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University of New South Wales
1.
Zhang, Shuai.
Personalized recommendation: neural architectures and beyond.
Degree: Computer Science & Engineering, 2019, University of New South Wales
URL: http://handle.unsw.edu.au/1959.4/64856 
;
https://unsworks.unsw.edu.au/fapi/datastream/unsworks:62792/SOURCE02?view=true
► Recommender system (RS) is a useful information filtering tool for guiding users in a personalized way of discovering products/services from a large space of possible…
(more)
▼ Recommender system (RS) is a useful information filtering tool for guiding users in a personalized way of discovering products/services from a large space of possible options. A good recommender system can not only ameliorate the prevalent issue of over-choice due to information explosion but can also promote sales and boost revenues. As such, it has become a vital and indispensable component in the modern internet industry. In this thesis, we aim to tackle several key prevalent tasks in recommender systems, including (1) modeling the complex relationships between users and items; (2) integrating side information; (3) modeling the temporal dynamics; and (4) cold-start problem. To this end, we investigate neural architectures and
geometric methods, aiming to tackle those challenges and improve recommendation performances.Recently, deep learning's revolutionary advances in speech recognition, computer vision, and natural language processing have gained significant attention. Many challenging problems such as feature representation learning and sequence modeling can be well addressed with deep neural models. Our key contributions on personalized recommendations with neural architectures are listed as follows: Firstly, we investigated feature representation learning for hybrid recommender systems, which involves learning items' feature representation with a contractive autoencoder. We proposed AutoSVD and AutoSVD++ to efficiently anticipate user's ratings for unseen items. Secondly, we investigated the personalized ranking task and proposed NeuRec and its extension, SNR, to model the complex and nonlinear relationships between users and items. Thirdly, we investigate the challenging cold-start problem and present a model that considers both item and user side information under a unified deep neural framework which can introduce personalization and collaborative effects to cold-start recommendations. Fourthly, we proposed a self-attentive metric learning framework to tackle the temporal dynamics in recommender systems. Beyond neural networks, we also investigate
geometric methods which concern modeling the intricate relations between users and items with
geometric inductive biases. We proposed FML to factorize the explicit Euclidean distance with standard learning algorithms. We also proposed a collaborative filtering model using Quaternion representations. Those
methods achieve comparable performances as neural networks with simpler formulation.
Advisors/Committee Members: Lina, Yao, Computer Science & Engineering, Faculty of Engineering, UNSW, Liming, Zhu, Computer Science & Engineering, Faculty of Engineering, UNSW, Xiwei, Xu, Computer Science & Engineering, Faculty of Engineering, UNSW.
Subjects/Keywords: Geometric methods; Recommender systems; Deep learning
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APA (6th Edition):
Zhang, S. (2019). Personalized recommendation: neural architectures and beyond. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/64856 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:62792/SOURCE02?view=true
Chicago Manual of Style (16th Edition):
Zhang, Shuai. “Personalized recommendation: neural architectures and beyond.” 2019. Doctoral Dissertation, University of New South Wales. Accessed February 27, 2021.
http://handle.unsw.edu.au/1959.4/64856 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:62792/SOURCE02?view=true.
MLA Handbook (7th Edition):
Zhang, Shuai. “Personalized recommendation: neural architectures and beyond.” 2019. Web. 27 Feb 2021.
Vancouver:
Zhang S. Personalized recommendation: neural architectures and beyond. [Internet] [Doctoral dissertation]. University of New South Wales; 2019. [cited 2021 Feb 27].
Available from: http://handle.unsw.edu.au/1959.4/64856 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:62792/SOURCE02?view=true.
Council of Science Editors:
Zhang S. Personalized recommendation: neural architectures and beyond. [Doctoral Dissertation]. University of New South Wales; 2019. Available from: http://handle.unsw.edu.au/1959.4/64856 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:62792/SOURCE02?view=true
Virginia Tech
2.
Sharma, Harsh Apurva.
Structure-preserving Numerical Methods for Engineering Applications.
Degree: PhD, Aerospace Engineering, 2020, Virginia Tech
URL: http://hdl.handle.net/10919/99912
► Accurate numerical simulation of dynamical systems over long time horizons is essential in applications ranging from particle physics to geophysical fluid flow to space hazard…
(more)
▼ Accurate numerical simulation of dynamical systems over long time horizons is essential in applications ranging from particle physics to geophysical fluid flow to space hazard analysis. In many of these applications, the governing physical equations derive from a variational principle and their solutions exhibit physically meaningful invariants such as momentum, energy, or vorticity. Unfortunately, most traditional numerical
methods do not account for the underlying
geometric structure of the physical system, leading to simulation results that may suggest nonphysical behavior. In this dissertation, tools from
geometric mechanics and computational
methods are used to develop numerical integrators that respect the qualitative features of the physical system. The research presented here focuses on numerical schemes derived from variational principles– schemes that are general enough to apply to a large class of engineering problems. Energy-preserving algorithms are developed for mechanical systems by exploiting the underlying
geometric properties. Numerical performance comparisons demonstrate that these algorithms provide almost exact energy preservation and lead to more accurate prediction. The advantages of these
methods in the numerical simulation are illustrated by various representative examples from engineering applications, which include limit cycle oscillations of an aeroelastic system, dynamics of a neutrally buoyant underwater vehicle, and optimization for spherical shape correlation and matching.
Advisors/Committee Members: Patil, Mayuresh J. (committeechair), Woolsey, Craig A. (committeechair), Ross, Shane D. (committee member), Lee, Taeyoung (committee member), Sultan, Cornel (committee member).
Subjects/Keywords: Structure-preserving methods; Geometric numerical integration; Variational integrators; Lie group methods
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APA (6th Edition):
Sharma, H. A. (2020). Structure-preserving Numerical Methods for Engineering Applications. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/99912
Chicago Manual of Style (16th Edition):
Sharma, Harsh Apurva. “Structure-preserving Numerical Methods for Engineering Applications.” 2020. Doctoral Dissertation, Virginia Tech. Accessed February 27, 2021.
http://hdl.handle.net/10919/99912.
MLA Handbook (7th Edition):
Sharma, Harsh Apurva. “Structure-preserving Numerical Methods for Engineering Applications.” 2020. Web. 27 Feb 2021.
Vancouver:
Sharma HA. Structure-preserving Numerical Methods for Engineering Applications. [Internet] [Doctoral dissertation]. Virginia Tech; 2020. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/10919/99912.
Council of Science Editors:
Sharma HA. Structure-preserving Numerical Methods for Engineering Applications. [Doctoral Dissertation]. Virginia Tech; 2020. Available from: http://hdl.handle.net/10919/99912
Clemson University
3.
Javier, Kayla Doris.
A Study of Quasi-Birth-Death Processes and Markovian Bitcoin Models.
Degree: PhD, School of Mathematical and Statistical Sciences, 2020, Clemson University
URL: https://tigerprints.clemson.edu/all_dissertations/2677
► In this dissertation we study a variety of continuous-time Markov chains (CTMCs) and present new formulas that can be used to find the stationary…
(more)
▼ In this dissertation we study a variety of continuous-time Markov chains (CTMCs) and present new formulas that can be used to find the stationary distribution and the Laplace transforms of the transition functions. Our first set of results involve a level-dependent Quasi-Birth-Death (QBD) processes. We study the distribution of the state and the associated running maximum level at a fixed time t. We present new expressions for the Laplace transforms of the transition functions containing this information. This work involves making use of a collection of R-matrices often found in matrix analytic literature. We also show how our
methods can be used to study the joint distribution of the running minimum level and state of a level-dependent Markov process of M/G/1-type. Our next set of results are based on a homogeneous QBD proccess. These results involve first computing a new class of R and G-matrices that can be used to find the Laplace transforms of the transition functions associated with a homogeneous QBD process with finitely many levels. Our final set of results are based on two CTMCs studied in Göbel et al. , which were created to model the interactions between a small pool of miners and a larger collection of miners within the Bitcoin network. We use the random-product technique, introduced by Buckingham and Fralix , to find the stationary distribution of this model when all miners are honest and when the small pool of miners implement the Selfish Mining strategy introduced by Eyal and Sirer in . We also study the Laplace transforms of the transition functions associated with these CTMCs and other performance measures such as the expected time it takes for a "fork" in the blockchain to be resolved.
Advisors/Committee Members: Brian Fralix, Jeff Kharoufeh, Peter Kiessler, Xin Liu.
Subjects/Keywords: blockchain; matrix-analytic methods; matrix-geometric methods; quasi-birth-death process; time-dependent behavior
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APA (6th Edition):
Javier, K. D. (2020). A Study of Quasi-Birth-Death Processes and Markovian Bitcoin Models. (Doctoral Dissertation). Clemson University. Retrieved from https://tigerprints.clemson.edu/all_dissertations/2677
Chicago Manual of Style (16th Edition):
Javier, Kayla Doris. “A Study of Quasi-Birth-Death Processes and Markovian Bitcoin Models.” 2020. Doctoral Dissertation, Clemson University. Accessed February 27, 2021.
https://tigerprints.clemson.edu/all_dissertations/2677.
MLA Handbook (7th Edition):
Javier, Kayla Doris. “A Study of Quasi-Birth-Death Processes and Markovian Bitcoin Models.” 2020. Web. 27 Feb 2021.
Vancouver:
Javier KD. A Study of Quasi-Birth-Death Processes and Markovian Bitcoin Models. [Internet] [Doctoral dissertation]. Clemson University; 2020. [cited 2021 Feb 27].
Available from: https://tigerprints.clemson.edu/all_dissertations/2677.
Council of Science Editors:
Javier KD. A Study of Quasi-Birth-Death Processes and Markovian Bitcoin Models. [Doctoral Dissertation]. Clemson University; 2020. Available from: https://tigerprints.clemson.edu/all_dissertations/2677
University of Pretoria
4.
[No author].
A systematic approach to model predictive controller
constraint handling : rigorous geometric methods
.
Degree: 2012, University of Pretoria
URL: http://upetd.up.ac.za/thesis/available/etd-10032011-163823/
► The models used by model predictive controllers (MPCs) to predict future outcomes are usually unconstrained forms like impulse or step responses and discrete state space…
(more)
▼ The models used by model predictive controllers
(MPCs) to predict future outcomes are usually unconstrained forms
like impulse or step responses and discrete state space models.
Certain MPC algorithms allow constraints to be imposed on the
inputs or outputs of a system; but they may be infeasible as they
are not checked for consistency via the process model. Consistent
constraint handling
methods - which account for their
interdependence and disambiguate the language used to specify
constraints – would therefore be an attractive aid when using any
MPC package. A rigorous and systematic approach to constraint
management has been developed, building on the work of Vinson
(2000), Lima (2007) and Georgakis et al. (2003) in interpreting
constraint interactions. The method supports linear steady-state
system models, and provides routines to obtain the following
information: effects of constraint changes on
the corresponding input and output constraints,
feasibility checks for constraints,
specification of constraint-set size
and optimal fitting of constraints within the
desirable input and output space.
Mathematical rigour and unambiguous language for identifying
constraint types were key design criteria. The outputs of the
program provide guidance when handling constraints, as opposed to
rules of thumb and experience, and promote understanding of the
system and its constraints. The metrics presented are not specific
to any commercial MPC and can be implemented in the user interfaces
of such MPCs. The method was applied to laboratory-scale test rigs
to illustrate the information obtained.
Advisors/Committee Members: Mr C Sandrock (advisor).
Subjects/Keywords: Constraint handling;
Model predictive controllers;
Geometric methods;
Operability index;
UCTD
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APA ·
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APA (6th Edition):
author], [. (2012). A systematic approach to model predictive controller
constraint handling : rigorous geometric methods
. (Masters Thesis). University of Pretoria. Retrieved from http://upetd.up.ac.za/thesis/available/etd-10032011-163823/
Chicago Manual of Style (16th Edition):
author], [No. “A systematic approach to model predictive controller
constraint handling : rigorous geometric methods
.” 2012. Masters Thesis, University of Pretoria. Accessed February 27, 2021.
http://upetd.up.ac.za/thesis/available/etd-10032011-163823/.
MLA Handbook (7th Edition):
author], [No. “A systematic approach to model predictive controller
constraint handling : rigorous geometric methods
.” 2012. Web. 27 Feb 2021.
Vancouver:
author] [. A systematic approach to model predictive controller
constraint handling : rigorous geometric methods
. [Internet] [Masters thesis]. University of Pretoria; 2012. [cited 2021 Feb 27].
Available from: http://upetd.up.ac.za/thesis/available/etd-10032011-163823/.
Council of Science Editors:
author] [. A systematic approach to model predictive controller
constraint handling : rigorous geometric methods
. [Masters Thesis]. University of Pretoria; 2012. Available from: http://upetd.up.ac.za/thesis/available/etd-10032011-163823/
University of Pretoria
5.
Campher, Andre
Herman.
A systematic
approach to model predictive controller constraint handling :
rigorous geometric methods.
Degree: Chemical Engineering, 2011, University of Pretoria
URL: http://hdl.handle.net/2263/28378
► The models used by model predictive controllers (MPCs) to predict future outcomes are usually unconstrained forms like impulse or step responses and discrete state space…
(more)
▼ The models used by model predictive controllers (MPCs) to
predict future outcomes are usually unconstrained forms like
impulse or step responses and discrete state space models. Certain
MPC algorithms allow constraints to be imposed on the inputs or
outputs of a system; but they may be infeasible as they are not
checked for consistency via the process model. Consistent
constraint handling
methods - which account for their
interdependence and disambiguate the language used to specify
constraints – would therefore be an attractive aid when using any
MPC package. A rigorous and systematic approach to constraint
management has been developed, building on the work of Vinson
(2000), Lima (2007) and Georgakis et al. (2003) in interpreting
constraint interactions. The method supports linear steady-state
system models, and provides routines to obtain the following
information: effects of constraint changes on
the corresponding input and output constraints,
feasibility checks for constraints,
specification of constraint-set size
and optimal fitting of constraints within the
desirable input and output space.
Mathematical rigour and unambiguous language for identifying
constraint types were key design criteria. The outputs of the
program provide guidance when handling constraints, as opposed to
rules of thumb and experience, and promote understanding of the
system and its constraints. The metrics presented are not specific
to any commercial MPC and can be implemented in the user interfaces
of such MPCs. The method was applied to laboratory-scale test rigs
to illustrate the information obtained.
Advisors/Committee Members: Sandrock, Carl (advisor).
Subjects/Keywords: Constraint
handling; Model
predictive controllers; Geometric
methods; Operability
index;
UCTD
Record Details
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Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Campher, A. (2011). A systematic
approach to model predictive controller constraint handling :
rigorous geometric methods. (Masters Thesis). University of Pretoria. Retrieved from http://hdl.handle.net/2263/28378
Chicago Manual of Style (16th Edition):
Campher, Andre. “A systematic
approach to model predictive controller constraint handling :
rigorous geometric methods.” 2011. Masters Thesis, University of Pretoria. Accessed February 27, 2021.
http://hdl.handle.net/2263/28378.
MLA Handbook (7th Edition):
Campher, Andre. “A systematic
approach to model predictive controller constraint handling :
rigorous geometric methods.” 2011. Web. 27 Feb 2021.
Vancouver:
Campher A. A systematic
approach to model predictive controller constraint handling :
rigorous geometric methods. [Internet] [Masters thesis]. University of Pretoria; 2011. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/2263/28378.
Council of Science Editors:
Campher A. A systematic
approach to model predictive controller constraint handling :
rigorous geometric methods. [Masters Thesis]. University of Pretoria; 2011. Available from: http://hdl.handle.net/2263/28378
6.
Imbach, Rémi.
Résolution de contraintes géométriques en guidant une méthode homotopique par la géométrie : Solving geometric constraints by a continuation method led by geometry.
Degree: Docteur es, Informatique, 2013, Université de Strasbourg
URL: http://www.theses.fr/2013STRAD033
► Suivant le domaine où on les sollicite, les solutions d’un système de contraintes géométriques (SCG) peuvent être : – formelles et exactes : elles prennent…
(more)
▼ Suivant le domaine où on les sollicite, les solutions d’un système de contraintes géométriques (SCG) peuvent être : – formelles et exactes : elles prennent par exemple la forme d’un plan de construction produisant toutes les solutions, obtenu en appliquant des règles dérivées de lemmes de géométrie. Beaucoup de SCG, surtout en 3D, résistent à cette approche ; – numériques et approchées : elles sont les solutions d’un système d’équations construit à partir des contraintes et trouvées grâce à des méthodes numériques efficaces quand elles ne recherchent qu’une solution. De par la nature des problèmes traités, chercher toutes les solutions conduit à une complexité exponentielle. Les méthodes par continuation, ou homotopie, permettent d’obtenir toutes les solutions d’un système d’équations polynomiales. Leur application à des SCG est coûteuse et difficilement sujette aux raisonnements permis par l’origine géométrique du problème car elles opèrent hors de l’espace des figures géométriques. Notre travail a pour objet la spécialisation d’une méthode par continuation à des SCG. La géométrie simplifie et justifie sa mise en œuvre dans l’espace des figures, ou des raisonnements géométriques sont possibles. On aborde également les cas ou l’ensemble de solutions d’un problème contient des éléments isolés et des continuums. Des solutions proches d’une esquisse fournie par un utilisateur sont d’abord trouvées. La recherche d’autres solutions, malgré sa complexité exponentielle, est rendue envisageable par une approche itérative. Une nouvelle méthode de décomposition est proposée pour maîtriser le coût de la résolution.
Depending on the required application field, the solutions of a geometric constraints system (GCS) are either : – symbolic and exact such as construction plans, providing all the solutions, obtained by applying geometric rules. Many problems, mostly in a 3D context, resist to this approach ; – or numerical and approximated : they are the solutions of a system of equations built from the constraints, provided by generical numerical methods that are efficient when only one solution is sought. However, searching all the solutions leads to an exponential computation cost, due to the nature of problems. Continuation methods, also called homotopic methods, find all the solutions of a polynomial system. Using them to solve systems of equations associated to systems of constraints is nevertheless costly. Moreover, combining them with geometric reasoning is a challenge, because they act in a projective complex space and not in the realizations space. The aim of this work is to specialize a continuation method to GCS. Geometry is exploited to simplify and justify its adaptation in the space of realizations, so allowing geometric reasoning. Cases where the connected components of the solution space of a problem have heterogeneous dimensions are addressed. The method discussed here provides in a first step solutions that are similar to a sketch drawn by the user. Then a procedure is proposed to search new solutions. Its…
Advisors/Committee Members: Schreck, Pascal (thesis director).
Subjects/Keywords: Résolution de contraintes géométriques; Méthodes par continuation; Homotopie; Méthodes Hybrides; Modélisation géométrique; Geometric constraints solving; Continuation methods; Homotopy; Hybrid methods; Geometric modeling; 514.2
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❌
APA ·
Chicago ·
MLA ·
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Manager
APA (6th Edition):
Imbach, R. (2013). Résolution de contraintes géométriques en guidant une méthode homotopique par la géométrie : Solving geometric constraints by a continuation method led by geometry. (Doctoral Dissertation). Université de Strasbourg. Retrieved from http://www.theses.fr/2013STRAD033
Chicago Manual of Style (16th Edition):
Imbach, Rémi. “Résolution de contraintes géométriques en guidant une méthode homotopique par la géométrie : Solving geometric constraints by a continuation method led by geometry.” 2013. Doctoral Dissertation, Université de Strasbourg. Accessed February 27, 2021.
http://www.theses.fr/2013STRAD033.
MLA Handbook (7th Edition):
Imbach, Rémi. “Résolution de contraintes géométriques en guidant une méthode homotopique par la géométrie : Solving geometric constraints by a continuation method led by geometry.” 2013. Web. 27 Feb 2021.
Vancouver:
Imbach R. Résolution de contraintes géométriques en guidant une méthode homotopique par la géométrie : Solving geometric constraints by a continuation method led by geometry. [Internet] [Doctoral dissertation]. Université de Strasbourg; 2013. [cited 2021 Feb 27].
Available from: http://www.theses.fr/2013STRAD033.
Council of Science Editors:
Imbach R. Résolution de contraintes géométriques en guidant une méthode homotopique par la géométrie : Solving geometric constraints by a continuation method led by geometry. [Doctoral Dissertation]. Université de Strasbourg; 2013. Available from: http://www.theses.fr/2013STRAD033
7.
Puschel Rouliez, Thomas.
Morpho-functional analyses of the primate skeleton:
applying 3D geometric morphometrics, finite element analysis and
phylogenetic comparative methods to assess ecomorphological
questions in extant and extinct anthropoids.
Degree: 2018, University of Manchester
URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:313627
► The overarching objective of this dissertation is to understand the relationship between form and ecological function in diverse skeletal elements belonging to different primate clades…
(more)
▼ The overarching objective of this dissertation is
to understand the relationship between form and ecological function
in diverse skeletal elements belonging to different primate clades
using
geometric morphometrics (GM), finite element analysis (FEA)
and phylogenetic comparative
methods (PCMs). GM provides a system
for quantifying morphology; while FEA allows measuring
biomechanical performance and PCMs are used to model how phenotypic
traits have evolved through time. Most chapters in this thesis
focus on the association between locomotion and morphology and how
to apply this information in the fossil record, while one analyses
the form–function relationship in a dietary context. Firstly, a
combined approach using FEA and GM is applied to analyse different
hominoid scapulae. The obtained results show that there is a
significant relationship between scapular shape and its
biomechanical performance. Hence at least part of scapular shape
variation is due to non-phylogenetic factors. Secondly, it is
tested whether there is a sclerocarpic specialization gradient in
the mandibular morphology of pitheciids. The results show that
there is indeed a relative specialization continuum for some
aspects of shape, although the story is more complex from a
biomechanical perspective. Subsequently, an analysis of the
phenetic affinities of extant platyrrhine tali and their Miocene
counterparts is carried out to explain the evolution of talar shape
and size in platyrrhines. The results suggest that talar shape
diversification can be explained by invoking a model representing a
phylogenetic hypothesis in which each platyrrhine family occupied a
separate adaptive optimum. Moreover, talar size diversification can
be characterised by a multidimensional niche model. Finally, the
main locomotor mode of different platyrrhine fossils is inferred by
applying a combination of GM, FEA and machine-learning (ML)
classification techniques. The ML algorithm applied to both
biomechanical and morphometric data categorised most of the fossil
sample as arboreal quadrupeds, which is consistent with previous
studies. Thus, it is expected to contribute to the understanding of
the correlation between form and ecological function, which is not
only relevant to appreciate the morphological diversity in extant
species, but also because it allows to infer past behaviours in
fossil taxa.
Advisors/Committee Members: KLINGENBERG, CHRISTIAN CP, Sellers, William, Klingenberg, Christian.
Subjects/Keywords: ecomorphology; primates; geometric morphometrics; finite element analysis; machine-learning; phylogenetic comparative methods
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Puschel Rouliez, T. (2018). Morpho-functional analyses of the primate skeleton:
applying 3D geometric morphometrics, finite element analysis and
phylogenetic comparative methods to assess ecomorphological
questions in extant and extinct anthropoids. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:313627
Chicago Manual of Style (16th Edition):
Puschel Rouliez, Thomas. “Morpho-functional analyses of the primate skeleton:
applying 3D geometric morphometrics, finite element analysis and
phylogenetic comparative methods to assess ecomorphological
questions in extant and extinct anthropoids.” 2018. Doctoral Dissertation, University of Manchester. Accessed February 27, 2021.
http://www.manchester.ac.uk/escholar/uk-ac-man-scw:313627.
MLA Handbook (7th Edition):
Puschel Rouliez, Thomas. “Morpho-functional analyses of the primate skeleton:
applying 3D geometric morphometrics, finite element analysis and
phylogenetic comparative methods to assess ecomorphological
questions in extant and extinct anthropoids.” 2018. Web. 27 Feb 2021.
Vancouver:
Puschel Rouliez T. Morpho-functional analyses of the primate skeleton:
applying 3D geometric morphometrics, finite element analysis and
phylogenetic comparative methods to assess ecomorphological
questions in extant and extinct anthropoids. [Internet] [Doctoral dissertation]. University of Manchester; 2018. [cited 2021 Feb 27].
Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:313627.
Council of Science Editors:
Puschel Rouliez T. Morpho-functional analyses of the primate skeleton:
applying 3D geometric morphometrics, finite element analysis and
phylogenetic comparative methods to assess ecomorphological
questions in extant and extinct anthropoids. [Doctoral Dissertation]. University of Manchester; 2018. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:313627
University of Bristol
8.
Navalon, Guillermo.
Evolution of the avian skull : evolutionary drivers of modern bird diversity.
Degree: PhD, 2019, University of Bristol
URL: http://hdl.handle.net/1983/e3908f4f-d4a3-4a23-8ee4-9834d88feccd
► Encompassing more than 11,000 species, birds are the most speciose group of tetrapods in modern-world ecosystems. The modern radiation of birds (Neornithes) originated in the…
(more)
▼ Encompassing more than 11,000 species, birds are the most speciose group of tetrapods in modern-world ecosystems. The modern radiation of birds (Neornithes) originated in the Mesozoic and greatly radiated in disparity following the K-Pg extinction, a radiation which is often believed to have been primarily driven by adaptation in response to ecological opportunity after this biotic crisis. This assumption largely rests on the presumption that the anatomy in birds, particularly the large variety of beak forms, is very correlated with their ecologies, particularly feeding ecology. In this thesis, this presumption is tested in a broad macroevolutionary scale for the first time. I find that this relationship is weaker and more complex than often assumed, suggesting that the diversification of beak morphologies in birds was likely shaped by a more complex set of evolutionary drivers than feeding adaptation, likely involving both extrinsic and intrinsic factors. Consequently, the roles of other intrinsic factors in craniofacial evolution are explored within some selected lineages of modern birds. First, I explore the patterns and strength of the coevolution between the beak and the rest of the skull (cranial integration), across all the lineages of landbirds (Inopinaves) and how these associations affected their craniofacial macroevolution. I find that variations in cranial integration had important implications for cranial evolution, specifically for the two classic avian adaptive radiations: Darwin's finches and Hawaiian honeycreepers. Secondly, I explore craniofacial shape variation over evolution and development in Strisores. My results suggest that evolutionary changes in development played a significant role in shaping macroevolution in this clade of birds. Finally, over this thesis geometric morphometrics and phylogenetic comparative methods are extensively used. I show some current limitations of these methods concerning the quantification of covariation patterns (integration and modularity). I propose a pipeline for identifying potential issues and offer some preliminary novel solutions to overcome them.
Subjects/Keywords: 550; birds; macroevolution; shape; skull; geometric morphometrics; adaptation; constraint; integration; phylogenetic comparative methods; development
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APA ·
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APA (6th Edition):
Navalon, G. (2019). Evolution of the avian skull : evolutionary drivers of modern bird diversity. (Doctoral Dissertation). University of Bristol. Retrieved from http://hdl.handle.net/1983/e3908f4f-d4a3-4a23-8ee4-9834d88feccd
Chicago Manual of Style (16th Edition):
Navalon, Guillermo. “Evolution of the avian skull : evolutionary drivers of modern bird diversity.” 2019. Doctoral Dissertation, University of Bristol. Accessed February 27, 2021.
http://hdl.handle.net/1983/e3908f4f-d4a3-4a23-8ee4-9834d88feccd.
MLA Handbook (7th Edition):
Navalon, Guillermo. “Evolution of the avian skull : evolutionary drivers of modern bird diversity.” 2019. Web. 27 Feb 2021.
Vancouver:
Navalon G. Evolution of the avian skull : evolutionary drivers of modern bird diversity. [Internet] [Doctoral dissertation]. University of Bristol; 2019. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/1983/e3908f4f-d4a3-4a23-8ee4-9834d88feccd.
Council of Science Editors:
Navalon G. Evolution of the avian skull : evolutionary drivers of modern bird diversity. [Doctoral Dissertation]. University of Bristol; 2019. Available from: http://hdl.handle.net/1983/e3908f4f-d4a3-4a23-8ee4-9834d88feccd
9.
Puschel Rouliez, Thomas.
Morpho-functional analyses of the primate skeleton : applying 3D geometric morphometrics, finite element analysis and phylogenetic comparative methods to assess ecomorphological questions in extant and extinct anthropoids.
Degree: PhD, 2018, University of Manchester
URL: https://www.research.manchester.ac.uk/portal/en/theses/morphofunctional-analyses-of-the-primate-skeleton-applying-3d-geometric-morphometrics-finite-element-analysis-and-phylogenetic-comparative-methods-to-assess-ecomorphological-questions-in-extant-and-extinct-anthropoids(68739f2a-e93f-42b2-9619-845165e2c7ec).html
;
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.771426
► The overarching objective of this dissertation is to understand the relationship between form and ecological function in diverse skeletal elements belonging to different primate clades…
(more)
▼ The overarching objective of this dissertation is to understand the relationship between form and ecological function in diverse skeletal elements belonging to different primate clades using geometric morphometrics (GM), finite element analysis (FEA) and phylogenetic comparative methods (PCMs). GM provides a system for quantifying morphology; while FEA allows measuring biomechanical performance and PCMs are used to model how phenotypic traits have evolved through time. Most chapters in this thesis focus on the association between locomotion and morphology and how to apply this information in the fossil record, while one analyses the form-function relationship in a dietary context. Firstly, a combined approach using FEA and GM is applied to analyse different hominoid scapulae. The obtained results show that there is a significant relationship between scapular shape and its biomechanical performance. Hence at least part of scapular shape variation is due to non-phylogenetic factors. Secondly, it is tested whether there is a sclerocarpic specialization gradient in the mandibular morphology of pitheciids. The results show that there is indeed a relative specialization continuum for some aspects of shape, although the story is more complex from a biomechanical perspective. Subsequently, an analysis of the phenetic affinities of extant platyrrhine tali and their Miocene counterparts is carried out to explain the evolution of talar shape and size in platyrrhines. The results suggest that talar shape diversification can be explained by invoking a model representing a phylogenetic hypothesis in which each platyrrhine family occupied a separate adaptive optimum. Moreover, talar size diversification can be characterised by a multidimensional niche model. Finally, the main locomotor mode of different platyrrhine fossils is inferred by applying a combination of GM, FEA and machine-learning (ML) classification techniques. The ML algorithm applied to both biomechanical and morphometric data categorised most of the fossil sample as arboreal quadrupeds, which is consistent with previous studies. Thus, it is expected to contribute to the understanding of the correlation between form and ecological function, which is not only relevant to appreciate the morphological diversity in extant species, but also because it allows to infer past behaviours in fossil taxa.
Subjects/Keywords: phylogenetic comparative methods; finite element analysis; machine-learning; primates; ecomorphology; geometric morphometrics
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APA ·
Chicago ·
MLA ·
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CSE |
Export
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APA (6th Edition):
Puschel Rouliez, T. (2018). Morpho-functional analyses of the primate skeleton : applying 3D geometric morphometrics, finite element analysis and phylogenetic comparative methods to assess ecomorphological questions in extant and extinct anthropoids. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/morphofunctional-analyses-of-the-primate-skeleton-applying-3d-geometric-morphometrics-finite-element-analysis-and-phylogenetic-comparative-methods-to-assess-ecomorphological-questions-in-extant-and-extinct-anthropoids(68739f2a-e93f-42b2-9619-845165e2c7ec).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.771426
Chicago Manual of Style (16th Edition):
Puschel Rouliez, Thomas. “Morpho-functional analyses of the primate skeleton : applying 3D geometric morphometrics, finite element analysis and phylogenetic comparative methods to assess ecomorphological questions in extant and extinct anthropoids.” 2018. Doctoral Dissertation, University of Manchester. Accessed February 27, 2021.
https://www.research.manchester.ac.uk/portal/en/theses/morphofunctional-analyses-of-the-primate-skeleton-applying-3d-geometric-morphometrics-finite-element-analysis-and-phylogenetic-comparative-methods-to-assess-ecomorphological-questions-in-extant-and-extinct-anthropoids(68739f2a-e93f-42b2-9619-845165e2c7ec).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.771426.
MLA Handbook (7th Edition):
Puschel Rouliez, Thomas. “Morpho-functional analyses of the primate skeleton : applying 3D geometric morphometrics, finite element analysis and phylogenetic comparative methods to assess ecomorphological questions in extant and extinct anthropoids.” 2018. Web. 27 Feb 2021.
Vancouver:
Puschel Rouliez T. Morpho-functional analyses of the primate skeleton : applying 3D geometric morphometrics, finite element analysis and phylogenetic comparative methods to assess ecomorphological questions in extant and extinct anthropoids. [Internet] [Doctoral dissertation]. University of Manchester; 2018. [cited 2021 Feb 27].
Available from: https://www.research.manchester.ac.uk/portal/en/theses/morphofunctional-analyses-of-the-primate-skeleton-applying-3d-geometric-morphometrics-finite-element-analysis-and-phylogenetic-comparative-methods-to-assess-ecomorphological-questions-in-extant-and-extinct-anthropoids(68739f2a-e93f-42b2-9619-845165e2c7ec).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.771426.
Council of Science Editors:
Puschel Rouliez T. Morpho-functional analyses of the primate skeleton : applying 3D geometric morphometrics, finite element analysis and phylogenetic comparative methods to assess ecomorphological questions in extant and extinct anthropoids. [Doctoral Dissertation]. University of Manchester; 2018. Available from: https://www.research.manchester.ac.uk/portal/en/theses/morphofunctional-analyses-of-the-primate-skeleton-applying-3d-geometric-morphometrics-finite-element-analysis-and-phylogenetic-comparative-methods-to-assess-ecomorphological-questions-in-extant-and-extinct-anthropoids(68739f2a-e93f-42b2-9619-845165e2c7ec).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.771426
Duke University
10.
Griffin, Randi Heesoo.
Macroevolution of Primate Skull Shape: Combining Geometric Morphometrics and Phylogenetic Comparative Methods
.
Degree: 2018, Duke University
URL: http://hdl.handle.net/10161/17444
► Primates span incredible behavioral and ecological diversity, and this diversity is reflected in the shape of the skull. This dissertation asks two questions surrounding…
(more)
▼ Primates span incredible behavioral and ecological diversity, and this diversity is reflected in the shape of the skull. This dissertation asks two questions surrounding the evolution of primate skull shape: 1) what are the macroevolutionary correlates of primate skull shape? And 2) what is the pattern of phenotypic integration in the primate skull at a macroevolutionary scale? To address these questions, I compiled a broad comparative dataset of anatomical landmarks identified from 3D scans of primate skulls and analyzed this data using statistical
methods that combine
geometric morphometrics and phylogenetic comparative
methods. To investigate the macroevolutionary correlates of skull shape, I used multivariate phylogenetic generalized linear models to test for relationships between skull shape and several variables that are predicted to be correlated with skull shape: allometry, typical diet, tree gouging behavior, activity pattern, and sexual dimorphism. I found strong phylogenetic signal for primate skull shape, confirming the need for phylogenetic comparative
methods. Allometry was a significant predictor of skull shape, with larger primates having relatively small, convergent orbits, and anteroposteriorly short skulls compared to small primates. Sexual dimorphism was associated with a dramatically lengthened rostrum, probably to facilitate a large gape in aggressive displays. Folivory was associated with deeper mandibles, which may improve mechanical advantage and strain resistance. To investigate patterns of phenotypic integration in the skull, I performed hierarchical clustering analyses on phylogenetically corrected inter-landmark covariance matrices. In contrast to previous research, I did not find evidence for distinct phenotypic modules in the primate skull, and I argue that this discrepancy is due to methodological shortcomings of past research that biased results towards identifying different anatomical regions as discrete modules. This dissertation represents one of the first investigations of primate skull shape at a macroevolutionary scale, and demonstrates that the combination of
geometric morphometrics and phylogenetic comparative
methods can yield novel insights into evolutionary morphology.
Advisors/Committee Members: Nunn, Charles L (advisor).
Subjects/Keywords: Morphology;
Zoology;
Evolution & development;
geometric morphometrics;
macroevolution;
phylogenetic comparative methods;
primates;
skull
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Griffin, R. H. (2018). Macroevolution of Primate Skull Shape: Combining Geometric Morphometrics and Phylogenetic Comparative Methods
. (Thesis). Duke University. Retrieved from http://hdl.handle.net/10161/17444
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Griffin, Randi Heesoo. “Macroevolution of Primate Skull Shape: Combining Geometric Morphometrics and Phylogenetic Comparative Methods
.” 2018. Thesis, Duke University. Accessed February 27, 2021.
http://hdl.handle.net/10161/17444.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Griffin, Randi Heesoo. “Macroevolution of Primate Skull Shape: Combining Geometric Morphometrics and Phylogenetic Comparative Methods
.” 2018. Web. 27 Feb 2021.
Vancouver:
Griffin RH. Macroevolution of Primate Skull Shape: Combining Geometric Morphometrics and Phylogenetic Comparative Methods
. [Internet] [Thesis]. Duke University; 2018. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/10161/17444.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Griffin RH. Macroevolution of Primate Skull Shape: Combining Geometric Morphometrics and Phylogenetic Comparative Methods
. [Thesis]. Duke University; 2018. Available from: http://hdl.handle.net/10161/17444
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Bristol
11.
Navalon, Guillermo.
Evolution of the avian skull : evolutionary drivers of modern bird diversity.
Degree: PhD, 2019, University of Bristol
URL: https://research-information.bris.ac.uk/en/studentTheses/e3908f4f-d4a3-4a23-8ee4-9834d88feccd
;
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782637
► Encompassing more than 11,000 species, birds are the most speciose group of tetrapods in modern-world ecosystems. The modern radiation of birds (Neornithes) originated in the…
(more)
▼ Encompassing more than 11,000 species, birds are the most speciose group of tetrapods in modern-world ecosystems. The modern radiation of birds (Neornithes) originated in the Mesozoic and greatly radiated in disparity following the K-Pg extinction, a radiation which is often believed to have been primarily driven by adaptation in response to ecological opportunity after this biotic crisis. This assumption largely rests on the presumption that the anatomy in birds, particularly the large variety of beak forms, is very correlated with their ecologies, particularly feeding ecology. In this thesis, this presumption is tested in a broad macroevolutionary scale for the first time. I find that this relationship is weaker and more complex than often assumed, suggesting that the diversification of beak morphologies in birds was likely shaped by a more complex set of evolutionary drivers than feeding adaptation, likely involving both extrinsic and intrinsic factors. Consequently, the roles of other intrinsic factors in craniofacial evolution are explored within some selected lineages of modern birds. First, I explore the patterns and strength of the coevolution between the beak and the rest of the skull (cranial integration), across all the lineages of landbirds (Inopinaves) and how these associations affected their craniofacial macroevolution. I find that variations in cranial integration had important implications for cranial evolution, specifically for the two classic avian adaptive radiations: Darwin's finches and Hawaiian honeycreepers. Secondly, I explore craniofacial shape variation over evolution and development in Strisores. My results suggest that evolutionary changes in development played a significant role in shaping macroevolution in this clade of birds. Finally, over this thesis geometric morphometrics and phylogenetic comparative methods are extensively used. I show some current limitations of these methods concerning the quantification of covariation patterns (integration and modularity). I propose a pipeline for identifying potential issues and offer some preliminary novel solutions to overcome them.
Subjects/Keywords: 550; birds; macroevolution; shape; skull; geometric morphometrics; adaptation; constraint; integration; phylogenetic comparative methods; development
Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Navalon, G. (2019). Evolution of the avian skull : evolutionary drivers of modern bird diversity. (Doctoral Dissertation). University of Bristol. Retrieved from https://research-information.bris.ac.uk/en/studentTheses/e3908f4f-d4a3-4a23-8ee4-9834d88feccd ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782637
Chicago Manual of Style (16th Edition):
Navalon, Guillermo. “Evolution of the avian skull : evolutionary drivers of modern bird diversity.” 2019. Doctoral Dissertation, University of Bristol. Accessed February 27, 2021.
https://research-information.bris.ac.uk/en/studentTheses/e3908f4f-d4a3-4a23-8ee4-9834d88feccd ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782637.
MLA Handbook (7th Edition):
Navalon, Guillermo. “Evolution of the avian skull : evolutionary drivers of modern bird diversity.” 2019. Web. 27 Feb 2021.
Vancouver:
Navalon G. Evolution of the avian skull : evolutionary drivers of modern bird diversity. [Internet] [Doctoral dissertation]. University of Bristol; 2019. [cited 2021 Feb 27].
Available from: https://research-information.bris.ac.uk/en/studentTheses/e3908f4f-d4a3-4a23-8ee4-9834d88feccd ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782637.
Council of Science Editors:
Navalon G. Evolution of the avian skull : evolutionary drivers of modern bird diversity. [Doctoral Dissertation]. University of Bristol; 2019. Available from: https://research-information.bris.ac.uk/en/studentTheses/e3908f4f-d4a3-4a23-8ee4-9834d88feccd ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782637
University of Oklahoma
12.
Stucky, Ben.
Cubulating one-relator products with torsion.
Degree: PhD, 2019, University of Oklahoma
URL: http://hdl.handle.net/11244/319548
► Since the resolution of the virtual Haken conjecture in the theory of hyperbolic 3-manifolds, there has been much attention devoted to CAT(0) cube complexes. These…
(more)
▼ Since the resolution of the virtual Haken conjecture in the theory of hyperbolic 3-manifolds, there has been much attention devoted to CAT(0) cube complexes. These non-positively curved metric spaces are powerful tools for understanding infinite, finitely generated groups in part because of their "cubical" combinatorics. Simply knowing that a group is cubulable (acts geometrically – properly and cocompactly by isometries – on a CAT(0) cube complex) is sufficient to unlock a good deal of structural information about it, and cubulating groups has become an important goal of modern
geometric group theory.
In 2013, Lauer and Wise showed that a one-relator group with torsion whose defining relator has exponent at least 4 is cubulable. To achieve this, they build a system of nicely-behaved codimension-1 subspaces ("walls") in the universal cover and invoke a construction due to Sageev.
In this thesis, we achieve a generalization of this result to one-relator products with torsion, namely, that a one-relator product of locally indicable groups whose defining relator has exponent at least 4 admits a
geometric action on a CAT(0) cube complex if the factors do. Our results are framed in the more general context of "staggered" quotients of free products of finitely many locally indicable and cubulable groups. The main tools are
geometric small-cancellation results for van Kampen diagrams over these groups, which allow us to argue that walls are plentiful and geometrically well-behaved in the universal cover. Relative hyperbolicity of these one-relator products and relative quasiconvexity of wall stabilizers both play a central role.
Using Agol's theorem that a hyperbolic, cubulable group is virtually special, we obtain as a corollary that the one-relator products we consider are virtually special provided that the factors are hyperbolic in addition to the other assumptions.
Advisors/Committee Members: Forester, Max (advisor), Jablonski, Michael (committee member), Tao, Jing (committee member), Greene, Scott (committee member), Brady, Noel (committee member).
Subjects/Keywords: Mathematics; Geometric group theory; Topological methods in group theory; Non-positively curved spaces and groups
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Stucky, B. (2019). Cubulating one-relator products with torsion. (Doctoral Dissertation). University of Oklahoma. Retrieved from http://hdl.handle.net/11244/319548
Chicago Manual of Style (16th Edition):
Stucky, Ben. “Cubulating one-relator products with torsion.” 2019. Doctoral Dissertation, University of Oklahoma. Accessed February 27, 2021.
http://hdl.handle.net/11244/319548.
MLA Handbook (7th Edition):
Stucky, Ben. “Cubulating one-relator products with torsion.” 2019. Web. 27 Feb 2021.
Vancouver:
Stucky B. Cubulating one-relator products with torsion. [Internet] [Doctoral dissertation]. University of Oklahoma; 2019. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/11244/319548.
Council of Science Editors:
Stucky B. Cubulating one-relator products with torsion. [Doctoral Dissertation]. University of Oklahoma; 2019. Available from: http://hdl.handle.net/11244/319548
Indian Institute of Science
13.
Vasista, Vinay V.
Automatic Optimization of Geometric Multigrid Methods using a DSL Approach.
Degree: MSc Engg, Faculty of Engineering, 2018, Indian Institute of Science
URL: http://etd.iisc.ac.in/handle/2005/3707
► Geometric Multigrid (GMG) methods are widely used in numerical analysis to accelerate the convergence of partial differential equations solvers using a hierarchy of grid discretizations.…
(more)
▼ Geometric Multigrid (GMG)
methods are widely used in numerical analysis to accelerate the convergence of partial differential equations solvers using a hierarchy of grid discretizations. These solvers find plenty of applications in various fields in engineering and scientific domains, where solving PDEs is of fundamental importance. Using multigrid
methods, the pace at which the solvers arrive at the solution can be improved at an algorithmic level. With the advance in modern computer architecture, solving problems with higher complexity and sizes is feasible - this is also the case with multigrid
methods. However, since hardware support alone cannot achieve high performance in execution time, there is a need for good software that help programmers in doing so.
Multiple grid sizes and recursive expression of multigrid cycles make the task of manual program optimization tedious and error-prone. A high-level language that aids domain experts to quickly express complex algorithms in a compact way using dedicated constructs for multigrid
methods and with good optimization support is thus valuable. Typical computation patterns in a GMG algorithm includes stencils, point-wise accesses, restriction and interpolation of a grid. These computations can be optimized for performance on modern architectures using standard parallelization and locality enhancement techniques.
Several past works have addressed the problem of automatic optimizations of computations in various scientific domains using a domain-specific language (DSL) approach. A DSL is a language with features to express domain-specific computations and compiler support to enable optimizations specific to these computations. Halide and PolyMage are two of the recent works in this direction, that aim to optimize image processing pipelines. Many computations like upsampling and downsampling an image are similar to interpolation and restriction in
geometric multigrid
methods.
In this thesis, we demonstrate how high performance can be achieved on GMG algorithms written in the PolyMage domain-specific language with new optimizations we added to the compiler. We also discuss the implementation of non-trivial optimizations, on PolyMage compiler, necessary to achieve high parallel performance for multigrid
methods on modern architectures. We realize these goals by:
• introducing multigrid domain-specific constructs to minimize the verbosity of the algorithm specification;
• storage remapping to reduce the memory footprint of the program and improve cache locality exploitation;
• mitigating execution time spent in data handling operations like memory allocation and freeing, using a pool of memory, across multiple multigrid cycles; and
• incorporating other well-known techniques to leverage performance, like exploiting multi-dimensional parallelism and minimizing the lifetime of storage buffers.
We evaluate our optimizations on a modern multicore system using five different benchmarks varying in multigrid cycle structure, complexity and size, for two-and…
Advisors/Committee Members: Uday Kumar Reddy, B (advisor).
Subjects/Keywords: Geometric Multigrid Methods; Automatic Optimization; Geometric Multigrid Method; Compiler Optimizations; PolyMage Compiler; DSL Approach; Automatic Optimization; Domain-specific Language Approach; GMG Algorithm; Polyhedral Optimization; Storage Optimization; Computer Science
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Vasista, V. V. (2018). Automatic Optimization of Geometric Multigrid Methods using a DSL Approach. (Masters Thesis). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/3707
Chicago Manual of Style (16th Edition):
Vasista, Vinay V. “Automatic Optimization of Geometric Multigrid Methods using a DSL Approach.” 2018. Masters Thesis, Indian Institute of Science. Accessed February 27, 2021.
http://etd.iisc.ac.in/handle/2005/3707.
MLA Handbook (7th Edition):
Vasista, Vinay V. “Automatic Optimization of Geometric Multigrid Methods using a DSL Approach.” 2018. Web. 27 Feb 2021.
Vancouver:
Vasista VV. Automatic Optimization of Geometric Multigrid Methods using a DSL Approach. [Internet] [Masters thesis]. Indian Institute of Science; 2018. [cited 2021 Feb 27].
Available from: http://etd.iisc.ac.in/handle/2005/3707.
Council of Science Editors:
Vasista VV. Automatic Optimization of Geometric Multigrid Methods using a DSL Approach. [Masters Thesis]. Indian Institute of Science; 2018. Available from: http://etd.iisc.ac.in/handle/2005/3707
Anna University
14.
Towheed, sultana.
Extraction of superficial and volumetric features in
three dimensional digital images using morphological
methods; -.
Degree: Information and Communication
Engineering, 2014, Anna University
URL: http://shodhganga.inflibnet.ac.in/handle/10603/24763
► The purpose of the work intended for research is to formulate techniques and strategies for detecting Superficial and Volumetric features of three dimensional digital images…
(more)
▼ The purpose of the work intended for research is to
formulate techniques and strategies for detecting Superficial and
Volumetric features of three dimensional digital images
Mathematical morphology plays an important role in such
formulations The structuring elements of various discrete
structures are studied using the algebraic tool called Geometric
Filters The concept of Geometric Filters was introduced by Rajan
and newlineothers in 1995 as Geometric interpretation of Extended
Filters which were introduced by Preston Hammer and others in 1985
Extended Filter is a set of theoretical concepts developed with the
help of set valued set functions of extended topology The
traditional topology deals with infinite spaces and constructs The
concept of Topological Filter was introduced by Cartan during 1950s
which is defined as a set of subsets of a power set with the
condition that the presence of an element in the filter ensures the
presence of all its super sets This concept is similar to that of
fundamental frequency and harmonics newline
newline
Appendix p.180-203, References
p.204-214.
Advisors/Committee Members: Rajan, E G.
Subjects/Keywords: Extended Filters; Geometric Filters; Information and communication engineering; Mathematical morphology; Morphological methods; Three dimensional digital images
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Towheed, s. (2014). Extraction of superficial and volumetric features in
three dimensional digital images using morphological
methods; -. (Thesis). Anna University. Retrieved from http://shodhganga.inflibnet.ac.in/handle/10603/24763
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Towheed, sultana. “Extraction of superficial and volumetric features in
three dimensional digital images using morphological
methods; -.” 2014. Thesis, Anna University. Accessed February 27, 2021.
http://shodhganga.inflibnet.ac.in/handle/10603/24763.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Towheed, sultana. “Extraction of superficial and volumetric features in
three dimensional digital images using morphological
methods; -.” 2014. Web. 27 Feb 2021.
Vancouver:
Towheed s. Extraction of superficial and volumetric features in
three dimensional digital images using morphological
methods; -. [Internet] [Thesis]. Anna University; 2014. [cited 2021 Feb 27].
Available from: http://shodhganga.inflibnet.ac.in/handle/10603/24763.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Towheed s. Extraction of superficial and volumetric features in
three dimensional digital images using morphological
methods; -. [Thesis]. Anna University; 2014. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/24763
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
INP Toulouse
15.
Goubinat, Damien.
Contrôle géométrique et méthodes numériques : application au problème de montée d'un avion. : Geometric control and numerical methods and the climbing problem of an aircraft.
Degree: Docteur es, Mathématiques Appliquées, 2017, INP Toulouse
URL: http://www.theses.fr/2017INPT0057
► Ce travail s’intéresse à la phase de montée d’un aéronef civil. Les trajectoires minimisant le temps de montée ainsi que que celles minimisant la consommation…
(more)
▼ Ce travail s’intéresse à la phase de montée d’un aéronef civil. Les trajectoires minimisant le temps de montée ainsi que que celles minimisant la consommation de carburant sont étudiées au travers du contrôle optimal géométrique. La dynamique associée à la phase de montée possède un phénomène dit de perturbation singulière. Ce phénomène, présent dans les systèmes multi-échelle, rend difficile la résolution numérique du problème de contrôle associé. La réduction desystème hamiltonien, permettant de s’affranchir de la difficulté numérique introduite par la perturbation singulière, est étudiée d’un point de vue théorique puis numérique. Dans un second temps, le système réduit est étudié géométriquement. L’utilisation des outils du contrôle géométrique combinée à celui des synthèses à temps court permet de déterminer des familles de trajectoires localement temps-optimales pour des temps courts. Cette étude est complétée par une étude des trajectoires temps-optimales en présence de contraintes d’état. D’un point de vue plus numérique, les méthodes directes et indirectes sont utilisées pour résoudre les différents problèmes. Une synthèse locale est alors réalisée en partant des familles de trajectoires déterminées pour des temps courts. Une étude des trajectoires minimisant la consommation de carburant est également réalisée.
This work concerns the climbing phase of a civil aircraft. The trajectories which minimize the climbing time and the one which minimize the fuel consumption are studied throughout geometric optimal control. The climbing phase dynamics presents a characteristics called singular perturbation. This phenomena exists in multi-scale dynamics which makes the numerical study of the associated control problem difficult. Theoretically and numerically we study the reduction of hamiltonian system. This concept allows to remove the numerical complexity induced by the singular perturbation. Secondly, the reduced system is studied geometrically. Families of timeoptimal trajectories in small time are determined thanks to geometric control tools and small time synthesis. A study of time-optimal trajectories with active state constraints completes this work. From a more numerical point of view, direct and indirect methods are used to solve the climbing problems. A local synthesis for time-optimal trajectory is established starting from the families of trajectory determined in small time. A study of minimum fuel consumption trajectories is also realized.
Advisors/Committee Members: Gergaud, Joseph (thesis director), Cots, Olivier (thesis director).
Subjects/Keywords: Trajectoire de montée; Perturbation singulière; Contrôle géométrique; Contraintes d’états; Méthodes numériques; Climbing trajectory; Singular perturbation; Geometric control; State constraints; Numerical methods
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APA (6th Edition):
Goubinat, D. (2017). Contrôle géométrique et méthodes numériques : application au problème de montée d'un avion. : Geometric control and numerical methods and the climbing problem of an aircraft. (Doctoral Dissertation). INP Toulouse. Retrieved from http://www.theses.fr/2017INPT0057
Chicago Manual of Style (16th Edition):
Goubinat, Damien. “Contrôle géométrique et méthodes numériques : application au problème de montée d'un avion. : Geometric control and numerical methods and the climbing problem of an aircraft.” 2017. Doctoral Dissertation, INP Toulouse. Accessed February 27, 2021.
http://www.theses.fr/2017INPT0057.
MLA Handbook (7th Edition):
Goubinat, Damien. “Contrôle géométrique et méthodes numériques : application au problème de montée d'un avion. : Geometric control and numerical methods and the climbing problem of an aircraft.” 2017. Web. 27 Feb 2021.
Vancouver:
Goubinat D. Contrôle géométrique et méthodes numériques : application au problème de montée d'un avion. : Geometric control and numerical methods and the climbing problem of an aircraft. [Internet] [Doctoral dissertation]. INP Toulouse; 2017. [cited 2021 Feb 27].
Available from: http://www.theses.fr/2017INPT0057.
Council of Science Editors:
Goubinat D. Contrôle géométrique et méthodes numériques : application au problème de montée d'un avion. : Geometric control and numerical methods and the climbing problem of an aircraft. [Doctoral Dissertation]. INP Toulouse; 2017. Available from: http://www.theses.fr/2017INPT0057
Universitat Politècnica de València
16.
Bader, Philipp Karl-Heinz.
Geometric Integrators for Schrödinger Equations
.
Degree: 2014, Universitat Politècnica de València
URL: http://hdl.handle.net/10251/38716
► The celebrated Schrödinger equation is the key to understanding the dynamics of quantum mechanical particles and comes in a variety of forms. Its numerical solution…
(more)
▼ The celebrated Schrödinger equation is the key to understanding the dynamics of
quantum mechanical particles and comes in a variety of forms. Its numerical solution
poses numerous challenges, some of which are addressed in this work.
Arguably the most important problem in quantum mechanics is the so-called harmonic
oscillator due to its good approximation properties for trapping potentials. In
Chapter 2, an algebraic correspondence-technique is introduced and applied to construct
efficient splitting algorithms, based solely on fast Fourier transforms, which
solve quadratic potentials in any number of dimensions exactly - including the important
case of rotating particles and non-autonomous trappings after averaging by Magnus
expansions. The results are shown to transfer smoothly to the Gross-Pitaevskii
equation in Chapter 3. Additionally, the notion of modified nonlinear potentials is
introduced and it is shown how to efficiently compute them using Fourier transforms.
It is shown how to apply complex coefficient splittings to this nonlinear equation and
numerical results corroborate the findings.
In the semiclassical limit, the evolution operator becomes highly oscillatory and standard
splitting
methods suffer from exponentially increasing complexity when raising
the order of the method. Algorithms with only quadratic order-dependence of the
computational cost are found using the Zassenhaus algorithm. In contrast to classical
splittings, special commutators are allowed to appear in the exponents. By construction,
they are rapidly decreasing in size with the semiclassical parameter and can be
exponentiated using only a few Lanczos iterations. For completeness, an alternative
technique based on Hagedorn wavepackets is revisited and interpreted in the light of
Magnus expansions and minor improvements are suggested. In the presence of explicit
time-dependencies in the semiclassical Hamiltonian, the Zassenhaus algorithm
requires a special initiation step. Distinguishing the case of smooth and fast frequencies,
it is shown how to adapt the mechanism to obtain an efficiently computable
decomposition of an effective Hamiltonian that has been obtained after Magnus expansion,
without having to resolve the oscillations by taking a prohibitively small
time-step.
Chapter 5 considers the Schrödinger eigenvalue problem which can be formulated as
an initial value problem after a Wick-rotating the Schrödinger equation to imaginary
time. The elliptic nature of the evolution operator restricts standard splittings to
low order, ¿ < 3, because of the unavoidable appearance of negative fractional timesteps
that correspond to the ill-posed integration backwards in time. The inclusion
of modified potentials lifts the order barrier up to ¿ < 5. Both restrictions can be
circumvented using complex fractional time-steps with positive real part and sixthorder
methods optimized for near-integrable Hamiltonians are presented.
Conclusions and pointers to further research are detailed in Chapter 6, with a special…
Advisors/Committee Members: Blanes Zamora, Sergio (advisor).
Subjects/Keywords: Numerical analysis;
Geometric integrators;
Splitting methods;
Magnus expansion;
Algebraic techniques;
Schrödinger equation;
Gross-Piatevskii equation;
Semiclassical limit;
Imaginary time
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Manager
APA (6th Edition):
Bader, P. K. (2014). Geometric Integrators for Schrödinger Equations
. (Doctoral Dissertation). Universitat Politècnica de València. Retrieved from http://hdl.handle.net/10251/38716
Chicago Manual of Style (16th Edition):
Bader, Philipp Karl-Heinz. “Geometric Integrators for Schrödinger Equations
.” 2014. Doctoral Dissertation, Universitat Politècnica de València. Accessed February 27, 2021.
http://hdl.handle.net/10251/38716.
MLA Handbook (7th Edition):
Bader, Philipp Karl-Heinz. “Geometric Integrators for Schrödinger Equations
.” 2014. Web. 27 Feb 2021.
Vancouver:
Bader PK. Geometric Integrators for Schrödinger Equations
. [Internet] [Doctoral dissertation]. Universitat Politècnica de València; 2014. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/10251/38716.
Council of Science Editors:
Bader PK. Geometric Integrators for Schrödinger Equations
. [Doctoral Dissertation]. Universitat Politècnica de València; 2014. Available from: http://hdl.handle.net/10251/38716
University of Lethbridge
17.
University of Lethbridge. Faculty of Arts and Science.
Spectrodirectional investigation of a geometric-optical canopy reflectance model by laboratory simulation
.
Degree: 2017, University of Lethbridge
URL: http://hdl.handle.net/10133/4855
► Canopy reflectance models (CRMs) can accurately estimate vegetation canopy biophysical-structural information such as Leaf Area Index (LAI) inexpensively using satellite imagery. The strict physical basis…
(more)
▼ Canopy reflectance models (CRMs) can accurately estimate vegetation canopy
biophysical-structural information such as Leaf Area Index (LAI) inexpensively using
satellite imagery. The strict physical basis which geometric-optical CRMs employ to
mathematically link canopy bidirectional reflectance and structure allows for the tangible
replication of a CRM's geometric abstraction of a canopy in the laboratory, enabling
robust CRM validation studies. To this end, the ULGS-2 goniometer was used to obtain
multiangle, hyperspectral (Spectrodirectional) measurements of a specially-designed
tangible physical model forest, developed based upon the Geometric-Optical Mutual
Shadowing (GOMS) CRM, at three different canopy cover densities. GOMS forwardmodelled
reflectance values had high levels of agreement with ULGS-2 measurements,
with obtained reflectance RMSE values ranging from 0.03% to 0.1%. Canopy structure
modelled via GOMS Multiple-Forward-Mode (MFM) inversion had varying levels of
success. The methods developed in this thesis can potentially be extended to more
complex CRMs through the implementation of 3D printing.
Subjects/Keywords: canopy reflectance models;
geometric-optical methods;
goniometer;
physical computational forest simulations;
remote sensing;
spectrodirectional data sampling
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Manager
APA (6th Edition):
Science, U. o. L. F. o. A. a. (2017). Spectrodirectional investigation of a geometric-optical canopy reflectance model by laboratory simulation
. (Thesis). University of Lethbridge. Retrieved from http://hdl.handle.net/10133/4855
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Science, University of Lethbridge. Faculty of Arts and. “Spectrodirectional investigation of a geometric-optical canopy reflectance model by laboratory simulation
.” 2017. Thesis, University of Lethbridge. Accessed February 27, 2021.
http://hdl.handle.net/10133/4855.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Science, University of Lethbridge. Faculty of Arts and. “Spectrodirectional investigation of a geometric-optical canopy reflectance model by laboratory simulation
.” 2017. Web. 27 Feb 2021.
Vancouver:
Science UoLFoAa. Spectrodirectional investigation of a geometric-optical canopy reflectance model by laboratory simulation
. [Internet] [Thesis]. University of Lethbridge; 2017. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/10133/4855.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Science UoLFoAa. Spectrodirectional investigation of a geometric-optical canopy reflectance model by laboratory simulation
. [Thesis]. University of Lethbridge; 2017. Available from: http://hdl.handle.net/10133/4855
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Virginia Tech
18.
Kashefi, Ali.
A Finite-Element Coarse-GridProjection Method for Incompressible Flows.
Degree: MS, Engineering Science and Mechanics, 2017, Virginia Tech
URL: http://hdl.handle.net/10919/79948
► Coarse grid projection (CGP) methodology is a novel multigrid method for systems involving decoupled nonlinear evolution equations and linear elliptic Poisson equations. The nonlinear equations…
(more)
▼ Coarse grid projection (CGP) methodology is a novel multigrid method for systems involving decoupled nonlinear evolution equations and linear elliptic Poisson equations. The nonlinear equations are solved on a fine grid and the linear equations are solved on a corresponding coarsened grid. Mapping operators execute data transfer between the grids. The CGP framework is constructed upon spatial and temporal discretization schemes. This framework has been established for finite volume/difference discretizations as well as explicit time integration
methods. In this article we present for the first time a version of CGP for finite element discretizations, which uses a semi-implicit time integration scheme. The mapping functions correspond to the finite-element shape functions. With the novel data structure introduced, the mapping computational cost becomes insignificant. We apply CGP to pressure correction schemes used for the incompressible Navier Stokes flow computations. This version is validated on standard test cases with realistic boundary conditions using unstructured triangular meshes. We also pioneer investigations of the effects of CGP on the accuracy of the pressure field. It is found that although CGP reduces the pressure field accuracy, it preserves the accuracy of the pressure gradient and thus the velocity field, while achieving speedup factors ranging from approximately 2 to 30. Exploring the influence of boundary conditions on CGP, the minimum speedup occurs for velocity Dirichlet boundary conditions, while the maximum speedup occurs for open boundary conditions. We discuss the CGP method as a guide for partial mesh refinement of incompressible flow computations and show its application for simulations of flow over a backward facing step and flow past a cylinder.
Advisors/Committee Members: Staples, Anne (committeechair), Saad Ragab (committee member), Traian Iliescu (committee member).
Subjects/Keywords: Semi-implicit time integration; Finite elements; Coarse-grid projection; Unstructured grids; Geometric multigrid methods; Pressure-correction schemes
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APA (6th Edition):
Kashefi, A. (2017). A Finite-Element Coarse-GridProjection Method for Incompressible Flows. (Masters Thesis). Virginia Tech. Retrieved from http://hdl.handle.net/10919/79948
Chicago Manual of Style (16th Edition):
Kashefi, Ali. “A Finite-Element Coarse-GridProjection Method for Incompressible Flows.” 2017. Masters Thesis, Virginia Tech. Accessed February 27, 2021.
http://hdl.handle.net/10919/79948.
MLA Handbook (7th Edition):
Kashefi, Ali. “A Finite-Element Coarse-GridProjection Method for Incompressible Flows.” 2017. Web. 27 Feb 2021.
Vancouver:
Kashefi A. A Finite-Element Coarse-GridProjection Method for Incompressible Flows. [Internet] [Masters thesis]. Virginia Tech; 2017. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/10919/79948.
Council of Science Editors:
Kashefi A. A Finite-Element Coarse-GridProjection Method for Incompressible Flows. [Masters Thesis]. Virginia Tech; 2017. Available from: http://hdl.handle.net/10919/79948
Swedish University of Agricultural Sciences
19.
Bergström, Dan.
Techniques and systems for boom-corridor thinning in young dense forests.
Degree: 2009, Swedish University of Agricultural Sciences
URL: http://pub.epsilon.slu.se/2154/
► Young dense stands could be thinned and the cut trees could be sold for bioenergy purposes, thus generating an income at an early stage of…
(more)
▼ Young dense stands could be thinned and the cut trees could be sold for bioenergy purposes, thus generating an income at an early stage of rotations. However, to make the utilization of young stands competitive, the costs of harvesting must be reduced while the value of the remaining stands is maintained at high levels. A possibility could be to develop a strip road and boom-corridor system for thinning young stands with high biomass, as an alternative to conventional pre-commercial thinning. The objectives of the studies underlying this thesis were to evaluate the effects of using new methods and techniques intended to promote efficient felling, bunching and compression of trees in boom-corridor thinning systems. As shown by simulations, combining boom-corridor thinning methods with conventional accumulating felling heads (AFHs), improved AFHs for multiple felling (AFH-2m2) and new techniques for continuous felling boom-corridor-wise (AFH-corr) would provide higher productivity in the order AFH-corr > AFH-2m2 > AFH (the AFH-corr system gave about two-fold higher productivity compared to the AFH system) (I). In field studies, boom-corridor thinning using a conventional AFH gave a significant, 16%, increase in productivity compared to a standard thinning from below treatment (II). The potential utility of a prototype felling head designed for continuous felling in boom-corridors in the field was also studied (III). The results show that felling speeds of about 1.3 m×s-1 can be achieved if cranes that allow higher movement speeds are used. Further, the performance of a prototype compression processing device was investigated in field studies, and the results show that the density of fresh Scots pine bunches could be increased by up to 160%, while reducing their ash contents (and hence nutrient losses) by 50% (IV). It was also found that load compression techniques can raise payloads (IV). In conclusion, if new techniques especially designed for boom-corridor thinning are developed and used in appropriate harvesting systems the productivity, cost-efficiency and profitability of the operation can be greatly increased.
Subjects/Keywords: thinning; methods; forestry equipment; forest stands; fuelwood; diameter; simulation; evaluation; geometric thinning; pre-commercial thinning; thinning systems; bioenergy; fuel wood; small diameter trees.
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Export
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APA (6th Edition):
Bergström, D. (2009). Techniques and systems for boom-corridor thinning in young dense forests. (Doctoral Dissertation). Swedish University of Agricultural Sciences. Retrieved from http://pub.epsilon.slu.se/2154/
Chicago Manual of Style (16th Edition):
Bergström, Dan. “Techniques and systems for boom-corridor thinning in young dense forests.” 2009. Doctoral Dissertation, Swedish University of Agricultural Sciences. Accessed February 27, 2021.
http://pub.epsilon.slu.se/2154/.
MLA Handbook (7th Edition):
Bergström, Dan. “Techniques and systems for boom-corridor thinning in young dense forests.” 2009. Web. 27 Feb 2021.
Vancouver:
Bergström D. Techniques and systems for boom-corridor thinning in young dense forests. [Internet] [Doctoral dissertation]. Swedish University of Agricultural Sciences; 2009. [cited 2021 Feb 27].
Available from: http://pub.epsilon.slu.se/2154/.
Council of Science Editors:
Bergström D. Techniques and systems for boom-corridor thinning in young dense forests. [Doctoral Dissertation]. Swedish University of Agricultural Sciences; 2009. Available from: http://pub.epsilon.slu.se/2154/
University of Michigan
20.
Rosu, Mihaela.
Dose computation in conformal radiation therapy including geometric uncertainties: Methods and clinical implications.
Degree: PhD, Pure Sciences, 2005, University of Michigan
URL: http://hdl.handle.net/2027.42/125485
► The aim of any radiotherapy is to tailor the tumoricidal radiation dose to the target volume and to deliver as little radiation dose as possible…
(more)
▼ The aim of any radiotherapy is to tailor the tumoricidal radiation dose to the target volume and to deliver as little radiation dose as possible to all other normal tissues. However, the motion and deformation induced in human tissue by ventilatory motion is a major issue, as standard practice usually uses only one computed tomography (CT) scan (and hence one instance of the patient's anatomy) for treatment planning. The interfraction movement that occurs due to physiological processes over time scales shorter than the delivery of one treatment fraction leads to differences between the planned and delivered dose distributions. Due to the influence of these differences on tumors and normal tissues, the tumor control probabilities and normal tissue complication probabilities are likely to be impacted upon in the face of organ motion. In this thesis we apply several
methods to compute dose distributions that include the effects of the treatment
geometric uncertainties by using the time-varying anatomical information as an alternative to the conventional Planning Target Volume (PTV) approach. The proposed
methods depend on the model used to describe the patient's anatomy. The dose and fluence convolution approaches for rigid organ motion are discussed first, with application to liver tumors and the rigid component of the lung tumor movements. For non-rigid behavior a dose reconstruction method that allows the accumulation of the dose to the deforming anatomy is introduced, and applied for lung tumor treatments. Furthermore, we apply the cumulative dose approach to investigate how much information regarding the deforming patient anatomy is needed at the time of treatment planning for tumors located in thorax. The results are evaluated from a clinical perspective. All dose calculations are performed using a Monte Carlo based algorithm to ensure more realistic and more accurate handling of tissue heterogeneities – of particular importance in lung cancer treatment planning.
Advisors/Committee Members: Haken, Randal K. Ten (advisor), Bielajew, Alex F. (advisor).
Subjects/Keywords: Clinical; Computation; Conformal Radiation Therapy; Deformation; Dose; Geometric Uncertainties; Implications; Including; Methods
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Export
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APA (6th Edition):
Rosu, M. (2005). Dose computation in conformal radiation therapy including geometric uncertainties: Methods and clinical implications. (Doctoral Dissertation). University of Michigan. Retrieved from http://hdl.handle.net/2027.42/125485
Chicago Manual of Style (16th Edition):
Rosu, Mihaela. “Dose computation in conformal radiation therapy including geometric uncertainties: Methods and clinical implications.” 2005. Doctoral Dissertation, University of Michigan. Accessed February 27, 2021.
http://hdl.handle.net/2027.42/125485.
MLA Handbook (7th Edition):
Rosu, Mihaela. “Dose computation in conformal radiation therapy including geometric uncertainties: Methods and clinical implications.” 2005. Web. 27 Feb 2021.
Vancouver:
Rosu M. Dose computation in conformal radiation therapy including geometric uncertainties: Methods and clinical implications. [Internet] [Doctoral dissertation]. University of Michigan; 2005. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/2027.42/125485.
Council of Science Editors:
Rosu M. Dose computation in conformal radiation therapy including geometric uncertainties: Methods and clinical implications. [Doctoral Dissertation]. University of Michigan; 2005. Available from: http://hdl.handle.net/2027.42/125485
Universidade do Rio Grande do Sul
21.
Maestri, Renan.
Evolução morfológica na radiação dos roedores sigmodontíneos : ecologia e história evolutiva.
Degree: 2017, Universidade do Rio Grande do Sul
URL: http://hdl.handle.net/10183/163695
► Radiações evolutivas estão entre os eventos mais fascinantes da evolução. Grande parte da diversidade da vida, tanto de espécies como ecológica, surgiu nos breves intervalos…
(more)
▼ Radiações evolutivas estão entre os eventos mais fascinantes da evolução. Grande parte da diversidade da vida, tanto de espécies como ecológica, surgiu nos breves intervalos temporais de rápida especiação que configuram as radiações. As causas ecológicas e não-ecológicas do surgimento da diversidade em radiações evolutivas, em especial nas radiações adaptativas, são tema de pesquisa há muito tempo, pelo menos desde que Darwin observou a imensa diversidade de um grupo de pássaros nas ilhas Galápagos. Desde então, as ilhas têm sido os ambientes ideais para o estudo desse fenômeno, e foi a partir das observações e experimentos em ilhas que toda a teoria ecológica das radiações evolutivas surgiu. Contudo, as causas ecológicas das radiações explosivas ocorridas em amplas escalas continentais permanecem tema de constante debate. Nesta tese, foram investigados os determinantes ecológicos e não-ecológicos (e.g., geografia, contingências históricas, efeitos filogenéticos) da evolução morfológica dos roedores sigmodontíneos durante sua radiação na região Neotropical, em especial no continente sul-americano. Para isso, foi quantificada a morfologia do crânio e mandíbula de mais de dois mil exemplares do grupo, e foram investigadas variações ecomorfológicas nos níveis interespecífico (I), intraespecífico (II), e entre assembleias de sigmodontíneos (III). Na Parte I da tese, foram investigadas duas predições da teoria da radiação adaptativa, a correlação-fenótipo ambiente (capítulo 1) e a funcionalidade do fenótipo através da força da mordida (capítulo 2), permitindo determinar o papel da divergência ecológica na evolução morfológica das espécies. Na Parte II (capítulo 3), foram investigadas as contribuições relativas de processos determinísticos e neutros sobre a variação morfológica entre populações de uma espécie de roedor sigmodontíneo amplamente distribuída, Akodon cursor. Na Parte III, a influência da variação ambiental e da distribuição espacial das linhagens filogenéticas de sigmodontíneos sobre o tamanho corporal (capítulo 4) e forma do crânio e mandíbula (capítulo 5), foram investigados no contexto biogeográfico da variação no tamanho e forma média entre assembleias de sigmodontíneos. As contribuições originais desta tese foram: (i) mostrar que a radiação evolutiva dos roedores sigmodontíneos foi guiada principalmente por fatores históricos e geográficos ao invés de fatores ecológicos; (ii) sugerir que radiações evolutivas ocorridas em escalas continentais, especialmente de roedores, têm um componente geográfico e histórico mais determinante do que o componente ecológico; (iii) revelar que a força da mordida varia pouco entre roedores sigmodontíneos herbívoros e granívoros, o que provavelmente é resultado do fenótipo generalista desses roedores; (iv) apontar que sigmodontíneos com dieta insetívora têm uma taxa de evolução mais rápida, e parecem estar evoluindo sua forma do crânio/mandíbula e sua força da mordida em uma direção diferente das demais espécies; (v) demonstrar que, dentro de uma espécie de sigmodontíneo…
Advisors/Committee Members: Freitas, Thales Renato Ochotorena de.
Subjects/Keywords: Morfologia animal; Adaptation; Evolutionary history; Akodon cursor; Sigmodontinae; Evolutionary radiation; Radiação; Functional biogeography; Geometric morphometrics; Macroecology; Macroevolution; Morphological evolution; Natural selection; Neotropics; Phylogenetic community ecology; Phylogenetic comparative methods
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APA ·
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MLA ·
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Manager
APA (6th Edition):
Maestri, R. (2017). Evolução morfológica na radiação dos roedores sigmodontíneos : ecologia e história evolutiva. (Thesis). Universidade do Rio Grande do Sul. Retrieved from http://hdl.handle.net/10183/163695
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Maestri, Renan. “Evolução morfológica na radiação dos roedores sigmodontíneos : ecologia e história evolutiva.” 2017. Thesis, Universidade do Rio Grande do Sul. Accessed February 27, 2021.
http://hdl.handle.net/10183/163695.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Maestri, Renan. “Evolução morfológica na radiação dos roedores sigmodontíneos : ecologia e história evolutiva.” 2017. Web. 27 Feb 2021.
Vancouver:
Maestri R. Evolução morfológica na radiação dos roedores sigmodontíneos : ecologia e história evolutiva. [Internet] [Thesis]. Universidade do Rio Grande do Sul; 2017. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/10183/163695.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Maestri R. Evolução morfológica na radiação dos roedores sigmodontíneos : ecologia e história evolutiva. [Thesis]. Universidade do Rio Grande do Sul; 2017. Available from: http://hdl.handle.net/10183/163695
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Vrije Universiteit Amsterdam
22.
Vargas Rivera, M.
Blowup in two geometric flows
.
Degree: 2011, Vrije Universiteit Amsterdam
URL: http://hdl.handle.net/1871/24161
Subjects/Keywords: wiskunde;
mathematics;
blowup;
geometric flows;
moving mesh methods;
matched asymptotics;
comparison principle
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APA (6th Edition):
Vargas Rivera, M. (2011). Blowup in two geometric flows
. (Doctoral Dissertation). Vrije Universiteit Amsterdam. Retrieved from http://hdl.handle.net/1871/24161
Chicago Manual of Style (16th Edition):
Vargas Rivera, M. “Blowup in two geometric flows
.” 2011. Doctoral Dissertation, Vrije Universiteit Amsterdam. Accessed February 27, 2021.
http://hdl.handle.net/1871/24161.
MLA Handbook (7th Edition):
Vargas Rivera, M. “Blowup in two geometric flows
.” 2011. Web. 27 Feb 2021.
Vancouver:
Vargas Rivera M. Blowup in two geometric flows
. [Internet] [Doctoral dissertation]. Vrije Universiteit Amsterdam; 2011. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/1871/24161.
Council of Science Editors:
Vargas Rivera M. Blowup in two geometric flows
. [Doctoral Dissertation]. Vrije Universiteit Amsterdam; 2011. Available from: http://hdl.handle.net/1871/24161
23.
Givois, Arthur.
Analyse numérique et expérimentale de vibrations non linéaires géométrique de structures élastiques et piézoélectriques. Modèles réduits et interactions modales : Numerical and experimental analysis of nonlinear vibrations of elastic and piezoelectric structures. Reduced-order models and modal interactions.
Degree: Docteur es, Procédés de fabrication - Génie mécanique, 2019, Paris, ENSAM
URL: http://www.theses.fr/2019ENAM0047
► Cette thèse de doctorat concerne l'analyse et la modélisation de structures minces en vibrations de grande amplitude avec transduction piézoélectrique. Ce type de système électromécanique…
(more)
▼ Cette thèse de doctorat concerne l'analyse et la modélisation de structures minces en vibrations de grande amplitude avec transduction piézoélectrique. Ce type de système électromécanique est utilisé dans de nombreuses applications, telles que les microsystèmes électromécaniques (MEMS) ainsi que les systèmes de contrôle ou de récupération d’énergie. Dans ce travail, on propose une stratégie numérique pour calculer efficacement la dynamique non-linéaire de ce problème couplé électromécanique avec des non-linéarités géométriques. La méthodologie est fondée sur des modèles réduits modaux, obtenus & partir de modèles analytiques ou par des formulations numériques éléments-finis originales. Dans ce dernier cas, les modèles réduits sont obtenus de manière non intrusive en utilisant des codes de calculs existants. Ces modèles sont ensuite résolus par une procédure de continuation de solutions périodiques. Cette thèse présente des résultats originaux de validation des méthodes non-intrusives, d'une part, et de convergence des modèles réduits, d'autre part, pour des structures minces de référence. Une stratégie expérimentale est également proposée pour mettre en évidence des phénomènes non-linéaires sur une structure avec actionnement et détection piézoélectriques complétement intégrés. Une méthode de continuation expérimentale, fondée sur le contrôle de la phase, est utilisée pour mesurer la réponse du système en régime libre (les modes non linéaires) et en régime forcé périodique. Des réponses vibratoires complexes, liées à des résonances internes entre modes, sont mesurés et caractérisées précisément, dans le cadre de vibrations asymétriques de plaques circulaires élastique et piézoélectrique.
This doctoral dissertation addresses the analysis and the modelling of the large amplitude nonlinear vibrations of thin structures with piezoelectric transduction. This type of system is used in numerous applications, such as Micro-Electromechanical Systems (MEMS), control-based systems or energy harvesting. This work proposes a numerical strategy to compute efficiently the nonlinear dynamics of electromechanical problems with geometric nonlinearities. The methodology is founded on the computation of modal reduced order models obtained from analytical and finite element approaches. In the latter case, the reduced order models are obtained by non-intrusive strategies using existing finite-element codes. Then, they are finally computed with a numerical method of continuation of periodic solutions. Original results are presented, about the validation of the non-intrusive methods and the convergence of the modal reduced order models, for reference thin structures. An experimental strategy is also proposed to highlight nonlinear phenomena on a structure with fully integrated piezoelectric actuation and detection. A phase locked-loop experimental continuation procedure is used to measure exchanges of energy due to internal resonances between asymmetric vibration modes in circular elastic and piezoelectric plates.
Advisors/Committee Members: Thomas, Olivier (thesis director), Deü, Jean-François (thesis director).
Subjects/Keywords: Vibrations; Non-Linéarités géométriques; Piézoélectricité; Réduction de modèles éléments finis; Méthodes de continuation; Analyse expérimentale; Vibrations; Geometric Nonlinearities; Piezoelectricity; Finite Element Reduced-Order Models; Continuation methods; Experimental analysis; 530
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Givois, A. (2019). Analyse numérique et expérimentale de vibrations non linéaires géométrique de structures élastiques et piézoélectriques. Modèles réduits et interactions modales : Numerical and experimental analysis of nonlinear vibrations of elastic and piezoelectric structures. Reduced-order models and modal interactions. (Doctoral Dissertation). Paris, ENSAM. Retrieved from http://www.theses.fr/2019ENAM0047
Chicago Manual of Style (16th Edition):
Givois, Arthur. “Analyse numérique et expérimentale de vibrations non linéaires géométrique de structures élastiques et piézoélectriques. Modèles réduits et interactions modales : Numerical and experimental analysis of nonlinear vibrations of elastic and piezoelectric structures. Reduced-order models and modal interactions.” 2019. Doctoral Dissertation, Paris, ENSAM. Accessed February 27, 2021.
http://www.theses.fr/2019ENAM0047.
MLA Handbook (7th Edition):
Givois, Arthur. “Analyse numérique et expérimentale de vibrations non linéaires géométrique de structures élastiques et piézoélectriques. Modèles réduits et interactions modales : Numerical and experimental analysis of nonlinear vibrations of elastic and piezoelectric structures. Reduced-order models and modal interactions.” 2019. Web. 27 Feb 2021.
Vancouver:
Givois A. Analyse numérique et expérimentale de vibrations non linéaires géométrique de structures élastiques et piézoélectriques. Modèles réduits et interactions modales : Numerical and experimental analysis of nonlinear vibrations of elastic and piezoelectric structures. Reduced-order models and modal interactions. [Internet] [Doctoral dissertation]. Paris, ENSAM; 2019. [cited 2021 Feb 27].
Available from: http://www.theses.fr/2019ENAM0047.
Council of Science Editors:
Givois A. Analyse numérique et expérimentale de vibrations non linéaires géométrique de structures élastiques et piézoélectriques. Modèles réduits et interactions modales : Numerical and experimental analysis of nonlinear vibrations of elastic and piezoelectric structures. Reduced-order models and modal interactions. [Doctoral Dissertation]. Paris, ENSAM; 2019. Available from: http://www.theses.fr/2019ENAM0047
University of the Western Cape
24.
Elsheikh, Sara Mohamed Ahmed Suleiman.
Analysis and implementation of robust numerical methods to solve mathematical models of HIV and Malaria co-infection
.
Degree: 2011, University of the Western Cape
URL: http://hdl.handle.net/11394/1784
► There is a growing interest in the dynamics of the co-infection of these two diseases. In this thesis, firstly we focus on studying the effect…
(more)
▼ There is a growing interest in the dynamics of the co-infection of these two diseases. In this thesis, firstly we focus on studying the effect of a distributed delay representing the incubation period for the malaria parasite in the mosquito vector to possibly reduce the initial transmission and prevalence of malaria. This model can be regarded as a generalization of SEI models (with a class for the latently infected mosquitoes) and SI models with a discrete delay for the incubation period in mosquitoes. We study the possibility of occurrence of backward bifurcation. We then extend these ideas to study a full model of HIV and malaria co-infection. To get further inside into the dynamics of the model, we use the
geometric singular perturbation theory to couple the fast and slow models from the full model. Finally, since the governing models are very complex, they cannot be solved analytically and hence we develop and analyze a special class of numerical
methods to solve them.
Advisors/Committee Members: Patidar, Kailash C (advisor), Ouifki, Rachid (advisor).
Subjects/Keywords: Human Immunodeficiency Virus (HIV);
Malaria;
HIV-Malaria Co-infection;
Distributed Delay;
Dynamical Systems;
Geometric Singular Perturbation Theory;
Bifurcation Analysis;
Local Asymptotic Stability;
Global Asymptotic Stability;
Numerical Methods
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Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Elsheikh, S. M. A. S. (2011). Analysis and implementation of robust numerical methods to solve mathematical models of HIV and Malaria co-infection
. (Thesis). University of the Western Cape. Retrieved from http://hdl.handle.net/11394/1784
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Elsheikh, Sara Mohamed Ahmed Suleiman. “Analysis and implementation of robust numerical methods to solve mathematical models of HIV and Malaria co-infection
.” 2011. Thesis, University of the Western Cape. Accessed February 27, 2021.
http://hdl.handle.net/11394/1784.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Elsheikh, Sara Mohamed Ahmed Suleiman. “Analysis and implementation of robust numerical methods to solve mathematical models of HIV and Malaria co-infection
.” 2011. Web. 27 Feb 2021.
Vancouver:
Elsheikh SMAS. Analysis and implementation of robust numerical methods to solve mathematical models of HIV and Malaria co-infection
. [Internet] [Thesis]. University of the Western Cape; 2011. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/11394/1784.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Elsheikh SMAS. Analysis and implementation of robust numerical methods to solve mathematical models of HIV and Malaria co-infection
. [Thesis]. University of the Western Cape; 2011. Available from: http://hdl.handle.net/11394/1784
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Duke University
25.
Lunagomez, Simon.
A Geometric Approach for Inference on Graphical Models
.
Degree: 2009, Duke University
URL: http://hdl.handle.net/10161/1354
► We formulate a novel approach to infer conditional independence models or Markov structure of a multivariate distribution. Specifically, our objective is to place informative prior…
(more)
▼ We formulate a novel approach to infer conditional independence models or Markov structure of a multivariate distribution. Specifically, our objective is to place informative prior distributions over graphs (decomposable and unrestricted) and sample efficiently from the induced posterior distribution. We also explore the idea of factorizing according to complete sets of a graph; which implies working with a hypergraph that cannot be retrieved from the graph alone. The key idea we develop in this paper is a parametrization of hypergraphs using the geometry of points in R
m. This induces informative priors on graphs from specified priors on finite sets of points. Constructing hypergraphs from finite point sets has been well studied in the fields of computational topology and random
geometric graphs. We develop the framework underlying this idea and illustrate its efficacy using simulations.
Advisors/Committee Members: Wolpert, Robert L (advisor), Mukherjee, Sayan (advisor).
Subjects/Keywords: Statistics;
Bayesian methods;
Computational topology;
Graphical models;
Random geometric graphs
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Lunagomez, S. (2009). A Geometric Approach for Inference on Graphical Models
. (Thesis). Duke University. Retrieved from http://hdl.handle.net/10161/1354
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Lunagomez, Simon. “A Geometric Approach for Inference on Graphical Models
.” 2009. Thesis, Duke University. Accessed February 27, 2021.
http://hdl.handle.net/10161/1354.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Lunagomez, Simon. “A Geometric Approach for Inference on Graphical Models
.” 2009. Web. 27 Feb 2021.
Vancouver:
Lunagomez S. A Geometric Approach for Inference on Graphical Models
. [Internet] [Thesis]. Duke University; 2009. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/10161/1354.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Lunagomez S. A Geometric Approach for Inference on Graphical Models
. [Thesis]. Duke University; 2009. Available from: http://hdl.handle.net/10161/1354
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Georgia Tech
26.
Niethammer, Marc.
Dynamic Level Sets for Visual Tracking.
Degree: PhD, Electrical and Computer Engineering, 2004, Georgia Tech
URL: http://hdl.handle.net/1853/7606
► This thesis introduces geometric dynamic active contours in the context of visual tracking, augmenting geometric curve evolution with physically motivated dynamics. Adding additional state information…
(more)
▼ This thesis introduces
geometric dynamic active contours in the context of visual tracking,
augmenting
geometric curve evolution with physically motivated dynamics. Adding additional state information to an evolving curve lifts the curve evolution problem to space dimensions larger than two and thus forbids the use of classical level set techniques.
This thesis therefore develops and explores level set
methods for problems of higher codimension,
putting an emphasis on the vector distance function based approach. This formalism is very general, it is interesting in its own right and still a challenging topic.
Two different implementations for
geometric dynamic active contours are explored:
the full level set approach as well as a simpler partial level set approach. The full level set approach results in full topological flexibility and can deal with curve intersections in the image plane. However, it is computationally expensive. On the other hand the partial level set approach gives up the topological flexibility
(intersecting curves cannot be represented) for increased computational efficiency. Contours colliding with different dynamic information (e.g., objects crossing in the image plane)
will be merged in the partial level set approach whereas they will correctly traverse each other
in the full level set approach. Both implementations are illustrated on synthetic and real examples.
Compared to the traditional static curve evolution case, fundamentally different evolution behaviors can be obtained by propagating additional information along with every point on a curve.
Advisors/Committee Members: Tannenbaum, Allen (Committee Chair), Egerstedt, Magnus (Committee Member), Jacobs, Laurence J. (Committee Member), Scott, Waymond (Committee Member), Yezzi, Anthony (Committee Member).
Subjects/Keywords: Dynamic active contours; Level set methods for higher codimensions; Geometric curve evolution theory
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APA ·
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Export
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Manager
APA (6th Edition):
Niethammer, M. (2004). Dynamic Level Sets for Visual Tracking. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/7606
Chicago Manual of Style (16th Edition):
Niethammer, Marc. “Dynamic Level Sets for Visual Tracking.” 2004. Doctoral Dissertation, Georgia Tech. Accessed February 27, 2021.
http://hdl.handle.net/1853/7606.
MLA Handbook (7th Edition):
Niethammer, Marc. “Dynamic Level Sets for Visual Tracking.” 2004. Web. 27 Feb 2021.
Vancouver:
Niethammer M. Dynamic Level Sets for Visual Tracking. [Internet] [Doctoral dissertation]. Georgia Tech; 2004. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/1853/7606.
Council of Science Editors:
Niethammer M. Dynamic Level Sets for Visual Tracking. [Doctoral Dissertation]. Georgia Tech; 2004. Available from: http://hdl.handle.net/1853/7606
27.
Rasheed, Md. Muhibur.
Predicting multibody assembly of proteins.
Degree: PhD, Computer Sciences, 2014, University of Texas – Austin
URL: http://hdl.handle.net/2152/26149
► This thesis addresses the multi-body assembly (MBA) problem in the context of protein assemblies. [...] In this thesis, we chose the protein assembly domain because…
(more)
▼ This thesis addresses the multi-body assembly (MBA) problem in the context of protein assemblies. [...] In this thesis, we chose the protein assembly domain because accurate and reliable computational modeling, simulation and prediction of such assemblies would clearly accelerate discoveries in understanding of the complexities of metabolic pathways, identifying the molecular basis for normal health and diseases, and in the designing of new drugs and other therapeutics. [...] [We developed] F²Dock (Fast Fourier Docking) which includes a multi-term function which includes both a statistical thermodynamic approximation of molecular free energy as well as several of knowledge-based terms. Parameters of the scoring model were learned based on a large set of positive/negative examples, and when tested on 176 protein complexes of various types, showed excellent accuracy in ranking correct configurations higher (F² Dock ranks the correcti solution as the top ranked one in 22/176 cases, which is better than other unsupervised prediction software on the same benchmark). Most of the protein-protein interaction scoring terms can be expressed as integrals over the occupied volume, boundary, or a set of discrete points (atom locations), of distance dependent decaying kernels. We developed a dynamic adaptive grid (DAG) data structure which computes smooth surface and volumetric representations of a protein complex in O(m log m) time, where m is the number of atoms assuming that the smallest feature size h is [theta](r[subscript max]) where r[subscript max] is the radius of the largest atom; updates in O(log m) time; and uses O(m)memory. We also developed the dynamic packing grids (DPG) data structure which supports quasi-constant time updates (O(log w)) and spherical neighborhood queries (O(log log w)), where w is the word-size in the RAM. DPG and DAG together results in O(k) time approximation of scoring terms where k << m is the size of the contact region between proteins. [...] [W]e consider the symmetric spherical shell assembly case, where multiple copies of identical proteins tile the surface of a sphere. Though this is a restricted subclass of MBA, it is an important one since it would accelerate development of drugs and antibodies to prevent viruses from forming capsids, which have such spherical symmetry in nature. We proved that it is possible to characterize the space of possible symmetric spherical layouts using a small number of representative local arrangements (called tiles), and their global configurations (tiling). We further show that the tilings, and the mapping of proteins to tilings on arbitrary sized shells is parameterized by 3 discrete parameters and 6 continuous degrees of freedom; and the 3 discrete DOF can be restricted to a constant number of cases if the size of the shell is known (in terms of the number of protein n). We also consider the case where a coarse model of the whole complex of proteins are available. We show that even when such coarse models do not show atomic positions, they can be…
Advisors/Committee Members: Bajaj, Chandrajit (advisor).
Subjects/Keywords: Spatial data structures; Dynamic data structures; Geometric optimization; Fast Fourier methods; Computational geometry; Tiling; Polyhedra molecular modeling; Molecular surface; Free energy; Uncertainty quantification
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APA ·
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MLA ·
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Export
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Manager
APA (6th Edition):
Rasheed, M. M. (2014). Predicting multibody assembly of proteins. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/26149
Chicago Manual of Style (16th Edition):
Rasheed, Md Muhibur. “Predicting multibody assembly of proteins.” 2014. Doctoral Dissertation, University of Texas – Austin. Accessed February 27, 2021.
http://hdl.handle.net/2152/26149.
MLA Handbook (7th Edition):
Rasheed, Md Muhibur. “Predicting multibody assembly of proteins.” 2014. Web. 27 Feb 2021.
Vancouver:
Rasheed MM. Predicting multibody assembly of proteins. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2014. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/2152/26149.
Council of Science Editors:
Rasheed MM. Predicting multibody assembly of proteins. [Doctoral Dissertation]. University of Texas – Austin; 2014. Available from: http://hdl.handle.net/2152/26149
University of Adelaide
28.
Haskard, Kathryn Anne.
An anisotropic Matern spatial covariance model: REML estimation and properties.
Degree: 2007, University of Adelaide
URL: http://hdl.handle.net/2440/47972
► This thesis concerns the development, estimation and investigation of a general anisotropic spatial correlation function, within model-based geostatistics, expressed as a Gaussian linear mixed model,…
(more)
▼ This thesis concerns the development, estimation and investigation of a general anisotropic spatial correlation function, within model-based geostatistics, expressed as a Gaussian linear mixed model, and estimated using residual maximum likelihood (REML).
The Matern correlation function is attractive because of its parameter which controls smoothness of the spatial process, and which can be estimated from the data. This function is combined with
geometric anisotropy, with an extension permitting different distance metrics, forming a flexible spatial covariance model which incorporates as special cases many infinite- range spatial covariance functions in common use.
Derivatives of the residual log-likelihood with respect to the four correlation-model parameters are derived, and the REML algorithm coded in Splus for testing and refinement as a precursor to its implementation into the software ASReml, with additional generality of linear mixed models. Suggestions are given regarding initial values for the estimation. A residual likelihood ratio test for anisotropy is also developed and investigated.
Application to three soil-based examples reveals that anisotropy does occur in practice, and that this technique is able to fit covariance models previously unavailable or inaccessible.
Simulations of isotropic and anisotropic data with and without a nugget effect reveal the following principal points. Inclusion of some closely-spaced locations greatly improves estimation, particularly of the Matern smoothness parameter, and of the nugget variance when present. The presence of
geometric anisotropy does not adversely affect parameter estimation. Presence of a nugget effect introduces greater uncertainty into the parameter estimates, most dramatically for the smoothness parameter, and also increases the chance of non-convergence and decreases the power of the test for anisotropy. Estimation is more difficult with very “unsmooth" processes (Matern smoothness parameter 0.1 or 0.25) | non- convergence is more likely and estimates are less precise and/or more biased. However it is still often possible to fit the full model including both anisotropy and nugget effect using REML with as few as 100 observations.
Additional simulations involving model misspecification reveal that ignoring anisotropy when it is present can substantially increase the mean squared error of prediction, but overfitting by attempting to model anisotropy when it is absent is less damaging. Further, plug-in estimates of prediction error variance are reasonable estimates of the actual mean squared error of prediction, regardless of the model fitted, weakening the argument requiring Bayesian approaches to properly allow for uncertainty in the parameter estimates when estimating prediction error variance.
The most valuable outcome of this research is the implementation of an anisotropic Matern correlation function in ASReml, including the full generality of Gaussian linear mixed models which permits additional fixed and random effects, making…
Advisors/Committee Members: Verbyla, Ari (advisor), Cullis, Brian R. (advisor), School of Agriculture, Food and Wine : Biometrics (school).
Subjects/Keywords: Matern correlation; geometric anisotropy; model-based geostatistics; residual maximum likehood; REML; Matern covariance; Geology – Statistical methods.; Soils – Analysis – Statistical methods.
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APA ·
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MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Haskard, K. A. (2007). An anisotropic Matern spatial covariance model: REML estimation and properties. (Thesis). University of Adelaide. Retrieved from http://hdl.handle.net/2440/47972
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Haskard, Kathryn Anne. “An anisotropic Matern spatial covariance model: REML estimation and properties.” 2007. Thesis, University of Adelaide. Accessed February 27, 2021.
http://hdl.handle.net/2440/47972.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Haskard, Kathryn Anne. “An anisotropic Matern spatial covariance model: REML estimation and properties.” 2007. Web. 27 Feb 2021.
Vancouver:
Haskard KA. An anisotropic Matern spatial covariance model: REML estimation and properties. [Internet] [Thesis]. University of Adelaide; 2007. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/2440/47972.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Haskard KA. An anisotropic Matern spatial covariance model: REML estimation and properties. [Thesis]. University of Adelaide; 2007. Available from: http://hdl.handle.net/2440/47972
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Universitat Politècnica de València
29.
Kopylov, Nikita.
Magnus-based geometric integrators for dynamical systems with time-dependent potentials
.
Degree: 2019, Universitat Politècnica de València
URL: http://hdl.handle.net/10251/118798
► [ES] Esta tesis trata sobre la integración numérica de sistemas hamiltonianos con potenciales explícitamente dependientes del tiempo. Los problemas de este tipo son comunes en…
(more)
▼ [ES] Esta tesis trata sobre la integración numérica de sistemas hamiltonianos con potenciales explícitamente dependientes del tiempo. Los problemas de este tipo son comunes en la física matemática, porque provienen de la mecánica cuántica, clásica y celestial.
La meta de la tesis es construir integradores para unos problemas relevantes no autónomos: la ecuación de Schrödinger, que es el fundamento de la mecánica cuántica; las ecuaciones de Hill y de onda, que describen sistemas oscilatorios; el problema de Kepler con la masa variante en el tiempo.
El Capítulo 1 describe la motivación y los objetivos de la obra en el contexto histórico de la integración numérica. En el Capítulo 2 se introducen los conceptos esenciales y unas herramientas fundamentales utilizadas a lo largo de la tesis.
El diseño de los integradores propuestos se basa en los métodos de composición y escisión y en el desarrollo de Magnus. En el Capítulo 3 se describe el primero. Su idea principal consta de una recombinación de unos integradores sencillos para obtener la solución del problema. El concepto importante de las condiciones de orden se describe en ese capítulo. En el Capítulo 4 se hace un resumen de las álgebras de Lie y del desarrollo de Magnus que son las herramientas algebraicas que permiten expresar la solución de ecuaciones diferenciales dependientes del tiempo.
La ecuación lineal de Schrödinger con potencial dependiente del tiempo está examinada en el Capítulo 5. Dado su estructura particular, nuevos métodos casi sin conmutadores, basados en el desarrollo de Magnus, son construidos. Su eficiencia es demostrada en unos experimentos numéricos con el modelo de Walker-Preston de una molécula dentro de un campo electromagnético.
En el Capítulo 6, se diseñan los métodos de Magnus-escisión para las ecuaciones de onda y de Hill. Su eficiencia está demostrada en los experimentos numéricos con varios sistemas oscilatorios: con la ecuación de Mathieu, la ec. de Hill matricial, las ecuaciones de onda y de Klein-Gordon-Fock.
El Capítulo 7 explica cómo el enfoque algebraico y el desarrollo de Magnus pueden generalizarse a los problemas no lineales. El ejemplo utilizado es el problema de Kepler con masa decreciente.
El Capítulo 8 concluye la tesis, reseña los resultados y traza las posibles direcciones de la investigación futura.; [CAT] Aquesta tesi tracta de la integració numèrica de sistemes hamiltonians amb potencials explícitament dependents del temps. Els problemes d'aquest tipus són comuns en la física matemàtica, perquè provenen de la mecànica quàntica, clàssica i celest.
L'objectiu de la tesi és construir integradors per a uns problemes rellevants no autònoms: l'equació de Schrödinger, que és el fonament de la mecànica quàntica; les equacions de Hill i d'ona, que descriuen sistemes oscil·latoris; el problema de Kepler amb la massa variant en el temps.
El Capítol 1 descriu la motivació i els objectius de l'obra en el context històric de la integració numèrica. En Capítol 2 s'introdueixen els conceptes essencials i unes ferramentes…
Advisors/Committee Members: Bader, Philipp Karl Heinz (advisor), Blanes Zamora, Sergio (advisor).
Subjects/Keywords: Numerical analysis;
Geometric numerical integration;
Symplectic integrator;
Structure preservation;
Differential equations;
Time-dependent;
Non-autonomous;
Magnus expansion;
Splitting methods;
Composition methods;
Schrödinger equation;
Wave equation;
Hill equation;
Mathieu equation;
Kepler problem;
Quasi-commutator-free;
Quasi-Magnus;
Magnus-splitting
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APA (6th Edition):
Kopylov, N. (2019). Magnus-based geometric integrators for dynamical systems with time-dependent potentials
. (Doctoral Dissertation). Universitat Politècnica de València. Retrieved from http://hdl.handle.net/10251/118798
Chicago Manual of Style (16th Edition):
Kopylov, Nikita. “Magnus-based geometric integrators for dynamical systems with time-dependent potentials
.” 2019. Doctoral Dissertation, Universitat Politècnica de València. Accessed February 27, 2021.
http://hdl.handle.net/10251/118798.
MLA Handbook (7th Edition):
Kopylov, Nikita. “Magnus-based geometric integrators for dynamical systems with time-dependent potentials
.” 2019. Web. 27 Feb 2021.
Vancouver:
Kopylov N. Magnus-based geometric integrators for dynamical systems with time-dependent potentials
. [Internet] [Doctoral dissertation]. Universitat Politècnica de València; 2019. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/10251/118798.
Council of Science Editors:
Kopylov N. Magnus-based geometric integrators for dynamical systems with time-dependent potentials
. [Doctoral Dissertation]. Universitat Politècnica de València; 2019. Available from: http://hdl.handle.net/10251/118798
Texas A&M University
30.
Parag, Parimal.
Delay-sensitive Communications Code-Rates, Strategies, and Distributed Control.
Degree: PhD, Electrical Engineering, 2012, Texas A&M University
URL: http://hdl.handle.net/1969.1/ETD-TAMU-2011-12-10699
► An ever increasing demand for instant and reliable information on modern communication networks forces codewords to operate in a non-asymptotic regime. To achieve reliability for…
(more)
▼ An ever increasing demand for instant and reliable information on modern communication networks forces codewords to operate in a non-asymptotic regime. To achieve reliability for imperfect channels in this regime, codewords need to be retransmitted from receiver to the transmit buffer, aided by a fast feedback mechanism. Large occupancy of this buffer results in longer communication delays. Therefore, codewords need to be designed carefully to reduce transmit queue-length and thus the delay experienced in this buffer. We first study the consequences of physical layer decisions on the transmit buffer occupancy. We develop an analytical framework to relate physical layer channel to the transmit buffer occupancy. We compute the optimal code-rate for finite-length codewords operating over a correlated channel, under certain communication service guarantees. We show that channel memory has a significant impact on this optimal code-rate.
Next, we study the delay in small ad-hoc networks. In particular, we find out what rates can be supported on a small network, when each flow has a certain end-to-end service guarantee. To this end, service guarantee at each intermediate link is characterized. These results are applied to study the potential benefits of setting up a network suitable for network coding in multicast. In particular, we quantify the gains of network coding over classic routing for service provisioned multicast communication over butterfly networks. In the wireless setting, we study the trade-off between communications gains achieved by network coding and the cost to set-up a network enabling network coding. In particular, we show existence of scenarios where one should not attempt to create a network suitable for coding.
Insights obtained from these studies are applied to design a distributed rate control algorithm in a large network. This algorithm maximizes sum-utility of all flows, while satisfying per-flow end-to-end service guarantees. We introduce a notion of effective-capacity per communication link that captures the service requirements of flows sharing this link. Each link maintains a price and effective-capacity, and each flow maintains rate and dissatisfaction. Flows and links update their respective variables locally, and we show that their decisions drive the system to an optimal point. We implemented our algorithm on a network simulator and studied its convergence behavior on few networks of practical interest.
Advisors/Committee Members: Chamberland, Jean-Francois (advisor), Shakkottai, Srinivas (advisor), Schlumprecht, Thomas (committee member), Georghiades, Costas N. (committee member), Datta, Aniruddha (committee member).
Subjects/Keywords: Matrix-geometric methods; correlated erasure channels; butterfly network; communication system; delay; quality of service (QoS); network coding; routing; tail asymptotics; tandem queues; wireless networks; wireless systems; utility maximization; distributed algorithm; resource allocation; congestion control
Record Details
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Record Details
Similar Records
Cite
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Parag, P. (2012). Delay-sensitive Communications Code-Rates, Strategies, and Distributed Control. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2011-12-10699
Chicago Manual of Style (16th Edition):
Parag, Parimal. “Delay-sensitive Communications Code-Rates, Strategies, and Distributed Control.” 2012. Doctoral Dissertation, Texas A&M University. Accessed February 27, 2021.
http://hdl.handle.net/1969.1/ETD-TAMU-2011-12-10699.
MLA Handbook (7th Edition):
Parag, Parimal. “Delay-sensitive Communications Code-Rates, Strategies, and Distributed Control.” 2012. Web. 27 Feb 2021.
Vancouver:
Parag P. Delay-sensitive Communications Code-Rates, Strategies, and Distributed Control. [Internet] [Doctoral dissertation]. Texas A&M University; 2012. [cited 2021 Feb 27].
Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2011-12-10699.
Council of Science Editors:
Parag P. Delay-sensitive Communications Code-Rates, Strategies, and Distributed Control. [Doctoral Dissertation]. Texas A&M University; 2012. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2011-12-10699
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Open Access Theses and Dissertations
