokes model. The third contribution of this thesis is the introduction of Radial Basis Function (RBF) methods in glaciology. Advantages of RBF methods in comparison to finite element methods or finite difference methods are demonstrated.eSSENCE
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Goswami, Ishan. "Computational and Experimental Investigation of the Critical Behavior Observed in Cell Signaling Related to Electrically Perturbed Lipid Systems." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/97564.
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Problem Statement: The use of pulsed electric fields (PEFs) as a tumor treatment modality is receiving increased traction. A typical clinical procedure involves insertion of a pair of electrodes into the tumor and administration of PEFs (amplitude: ~1 kV/cm; pulse-width: 100 μs). This leaves a zone of complete cell death and a sub-lethal zone where a fraction of the cells survive. There is substantial evidence of an anti-tumor systemic immune profile in animal patients treated with PEFs. However, the mechanism behind such immune profile alterations remains unknown, and the effect of PEFs on cell signaling within sub-lethal zones remains largely unexplored. Moreover, different values of a PEF pulse parameter, for e.g. the pulse-widths of 100 μs and 100 ns, may have different effects on cell signaling. Thus, the challenge of answering the mechanistic questions is compounded by the large PEF parameter space consisting of different combinations of pulse-widths, amplitudes, and exposure times.
Intellectual merit: This Ph.D. research provides proof that sub-lethal PEFs can enhance anti-tumor signaling in triple negative breast cancer cells by abrogating thymic stromal lymphopoietin signaling and enhancing stimulatory proteins such as the tumor necrosis factor. Furthermore, experimental evidence produced during this Ph.D. research demonstrates that PEFs may not directly impact the intracellular mitochondrial membrane at clinically relevant field amplitudes. As demonstrated in this work, PEFs may influence the mitochondria via an indirect route such as disruption of the actin cytoskeleton and/or alteration of ionic environment in the cytoplasm due to cell membrane permeabilization. Thus, a reductionist approach to understanding the influence of PEFs on cell signaling is proposed by limiting the study to membrane dynamics. To overcome the problem of investigating the entire PEF parameter space, this Ph.D. research proposes a first-principle thermodynamic approach of scaling the PEF parameter space such that an understanding developed in one regime of PEF pulse parameter values can be used to understand other regimes of the parameter space. Demonstration of the validity of this scaling model is provided by coupling Monte-Carlo methods for density-of-states with the steepest-entropy-ascent quantum thermodynamic framework for the non-equilibrium prediction of the lipid membrane dynamics.Ph. D.
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Osbild, Ralf Verfasser], and Kurt [Akademischer Betreuer] [Mehlhorn. "General analysis tool box for controlled perturbation algorithms and complexity and computation of Θ-guarded regions / Ralf Osbild. Betreuer: Kurt Mehlhorn." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2013. http://d-nb.info/1053634994/34.
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Johansson, Pedher. "Software tools for matrix canonical computations and web-based software library environments." Doctoral thesis, Umeå : Dept. of Computing Science, Umeå University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-890.
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Yasmin, Sabina. "Computational Studies of Plant Toxin Blockers of Potassium Channels, and Affinity & Aggregation of Antibodies." Thesis, The University of Sydney, 2018. http://hdl.handle.net/2123/18907.
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The voltage activated potassium channel Kv1.3 is an important therapeutic target due to its vital role in the treatment of autoimmune diseases. A family of plant toxins identified recently but their binding affinities for Kv1 channels have not been characterized. Here we have studied the binding of four plant toxins EgK1, SmK1, JrK1, and CcK1 with Kv1 channels using molecular docking and molecular dynamics (MD) simulations. The EgK1 toxin has been found as a potent blocker of Kv1.3 and highly selective for Kv1.3 over Kv1.1. Umbrella sampling MD simulations are performed for the Kv1.3–EgK1 complex to calculate binding free energy. The binding modes of all toxins are compared to design an EgK1 analog with higher affinity for Kv1.3 which could be a potential therapeutic lead for the treatment of autoimmune diseases. Herceptin is used in the treatment of breast cancer for patients whose tumors excessively express the HER2 protein. Here we have performed a computational study of HER2–herceptin-Fab complex and identified three mutations on herceptin to increase its binding affinity for HER2. Using MD simulations and Free energy perturbation method, D28R mutation found as the most promising one for improving the binding affinity of herceptin for HER2. Aggregation of protein is an undesired phenomena which reduces the antibody activity, so it is vitally necessary to understand the mechanism of aggregation at a molecular level for designing aggregation resistant versions of therapeutic antibodies. Here, we use higher temperature MD simulations to identify the aggregation prone regions in an antibody with a crystal structure (1HZH). The role of glycosylation in 1HZH is found to increase the overall stability of the antibody. The identified aggregation prone regions are modified via mutations to increase the aggregation resistance of the antibody.
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Wikström, Gunilla. "Computation of Parameters in some Mathematical Models." Doctoral thesis, Umeå University, Computing Science, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-565.
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In computational science it is common to describe dynamic systems by mathematical models in forms of differential or integral equations. These models may contain parameters that have to be computed for the model to be complete. For the special type of ordinary differential equations studied in this thesis, the resulting parameter estimation problem is a separable nonlinear least squares problem with equality constraints. This problem can be solved by iteration, but due to complicated computations of derivatives and the existence of several local minima, so called short-cut methods may be an alternative. These methods are based on simplified versions of the original problem. An algorithm, called the modified Kaufman algorithm, is proposed and it takes the separability into account. Moreover, different kinds of discretizations and formulations of the optimization problem are discussed as well as the effect of ill-conditioning.
Computation of parameters often includes as a part solution of linear system of equations Ax = b. The corresponding pseudoinverse solution depends on the properties of the matrix A and vector b. The singular value decomposition of A can then be used to construct error propagation matrices and by use of these it is possible to investigate how changes in the input data affect the solution x. Theoretical error bounds based on condition numbers indicate the worst case but the use of experimental error analysis makes it possible to also have information about the effect of a more limited amount of perturbations and in that sense be more realistic. It is shown how the effect of perturbations can be analyzed by a semi-experimental analysis. The analysis combines the theory of the error propagation matrices with an experimental error analysis based on randomly generated perturbations that takes the structure of A into account
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Stefan, Andreea. "An approach to the automatic generation of reduced chemical mechanisms using Computational Singular Perturbation (CSP) and Rate-Controlled Constrained Equilibrium (RCCE)." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/29951.
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Computer simulations using accurate chemical kinetic models are increasingly being used to support the development of combustion technologies and fuels. This action is essential for the reduction of hazardous and green-house gas emissions as well as for efficiency improvement of combustion applications. Consequently, the need to incorporate detailed chemistry in the simulation of combustion processes resulted in an increased interest in developing effective tools for mechanism reduction, from both accuracy and efficiency point of view. In this work, the Rate-Controlled Constrained Equilibrium (RCCE) and the Computational Singular Perturbation (CSP) methods are combined in order to generate an automatic technique for chemical kinetics reduction. The former method identifies the steady-state species and fast reactions while the latter simplifies the kinetics of complex reacting systems. The non steady state species provided by CSP represent the constraints employed in the RCCE code which systematically reduces the detailed mechanism. The benefits of combining the two reduction methods are briefly assessed for H2-air and C2H2-air chemical mechanisms and other two laminar premixed flames are thoroughly investigated i.e. the CH4-air and C3H8-air flames. The detailed chemical kinetics mechanisms used for describing the later two gas mixtures consist of 53 species and 325 reactions and 118 species and $665$ reactions, respectively. The direct numerical solution of 1-D laminar premixed flames is computed using the premixed flame code, providing accurate data for the proposed methodology of detailed chemistry reduction for methane-air and propane-air mixtures. The computational work involves the investigation of several chemical reduced models for each of the above gas mixtures in order to test the potential of the synergy between the two chemical mechanism reduction methodologies. These models are obtained by gradually increasing the number of constraints used for RCCE (resulting in reduced schemes with 12, 16 and 20 constraints for the methane/air flame and 15, 25, 35 and 45 constraints for the propane/air flame) as well as varying the equivalence ratio in the range of (0.8-1.2). The comparison with the results obtained from direct numerical simulations shows that the reduced models containing 20 constraints for the methane case and 45 constraints for the propane case provide good predictions of the laminar flame structure, including steady-state minor species both at stoichiometric and rich/lean mixtures, as well as adequate values of the corresponding burning velocities. Very good agreement with the detailed kinetic model as well as a significant computational time gain are observed. The study also derived a reduced chemical model that can predict flames of various mixture composition at specific pressure value. This reduced chemical model uses the same set of constraints for various equivalence ratio cases and it is able to predict global variables and species concentration within acceptable accuracy limits. The computation time by using this RCCE-CSP scheme is reduced to a third of the simulation time required in the case of applying the direct integration method. Overall, the results suggest that the combined RCCE-CSP is potentially a very reliable time-scale separation method for deriving low-dimensional models by the use of a fully automatic reduction algorithm. Since the proposed technique is an approach to automatically generate reduced chemical models and requires minor computations, it is recommended for the simplification of large detailed chemical kinetic mechanisms as well as for applications to turbulent combustion due to its potential for tabulation.
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YANG, Qin. "Accurate Spectral Predictions of Medium-to-large Molecular Systems: Balancing Performance and Reliability." Doctoral thesis, Scuola Normale Superiore, 2021. http://hdl.handle.net/11384/108450.
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Computational spectroscopy is being commonly used to understand the observed spectra of
molecular systems, like biological molecules or photosensitive molecules that attract significant
interest for solar energy conversion, organic display, or bio-probes. The correct prediction of the
physicochemical properties of these systems can provide guidelines to understand their activities
and optimize their applications. However, the methods commonly used for such studies have
become insufficiently accurate to match the most advanced spectroscopic techniques or those of
higher sensitivity, like chiroptical ones. While more advanced models have been proposed in the
literature, they have been mostly confined to small or simple molecules. The scale-up to larger
and more complex structures presents several challenges, which were at the core of this thesis.
For vibrational spectra, the double harmonic approximation remains the standard, despite
its systematic overestimation of the energy levels and its inability to predict overtones and
combinations. Anharmonic simulations do not have these deficiencies, but have a steep increase
in the computational cost. Among them, variational methods provide a systematic improvement,
but become quickly prohibitive, making them only feasible on very small molecules without
significant approximations. While second-order vibrational perturbation theory (VPT2) can be
used on systems with dozens of atoms, the resonances present in the system can induce significant
errors in the simulations. To deal with the problem of resonances, deperturbed (DVPT2) and
generalized (GVPT2) VPT2 have been proposed. Using these two models as reference, a series of
benchmarks have been designed during this thesis targeting medium-to-large molecular systems,
and new protocols have been proposed to identify the potential pitfalls and maximize the accuracy
and performance of anharmonic simulations. 15 molecules ranging from small to large have thus
been studied, classified into three groups. The first group is composed of 8 small molecules, with
less than 7 atoms. These small molecules have been used for a systematic benchmark of DVPT2
and GVPT2, including the intensity of vibrational spectra. With the aim of determining the
achievable accuracy and reliability of DFT-based VPT2 calculations, several DFT functionals
with different basis sets have been tested, as well as hybridization schemes combining different
levels for the harmonic base and the anharmonic correction. The best performing electronic
structure methods (ESCMs) are then used to treat medium-sized molecular systems (the second
group). The second group comprises furan, fluorobenzene, methyloxirane, and glycine, with
more complex topologies and resonance patterns. The definition of the most suitable ESCMs
has been further refined with this second group, especially the hybrid schemes. However, the
presence of new resonance patterns and large amplitude motions (LAMs) in methyloxirane and
glycine are two other important factors that can influence the accuracy of VPT2 in general.
Methods dealing with resonance patterns and LAMs have been tested on the molecules of
the second group, which paved the way to the simulation of large-sized molecules in group
three. For intensity, a more complete version of DVPT2, called IDVPT2, was implemented to
correctly remove resonances of all types. Three molecules have been chosen to represent large
molecules, naphthalene, -pinene and artemisinin. More in-depth studies on resonance have been
carried out on these three molecules, especially on -pinene. With pinene, a new class of Fermi
resonances (FRs), specific to intensity, was identified, and new correction schemes were devised,
implemented, and tested. Artemisinin was chosen in the study as an example of a large and
complex system, with 42 atoms and 7 chiral centers. It is an important pharmaceutical molecule,
which is known for its high anti-malaria and anticancer bioactivity. The final computational
protocol has been used to simulate the vibrational circular dichroism (VCD) and Raman optical
activity (ROA) spectra of artemisinin at a very accurate level. Thanks to this, we can proceed
to describe qualitatively the coupling between the reactive and recognition sites. This result
is also an interesting contribution for the bioactivity and structural studies of pharmaceutical
molecules. For electronic spectra, pure electronic transitions are often used, completely ignoring the
vibronic effects. This has been shown to be insufficient when used for high-resolution UV-visible
spectra or many chiroptical spectra. Several models have been developed to properly consider
the vibrational effects in electronic spectra, which can help balance accuracy and feasibility in
terms of computational cost. There are generally two groups according to the extrapolation
of the potential energy surface, which are the adiabatic models (Adiabatic Hessian, AH, and
Adiabatic Shift, AS) and vertical models (Vertical Hessian, VH, and Vertical Gradient, VG).
The Duschinsky transformation describes the evolution of the vibrational modes in relation to
the electronic transition. Then Franck-Condon (FC) and its extension, Herzberg-Teller (FCHT),
are used to represent the dependence of the transition properties on the nuclear positions. The
final spectra can be generated through two algorithms, the time-independent (TI) and the timedependent
(TD) methods. TI is based on an explicit sum of all transitions, while TD describes
the evolution of a wave packet after the transition. Because of the many possible combinations
offered by these models, vibronic simulations require specific knowledge and experience to select
the proper modal, depending on the targeted accuracy and characteristics of the system. A
significant hurdle to the definition of reliable protocols is that the strengths and weaknesses of
these models have not yet been extensively studied for large and complex systems, which may
exhibit some degree of flexibility, especially for chiroptical spectra. Hence, a protocol has been
built for the study of a family of Ir-complexes, which emit deep blue phosphorescence. Through
the step-up study of the molecules in this family, from prototype to more complex molecules,
the available methods were systematically assessed and compared. Because of the size and
complexity of the system, reduced-dimensionality schemes on top of internal coordinates were
used and defined to achieve good reliability and accuracy. Based on the vibronic simulations,
the most relevant transitions and the associated vibrational modes were identified, and possible
improvements on the experimental side have been proposed. This extensive study served as a
basis for the investigation of a chiral boron dipyrromethene dye (BODIPY) and a porphyrin
derivative (zinc octaethylporphyrin, ZnOEP). All these examples have shown the importance
of including the vibrational effects, not only to improve the accuracy of the results, but also
in some cases to get a correct understanding of the underlying physicochemical properties.
They are also good targets to study the importance of balancing the computational cost and
accuracy. From the study of these molecules, a complete protocol for vibronic simulation has
been built for organic and organometallic systems. In these studies, we also investigate the
value of visualization tools, in particular the electronic transition current density, to gain further
insights on the origin of the chiroptical signal at a local level.
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Ringer, Ashley L. "From small to big." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28089.
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Thesis (M. S.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009.Committee Chair: Sherrill, C. David; Committee Member: Bredas, Jean-Luc; Committee Member: El-Sayed, Mostafa A.; Committee Member: Harvey, Stephen C; Committee Member: Hernandez, Rigoberto.
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Lind, Christoffer. "Computational Studies of Protein Synthesis on the Ribosome and Ligand Binding to Riboswitches." Doctoral thesis, Uppsala universitet, Beräkningsbiologi och bioinformatik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-328583.
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The ribosome is a macromolecular machine that produces proteins in all kingdoms of life. The proteins, in turn, control the biochemical processes within the cell. It is thus of extreme importance that the machine that makes the proteins works with high precision. By using three dimensional structures of the ribosome and homology modelling, we have applied molecular dynamics simulations and free-energy calculations to study the codon specificity of protein synthesis in initiation and termination on an atomistic level. In addition, we have examined the binding of small molecules to riboswitches, which can change the expression of an mRNA. The relative affinities on the ribosome between the eukaryotic initiator tRNA to the AUG start codon and six near-cognate codons were determined. The free-energy calculations show that the initiator tRNA has a strong preference for the start codon, but requires assistance from initiation factors 1 and 1A to uphold discrimination against near-cognate codons. When instead a stop codon (UAA, UGA or UAG) is positioned in the ribosomal A-site, a release factor binds and terminates protein synthesis by hydrolyzing the nascent peptide chain. However, vertebrate mitochondria have been thought to have four stop codons, namely AGA and AGG in addition to the standard UAA and UAG codons. Furthermore, two release factors have been identified, mtRF1 and mtRF1a. Free-energy calculations were used to determine if any of these two factors could bind to the two non-standard stop codons, and thereby terminate protein synthesis. Our calculations showed that the mtRF’s have similar stop codon specificity as bacterial RF1 and that it is highly unlikely that the mtRF’s are responsible for terminating at the AGA and AGG stop codons. The eukaryotic release factor 1, eRF1, on the other hand, can read all three stop codons singlehandedly. We show that eRF1 exerts a high discrimination against near-cognate codons, while having little preference for the different cognate stop codons. We also found an energetic mechanism for avoiding misreading of the UGG codon and could identify a conserved cluster of hydrophobic amino acids which prevents excessive solvent molecules to enter the codon binding site. The linear interaction energy method was used to examine binding of small molecules to the purine riboswitch and the FEP method was employed to explicitly calculate the LIE b-parameters. We show that the purine riboswitches have a remarkably high degree of electrostatic preorganization for their cognate ligands which is fundamental for discriminating against different purine analogs.
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Fukasaku, Kotaro. "Explorative study for stochastic failure analysis of a roughened bi-material interface: implementation of the size sensitivity based perturbation method." Thesis, Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/41114.
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In our age in which the use of electronic devices is expanding all over the world, their reliability and miniaturization have become very crucial. The thesis is based on the study of one of the most frequent failure mechanisms in semiconductor packages, the delamination of interface or the separation of two bonded materials, in order to improve their adhesion and a fortiori the reliability of microelectronic devices. It focuses on the metal (-oxide) / polymer interfaces because they cover 95% of all existing interfaces.
Since several years, research activities at mesoscopic scale (1-10µm) have proved that the more roughened the surface of the interface, i.e., presenting sharp asperities, the better the adhesion between these two materials. Because roughness exhibits extremely complex shapes, it is difficult to find a description that can be used for reliability analysis of interfaces. In order to investigate quantitatively the effect of roughness variation on adhesion properties, studies have been carried out involving analytical fracture mechanics; then numerical studies were conducted with Finite Element Analysis. Both were done in a deterministic way by assuming an ideal profile which is repeated periodically.
With the development of statistical and stochastic roughness representation on the one hand, and with the emergence of probabilistic fracture mechanics on the other, the present work adds a stochastic framework to the previous studies. In fact, one of the Stochastic Finite Element Methods, the Perturbation method is chosen for implementation, because it can investigate the effect of the geometric variations on the mechanical response such as displacement field. In addition, it can carry out at once what traditional Finite Element Analysis does with numerous simulations which require changing geometric parameters each time.
This method is developed analytically, then numerically by implementing a module in a Finite Element package MSc. Marc/Mentat. In order to get acquainted and to validate the implementation, the Perturbation method is applied analytically and numerically to the 3 point bending test on a beam problem, because the input of the Perturbation method in terms of roughness parameters is still being studied. The capabilities and limitations of the implementation are outlined.
Finally, recommendations for using the implementation and for furture work on roughness representation are discussed.
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Boukharta, Lars. "Computational Modelling of Ligand Complexes with G-Protein Coupled Receptors, Ion Channels and Enzymes." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-212103.
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Accurate predictions of binding free energies from computer simulations are an invaluable resource for understanding biochemical processes and drug action. The primary aim of the work described in the thesis was to predict and understand ligand binding to several proteins of major pharmaceutical importance using computational methods. We report a computational strategy to quantitatively predict the effects of alanine scanning and ligand modifications based on molecular dynamics free energy simulations. A smooth stepwise scheme for free energy perturbation calculations is derived and applied to a series of thirteen alanine mutations of the human neuropeptide Y1 G-protein coupled receptor and a series of eight analogous antagonists. The robustness and accuracy of the method enables univocal interpretation of existing mutagenesis and binding data. We show how these calculations can be used to validate structural models and demonstrate their ability to discriminate against suboptimal ones. Site-directed mutagenesis, homology modelling and docking were further used to characterize agonist binding to the human neuropeptide Y2 receptor, which is important in feeding behavior and an obesity drug target. In a separate project, homology modelling was also used for rationalization of mutagenesis data for an integron integrase involved in antibiotic resistance. Blockade of the hERG potassium channel by various drug-like compounds, potentially causing serious cardiac side effects, is a major problem in drug development. We have used a homology model of hERG to conduct molecular docking experiments with a series of channel blockers, followed by molecular dynamics simulations of the complexes and evaluation of binding free energies with the linear interaction energy method. The calculations are in good agreement with experimental binding affinities and allow for a rationalization of three-dimensional structure-activity relationships with implications for design of new compounds. Docking, scoring, molecular dynamics, and the linear interaction energy method were also used to predict binding modes and affinities for a large set of inhibitors to HIV-1 reverse transcriptase. Good agreement with experiment was found and the work provides a validation of the methodology as a powerful tool in structure-based drug design. It is also easily scalable for higher throughput of compounds.
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Shamsudin, Khan Yasmin. "Non-Steroidal Anti-Inflammatory Drugs in Cyclooxygenases 1 and 2 : Binding modes and mechanisms from computational methods and free energy calculations." Doctoral thesis, Uppsala universitet, Beräkningsbiologi och bioinformatik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-328478.
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Non-steroidal anti-inflammatory drugs (NSAIDs) are one of the most commonly used classes of drugs. They target the cyclooxygenases (COX) 1 and 2 to reduce the physiological responses of pain, fever, and inflammation. Due to their role in inducing angiogenesis, COX proteins have also been identified as targets in cancer therapies. In this thesis, I describe computational protocols of molecular docking, molecular dynamics simulations and free energy calculations. These methods were used in this thesis to determine structure-activity relationships of a diverse set of NSAIDs in binding to their target proteins COX-1 and 2. Binding affinities were calculated and used to predict the binding modes. Based on combinations of molecular dynamics simulations and free energy calculations, binding mechanisms of sub-classes of NSAIDs were also proposed. Two stable conformations of COX were probed to understand how they affect inhibitor affinities. Finally, a brief discussion on selectivity towards either COX isoform is discussed. These results will be useful in future de novo design and testing of third-generation NSAIDs.
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Eslick, John. "A Dynamical Study of the Evolution of Pressure Waves Propagating through a Semi-Infinite Region of Homogeneous Gas Combustion Subject to a Time-Harmonic Signal at the Boundary." ScholarWorks@UNO, 2011. http://scholarworks.uno.edu/td/1367.
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In this dissertation, the evolution of a pressure wave driven by a harmonic signal on the boundary during gas combustion is studied. The problem is modeled by a nonlinear, hyperbolic partial differential equation. Steady-state behavior is investigated using the perturbation method to ensure that enough time has passed for any transient effects to have dissipated. The zeroth, first and second-order perturbation solutions are obtained and their moduli are plotted against frequency. It is seen that the first and second-order corrections have unique maxima that shift to the right as the frequency decreases and to the left as the frequency increases. Dispersion relations are determined and their limiting behavior investigated in the low and high frequency regimes. It is seen that for low frequencies, the medium assumes a diffusive-like nature. However, for high frequencies the medium behaves similarly to one exhibiting relaxation. The phase speed is determined and its limiting behavior examined. For low frequencies, the phase speed is approximately equal to sqrt[ω/(n+1)] and for high frequencies, it behaves as 1/(n+1), where n is the mode number. Additionally, a maximum allowable value of the perturbation parameter, ε = 0.8, is determined that ensures boundedness of the solution. The location of the peak of the first-order correction, xmax, as a function of frequency is determined and is seen to approach the limiting value of 0.828/sqrt(ω) as the frequency tends to zero and the constant value of 2 ln 2 as the frequency tends to infinity. Analytic expressions are obtained for the approximate general perturbation solution in the low and high-frequency regimes and are plotted together with the perturbation solution in the corresponding frequency regimes, where the agreement is seen to be excellent. Finally, the solution obtained from the perturbation method is compared with the long-time solution obtained by the finite-difference scheme; again, ensuring that the transient effects have dissipated. Since the finite-difference scheme requires a right boundary, its location is chosen so that the wave dissipates in amplitude enough so that any reflections from the boundary will be negligible. The perturbation solution and the finite-difference solution are found to be in excellent agreement. Thus, the validity of the perturbation method is established.
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Dekhli, Faiza. "Étude et réalisation de logiciels d'optimisation contrainte avec analyse des erreurs de calculs et de données." Paris 6, 1985. http://www.theses.fr/1985PA066413.
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Timpanaro, André Martin. "Mudanças de opinião em redes complexas." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/43/43134/tde-11032013-103856/.
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Nos últimos anos, uma míriade de modelos de propagação de opinião foram propostos, motivados pelo interesse crescente dos físicos por problemas interdisciplinares tanto em sociologia, quanto em economia e biologia. Um dos objetivos desse trabalho é unificar alguns desses modelos em uma mesma formulação. Para isso, generalizamos a noção de confiança limitada para o que chamamos de regras de confiança, que podem ser interpretadas como a introdução de viéses ou preconceitos nas interações de agentes com opiniões distintas. Munidos dessa formulação, nos propusemos a estudar como modelos que promovem localmente conformidade (o que está de acordo com experimentos para grupos pequenos conduzidos por psicólogos), poderiam gerar diversidade globalmente (explicando a persistência de pontos de vista distintos em sociedades, por exemplo). Nós estudamos o campo médio do modelo do votante e de variantes do modelo Sznajd. Aplicando ferramentas de sistemas dinâmicos, conseguimos resolver analiticamente o comportamento qualitativo dos modelos na ausência de ruído e desenvolvemos uma teoria de perturbação para o modelo Sznajd com ruído infinitesimal, que nos forneceu um retrato parcial do comportamento na presença de ruído. Na ausência de ruído, chegamos a conclusão que o modelo do votante se comporta de maneira completamente diferente, enquanto que os outros modelos tem essencialmente o mesmo comportamento. Também fizemos simulações em redes Barabási-Albert e Watts-Strogatz para os modelos votante e Sznajd e, em colaboração com o grupo de pesquisa do Institute for Complex Systems and Mathematical Biology da Universidade de Aberdeen, estudamos um modelo de biodiversidade que pode ser encarado como uma variante do modelo do votante em uma rede quadrada. As nossas conclusões apontam que os resultados de campo médio podem ser compreendidos através de conexões com teoria de grafos e que os diversos modelos simulados se comportam em um certo sentido da mesma maneira, reforçando a idéia de universalidade entre eles (na verdade é essencial que existam aspectos universais no comportamento humano para que a modelagem de sistemas sociais seja factível, dadas as dificuldades óbvias de se construir um modelo realista para uma pessoa ou uma sociedade). Grosso modo, em todos os sistemas estudados, a coexistência ou não de pontos de vista diferentes parece depender mais crucialmente da rede e do tipo de regra de confiança, do que de outros detalhes específicos do modelo.In the recent years, a great number of opinion propagation models were proposed, motivated by the increasing interest among physicists in interdisciplinary problems, not only in sociology, but also in economics and biology. One of the goals of this work is to unify some of these models under a same formulation. In order to do that, we generalized the notion of bounded confidence to what we called confidence rules, that can be interpreted as the introduction of biases and prejudices in the interactions among agents holding differing points of view. Using this formulation, we decided to study how models that locally breed conformity (what is in accordance with experiments conducted by psichologists for small groups) could sustain diversity globally (explaining the persistence of different points of view in societies, for example). We studied the mean field version of the voter model and of variants of the Sznajd model. We used dynamical systems techniques and were able to solve analytically the qualitative behaviour of the models in the absence of noise and developed a perturbation theory for the Sznajd model with infinitesimal noise, that yielded a partial picture of the behaviour with noise. In the absence of noise, we found that the voter model has a completely different behaviour, while the other models have essentially the same behaviour. We also did simulations in Barabási-Albert and Watts-Strogatz networks for the voter and the Sznajd models and we collaborated with the research group of the Institute for Complex Systems and Mathematical Biology from the University of Aberdeen, studying a biodiversity model that can be seen as a modification of the voter model in a square lattice. Our conclusions point that the mean field results can be understood through connections with graph theory problems and that the different models that were simulated, in some sense, have the same behaviour, reinforcing the idea of universality for these models (due to the obvious difficulties in modelling human beings in a reliable and realistic way, some degree of universality in human behaviour is actually essential, in order for social modelling to be feasible). Roughly speaking, in all the systems that were studied, the coexistence or not of differing opinions, seems to depend more strongly on the network and on the type of confidence rule used, than in other specific details of the model.
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Prescott, Thomas Paul. "Large-scale layered systems and synthetic biology : model reduction and decomposition." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:205a18fb-b21f-4148-ba7d-3238f4b1f25b.
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This thesis is concerned with large-scale systems of Ordinary Differential Equations that model Biomolecular Reaction Networks (BRNs) in Systems and Synthetic Biology. It addresses the strategies of model reduction and decomposition used to overcome the challenges posed by the high dimension and stiffness typical of these models. A number of developments of these strategies are identified, and their implementation on various BRN models is demonstrated. The goal of model reduction is to construct a simplified ODE system to closely approximate a large-scale system. The error estimation problem seeks to quantify the approximation error; this is an example of the trajectory comparison problem. The first part of this thesis applies semi-definite programming (SDP) and dissipativity theory to this problem, producing a single a priori upper bound on the difference between two models in the presence of parameter uncertainty and for a range of initial conditions, for which exhaustive simulation is impractical. The second part of this thesis is concerned with the BRN decomposition problem of expressing a network as an interconnection of subnetworks. A novel framework, called layered decomposition, is introduced and compared with established modular techniques. Fundamental properties of layered decompositions are investigated, providing basic criteria for choosing an appropriate layered decomposition. Further aspects of the layering framework are considered: we illustrate the relationship between decomposition and scale separation by constructing singularly perturbed BRN models using layered decomposition; and we reveal the inter-layer signal propagation structure by decomposing the steady state response to parametric perturbations. Finally, we consider the large-scale SDP problem, where large scale SDP techniques fail to certify a system’s dissipativity. We describe the framework of Structured Storage Functions (SSF), defined where systems admit a cascaded decomposition, and demonstrate a significant resulting speed-up of large-scale dissipativity problems, with applications to the trajectory comparison technique discussed above.
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Jobst, Beatrice M. "Mechanistic insights into the large-scale dynamics underlying different brain states." Doctoral thesis, Universitat Pompeu Fabra, 2018. http://hdl.handle.net/10803/563080.
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Brain activity during rest exhibits a robust intrinsic spatio-temporal structure characterized by correlated patterns of neural activity. The study of the brain in altered states of vigilance or drug-induced brain states has revealed a number of local and global alterations of this activity and changes in the spatio-temporal correlation patterns. Yet, we are still missing a mechanistic explanation of the dynamics underlying these experimentally observed phenomena. In this thesis we will use whole-brain computational modeling to try to elucidate the dynamical processes governing these distinct brain states. We will show how models of whole-brain activity and dynamical alterations thereof on a local level can be applied to efficiently dissociate between different brain states by their dynamical properties and how they therefore provide a mechanistic characterization of each state. We will demonstrate that one unified framework can account for an effective description and identification of several entirely distinct brain states.La actividad cerebral en reposo presenta una estructura espacio-temporal intrínseca robusta caracterizada por patrones de actividad neuronal correlacionados. El estudio del cerebro en estados alterados de conciencia o estados bajo influencia de drogas ha revelado alteraciones locales y globales de esta actividad así como cambios en los patrones de correlación. Sin embargo, los mecanismos de la dinámica subyacente no han sido revelados del todo. En esta disertación se aplicarán modelos computacionales de actividad cerebral a gran escala para intentar a esclarecer los procesos dinámicos que dominan dichos estados cerebrales. Se mostrará como las alteraciones de las dinámicas locales pueden ser aplicadas para diferenciar estados cerebrales distintos así como para proporcionar una caracterización mecanística de cada estado. Finalmente, se revelará como un único marco teórico puede ser utilizado para describir e identifocar de manera efectiva estados cerebrales completamente diferentes.
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Lani, Giovanna. "Vers une nouvelle méthode de calcul pour la fonction de Green à un corps." Phd thesis, Ecole Polytechnique X, 2011. http://pastel.archives-ouvertes.fr/pastel-00667923.
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Dans ce travail, une nouvelle voie pour le calcul de la fonction de Green (GF) à une particule a été développée. L' objectif est de remédier aux défauts de nombreuses autres approches à plusieurs corps, par exemple l'approximation GW (GWA), dans le traitement des forts effets de corrélation dans les solides. L'idée consiste à résoudre un ensemble d'équations différentielles fonctionnelles et non-linéaires, qui sont centrales à la théorie des perturbations à plusieurs corps. Dans un premier temps, ce qu'on appelle le modèle à un 1-point est employé (une seule valeur pour chaque variable d'espace, temps, spin est retenue) et l'ensemble des équations se réduit alorsà une seule équation algébrique, pour laquelle une solution exacte et explicite est obtenue. La solution est utilisée comme outil de référence pour analyser les performances des autres méthodes bien établies (par exemple, des versions différentes de GW). Par ailleurs, des approximations alternatives sont conçues et pour les plus prometteuses la généralisation à la forme fonctionnelle (complète) est discutée. La dernière partie de cetravail aborde la généralisation de l'approche au-delà du cadre à1-point. Tout d'abord la dépendance en fréquence de la GF est restaurée (tout en conservant le modèle à un 1-point pour les variables d'espace et despin) et l'ensemble des équations est résolu. Il est montré que dans un tel cadre, il est possible de retrouver ce que l'on appelle "l'expansion en cumulants" pour GF- une approximation qui va au-delà de GW et fournit des fonctions spectrales en bon accord avec les expériences de photo-émission . Enfin, à l'aide d'un ansatz, une famille de solutions pour les equations dans leur forme fonctionnelle est obtenue et des moyens sont proposés, allant bien au delà de l'état de l'art, afin d'obtenir des approximations pour celles ayant une signification physique.
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Gusev, Yuri Vladimirovich. "Covariant computations of heat kernels in perturbation theory." 1996. http://hdl.handle.net/1993/19182.
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CHEN, WEI-JU, and 陳薇如. "Perturbation Property and the Computation of Best Approximations in Hilbert Spaces." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/5mg8p7.
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碩士輔仁大學
數學系研究所
93
In a Hilbert space , a constrained best approximation problem is considered.Let be a closed convex set and be a finite collection of half-spaces. Under the assumption that not equal to empty set, the best approximation from to any belongs to is considered. Of the most notable, the strong conical hull intersection property (strong CHIP) was shown [5] to characterize the purturbation property . In particular, by defining , and , then the assumption becomes and the perturbation property can be written as . This is the one that we used for computation. Finally, some examples are given.
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Ettenhuber, Christian [Verfasser]. "Computational approaches for metabolic flux analysis in 13C perturbation experiments / Christian Ettenhuber." 2005. http://d-nb.info/974209961/34.
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Sung, Cheng Yang, and 宋承陽. "Second and Third-order Perturbation Computations on Phonon Transport in Thermoelectric Materials and Parametric Analyses on the Figure of Merit." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/11146777767522857437.
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碩士國立清華大學
動力機械工程學系
104
As the economic develops, the production and usage of the energy has become an increasing important issue. Thermoelectric materials are one of the most promising energy material. At the same time, light and low dimension are the ways that technology develops nowadays. For thermoelectric materials, the reduction of the scale can also lead to higher conversion efficiency. We use computational quantum mechanics to simulate thermoelectric materials in nanoscale, and obtain their thermal and electrical properties, and then finally calculate the figure of merit to find out whether it is a good thermoelectric material. In the end, we aim to optimize the figure of merit by changing the composition, structure and doping. As a result of the commercial materials nowadays are rare and expensive, we choose silicon and germanium to set up our model. The study uses Kohn-Sham equation, plane wave basis and self-consistent field to optimize the model. After that, density functional perturbation theory (DFPT) is employed to calculate the phonon dispersion relation and phonon density of states, which can be further analyzed to achieve the group velocity, heat capacity, phonon relaxation time and finally the thermal conductivity. Next, we use density functional theory (DFT) to calculate the band structure and the density of states. Implementing the above parameters into the Boltzmann Transport Equation (BTE) and artificial doping, the electrical properties can be calculated. In conclusion, no matter what the structure the nanowire is, low frequency phonons dominate the heat transfer, while the silicon core germanium shell nanowire leads to the lowest thermal conductivity, and the thermal conductivity decreases with the increasing thickness of the germanium shell at the same nanowire diameter.
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Hernández, Antonio. "In vivo dynamic function of lower extremity human biarticular muscles as measured by novel electrical stimulation protocols juxtaposed to computational perturbation studies /." 2009. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Song, Wonsik. "High Fidelity Numerical Simulations and Diagnostics of Complex Reactive Systems." Diss., 2021. http://hdl.handle.net/10754/669072.
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To contribute to the design of next-generation high performance and low emission combustion devices, this study provides a series of high fidelity numerical simulations of turbulent premixed combustion and autoignition with different clean fuels. The first part of the thesis consists of the direct numerical simulations (DNS) of the lean hydrogen-air turbulent premixed flames at a wide range of Karlovitz number (Ka) conditions up to Ka = 1,126. Turbulence-chemistry interaction is discussed in terms of statistical analysis of the turbulent flame speed and flame structure. Global and local flame speed are separately studied through the fuel consumption speed and displacement speed of the flame front, respectively, and the results are compared with the reference laminar flames as well as similar studies in the literature. The global flame structure is assessed via cross-sectional and conditional averages, and modeling implication is further discussed. Detailed analysis of the local flame structure along the positive and negative curvature is also conducted, providing an understanding of the different behavior of local heat release response. Finally, as the modeling perspectives for Reynolds-averaged Navier-Stokes (RANS) and large eddy simulations (LES), the mean quantities of major species, intermediate species, density, the reaction rate of the progress variable, and heat release rate are assessed in the context of the probability density function (PDF). The second part of the thesis consists of applications of the advanced mathematical tool called the computational singular perturbation (CSP). A skeletal chemical mechanism is developed using the CSP algorithm for the autoignition of methanol and dimethyl ether blends, and the ignition delay time and laminar flame speed are validated for a wide range of mixture conditions. A series of autoignition simulations are carried out in the canonical counter flow mixing layer using the developed skeletal mechanism, and detailed analyses of the autoignition for the methanol and dimethyl ether blends at a wide range of strain rate conditions are provided using the CSP diagnostics tools for a wide range of chemical and fluid combinations.
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Xing, X. Q., Murali Damodaran, and Chung Piaw Teo. "Aerodynamic Shape Design of Transonic Airfoils Using Hybrid Optimization Techniques and CFD." 2003. http://hdl.handle.net/1721.1/3710.
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This paper will analyze the effects of using hybrid optimization methods for optimizing objective functions that are determined by computational fluid dynamics solvers for compressible viscous flow for optimal design of airfoils. Previous studies on this topic by the authors had examined the application of deterministic optimization methods and stochastic optimization methods such as Simulated Annealing and Simultaneous Perturbation Stochastic Analysis (SPSA). The studies indicated that SPSA method has a greater or equal efficiency as compared with SA method in reaching optimal airfoil designs for the design problem in question. However, in some situations SPSA method has a tendency to demonstrate an oscillatory behavior in the vicinity of a local optima. To overcome this tendency, a hybrid method designed to take full advantage of SPSA’s high rate of reduction of the objective function at the inception of the design process to drive the design cycles towards the optimal zone at first, and then combining with other methods to perform the final stages of the convergence towards the optimal solutions is considered. SPSA method has been combined with the gradient-based Broydon-Fletcher-Goldfarb-Shanno (BFGS) method as well as Simulated Annealing method for the transonic inverse airfoil design problem that is concerned with the specification of a target airfoil surface pressure distribution and starting from an initial guess of an airfoil shape, the target airfoil shape is reached by way of minimization of a quantity that depends on the difference between the target and current airfoil surface pressure distribution. For a typical transonic flow test case, the effects of using hybrid optimization techniques such as SPSA+BFGS and SPSA+SA as opposed to using SPSA alone can be seen in Figure 1. After 800 design cycles using SPSA, the hybrid SPSA+SA method took 2521 function evaluations of SA while the SPSA+BFGS method took 271 function evaluations to reach similar values which are much better than that reached by using SPSA alone in the entire minimization process. Results indicate that both of the two hybrid methods have capability to find a global optimum more efficiently than the SPSA method. The paper will address issues related to hybridization and its impact on the optimal airfoil shape designs in various contexts.Singapore-MIT Alliance (SMA)
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Abdulla, Mohammed Shahid. "Simulation Based Algorithms For Markov Decision Process And Stochastic Optimization." Thesis, 2008. http://hdl.handle.net/2005/812.
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In Chapter 2, we propose several two-timescale simulation-based actor-critic algorithms for solution of infinite horizon Markov Decision Processes (MDPs) with finite state-space under the average cost criterion. On the slower timescale, all the algorithms perform a gradient search over corresponding policy spaces using two different Simultaneous Perturbation Stochastic Approximation (SPSA) gradient estimates. On the faster timescale, the differential cost function corresponding to a given stationary policy is updated and averaged for enhanced performance. A proof of convergence to a locally optimal policy is presented. Next, a memory efficient implementation using a feature-vector representation of the state-space and TD (0) learning along the faster timescale is discussed. A three-timescale simulation based algorithm for solution of infinite horizon discounted-cost MDPs via the Value Iteration approach is also proposed. An approximation of the Dynamic Programming operator T is applied to the value function iterates. A sketch of convergence explaining the dynamics of the algorithm using associated ODEs is presented. Numerical experiments on rate based flow control on a bottleneck node using a continuous-time queueing model are presented using the proposed algorithms.
Next, in Chapter 3, we develop three simulation-based algorithms for finite-horizon MDPs (FHMDPs). The first algorithm is developed for finite state and compact action spaces while the other two are for finite state and finite action spaces. Convergence analysis is briefly sketched. We then concentrate on methods to mitigate the curse of dimensionality that affects FH-MDPs severely, as there is one probability transition matrix per stage. Two parametrized actor-critic algorithms for FHMDPs with compact action sets are proposed, the ‘critic’ in both algorithms learning the policy gradient. We show w.p1convergence to a set with the necessary condition for constrained optima. Further, a third algorithm for stochastic control of stopping time processes is presented. Numerical experiments with the proposed finite-horizon algorithms are shown for a problem of flow control in communication networks.
Towards stochastic optimization, in Chapter 4, we propose five algorithms which are variants of SPSA. The original one measurement SPSA uses an estimate of the gradient of objective function L containing an additional bias term not seen in two-measurement SPSA. We propose a one-measurement algorithm that eliminates this bias, and has asymptotic convergence properties making for easier comparison with the two-measurement SPSA. The algorithm, under certain conditions, outperforms both forms of SPSA with the only overhead being the storage of a single measurement. We also propose a similar algorithm that uses perturbations obtained from normalized Hadamard matrices. The convergence w.p.1 of both algorithms is established. We extend measurement reuse to design three second-order SPSA algorithms, sketch the convergence analysis and present simulation results on an illustrative minimization problem. We then propose several stochastic approximation implementations for related algorithms in flow-control of communication networks, beginning with a discrete-time implementation of Kelly’s primal flow-control algorithm. Convergence with probability1 is shown, even in the presence of communication delays and stochastic effects seen in link congestion indications. Two relevant enhancements are then pursued :a) an implementation of the primal algorithm using second-order information, and b) an implementation where edge-routers rectify misbehaving flows. Also, discrete-time implementations of Kelly’s dual algorithm and primal-dual algorithm are proposed. Simulation results a) verifying the proposed algorithms and, b) comparing stability properties with an algorithm in the literature are presented.
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Gregory, Kasimir Phennah. "A quantum chemical investigation of Hofmeister effects in non-aqueous solvents." Thesis, 2022. http://hdl.handle.net/1959.13/1460595.
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Research Doctorate - Doctor of Philosophy (PhD)Specific ion effects (SIEs) encompass any phenomenon induced by ions that is dependent on the identity of the ions, and not just their charge or concentration. These occur in salts, electrolyte solutions, ionic liquids, acids and bases and have been known for over 130 years, from which the Hofmeister series originated. They are important in biology, nutrition, electrochemistry and various interfacial or geophysico-phenomena. It is perhaps harder to find a “real-world” system in which specific ion effects don’t occur, than systems where they do. Nonetheless, despite such ubiquity and effect on our daily lives, our understanding of these salty solutions is limited. This thesis addresses the knowledge gap surrounding the lack of parameters (for both ion and solvent) for quantifying SIEs in aqueous and nonaqueous environments. This thesis begins with a deeper introduction to the topic of SIEs and highlights the current state-of-play. The theories underlying quantum mechanics and computational chemistry are discussed to highlight how they may be applied to elucidate some of the fundamental origins of SIEs. These methods were subsequently used to investigate possible energetic origins of counterion and solvent induced reversals to the Hofmeister series, and highlights that the Lewis acidity and basicity (collectively Lewis strength) indices of the cations and anions respectively, can quantify SIEs. Following this revelation, these empirical parameters were recast in terms of intermolecular forces. Electrostatics appeared to govern the Lewis strength indices, so these were replaced with an electrostatic parameter, ϸ (“sho”), that originates from Coulomb’s Law. For anions, ϸ is shown to quantify SIE trends observed in enthalpies of hydration, polymer lower critical solution temperatures, enzyme and viral activities, SN2 reaction rates and Gibbs free energies of transfer from water to nonaqueous solvents highlighting the versatility of ϸ as a new SIE parameter. Cation interactions are more prone to deviations from ϸ correlations. In the absence of any cosolute (i.e., pure ion-solvent interactions) however, cation solvent interactions follow a strong trend with Coulomb’s Law for ~15 different solvents. This supports a conclusion that competing electrostatic interactions between the solvent and a cosolute for the cation may mask each other allowing non-electrostatic contributions to play a dominant role. Furthermore, with similarity to the ion parameterisation, the ϸ values at the negative and positive solvent dipolar atoms correlate with the solvent’s Lewis basicity and acidity respectively. Additionally, these analyses can be related to macroscopic solvent parameters such as the relative permittivity. The data deficiency issue facing the SIE field was more generally addressed in this thesis by the generation of IonSolvR, a repository containing over 3000 distinct QM/MD trajectories of up to 52 ions in 28 bulk solvents on nanosecond-scales. Finally, the key findings of this thesis are summarised and an outlook on the field of SIEs and the broader implications arising from this thesis is presented.
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Ulerich, Rhys David. "Reducing turbulence- and transition-driven uncertainty in aerothermodynamic heating predictions for blunt-bodied reentry vehicles." Thesis, 2014. http://hdl.handle.net/2152/26886.
Full textAbstract:
Turbulent boundary layers approximating those found on the NASA Orion Multi-Purpose Crew Vehicle (MPCV) thermal protection system during atmospheric reentry from the International Space Station have been studied by direct numerical simulation, with the ultimate goal of reducing aerothermodynamic heating prediction uncertainty. Simulations were performed using a new, well-verified, openly available Fourier/B-spline pseudospectral code called Suzerain equipped with a ``slow growth'' spatiotemporal homogenization approximation recently developed by Topalian et al. A first study aimed to reduce turbulence-driven heating prediction uncertainty by providing high-quality data suitable for calibrating Reynolds-averaged Navier--Stokes turbulence models to address the atypical boundary layer characteristics found in such reentry problems. The two data sets generated were Ma[approximate symbol] 0.9 and 1.15 homogenized boundary layers possessing Re[subscript theta, approximate symbol] 382 and 531, respectively. Edge-to-wall temperature ratios, T[subscript e]/T[subscript w], were close to 4.15 and wall blowing velocities, v[subscript w, superscript plus symbol]= v[subscript w]/u[subscript tau], were about 8 x 10-3 . The favorable pressure gradients had Pohlhausen parameters between 25 and 42. Skin frictions coefficients around 6 x10-3 and Nusselt numbers under 22 were observed. Near-wall vorticity fluctuations show qualitatively different profiles than observed by Spalart (J. Fluid Mech. 187 (1988)) or Guarini et al. (J. Fluid Mech. 414 (2000)). Small or negative displacement effects are evident. Uncertainty estimates and Favre-averaged equation budgets are provided. A second study aimed to reduce transition-driven uncertainty by determining where on the thermal protection system surface the boundary layer could sustain turbulence. Local boundary layer conditions were extracted from a laminar flow solution over the MPCV which included the bow shock, aerothermochemistry, heat shield surface curvature, and ablation. That information, as a function of leeward distance from the stagnation point, was approximated by Re[subscript theta], Ma[subscript e], [mathematical equation], v[subscript w, superscript plus sign], and T[subscript e]/T[subscript w] along with perfect gas assumptions. Homogenized turbulent boundary layers were initialized at those local conditions and evolved until either stationarity, implying the conditions could sustain turbulence, or relaminarization, implying the conditions could not. Fully turbulent fields relaminarized subject to conditions 4.134 m and 3.199 m leeward of the stagnation point. However, different initial conditions produced long-lived fluctuations at leeward position 2.299 m. Locations more than 1.389 m leeward of the stagnation point are predicted to sustain turbulence in this scenario.text