Dissertations / Theses on the topic 'Computational stress'
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1
Fallah, Nosrat Allah. "Computational stress analysis using finite volume methods." Thesis, University of Greenwich, 2000. http://gala.gre.ac.uk/6166/.
Full textAbstract:
There is a growing interest in applying finite volume methods to model solid mechanics problems and multi-physics phenomena. During the last ten years an increasing amount of activity has taken place in this area. Unlike the finite element formulation, which generally involves volume integrals, the finite volume formulation transfers volume integrals to surface integrals using the divergence theorem. This transformation for convection and diffusion terms in the governing equations, ensures conservation at the local element level. This is seen as a major attraction for finite volume methods. The research presented in this thesis details the development of a cell vertex based finite volume formulation for complex analysis like geometrically nonlinear modelling and plate analysis. For both geometrically nonlinear and plate analysis a series of simulation results are presented and are compared with conventional finite element results. Further research has been carried out to solve stress problems in multi-physics phenomena using a Computational Fluid Dynamics(CFD) frame-work. This approach has the advantage in that it uses the similarities between fluid and solid momentum equations to introduce some modifications in a CFD code that allows a complete CFD solution procedure to be used for the simultaneous calculation of the velocity, temperature and displacement variables. The results of this integrated approach are compared with results obtained by using techniques which solve the problem by 111 using two solvers (one for solid regions, one for fluid regions). In summary, the novelty of the research detailed in this thesis is: • Finite volulne formulation for elastic large strain analysis. Comparison of this approach with traditional finite element techniques: - Cell-vertex finite volume method is as accurate as finite element approach but slower in solution time. • Finite volume formulation for structural plate analysis. Comparison with traditional finite element method: - Novel finite volume approach is as accurate as finite element approach. - Does not display locking problems (observed with finite element methods) and is comparable in solution times. • Formulation of an integrated CFD solver for coupled flow, heat transfer and stress calculations. Comparison with a 2-solver approach: - Integrated approach is much faster and substantially less memory intensive than 2-solver approach. Comparisons between the new formulation and traditional approaches are made in terms of accuracy and solution speed.
2
Marklund, Sarah. "Reverse Stress Test Optimization : A study on how to optimize an algorithm for reverse stress testing." Thesis, Umeå universitet, Institutionen för fysik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-149178.
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In this thesis we investigate how to optimize an algorithm that determines a scenario multiplier for a reverse stress test with a method where predefined scenarios are scaled. The scenarios are composed by different risk factors that represents market events. A reverse stress test is used for risk estimation and explains for what market condition a given portfolio will lose a particular amount. In this study we consider a reverse stress test where the goal is to find for what scenario a clearing house become insolvent, that is when the clearing house's loss is equal to its resource pool. The goal with this work is to find a more efficient algorithm than the current bisection algorithm for finding the scenario multiplier in the reverse stress test. The algorithms that were examined were one bracketing algorithm (the false-position algorithm) and two iterative algorithms (the Newton-Raphson and Halley's algorithms), which were implemented in MATLAB. A comparative study was made where the efficiency of the optimized algorithms were compared with the bisection algorithm. The algorithms were evaluated by comparing the running times and number of iterations needed to find the scenario multiplier in the reverse stress test. Other optimization strategies that were investigated were to reduce the number of scenarios in the predefined scenario matrix to decrease the running time and determine an appropriate initial multiplier to use in the iterative algorithms. The reduction of scenarios consisted of removing the scenarios that were multiples of other scenarios by comparing the risk factors in each scenario. We used Taylor approximation to simplify the loss function and thereby approximate an initial multiplier, which would reduce the manually input from the user. Furthermore, we investigated the running times and number of iterations needed to find the scenario multiplier when several initial multipliers were used in the iterative algorithms to increase the chance of finding a solution. The result shows that both the Newton-Raphson algorithm and Halley's algorithm are more efficient and need less iterations to find the scenario multiplier than the current bisection algorithm. Halley's algorithm is the most efficient, which is on average 200-470% faster than the current algorithm depending on how many initial multipliers that are used (one, two or three), while the Newton-Raphson algorithm is on average 150-300% faster than the current algorithm. Furthermore, the result shows that the false-position algorithm is not efficient for this aim. The result from the reduction of scenarios shows that scenarios could be removed by this approach, where the real scenario obtained from performing a reverse stress test was never among the removed scenarios. Moreover, the initial multiplier approximation could be used when the scenario matrix contains a certain type of risk factors. Finally, this study shows that the current bisection algorithm can be optimized by the Newton-Raphson algorithm and Halley's algorithm.
3
Aharon, Ofer S. M. Massachusetts Institute of Technology. "Stress distributions around hydrofoils using computational fluid dynamics." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/46382.
Full textAbstract:
Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references (leaf 108).
This research describes the reciprocal influence between two foils, vertically and horizontally oriented, on each other for different gaps between them. Those cases are the focus part of a bigger process of lowering significantly the drag of a ship when hydrofoils are attached to its hull. The research results are based on CFD analyses using the ADINA software. In order to verify the CFD process, a comparison was made between analytical, experimental and ADINA?s results for a single foil. The chosen foil was the famous Clark-Y foil; however a correction to its geometry was made using the Unigraphics software. Using the corrected geometry with an analytical solution well detailed and explained, the results of the CFD model were compared to experimental and analytical solutions. The matching of the results and the obtained accuracy are very high and satisfactory. In addition, the research contains an examination of the results when one of the boundary conditions is changed. Surprisingly, it was discovered that the FREE slip condition along the foil is much closer to reality than the NO slip condition. Another examination was stretching horizontally the foil and checking the pressure distribution behavior. Those results met exactly the expectations. As for the main core of this research, both the bi-plane case and the stagger case were found to be less effective than using a single foil. The conclusion of those investigations is that using those cases a few decades ago was for a structural reason rather than stability or speed. Since this research is very wide but also deep in its knowledge, references and academic work, many future research works may be based on it or go on from its detailed stages.
by Ofer Aharon.
S.M.
4
Heldt, Thomas 1972. "Computational models of cardiovascular response to orthostatic stress." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/28761.
Full textAbstract:
Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2004.Includes bibliographical references (p. 163-185).
The cardiovascular response to changes in posture has been the focus of numerous investigations in the past. Yet despite considerable, targeted experimental effort, the mechanisms underlying orthostatic intolerance (OI) following spaceflight remain elusive. The number of hypotheses still under consideration and the lack of a single unifying theory of the pathophysiology of spaceflight-induced OI testify to the difficulty of the problem. In this investigation, we developed and validated a comprehensives lumped-parameter model of the cardiovascular system and its short-term homeostatic control mechanisms with the particular aim of simulating the short-term, transient hemodynamic response to gravitational stress. Our effort to combine model building with model analysis led us to conduct extensive sensitivity analyses and investigate inverse modeling methods to estimate physiological parameters from transient hemodynamic data. Based on current hypotheses, we simulated the system-level hemodynamic effects of changes in parameters that have been implicated in the orthostatic intolerance phenomenon. Our simulations indicate that changes in total blood volume have the biggest detrimental impact on blood pressure homeostasis in the head-up posture. If the baseline volume status is borderline hypovolemic, changes in other parameters can significantly impact the cardiovascular system's ability to maintain mean arterial pressure constant. In particular, any deleterious changes in the venous tone feedback impairs blood pressure homeostasis significantly. This result has important implications as it suggests that al-adrenergic agonists might help alleviate the orthostatic syndrome seen post-spaceflight.
by Thomas Heldt.
Ph.D.
5
Potter, Tavis L. "Computational Stress and Deformation Analysis of Mammary Prosthesis." Thesis, Virginia Tech, 2003. http://hdl.handle.net/10919/41795.
Full textAbstract:
A linear and non-linear material model for the breast implants was developed through axial tension testing, while linear and non-linear breast tissue models were assumed based on smooth muscle. These material models were to develop axisymmetric finite element models to determine the stresses in the implant walls under tissue loading. The non-linear material models were used to more accurately model the complex nature of the implant stresses. After analysis it was found that the implants were under compressive loading which meant that local buckling in the implant might be possible.
For accurate stress prediction in the implant walls and to fully characterize implant buckling a more accurate non-linear breast tissue material model needs to be developed. Having this material model would allow for a full three-dimensional finite element model can be developed. With the development of a three-dimensional FEA model the implant buckling and implant stresses could be fully characterized. Ultimately allowing for accurate implant stress estimation and fatigue life calculation using the Palmgren-Miner rule, S-N curves, and an external load spectra.Master of Science
6
Rimoli, Julian Jose Ortiz Michael Ortiz Michael. "A computational model for intergranular stress corrosion cracking /." Diss., Pasadena, Calif. : California Institute of Technology, 2009. http://resolver.caltech.edu/CaltechETD:etd-05142009-135909.
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Vorobtsova, Natalya. "Computational model of coronary tortuosity." Thesis, Virginia Tech, 2015. http://hdl.handle.net/10919/51267.
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Coronary tortuosity is the abnormal curving and twisting of the coronary arteries. Although the phenomenon of coronary tortuosity is frequently encountered by cardiologists its clinical significance is unclear. It is known that coronary tortuosity has significant influence on the hemodynamics inside the coronary arteries, but it is difficult to draw definite conclusions due to the lack of patient-specific studies and an absence of a clear definition of tortuosity.
In this work, in order to investigate a relation of coronary tortuosity to such diseases as atherosclerosis, ischemia, and angina, a numerical investigation of coronary tortuosity was performed. First, we studied a correlation between a degree of tortuosity and flow parameters in three simplified vessels with curvature and zero torsion. Next, a statistical analysis based on flow calculations of 23 patient-based real tortuous arteries was performed in order to investigate a correlation between tortuosity and flow parameters, such as pressure drop, wall shear stress distribution, and a strength of helical flow, represented by a helicity intensity, and concomitant risks.
Results of both idealized and patient-specific studies indicate that a risk of perfusion defects grows with an increased degree of tortuosity due to an increased pressure drop downstream an artery. According to the results of the patient-specific study, a risk of atherosclerosis decreases in more tortuous arteries - a result different from an outcome of the idealized study of arteries with zero torsion. Consequently, a modeling of coronary tortuosity should take into account all aspects of tortuosity including a heart shape that introduces additional torsion to arteries. Moreover, strength of a helical flow was shown to depend strongly on a degree of tortuosity and affect flow alterations and accompanying risks of developing atherosclerosis and perfusion defects. A corresponding quantity, helicity intensity, might have a potential to be implemented in future studies as a universal single parameter to describe tortuosity and assess congruent impact on the health of a patient.Master of Science
8
McGoldrick, Christopher R. "Computational methods for contact stress problems with normal and tangential loading /." Online version of thesis, 1991. http://hdl.handle.net/1850/10612.
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9
Ressler, Barbara G. H. (Barbara Grace Hammer) 1970. "Airway mechanics in asthma : computational modeling and molecular responses to stress." Thesis, Massachusetts Institute of Technology, 1999. http://hdl.handle.net/1721.1/80021.
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10
Rojano, Aguilar Fernando. "Computational Modeling to Reduce Impact of Heat Stress in Lactating Cows." Diss., The University of Arizona, 2013. http://hdl.handle.net/10150/272838.
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Climatic conditions inside the dairy barn do not concern dairy farmers until those conditions begin to affect productivity and, consequently, profits. As heat and humidity increase beyond the cow's comfort levels, milk production declines, as does fertility and the welfare of the cow in general. To reinforce the cooling mechanisms currently used, this work proposes an alternative system for reducing the risk of heat stress. This innovative conductive cooling system does not depend on current weather conditions, and it does not require significant modifications when it is installed or during its operation. Also, the system circulates water that can be reused. Given that a review of the literature found very few related studies, it is suggested that each freestall be equipped with a viable prototype in the form of a waterbed able to exchange heat. Such a prototype has been simulated using Computational Fluid Dynamics (CFD) and later verified by a set of experiments designed to confirm its cooling capacity. Furthermore, this investigation sets the foundation for modeling temperature in a water supply system linked to the waterbeds. EPANET, a software program developed by the Environmental Protection Agency, simulates the hydraulic model. Its Water Quality Solver has been modified according to an analogy in the governing equation that compares mass to heat transfer and serves to simulate water temperature as the water is transported from its source to the point of delivery and then as it returns to the same source.
11
Anandakrishnan, Shivendren. "Computational investigation into states of self-stress of pin-jointed bar assemblies." Thesis, University of Bristol, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.434796.
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12
Hoyos, Laureano R. Jr. "Experimental and computational modeling of unsaturated soil behavior under true triaxial stress states." Diss., Georgia Institute of Technology, 1998. http://hdl.handle.net/1853/32773.
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13
(unal), Kutlu Ozge. "Computational 3d Fracture Analysis In Axisymmetric Media." Master's thesis, METU, 2008. http://etd.lib.metu.edu.tr/upload/12609872/index.pdf.
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In this study finite element modeling of three dimensional elliptic and semielliptic
cracks in a hollow cylinder is considered. Three dimensional crack and
cylinder are modeled by using finite element analysis program ANSYS.
The main objectives of this study are as follows. First, Ansys Parametric
Design Language (APDL) codes are developed to facilitate modeling of different
types of cracks in cylinders. Second, by using these codes the effect of some
parameters of the problem like crack location, cylinder&rsquos radius to thickness ratio (R/t), the crack geometry ratio (a/c) and crack minor axis to cylinder thickness ratio (a/t) on stress intensity factors for surface and internal cracks are examined. Mechanical and thermal loading cases are considered. Displacement Correlation Technique (DCT) is used to obtain Stress Intensity Factors.
14
Johnson, Kevin Robert. "In Vivo Coronary Wall Shear Stress Determination Using CT, MRI, and Computational Fluid Dynamics." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/14482.
Full textAbstract:
Wall shear stress (WSS) has long been identified as a factor in the development of atherosclerotic lesions. Autopsy studies have revealed a strong tendency for lesion development at arterial branch sites and along the inner walls of curvature areas that, in theory, should experience low WSS. Calculations of coronary artery WSS have typically been based upon average models of coronary artery geometry with average flow conditions and then compared to average lesion distributions. With all the averaging involved, a more detailed knowledge of the correlation between WSS and atherosclerotic lesion development might be obscured. Recent advancements in hemodynamic modeling now enable the calculation of WSS in individual subjects. An image-based approach for patient-specific calculation of in vivo WSS using computational fluid dynamics (CFD) would allow a more direct study of this correlation. New state-of-the-art technologies in multi-detector computed tomography (CT) and 3.0 Tesla magnetic resonance imaging (MRI) offer potential improvements for the measurement of coronary artery geometry and blood flow.
The overall objective of this research was to evaluate the quantitative accuracy of multi-detector CT and 3.0 Tesla MRI and incorporate those imaging modalities into a patient-specific CFD model of coronary artery WSS. Using a series of vessel motion phantoms, it has been shown that 64-detector CT can provide accurate measurements of coronary artery geometry for heart rates below 70 beats per minute. A flow phantom was used to validate the use of navigator-echo gated, phase contrast MRI at 3.0 Tesla to measure velocity of coronary blood flow. Patient-specific, time-resolved CFD models of coronary WSS were created for two subjects. Furthermore, it was determined that population-average velocity curves or steady state velocities can predict locations of high or low WSS with high degrees of accuracy compared to the use of patient-specific blood flow velocity measurements as CFD boundary conditions. This work is significant because it constitutes the first technique to non-invasively calculate in vivo coronary artery WSS using image-based, patient-specific modeling.
15
Takahashi, Andrew Rikio. "Computational studies of stress and structure development resulting from the coalescence of metallic islands." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/42163.
Full textAbstract:
Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2007.Includes bibliographical references (leaves 63-65).
Thin film component properties are critical design elements in almost all industries. These films are particularly important in the performance of micro- and nano-electromechanical systems (MEMS and NEMS). Residual stress in thin film components is often treated as an unavoidable side effect of processing steps and the degree of residual stress can drastically affect the performance and properties of the final product. While high levels of residual stress are often detrimental to performance, control of the stress and stress gradients can also be used to enhance performance and even generate new capabilities. The work presented in this thesis examines the role of island coalescence in the development of structure and stress in thin films. The primary methods of investigation are molecular dynamics (MD) and finite element analysis (FEA). The semi-empirical MD calculations show that coalescence is a very rapid process for unconstrained spheres and for hemispheres allowed to slide on a frictionless substrate. Particle rotations are commonly observed during the coalescence calculations. The extent of neck formation between 2 particles is consistent with continuum models even down to length scales which would normally be outside the range in which the models might be expected to be applicable. The MD calculations also show that internal island defects may be induced by the island coalescence process, but only for a particular range of island sizes. We present an energetic model for the existence of such a size range and have located experimental evidence in the literature for such defects. Our FEA work extends an earlier study on the effects of contact angle on island coalescence. Our FEA study of islands with greater than 90 degree contact angle coalescence shows that neck formation occurs very similarly to the free sphere coalescence case. We conclude that MD and FEA calculations are useful tools in analyzing the island coalescence process and can provide mechanistic insight beyond what is available from the more general continuum models.
by Andrew Rikio Takahashi.
S.M.
16
Bryan, Rebecca. "Large scale, multi femur computational stress analysis using a statistical shape and intensity model." Thesis, University of Southampton, 2010. https://eprints.soton.ac.uk/185087/.
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Suga, Kazuhiko. "Development and application of a non-linear eddy viscosity model sensitized to stress and strain variants." Thesis, University of Manchester, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296470.
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18
Brock, Kelly Paige. "Protein structure and interaction under environmental stress : from quality control recognition to evolution of collective behavior." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104575.
Full textAbstract:
Thesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, 2016.Cataloged from PDF version of thesis.
Includes bibliographical references.
A protein's function in the cell depends on its structure, which in turn depends on the intracellular environment. Stress like heat shock or nutrient starvation can alter intracellular conditions, leading to protein misfolding - i.e. the inability of a protein to reach or maintain its native conformation. Since many proteins interact with each other, protein misfolding and cellular stress response must be examined both on the scale of individual protein conformational changes and on a more global level, where interaction patterns can reveal larger-scale protein responses to cellular stress. On the individual scale, one example of a protein particularly susceptible to misfolding is the human von Hippel-Lindau (VHL) tumor suppressor. When expressed in the absence of its cofactors, VHL cannot fold correctly and is quickly degraded by the cell's quality control machinery. Here, I present a biophysical characterization of a VHL mutation that confers increased resistance to misfolding. Mathematical modeling provides an explanation for this mutant's increased stability in the cell by predicting how its cofactor and chaperone interaction sites are buried or exposed in the protein's predicted conformation. On a more global level, a budding yeast cell undergoing glucose deprivation both acidifies its cytosol and exhibits widespread protein clustering. By employing a proteome-wide computational assay, I examine how this drop in pH could lead to the formation of higher order protein structures. This modeling framework also provides a rationale for why these two related phenotypes might be beneficial, since protein clustering can help regulate relevant metabolic pathways and provide protection from protein misfolding and/or degradation.
by Kelly Paige Brock.
Ph. D.
19
Salihu, B. M. "Stress analysis of drillstring threaded connections." Thesis, Cranfield University, 2011. http://dspace.lib.cranfield.ac.uk/handle/1826/7752.
Full textAbstract:
The demand for energy from developed and developing economies of the world is
driving the search for energy resources to more challenging environments. The
exploration and exploitation of hydrocarbons now requires the drillbit to hit pay zones
from drillships or platforms that are located on water surfaces below which is, possibly,
in excess of ten thousand feet of water above the sea bed. From Brazil, to the Gulf of
Mexico and the Gulf of Guinea on the western coast of Africa, hitherto unfamiliar, but
now common, concepts in the drilling parlance such as ultra-deep drilling (UDD), ultraextended-
reach drilling (uERD) and slimhole drilling, are employed to reach and
produce reservoirs which a few decades ago would seem technologically impossible to
produce.
This is expected to exert tremendous demands on the physical and mechanical
properties of the drillstring components. Limiting factors for reaching and producing oil
and gas resources hidden very deep in the subsurface are both the capacity of the
drilling rig to support the weight of the drillstring, which in some instances can be
several kilometres long, and the bending, tensile and impact stresses the string has to
withstand in well trajectories that are getting both longer and more tortuous.
Associated with this increased well depths and complex well trajectories is the
prohibitive cost penalty of a failed drillstring. The in-service failure of drillstrings has
always been an issue in the industry long before the wells become this deep and
complex. The global oil and gas industry estimates the cost of string failure to be in
excess of quarter of a billion dollars annually.
Researchers are continuously looking for ways to design against string failure and
improve the level of confidence in drillstrings. Defect-tolerant design, tooljoint geometry
modification and surface coldworking are just a few of the ideas that have gained
mileage in this effort. Others that are now in consideration are the use of nonconventional
materials such as aluminium and titanium alloys for drillstring
components. More novel, still, is the use of a combination of two materials - one ‘softer’
than the other to form a hybrid string of two materials of unequal moduli of elasticity.
This is done to make the string lighter, reduce stress concentration factor at the
connections and place fatigue resistant materials in areas of high well bore curvature.In this work a computational technique in the form of two-dimensional finite element
analysis is used to develop a robust model of a drillstring connection and to analyse the
stresses on the model of a threaded connection of standard drillstring tooljoint made
from alloy steel. Further comparative analyses were undertaken on models of
drillstrings made from a newly developed drillstring material for ultra-deep drilling, the
UD-165, aluminium and titanium alloys and, finally, on hybrid drillstrings made from two
different materials of unequal moduli of elasticity.
The aim is not only to develop and validate a better method of computational drillstring
analysis but also to use the model to investigate and suggest areas of optimisation that
will benefit industry especially in the areas hybrid strings.
20
Stockman, Tyler Joseph. "Early targeting of knee osteoarthritis : validation of computational methods." Thesis, University of Iowa, 2014. https://ir.uiowa.edu/etd/2149.
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Osteoarthritis (OA) is the most common type of arthritis, a disease in which inflammation and stiffness of the joints occur. This debilitating disease of the joints currently reigns as the most prevalent among the world's populations. Of particular interest to our group is the study of the biomechanical factors relating to knee OA. Studies have shown that knee OA is related to multiple biomechanical factors, all of which are complexly interrelated. These factors have been seen to produce varied effects on the structures of the knee. This work examines validation of a computational model implementing discrete element analysis, and discusses the potential for large-scale, subject-specific modeling of the knee. In particular, contact stress can be estimated using this technique, and these estimates can potentially be related to OA onset in subjects.
21
Surujon, Defne. "Computational approaches in infectious disease research: Towards improved diagnostic methods." Thesis, Boston College, 2020. http://hdl.handle.net/2345/bc-ir:109089.
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Thesis advisor: Kenneth WilliamsDue to overuse and misuse of antibiotics, the global threat of antibiotic resistance is a growing crisis. Three critical issues surrounding antibiotic resistance are the lack of rapid testing, treatment failure, and evolution of resistance. However, with new technology facilitating data collection and powerful statistical learning advances, our understanding of the bacterial stress response to antibiotics is rapidly expanding. With a recent influx of omics data, it has become possible to develop powerful computational methods that make the best use of growing systems-level datasets. In this work, I present several such approaches that address the three challenges around resistance. While this body of work was motivated by the antibiotic resistance crisis, the approaches presented here favor generalization, that is, applicability beyond just one context. First, I present ShinyOmics, a web-based application that allow visualization, sharing, exploration and comparison of systems-level data. An overview of transcriptomics data in the bacterial pathogen Streptococcus pneumoniae led to the hypothesis that stress-susceptible strains have more chaotic gene expression patterns than stress-resistant ones. This hypothesis was supported by data from multiple strains, species, antibiotics and non-antibiotic stress factors, leading to the development of a transcriptomic entropy based, general predictor for bacterial fitness. I show the potential utility of this predictor in predicting antibiotic susceptibility phenotype, and drug minimum inhibitory concentrations, which can be applied to bacterial isolates from patients in the near future. Predictors for antibiotic susceptibility are of great value when there is large phenotypic variability across isolates from the same species. Phenotypic variability is accompanied by genomic diversity harbored within a species. I address the genomic diversity by developing BFClust, a software package that for the first time enables pan-genome analysis with confidence scores. Using pan-genome level information, I then develop predictors of essential genes unique to certain strains and predictors for genes that acquire adaptive mutations under prolonged stress exposure. Genes that are essential offer attractive drug targets, and those that are essential only in certain strains would make great targets for very narrow-spectrum antibiotics, potentially leading the way to personalized therapies in infectious disease. Finally, the prediction of adaptive outcome can lead to predictions of future cross-resistance or collateral sensitivities. Overall, this body of work exemplifies how computational methods can complement the increasingly rapid data generation in the lab, and pave the way to the development of more effective antibiotic stewardship practices
Thesis (PhD) — Boston College, 2020
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
22
Folkes, Leighton. "Computational analysis of small RNAs and the RNA degradome with application to plant water stress." Thesis, University of East Anglia, 2014. https://ueaeprints.uea.ac.uk/52038/.
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Water shortage is one of the most important environmental stress factors that affects plants, limiting crop yield in large areas worldwide. Plants can survive water stress by regulating gene expression at several levels. One of the recently discovered regulatory mechanisms involves small RNAs (sRNAs), which can regulate gene expression by targeting messenger RNAs (mRNAs) and directing endonucleolytic cleavage resulting in mRNA degradation. A snapshot of an mRNA degradation profile (degradome) can be captured through a new high-throughput technique called Parallel Analysis of RNA Ends (PARE) by using next generation sequencing technologies. In this thesis we describe a new user friendly degradome analysis software tool called PAREsnip that we have used for the rapid genome-wide discovery of sRNA/target interactions evidenced through the degradome. In addition to PAREsnip and based upon PAREsnip’s rapid capability, we also present a new software tool for the construction, analysis and visualisation of sRNA regulatory interaction networks. The two new tools were used to analyse PARE datasets obtained fromMedicago truncatula and Arabidopsis thaliana. In particular, we have used PAREsnip for the high-throughput analysis of PARE data obtained from Medicago when subjected to dehydration and found several sRNA/mRNA interactions that are potentially responsive to water stress. We also present how we used our new network visualisation and analysis tool with PARE datasets obtained from Arabidopsis and discovered several novel sRNA regulatory interaction networks. In building tools and using them for this kind of analysis, we gain a better understanding of the processes and mechanisms involved in sRNA mediated gene regulation and how plants respond to water stress which could lead to new strategies in improving stress tolerance.
23
Borghi, Alessandro. "Computational analysis of flow and stress patterns in thoracic aortic aneurysms : a patient specific study." Thesis, Imperial College London, 2007. http://hdl.handle.net/10044/1/7600.
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24
Cid, Samper Fernando 1991. "Computational approaches to characterize RNP granules." Doctoral thesis, Universitat Pompeu Fabra, 2020. http://hdl.handle.net/10803/668449.
Full textAbstract:
Ribonucleoprotein granules (RNP granules) are liquid-liquid phase separated
complexes composed mainly by proteins and RNA. They are responsible of many
processes involved in RNA regulation. Alterations in the dynamics of these proteinRNA complexes are associated with the appearance of several neurodegenerative
disorders such as Amyotrophic Lateral Sclerosis ALS or Fragile X Tremor Ataxia
Syndrome FXTAS. Yet, many aspects of their organization as well as the specific
roles of the RNA on the formation and function of these complexes are still unknown.
In order to study RNP granules structure and formation, we integrated several state of
the art high-throughput datasets. This includes protein and RNA composition obtained
from RNP pull-downs, protein-RNA interaction data from eCLIP experiments and
transcriptome-wide secondary structure information (produced by PARS). We used
network analysis and clustering algorithms to understand the fundamental properties
of granule RNAs. By integrating these properties, we produced a model to identify
scaffolding RNA. Scaffolding RNAs are able to recruit many protein components into
RNP granules. We found that the main protein components of stress granules (a kind
of RNP granules) are connected through protein-RNA interactions. We also analyzed
the contribution of RNA-RNA interactions and RNA post-transcriptional
modifications on the granule internal organization.
We applied these findings to understand the biochemical pathophysiology of FXTAS
disease, employing as well some novel experimental data. In FXTAS, a mutation on
the FMR1 gene produces a 5´microsatellite repetition that enhances its scaffolding
ability. This mutated mRNA is able to sequester some important proteins into nuclear
RNP granules, such as TRA2A (i.e. a splicing factor), impeding their normal function
and therefore producing some symptoms associated with the progress of the disease.
The better understanding of the principles governing granules formation and structure
will enable to develop novel therapies (e.g. aptamers) to mitigate the development of
several neurodegenerative diseases.Los gránulos ribonucleoproteicos (gránulos RNP, por sus siglas en inglés) son complejos producidos mediante separación líquido-líquido y están constituidos principalmente por proteínas y ARN. Son responsables de numerosos procesos involucrados con la regulación del ARN. Alteraciones en la dinámica de estos complejos de proteínas y ARN están asociadas con la aparición de diversas enfermedades neurodegenerativas como el ELA o FXTAS. Sin embargo, todavía se desconocen muchos aspectos relativos a su organización interna así como las contribuciones específicas del RNA en la formación y funcionamiento de estos complejos. A fin de estudiar la estructura y formación de los gránulos RNP, hemos integrado varias bases de datos de alto rendimiento de reciente aparición. Esto incluye datos sobre la composición proteica y en ARN de los RNP, sobre la interacción de proteínas y ARN extraída de experimentos de eCLIP y sobre la estructura secundaria del transcriptoma (producida mediante PARS). Todos estos datos han sido procesados para comprender las propiedades fundamentales de los ARNs que integran los gránulos, mediante el empleo de métodos computacionales como el análisis de redes o algoritmos de agrupamiento. De esta manera, hemos producido un modelo que integra varias de estas propiedades e identifica candidatos denominados ARNs de andamiaje. Definimos ARNs de andamiaje como moléculas de ARN con una alta propensión a formar gránulos y reclutar un gran número de componentes proteicos a los gránulos RNP. También hemos encontrado que las interacciones proteína-ARN conectan los principales componentes proteicos de consenso de los gránulos de estrés (un tipo específico de gránulos RNP). También hemos estudiado la contribución de las interacciones ARN-ARN y las modificaciones post-transcriptionales del RNA en la organización interna del gránulo. Hemos aplicado estos resultados para la comprensión de la fisiopatología molecular de FXTAS, empleando también algunos datos experimentales originales. En FXTAS, una mutación en el gen FMR1 produce una repetición de microsatélite en 5´ que incrementa su capacidad como ARN de andamiaje. Este mARN mutado es capaz de secuestrar algunas proteínas importantes como TRA2A (un factor de ayuste alternativo) en gránulos RNP nucleares, impidiendo su normal funcionamiento y por consiguiente produciendo algunos síntomas asociados con el progreso de la enfermedad. Una mejor comprensión de los principios que gobiernan la formación y estructura de los gránulos puede permitir desarrollar nuevas terapias (ej: aptámeros) para mitigar el desarrollo de diversas enfermedades neurodegenerativas.
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Lau, Chung Yin. "Computational stress analysis for ball grid array reliability and passive component reliability in board level assemblies /." View abstract or full-text, 2005. http://library.ust.hk/cgi/db/thesis.pl?MECH%202005%20LAU.
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Singh, Shelly Deokie. "Computational analysis of blood flow and stress patterns in the aorta of patients with Marfan syndrome." Thesis, Imperial College London, 2016. http://hdl.handle.net/10044/1/45539.
Full textAbstract:
Personalised external aortic root support (PEARS) was designed to prevent progressive aortic dilatation, and the associated risk of aortic dissection, in patients with Marfan syndrome by providing an additional support to the aorta. The objective of this thesis was to understand the biomechanical implications of PEARS surgery as well as to investigate the altered haemodynamics associated with the disease and its treatment. Finite element (FE) models were developed using patient-specific aortic geometries reconstructed from pre and post-PEARS magnetic resonance (MR) images of three Marfan patients. The wall and PEARS materials were assumed to be isotropic, incompressible and linearly elastic. A static load on the inner wall corresponding to the patients’ pulse pressure was applied with a zero-displacement constraint at all boundaries. Results showed that peak aortic stresses and displacements before PEARS were located at the sinuses of Valsalva but following PEARS surgery, they were shifted to the aortic arch, at the intersection between the supported and unsupported aorta. The zero-displacement constraint at the aortic root was subsequently removed and replaced with downward motion measured from in vivo images. This revealed significant increases in the longitudinal wall stress, especially in the pre-PEARS models. Computational fluid dynamics (CFD) models were developed to evaluate flow characteristics. The correlation-based transitional Shear Stress Transport (SST-Tran) model was adopted to simulate potential transitional and turbulence flow during part of the cardiac cycle and flow waveforms derived from phase-contrast MR images were imposed at the inlets. Qualitative patterns of the haemodynamics were similar pre- and post-PEARS with variations in mean helicity flow index (HFI) of -10%, 35% and 20% in the post-PEARS aortas of the three patients. A fluid-structure interaction (FSI) model was developed for one patient, pre- and post-PEARS in order to examine the effect of wall compliance on aortic flow as well as the effect of pulsatile flow on wall stress. This model excluded the sinuses and was based on the laminar flow assumption. The results were similar to those obtained using the rigid wall and static structural models, with minor quantitative differences. Considering the higher computational cost of FSI simulations and the relatively small differences observed in peak wall stress, it is reasonable to suggest that static structural models would be sufficient for wall stress prediction. Additionally, aortic root motion had a more profound effect on wall stress than wall compliance. Further studies are required to assess the statistical significance of the findings outlined in this thesis. Recommendations for future work were also highlighted, with emphasis on model assumptions including material properties, residual stress and boundary conditions.
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Thomas, Holly Dominique. "A computational investigation of patient factors contributing to contact stress abnormalities in the dysplastic hip joint." Thesis, University of Iowa, 2017. https://ir.uiowa.edu/etd/6005.
Full textAbstract:
Acetabular dysplasia, a deformity characterized by the presence of a shallow acetabulum inadequately covering the femoral head, alters force transfer through a joint, causing early-onset hip pain and degeneration. Dysplasia is often treated surgically with a periacetabular osteotomy (PAO), which permits multiplanar acetabular reorientation to stabilize the joint and alleviate pain. PAO alters joint mechanics, including contact stress, which can be assessed via computational methods.
This work sought to enhance a discrete element analysis (DEA) model for assessment of the dysplastic hip. The primary focus was on understanding how the gait parameters used to load a DEA model affect the computed contact stress. Several additional studies focused on understanding specific anatomic and demographic factors contributing to the contact stress evaluation were also performed.
Implementation of a dysplastic gait pattern to load the DEA models resulted in more cases with improved contact stress and clinical measures after PAO, which concurred with clinical findings. Patient demographics and acetabular and femoral geometry all affected the computed contact stress distributions, emphasizing the importance of proper cohort categorization prior to interpretation of DEA-calculated contact stress. These results indicate that accurate modeling of the particular deformity in this cohort likely requires evaluation of both functional and anatomic differences.
These studies improve the ability to realistically model and characterize dysplastic hip contact mechanics. DEA is a valuable tool for assessing contact stress in dysplastic joints, which has the potential to improve patient outcomes by guiding clinicians in non-operative treatment, pre-operative PAO planning, and evaluating intraoperative success.
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Loomis, Nicholas C. (Nicholas Charles). "Computational imaging and automated identification for aqueous environments." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/67589.
Full textAbstract:
Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2011."June 2011." Cataloged from PDF version of thesis.
Includes bibliographical references (p. 253-293).
Sampling the vast volumes of the ocean requires tools capable of observing from a distance while retaining detail necessary for biology and ecology, ideal for optical methods. Algorithms that work with existing SeaBED AUV imagery are developed, including habitat classification with bag-of-words models and multi-stage boosting for rock sh detection. Methods for extracting images of sh from videos of long-line operations are demonstrated. A prototype digital holographic imaging device is designed and tested for quantitative in situ microscale imaging. Theory to support the device is developed, including particle noise and the effects of motion. A Wigner-domain model provides optimal settings and optical limits for spherical and planar holographic references. Algorithms to extract the information from real-world digital holograms are created. Focus metrics are discussed, including a novel focus detector using local Zernike moments. Two methods for estimating lateral positions of objects in holograms without reconstruction are presented by extending a summation kernel to spherical references and using a local frequency signature from a Riesz transform. A new metric for quickly estimating object depths without reconstruction is proposed and tested. An example application, quantifying oil droplet size distributions in an underwater plume, demonstrates the efficacy of the prototype and algorithms.
by Nicholas C. Loomis.
Ph.D.
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Johnson, Shane Miguel. "Computational modeling, stochastic and experimental analysis with thermoelastic stress analysis for fiber reinforced polymeric composite material systems." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/34668.
Full textAbstract:
Many studies with Thermoelastic Stress Analysis (TSA) and Infrared Thermography, in Fiber Reinforced Polymeric materials (FRPs), are concerned with surface detection of "hot spots" in order to locate and infer damage. Such experimental analyses usually yield qualitative relations where correlations between stress state and damage severity cannot be obtained. This study introduces quantitative experimental methodologies for TSA and Digital Image Correlation to expand the use of remote sensing technologies for static behavior, static damage initiation detection, and fatigue damage in FRPs. Three major experimental studies are conducted and coupled with nonlinear anisotropic material modeling: static and TSA of hybrid bio-composite material systems, a new stochastic model for fatigue damage of FRPs, and fracture analysis for FRP single-lap joints. Experimental calibration techniques are developed to validate the proposed macromechanical and micromechanical nonlinear anisotropic modeling frameworks under multi-axial states of stress. The High Fidelity Generalized Method of Cells (HFGMC) is a sophisticated micromechanical model developed for analysis of multi-phase composites with nonlinear elastic and elastoplastic constituents is employed in this study to analyze hybrid bio-composites. Macro-mechanical nonlinear anisotropic models and a linear orthotropic model for fracture behavior using the Extended Finite Element method (XFEM) are also considered and compared with the HFGMC method. While micromechanical and FE results provide helpful results for correlating with quasi-static behavior, analyzing damage progression after damage initiation is not straightforward and involves severe energy dissipation, especially with increasing damage progression. This is especially true for fatigue damage evolution, such as that of composite joints as it is associated with uncertainty and randomness. Towards that goal, stochastic Markov Chain fatigue damage models are used to predict cumulative damage with the new damage indices proposed using full-field TSA image analysis algorithms developed for continuously acquired measurements during fatigue loading of S2-Glass/E733FR unidirectional single-lap joints. Static damage initiation is also investigated experimentally with TSA in single-lap joints with thick adherends providing for new design limitations. The computational modeling, stochastic and experimental methods developed in this study have a wide range of applications for static, fracture and fatigue damage of different FRP material and structural systems.
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Attaway, Stephen Wayne. "A stress-based finite element method for computational elasto-plastic analysis, using an endochronic theory of plasticity." Diss., Georgia Institute of Technology, 1986. http://hdl.handle.net/1853/20792.
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Qi, Gang. "Computational modeling for stress analysis of overhead transmission line stranded conductors under design and fretting fatigue conditions." Thesis, McGill University, 2014. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=121122.
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While great efforts have been made in the electrical utility industry to engineer various stranded conductors with enhanced strength and vibrational characteristics, research devoted to understanding the complex mechanical behavior of complete conductors has been scarce, especially from a computational mechanics perspective. In the meanwhile, the long-lasting problem of conductor fretting fatigue becomes increasingly critical for overhead line design and maintenance, especially with the world-wide aging of electrical transmission grids. Aging of conductors contributes to significant degradation of their local fatigue strength, leading to drastic reduction of their service life. However, the complex mechanical response of stranded conductors cannot be well predicted by either experimental testing or simplified theoretical models, owing to the physical complexity introduced by their multi-layer stranded geometry, nonlinear material properties, substantial frictions among the wires and between the wires and hardware clamping systems, as well as the comprehensive contact interactions amongst their components. Simplified beam models and coarse 3-D models of earlier computational studies also fail to calculate the accurate stress variations inside a conductor strand and capture the stress gradients near the contact interfaces. Moreover, the estimations of fretting fatigue life are very dependent on the high accuracy of the stress predictions in the conductor wires. Therefore, reliable high-fidelity computational models have been long expected for a better understanding of the contact damage of transmission line conductors under both design and fretting fatigue conditions. The main objective of this thesis is to study the complex stress states and relevant influencing factors of stranded electrical conductors, using finite element analysis approaches. The research was carried out in three stages. First of all, a study focused on the finite element (FE) modeling of an optical ground wire (OPGW) cable strand for its detailed stress analysis. A refined 3-D FE model including all essential nonlinear characteristics was successfully constructed. As a result, a high-fidelity physics-based macroscopic modeling methodology was developed for detailed and accurate computational stress analysis of stranded conductors. A 795 kcmil Drake ACSR conductor was then selected as a benchmark conductor to investigate the tensile strength and critical stress states of a complete conductor under extreme design conditions. Furthermore, a sensitivity study explored the relative importance of friction effects among conductor wires on the mechanical response.A large scale 3-D FE stress analysis model with comprehensive nonlinearities was developed and implemented to simulate an actual ACSR fretting fatigue test. The computational results showed good agreement with some experimental measurements and field observations reported in the open literature. Based on the accurate stress analysis, a practical multi-axial fatigue lifing methodology was developed to estimate local fretting fatigue strength of electrical conductors. Subsequently, a parametric study was performed to examine the influence of fretting amplitudes on the mechanical response of the conductor-clamp system.In conclusion, this research shows the reliability and significance of using reliable FE modeling in predicting the complex response of stranded conductors, which has contributed to fill some of the current knowledge gaps. Furthermore, the computational modeling and lifing approaches developed in this thesis provide a different perspective from existing practices and may become a starting block of further exploration of the mechanisms of conductor fretting fatigue and future development of improved fatigue lifing methods for the increasingly aging overhead transmission line conductors.Malgré les efforts déployés par l'industrie des lignes de transport d'électricité pour la conception de conducteurs toronnés de haute résistance mécanique, la recherche dédiée à la compréhension physique du comportement mécanique des conducteurs s'est faite plus rare, surtout du point de vue de la mécanique computationnelle. Le problème du vieillissement des conducteurs de lignes aériennes à haute tension, en particulier celui de l'usure en fatigue des brins et torons, n'est toujours pas complètement compris ni donc résolu. Le vieillissement des conducteurs se manifeste par une dégradation importante de leur résistance locale à l'usure en fatigue, réduisant par le fait même leur vie utile et la robustesse mécanique de l'ensemble de la ligne. Il faut reconnaître que les études expérimentales et les modèles théoriques simplifiés ne peuvent pas prédire le comportement mécanique détaillé des conducteurs toronnés à cause de la complexité physique de ces câbles: torons et brins multicouches, matériaux inélastiques non-linéaires, effets des frictions substantielles entre les brins, torons et les surfaces des accessoires d'attache, ainsi que les interactions de contact entre ces éléments.Les travaux rapportés dans la thèse procèdent en trois étapes principales, décrites ci-après. La première partie consiste à préparer un modèle de section de câble de garde à fibre optique (CGFO) de construction complexe et d'en faire l'analyse détaillée sous déplacement axial contrôlé. Cette étape a servi à établir les bases de la méthodologie proposée, lesquelles sont discutées de manière exhaustive. La deuxième partie de la recherche porte sur la modélisation raffinée du conducteur de ligne ACSR 795 kcmil qui porte le nom de code « Drake », sélectionné comme cas de référence pour étudier la résistance en traction et les états de contraintes complexes du conducteur sous des conditions de conception extrêmes de conception. sensibilité a également exploré l'importance relative des effets frictionnels entre les brins du câble sur les contraintes calculées par le modèle. Finalement, un modèle détaillé 3-D est créé pour simuler les conditions précises d'un essai typique de fatigue en flexion pour le conducteur « Drake » jumelé à une pince de suspension. Le modèle retient toutes les non-linéarités du problème d'un point de vue mécanique. l'auteur suggère une méthode pratique pour évaluer la résistance locale en fatigue multiaxiale des conducteurs du type ACSR au droit des points de contact des pinces de suspension. Cette méthode est relativement simple d'application (une fois les analyses de contraintes disponibles) et donne des résultats en accord avec les valeurs recommandées par les manufacturiers pour le câble « Drake ». Par la suite, une étude paramétrique est faite pour vérifier l'influence de l'amplitude des mouvements de glissement sur les états de contraintes déterminés dans le conducteur dans la région de contact avec la pince sous l'effet d'un cycle complet de chargement flexionnel. En conclusion, cette recherche démontre la faisabilité et la pertinence de l'usage des méthodes computationnelles avancées pour l'analyse des contraintes d'un problème complexe comme celui des conducteurs toronnés multicouches. La méthodologie de construction des modèles est une contribution scientifique importante qui permet d'améliorer notre compréhension du comportement mécanique des conducteurs sous charges extrêmes ou dans des conditions de fatigue flexionnelle. La méthode proposée pour l'estimation de la résistance à l'usure en fatigue est également utile pour l'industrie des lignes de transport et pour les manufacturiers de câbles et il est envisageable que cette recherche servira de tremplins à plusieurs autres études computationnelles pertinentes sur les conducteurs de lignes afin d'améliorer leur fiabilité et leur robustesse mécanique.
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Kadel, Saurav. "Computational Assessment of Aortic Valve Function and Mechanics under Hypertension." Wright State University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=wright1594243694736478.
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Gao, Hao. "Carotid plaque stress analysis by fluid structure interaction based on in-vivo MRI : implications to plaque vulnerability assessment." Thesis, Brunel University, 2010. http://bura.brunel.ac.uk/handle/2438/4731.
Full textAbstract:
Stroke is one of the leading causes of death in the world, resulting mostly from the sudden rupture of atherosclerotic plaques. From a biomechanical view, plaque rupture can be considered as a mechanical failure caused by extremely high plaque stress. In this PhD project, we are aiming to predict 3D plaque stress based on in-vivo MRI by using fluid structure interaction (FSI) method, and provide information for plaque rupture risk assessment. Fluid structure interaction was implemented with ANSYS 11.0, followed by a parameter study on fibrous cap thickness and lipid core size with realistic carotid plaque geometry. Twenty patients with carotid plaques imaged by in-vivo MRI were provided in the project. A framework of reconstructing 3D plaque geometry from in-vivo multispectral MRI was designed. The followed reproducibility study on plaque geometry reconstruction procedure and its effect on plaque stress analysis filled the gap in the literature on imaging based plaque stress modeling. The results demonstrated that current MRI technology can provide sufficient information for plaque structure characterization; however stress analysis result is highly affected by MRI resolution and quality. The application of FSI stress analysis to 4 patients with different plaque burdens has showed that the whole procedure from plaque geometry reconstruction to FSI stress analysis was applicable. In the study, plaque geometries from three patients with recent transient ischemic attack were reconstructed by repairing ruptured fibrous cap. The well correlated relationship between local stress concentrations and plaque rupture sites indicated that extremely high plaque stress could be a factor responsible for plaque rupture. Based on the 20 reconstructed carotid plaques from two groups (symptomatic and asymptomatic), fully coupled fluid structure interaction was performed. It was found that there is a significant difference between symptomatic and asymptomatic patients in plaque stress levels, indicating plaque stress could be used as one of the factors for plaque vulnerability assessment. A corresponding plaque morphological feature study showed that plaque stress is significantly affected by fibrous cap thickness, lipid core size and fibrous cap surface irregularities (curvedness). A procedure was proposed for predicting plaque stress by using fibrous cap thickness and curvedness, which requires much less computational time, and has the potential for clinical routine application. The effects of residual stress on plaque stress analysis and arterial wall material property characterization by using in-vivo MRI data were also discussed for patient specific modeling. As the further development, histological study of plaque sample has been combined with conventional plaque stress analysis by assigning material properties to each computational element, based on the data from histological analysis. This method could bridge the gap between biochemistry and biomechanical study of atherosclerosis plaques. In conclusion, extreme stress distributions in the plaque region can be predicted by modern numerical methods, and used for plaque rupture risk assessment, which will be helpful in clinical practice. The combination of plaque MR imaging analysis, computational modelling, and clinical study/ validation would advance our understandings of plaque rupture, prediction of future rupture, and establish new procedures for patient diagnose, management, and treatment.
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Kida, Naoki. "Finite element formulation and analysis for an arterial wall with residual and active stresses." Kyoto University, 2014. http://hdl.handle.net/2433/189352.
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上原, 拓也, Takuya UEHARA, 貴洋 辻野, and Takahiro TSUJINO. "フェーズフィールドモデルを用いた変態‐熱‐応力連成解析の定式化." 日本機械学会, 2006. http://hdl.handle.net/2237/9012.
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Thanoon, David. "Computational framework for local breast cancer treatment." Thesis, Bordeaux 1, 2011. http://www.theses.fr/2011BOR14387/document.
Full textAbstract:
Le cancer du sein est le cancer le plus fréquent chez les femmes. Il y a une multitude de solutions proposées concernant une éventuelle intervention médicale pour le cancer du sein ‐ une en particulier est la chirurgie mammaire conservatrice (tumoréctomie). Le but de la tumoréctomie est de parvenir à un contrôle local du cancer, ainsi que de préserver une forme du sein qui satisfait les besoins esthétiques de la femme. Bien que ces objectifs sont généralement atteint, il reste encore parfois des résultats inattendus,tels qu'une tumeur récurrence locale, ou des résultats cosmétiques insuffisants.L'objectif de cette thèse est de proposer une plateforme de calcul, qui contribue à la tumoréctomie. Cela comprend:1) Une étude de la dynamique de croissance des tumeurs du sein.2) Une étude sur la prédiction du contour du sein grâce a la chirurgie virtuelle.3) Un modèle de calcul de la forme finale du sein après cicatrisationBreast cancer is the most common cancer among women in the developed as well as the developing countries. There are a plethora of proposed solutions regarding possible medical interventions for breast cancer–one in particular is Breast Conserving Therapy (BCT). BCT comprises of complete surgical excision of the tumor (partialmastectomy), and post-operative radiotherapy for the remaining breast tissue. This is a feasible treatment for most women with breast cancer. The goal of BCT is toachieve local control of the cancer, as well as to preserve breast shape that appeases awoman’s cosmetic concerns. Although these goals are usually achieved, there are still occasional unexpected results, such as reexcision of the tumor due to a positive margin assessment, tumor local recurrence, unsatisfactory cosmetic results, and breastpain. Other than surgical experience and judgment, there are currently no toolswhich can predict the outcome of partial mastectomy on the contour and deformity of the treated breast. The objective of this dissertation is to propose computational framework, which contributes to BCT operations, this was achieve by exploring two areas.On the one hand we developed a multiscale model adapted for breast cancer tumor growth, ductal carcinoma in situ (DCIS). The model features included: nutrients growth limitation, wall degradation enzyme and HER2 chemical expression tumor phenotype. Our model successfully simulate some pattern of DCIS carcinoma.Among the interesting result we showed that the enzyme contributed to a greater tumor size and that when HER2 was over expressed, the growth limiting factor wasthe EGFR. On the other hand, we developed a virtual surgery box to simulate BCT surgery. The box will input MRI patient data and will output cosmetic and functional indicator to rate the impact of the surgery. It appears that stiffness of the tissue, resection radius as well as the lump quadrant location are the most sensitive parameters to the indicators. A healing model was also embedded to simulate the wound closure after resection, this model was stress dependent and illustrate anasymmetric wound closure progression.The tools developed in this research allows a new type of field convergence between the surgery and computation field. At the local level it will allow surgeons and patient to be able to communicate on the pertinence and necessity of performing alumpectomy surgery, enabling to anticipate the possible outcome of the operation.On the global aspect this type of tool gives birth to a new type of field: computational surgery, where computer scientist and surgeons work hand in hand to provide the best and the most reliable service to the patients
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Kucharavy, Andrei. "Molecular mechanisms of aneuploidy-mediated stress-resistance." Electronic Thesis or Diss., Paris 6, 2017. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2017PA066734.pdf.
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L’aneuploïdie a été historiquement associé à des phénotypes nuisibles, notamment le cancer et le syndrome de Down. Cependant, des résultats expérimentaux récents suggèrent que l’aneuploïdie permettrait l'adaptation à des stresseurs variés, notamment résistance aux médicaments, en rendant la compréhension critique au domaine biomédical. Cependant, les mécanismes moléculaires permettant cette adaptation restaient à élucider. Une telle élucidation selon plusieurs axes a été justement l'objet de ce travail. Premièrement, nous avons développé un modèle mathématique représentant l'adaptation aux environnements adverses comme un compromis dans la position dans un espace des traits. L’aneuploïdie y permet une exploration plus rapide. Ce modèle a été validé sur des données expérimentaux et a été utilisé pour prédire une combinaison médicamenteuse ciblant les populations cellulaires hétérogènes dans le cancer du sein. Deuxièmement, nous avons utilisé les concepts du domaine de la biologie en réseaux et des résultats de théorie de graphes pour prédire la distribution des gènes essentiels, des interactions létales et des gènes essentiels évolutifs - des gènes essentiels qui peuvent être supprimés dans des organismes devenus aneuploïdes. Nous avons également construit un algorithme pour prédire les mécanismes moléculaires qui expliquerait les phénotypes associés à des perturbations génétiques à grande échelle. Finalement, nous avons exploré plusieurs mécanismes par lesquels l’aneuploïdie pourrait impacter la régulation génétique, conduisant au développement des outil informatiques publiésAneuploidy has historically been associated with detrimental phenotypes and diseases, notably cancer and Down Syndrome. However, recent experimental evidence suggests aneuploidy provides adaptation to numerous stressors, including drug resistance, making aneuploidy study critical to biomedical research. However, the molecular mechanisms underlying this process remained elusive until now. This work focused on exploring several approaches to understanding those mechanisms. Frist, we have developed a general mathematical model of organism adaptation to adverse environments. In our model, the adaptation to environments takes place as a trade-off in the space of traits, of which aneuploidy allows a more efficient and rapid sampling. This model was validated on experimental data and used to predict optimal drug combinations targeting heterogeneous populations breast tumor cells. Second, we used the framework of network biology to model biomolecular networks and apply to them results from the graph theory and existing results on weighted graphs from other domains. We were able to predict the distribution of essential genes, lethal genetic interactions and essential evolvable genes - essential genes that can be deleted in the aneuploid background. We were as well able to build a predictive model for inferring most likely pathways underlying the phenotype of large-scale genetic perturbations. Finally, we attempted to explore several possible modes besides dosage effects by which aneuploidy could impact the gene expression regulation. This required a development of an image analysis toolkit that was validated and released for as open-source software
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Singh, Harminder. "Modelling of shear sensitive cells in stirred tank reactor using computational fluid dynamics." Thesis, University of Canterbury. Chemical and Process Engineering, 2011. http://hdl.handle.net/10092/5684.
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Animal cells are often cultured in stirred tank reactors. Having no cell wall, these animal cells are very sensitive to the fluid mechanical stresses that result from agitation by the impeller and from the rising and bursting of bubbles, which are generated within the culture medium in the stirred tank to supply oxygen by mass transfer to the cells. If excessive, these fluid mechanical stresses can result in damage/death of animal cells. Stress due to the rising and bursting of bubbles can be avoided by using a gas-permeable membrane, in the form of a long coiled tube (with air passing through it) within the stirred tank, instead of air-bubbles to oxygenate the culture medium. Fluid mechanical stress due to impeller agitation can be controlled using appropriate impeller rotational speeds. The aim of this study was to lay the foundations for future work in which a correlation would be developed between cell damage/death and the fluid mechanical stresses that result from impeller agitation and bubbling. Such a correlation could be used to design stirred-tank reactors at any scale and to determine appropriate operating conditions that minimise cell damage/death due to fluid mechanical stresses.
Firstly, a validated CFD model of a baffled tank stirred with a Rushton turbine was developed to allow fluid mechanical stresses due to impeller agitation to be estimated. In these simulations, special attention was paid to the turbulence energy dissipation rate, which has been closely linked to cell damage/death in the literature. Different turbulence models, including the k-ε, SST, SSG-RSM and the SAS-SST models, were investigated.
All the turbulence models tested predicted the mean axial and tangential velocities reasonably well, but under-predicted the decay of mean radial velocity away from the impeller. The k-ε model predicted poorly the generation and dissipation of turbulence in the vicinity of the impeller. This contrasts with the SST model, which properly predicted the appearance of maxima in the turbulence kinetic energy and turbulence energy dissipation rate just off the impeller blades. Curvature correction improved the SST model by allowing a more accurate prediction of the magnitude and location of these maxima. However, neither the k-ε nor the SST models were able to properly capture the chaotic and three-dimensional nature of the trailing vortices that form downstream of the blades of the impeller. In this sense, the SAS-SST model produced more physical predictions. However,this model has some drawbacks for modelling stirred tanks, such as the large number of modelled revolutions required to obtain good statistical averaging for calculating turbulence quantities. Taking into consideration both accuracy and solution time, the SSG-RSM model was the least satisfactory model tested for predicting turbulent flow in a baffled stirred tank with a Rushton turbine.
In the second part of the work, experiments to determine suitable oxygen transfer rates for culturing cells were carried out in a stirred tank oxygenated using either a sparger to bubble air through the culture medium or a gas-permeable membrane. Results showed that the oxygen transfer rates for both methods of oxygenation were always above the minimum oxygen requirements for culturing animal cells commonly produced in industry, although the oxygen transfer rate for air-bubbling was at-least 10 times higher compared with using a gas-permeable membrane. These results pave the way for future experiments, in which animal cells would be cultured in the stirred tank using bubbling and (separately) a gas-permeable membrane for oxygenation so that the effect of rising and bursting bubbles on cell damage/death rates can be quantified. The effect of impeller agitation on cell damage/death would be quantified by using the gas permeable membrane for oxygenation (to remove the detrimental effects of bubbling), and changing the impeller speed to observe the effect of agitation intensity.
In the third and final part of this work, the turbulent flow in the stirred tank used in the oxygenation experiments was simulated using CFD. The SST turbulence model with curvature correction was used in these simulations, since it was found to be the most accurate model for predicting turbulence energy dissipation rate in a stirred tank. The predicted local maximum turbulence energy dissipation rate of 8.9x10¹ m2/s3 at a rotational speed of 900 rpm was found to be substantially less than the value of 1.98x10⁵ m2/s3 quoted in the literature as a critical value above which cell damage/death becomes significant. However, the critical value for the turbulence energy dissipation rate quoted in the literature was determined in a single-pass flow device, whereas animal cells in a stirred tank experience frequent exposure to high turbulence energy dissipation rates (in the vicinity of the impeller) due to circulation within the stirred tank and long culture times. Future cell-culturing experiments carried out in the stirred tank of this work would aim to determine a more appropriate critical value for the turbulence energy dissipation rate in a stirred tank, above which cell damage/death becomes a problem.
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Karolyi, Daniel Roberts. "Hemodynamic wall shear stress in models of atherosclerotic plaques using phase contrast magnetic resonance velocimetry and computational fluid dynamics." Diss., Georgia Institute of Technology, 2002. http://hdl.handle.net/1853/20132.
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Papadopoulou, Virginie. "Computational and experimental techniques towards optimising the cardiovascular risk assessment of hyperbaric decompression stress caused by circulatory bubble dynamics." Thesis, Imperial College London, 2015. http://hdl.handle.net/10044/1/52254.
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This work focuses on developing new techniques towards the quantification of hyperbaric decompression stress. Instead of just preventing decompression sickness (DCS), the aim is to go towards developing an environmental cardiovascular personalised stress index, especially as sub-clinical long terms effects of even recreational scuba diving have been demonstrated. From an engineering perspective, despite the longevity of the research field, a number of fundamental issues that remain unknown have prevented efficient modelling. The aim of this thesis is to directly tackle the research methodology by developing three tailored tools. Firstly, we develop a simulation platform in MatLab to model the diving process by optimizing the implementation of dissolved gas phase tracking decompression algorithms. This platform can be used to simulate diving scenarios, but also analyse real dive profiles. From a first analysis on real profiles provided to us by the European Divers Alert Network database, we find as expected that these existing models are poor predictors of accidents, but also demonstrate that ascent rate seems to be an important predictor of DCS for the range of profiles considered. Secondly, a fundamental issue for modelling the decompression phenomenon is that the precise formation site and growth mechanism of decompression bubbles in vivo remains unknown. We develop a novel experimental set-up and analysis code for the real-time optical study of decompression induced bubble growth dynamics. Looking at bubble growth from a gas saturated solution on ex-vivo muscle and fat tissues, we show that the role of the substrate from which bubble detach plays a significant role. Bubble density, nucleation threshold, detachment size and coalescence behaviour are shown significantly different for the two substrates, whereas growth rates after a critical size are governed by diffusion as expected, and a competition for dissolved gas between adjacent multiple bubbles is demonstrated. These findings are not accounted for in current modelling efforts so our experimental set-up could be used in the development of a more physiologically relevant decompression model. Thirdly, an important question in terms of decompression modelling optimisation is the precise definition of the evaluation endpoint. Vascular circulating bubbles are normally assessed semi-quantitatively by trained human raters who grade the severity on echocardiograms. We show statistically that this is highly rater-dependent compared to a new counting methodology which is found to perform significantly better but is more time-consuming. We then use image processing techniques to semi-automate this new counting methodology with good comparison to human raters, significantly reducing the time needed for the assessment. This new method could be added to decompression model validation protocols, as well as used in physiology experiments looking at predictive parameters for, or preventive measures against, circulating gas bubbles post-dive. The proposed experimental and computational techniques could be used towards optimising the cardiovascular risk assessment of hyperbaric decompression stress caused by circulatory bubble dynamics.
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VanDenBosch, Leah M. "Investigating the effect of fluid shear stress on the failure of cancer cell membranes: an experimental and computational analysis." Thesis, University of Iowa, 2018. https://ir.uiowa.edu/etd/6318.
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Cancer metastasis, or the formation of a secondary tumor at a site distant from the primary tumor, is known to be an inefficient process. Historically, it was believed that the shear stresses and forces experienced by cancer cells traveling through the circulatory system are major limiting factors to their metastatic potential and viability. High levels of fluid shear stress are known to be capable of destroying tumor cells. However, more recent research has shown that cancer cells survive migration through the circulatory system and extravasation into distant tissues with a high degree of efficiency, indicating that hemodynamic forces are not primarily responsible for metastatic cancer cell death. A current subject of investigation is the biomechanical effect of fluid shear stress on cancer cells – how do cancer cells react to the fluidic forces and stresses they experience in circulation? This study focused on quantifying the elastic modulus and rupture behavior of prostate cancer and prostate epithelial cells, with and without exposure to fluid shear stress. Micropipette aspiration was the means of inducing deformation and rupture of the cell membrane. Images obtained through micropipette aspiration were analyzed to calculate elastic modulus and to quantify local stresses along the aspirated cell membrane. An axisymmetric stress model of the aspirated cell membrane was solved using MATLAB; the trends for direction and relative magnitude of stresses were confirmed by an Abaqus finite element model.
Results of the micropipette aspiration included statistically significant differences in elastic modulus and rupture pressure between experimental groups. The elastic modulus of epithelial cells exposed to shear stress was significantly higher than that of the cancer cell groups, both exposed and unexposed to shear stress. There was no difference in elastic modulus between cancer cells exposed to shear stress and unexposed to shear stress. This is contrary to the findings of a previous study; prostate cancer cells have been observed to stiffen after exposure to shear stress. It has also been well documented that epithelial cells exhibit higher elastic moduli than cancer cells; however, no difference was observed in this study in the comparison of elastic moduli of cancer and epithelial cells that were unexposed to shear stress. The rupture pressure of the cancer cells unexposed to shear stress was significantly lower than any other group. This suggests a strengthening reaction of the cancer cell membrane in response to shear stress exposure. This effect was observed to be transient; the increase in rupture pressure disappeared by an hour after the shear stress exposure. The epithelial cells did not exhibit any change in rupture pressure after exposure to shear stress. There was no correlation between elastic modulus and rupture pressure; the stiffness of the cells did not indicate how likely they were to rupture.
The MATLAB and Abaqus models agreed well for trends of principal stresses and von Mises stress. The MATLAB model was quite sensitive to the curvature of the spline fitted to the membrane edge, resulting in irregular patterns and some extreme values of stress and making the results difficult to interpret. The maximum stress did tend to increase with increased aspiration pressure. The location of the maximum stress along the membrane did not reliably correspond to the location of rupture during micropipette aspiration. This model may be improved by automating the process of fitting a spline to the edge of the membrane to reduce user error in plotting individual points.
Further studies to characterize the effects of fluid shear stress on cancer cell mechanics will be useful to confirm differences in elastic modulus and rupture pressure and to investigate the effect of time, temperature, cancer cell line, culture medium, and other variables on cancer cell properties.
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Grytsan, Andrii. "Abdominal aortic aneurysm inception and evolution - A computational model." Doctoral thesis, KTH, Biomekanik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-197289.
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Abdominal aortic aneurysm (AAA) is characterized by a bulge in the abdominal aorta. AAA development is mostly asymptomatic, but such a bulge may suddenly rupture, which is associated with a high mortality rate. Unfortunately, there is no medication that can prevent AAA from expanding or rupturing. Therefore, patients with detected AAA are monitored until treatment indication, such as maximum AAA diameter of 55 mm or expansion rate of 1 cm/year. Models of AAA development may help to understand the disease progression and to inform decision-making on a patient-specific basis. AAA growth and remodeling (G&R) models are rather complex, and before the challenge is undertaken, sound clinical validation is required. In Paper A, an existing thick-walled model of growth and remodeling of one layer of an AAA slice has been extended to a two-layered model, which better reflects the layered structure of the vessel wall. A parameter study was performed to investigate the influence of mechanical properties and G&R parameters of such a model on the aneurysm growth. In Paper B, the model from Paper A was extended to an organ level model of AAA growth. Furthermore, the model was incorporated into a Fluid-Solid-Growth (FSG) framework. A patient-specific geometry of the abdominal aorta is used to illustrate the model capabilities. In Paper C, the evolution of the patient-specific biomechanical characteristics of the AAA was investigated. Four patients with five to eight Computed Tomography-Angiography (CT-A) scans at different time points were analyzed. Several non-trivial statistical correlations were found between the analyzed parameters. In Paper D, the effect of different growth kinematics on AAA growth was investigated. The transverse isotropic in-thickness growth was the most suitable AAA growth assumption, while fully isotropic growth and transverse isotropic in-plane growth produced unrealistic results. In addition, modeling of the tissue volume change improved the wall thickness prediction, but still overestimated thinning of the wall during aneurysm expansion.Bukaortaaneurysm (AAA) kännetecknas av en utbuktning hos aortaväggen i buken. Tillväxt av en AAA är oftast asymtomatisk, men en sådan utbuktning kan plö̈tsligt brista, vilket har hög dödlighet. Tyvärr finns det inga mediciner som kan förhindra AAA från att expandera eller brista. Patienter med upptä̈ckt AAA hålls därför under uppsikt tills operationskrav är uppnådda, såsom maximal AAA-diameter på 55 mm eller expansionstakt på 1 cm/år. Modeller för AAA-tillväxt kan bidra till att öka förståelsen för sjukdomsförloppet och till att förbättra beslutsunderlaget på en patientspecifik basis. AAA modeller för tillväxt och strukturförändring (G&R) är ganska komplicerade och innan man tar sig an denna utmaning krävs de god klinisk validering. I Artikel A har en befintlig tjockväggig modell för tillväxt av ett skikt av en AAA-skiva utö̈kats till en två-skiktsmodell. Denna modell återspeglar bättre den skiktade strukturen hos kärlväggen. Genom en parameterstudie undersö̈ktes påverkan av mekaniska egenskaper och G&R-parametrar hos en sådan modell för AAA-tillväxt. I Artikel B utvidgades modellen från Artikel A till en organnivå-modell för AAA-tillväxt. Vidare inkorporerades modellen i ett “Fluid–Solid–Growth” (FSG) ramverk. En patientspecifik geometri hos bukaortan användes för att illustrera möjligheterna med modellen. I Artikel C undersöktes utvecklingen av patientspecifika biomekaniska egenskaper hos AAA. Fyra patienter som skannats fem till åtta gånger med “Computed Tomography-Angiography” (CT-A) vid olika tillfällen analyserades. Flera icke triviala statistiska samband konstaterades mellan de analyserade parametrarna. I Artikel D undersöktes effekten av olika tillväxt-kinematik för AAA tillväxt. En modell med transversellt-isotrop-i-tjockleken-tillväxt var den bäst lämpade för AAA tillväxt, medans antagandet om fullt-isotrop-tillväxt och transversellt-isotrop-i-planet-tillväxt producerade orimliga resultat. Dessutom gav modellering av vävnadsvolymsförändring ett förbättrat väggtjockleks resultat men en fortsatt överskattning av väggförtunningen under AAA-expansionen.
QC 20161201
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Franaszek, Krzysztof. "Translation-mediated stress responses : mining of ribosome profiling data." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/269473.
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Advances in next-generation sequencing platforms during the past decade have resulted in exponential increases in biological data generation. Besides applications in determining the sequences of genomes and other DNA elements, these platforms have allowed the characterization of cell-wide mRNA pools under different conditions and in different tissues. In 2009, Ingolia and colleagues developed an extension of high-throughput sequencing that provides a snapshot of all cellular mRNA fragments protected by translating ribosomes, dubbed ribosome profiling. This approach allows detection of differential translation activity, annotation of novel protein coding sequences and variants, identification of ribosome pause sites and estimates of de novo protein synthesis. As with other sequencing based methodologies, a major challenge of ribosome profiling has been sorting, filtering and interpreting the gigabytes of data produced during the course of a typical experiment. In this thesis, I developed and applied computational pipelines to interrogate ribosome profiling data in relation to gene expression in several viruses and eukaryotic species, as well as to identify sites of ribosomal pausing and sites of non-canonical translation activity. Specifically, I applied various control analyses for characterizing the quality of profiling data and developed scripts for visualizing genome-based (exon-by-exon) rather than transcript-based ribosome footprint alignments. I also examined the challenge of mapping footprints to repetitive sequences in the genome and propose ways to mitigate the associated problems. I performed differential expression analyses on data from coronavirus-infected murine cells, retrovirus-infected human cells and temperature-stressed Arabidopsis thaliana plants. Dissection of translational responses in Arabidopsis thaliana during heat shock or cold shock revealed several groups of genes that were highly upregulated within 10 minutes of temperature challenge. Analysis of the branches of the unfolded protein and integrated stress responses during coronavirus infection allowed for deconvolution of transcriptional and translational contributions. During the course of these analyses, I identified errors in a recently publicized algorithm for detection of differential translation, and wrote corrections that have now been pulled into the repository for this package. Comparison of the translational kinetics of the dengue virus infection in mosquito and human cell lines revealed host-specific sites of ribosome pausing and RNA accumulation. Analysis of HIV profiling data revealed footprint peaks which were in agreement with previously proposed models of peptide or RNA mediated ribosome stalling. I also developed a simulation to identify transcripts that are prone to generating RPFs with multiple alignments during the read mapping process. Together, the scripts and pipelines developed during the course of this work will serve to expedite future analyses of ribosome profiling data, and the results will inform future studies of several important pathogens and temperature stress in plants.
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Riera, Sardà Alexandre. "Computational Intelligence Techniques for Electro-Physiological Data Analysis." Doctoral thesis, Universitat de Barcelona, 2012. http://hdl.handle.net/10803/107818.
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This work contains the efforts I have made in the last years in the field of Electrophysiological data analysis. Most of the work has been done at Starlab Barcelona S.L. and part of it at the Neurodynamics Laboratory of the Department of Psychiatry and Clinical Psychobiology of the University of Barcelona. The main work deals with the analysis of electroencephalography (EEG) signals, although other signals, such as electrocardiography (ECG), electroculography (EOG) and electromiography (EMG) have also been used. Several data sets have been collected and analysed applying advanced Signal Processing techniques. On a later stage Computational Intelligence techniques, such as Machine Learning and Genetic Algorithms, have been applied, mainly to classify the different conditions from the EEG data sets. 3 applications involving EEG and classification are proposed corresponding to each one of the 3 case studies presented in this thesis.
Analysis of Electrophysiological signals for biometric purposes:
We demonstrate the potential of using EEG signals for biometric purposes. Using the ENOBIO EEG amplifier, and using only two frontal EEG channels, we are able to authenticate subjects with a performance up to 96.6%. We also looked for features extracted from the ECG signals and in that case the performance was equal to 97.9%. We also fused the results of both modalities achieving a perfect performance. Our system is ready to use and since it only uses 4 channels (2 for EEG, 1 for ECG in the left wrist and 1 as active reference in the right ear lobe), the wireless ENOBIO sensor is perfectly suited for our application.
EEG differences in First Psychotic Episode (FPE) Patients:
From an EEG data set of 15 FPE patients and the same number of controls, we studied the differences in their EEG signals in order to train a classifier able to recognise to which group an EEG sample comes from. The feature we use are extracted from the EEG by computing the Synchronization Likelihood feature between all possible pairs of channels. The next step is to build a graph and from that graph we extracted the Mean Path Length and the Clustering Coefficient. Those features as a function of the connectivity threshold are then used in our classifiers. We then create several classification problems and we reach up to 100% of classification in some cases.
Markers of stress in the EEG signal:
In this research, we designed a protocol in which the participants where asked to perform different tasks, each one with a different stress level. Among these tasks we can find the Stroop Test, Mathematical arithmetics and also a fake blood sample test. By extracting the alpha asymmetry and the beta/alpha ration, we where able to discriminate between the different tasks with performances up to 88%. This application can be used with only 3 EEG electrodes, and it can also work in real time. Finally this application can also be used as a neurofeedback training to learn how to cope with stress.Este trabajo contiene los esfuerzos que he realizado en los últimos años en el campo del análisis de datos electro-fisiológicos. La mayor parte del trabajo se ha hecho en Starlab Barcelona SL y otra parte en el Laboratorio de Neurodinámica del Departamento de Psiquiatría y Psicobiología Clínica de la Universidad de Barcelona. La parte central de esta tesis está relacionado con el análisis de la señales de electroencefalografía (EEG), aunque otras señales, tales como electrocardiografía (ECG), electroculografía (EOG) y electromiografía (EMG) también se han utilizado. Varios conjuntos de datos se han recogido y analizado aplicando técnicas avanzadas de procesamiento de señales. En una fase posterior, técnicas de inteligencia computacional, tales como 'Machine Learning' y algoritmos genéticos, se han aplicado, principalmente para clasificar las diferentes condiciones de los conjuntos de datos de EEG. Las 3 aplicaciones, que involucran EEG y técnicas de clasificación, que se presentan en esta tesis son: -Análisis de señales electro-fisiológicas para aplicaciones de biometría -Diferencias en las características del EEG en pacientes de primer brote psicótico -Marcadores de estrés en la señal de EEG
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Fadeel, Abdalsalam. "Development and Application of a Computational Modeling Scheme for Periodic Lattice Structures." Wright State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=wright162248153014535.
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Grover, Susan M. "Computational study of stress concentration about an oblique hole in a thick walled tube toward understanding structural improvements in bone /." [Gainesville, Fla.] : University of Florida, 2004. http://purl.fcla.edu/fcla/etd/UFE0006801.
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Matek, Christian C. A. "Statistical mechanics of nucleic acids under mechanical stress." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:ce44cf50-2001-4f54-8e57-d1757f709fd6.
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In this thesis, the response of DNA and RNA to linear and torsional mechanical stress is studied using coarse-grained models. Inspired by single-molecule assays developed over the last two decades, the end-to-end extension, buckling and torque response behaviour of the stressed molecules is probed under conditions similar to experimentally used setups. Direct comparison with experimental data yields excellent agreement for many conditions. Results from coarse-grained simulations are also compared to the predictions of continuum models of linear polymer elasticity. A state diagram for supercoiled DNA as a function of twist and tension is determined. A novel confomational state of mechanically stressed DNA is proposed, consisting of a plectonemic structure with a denaturation bubble localized in its end-loop. The interconversion between this novel state and other, known structural motifs of supercoiled DNA is studied in detail. In particular, the influence of sequence properties on the novel state is investigated. Several possible implications for supercoiled DNA structures in vivo are discussed. Furthermore, the dynamical consequences of coupled denaturation and writhing are studied, and used to explain observations from recent single molecule experiments of DNA strand dynamics. Finally, the denaturation behaviour, topology and dynamics of short DNA minicircles is studies using coarse-grained simulations. Long-range interactions in the denaturation behaviour of the system are observed. These are induced by the topology of the system, and are consistent with results from recent molecular imaging studies. The results from coarse-grained simulations are related to modelling of the same system in all-atom simulations and a local denaturation model of DNA, yielding insight into the applicability of these different modelling approaches to study different processes in nucleic acids.
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von, Stillfried Florian. "Computational fluid-dynamics investigations of vortex generators for flow-separation control." Doctoral thesis, KTH, Turbulens, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-94879.
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Many flow cases in fluid dynamics face undesirable flow separation due to ad-verse pressure gradients on wall boundaries. This occurs, for example, due togeometrical reasons as in a highly curved turbine-inlet duct or on flow-controlsurfaces such as wing trailing-edge flaps within a certain angle-of-attack range.Here, flow-control devices are often used in order to enhance the flow and delayor even totally eliminate flow separation. Flow control can e.g. be achieved byusing passive or active vortex generators (VGs) for momentum mixing in theboundary layer of such flows. This thesis focusses on such passive and activeVGs and their modelling for computational fluid dynamics investigations. First, a statistical VG model approach for passive vane vortex genera-tors (VVGs), developed at the Royal Institute of Technology Stockholm andthe Swedish Defence Research Agency, was evaluated and further improvedby means of experimental data and three-dimensional fully-resolved computa-tions. This statistical VVG model approach models those statistical vortexstresses that are generated at the VG by the detaching streamwise vortices.This is established by means of the Lamb-Oseen vortex model and the Prandtllifting-line theory for the determination of the vortex strength. Moreover, thisansatz adds the additional vortex stresses to the turbulence of a Reynolds-stresstransport model. Therefore, it removes the need to build fully-resolved three-dimensional geometries of VVGs in a computational fluid dynamics mesh. Usu-ally, the generation of these fully-resolved geometries is rather costly in termsof preprocessing and computations. By applying VVG models, the costs arereduced to that of computations without VVGs. The original and an improvedcalibrated passive VVG model show sensitivity for parameter variations suchas the modelled VVG geometry and the VVG model location on a flat plate inzero- and adverse-pressure-gradient flows, in a diffuser, and on an airfoil withits high-lift system extracted. It could be shown that the passive VG modelqualitatively and partly quantitatively describes correct trends and tendenciesfor these different applications. In a second step, active vortex-generator jets (VGJs) are considered. They were experimentally investigated in a zero-pressure-gradient flat-plate flow atTechnische Universitä̈t Braunschweig, Germany, and have been re-evaluated for our purposes and a parameterization of the generated vortices was conducted. Dependencies of the generated vortices and their characteristics on the VGJsetup parameters could be identified and quantified. These dependencies wereused as a basis for the development of a new statistical VGJ model. This modeluses the ansatz of the passive VVG model in terms of the vortex model, theadditional vortex-stress tensor, and its summation to the Reynolds stress ten-sor. Yet, it does not use the Prandtl lifting-line theory for the determinationof the circulation but an ansatz for the balance of the momentum impact thatthe VGJ has on the mean flow. This model is currently under developmentand first results have been evaluated against experimental and fully-resolvedcomputational results of a flat plate without pressure gradient.QC 20120511
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Weidner, Katherine Lourene. "Evaluation of the Jet Test Method for determining the erosional properties of Cohesive Soils; A Numerical Approach." Thesis, Virginia Tech, 2012. http://hdl.handle.net/10919/72983.
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Estimates of bank erosion typically require field measurements to determine the soil erodibility since soil characteristics are highly variable between sites, especially for cohesive soils. The submerged jet test device is an in situ method of determining the critical shear stress and soil erodibility of cohesive soils. A constant velocity jet, applied perpendicular to the soil surface, creates a scour hole which is measured at discrete time intervals. While the results of these tests are able to provide values of critical shear stress and soil erodibility, the results are often highly variable and do not consider certain aspects of scour phenomena found in cohesive soils. Jet test measurements taken on the lower Roanoke River showed that the results varied for samples from similar sites and bulk failures of large areas of soil were common on the clay banks. Computational Fluid Dynamics (CFD) can be used to determine the effect of scour hole shape changes on the applied shear stress. Previous calculation methods assumed that the depth of the scour hole was the only parameter that affected the applied shear stress. The analysis of the CFD models showed that depth did heavily influence the maximum shear stress applied to the soil boundary. However, the scour hole shape had an impact on the flow conditions near the jet centerline and within the scour hole. Wide, shallow holes yielded results that were similar to the flat plate, therefore it is recommended that field studies only use jet test results from wide, shallow holes to determine the coefficient of erodibility and the critical shear stress of cohesive soils.
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Krishnamoorthy, Mahesh kumaar. "Investigations on Linkages Between Blood Flow Dynamics and Histological Endpoints in Dialysis Access Fistula." University of Cincinnati / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1267718697.
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