subject:(Biological systems Mathematical models)

University of Oxford

1. Bull, Joshua. Characterisation of macrophage infiltration into solid tumours via image analysis and computational modelling.

Degree: PhD, 2018, University of Oxford

URL: http://ora.ox.ac.uk/objects/uuid:6319ffed-8db3-4e10-924b-cfa677923d34 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.780574

► Macrophages are innate immune cells that play a key role in conditions as diverse as wound healing, atherosclerosis and cancer. In cancer, macrophages may be… (more)

▼ Macrophages are innate immune cells that play a key role in conditions as diverse as wound healing, atherosclerosis and cancer. In cancer, macrophages may be characterised as anti-tumour, promoting a wider immune response and phagocytosing tumour cells, or as pro-tumour, suppressing the immune response and promoting blood vessel growth and metastasis. The spatial distribution of macrophages inside a tumour correlates with patient prognosis and treatment response, and is hypothesised to be predictive of macrophage phenotype. In this thesis, we use a combination of mathematical modelling and image analysis to characterise these distribution patterns and understand the mechanisms by which macrophages may infiltrate solid tumours. We have developed an image analysis pipeline for the automated analysis of whole slide histology images, a rich source of spatial data for the investigation of immune cell distributions in vivo. Our pipeline automatically identifies macrophages and other cell types using a combination of superpixellation and Support Vector Machines (SVMs), and we develop summary statistics which characterise distinct macrophage distributions across different tumour indications based on detected cell locations. We validate our pipeline against real data and benchmark it against human pathologists. We then demonstrate its flexibility and robustness in a range of applications across a variety of datasets. We investigate the observed distributions of macrophages further by using the Chaste (Cancer, Heart and Soft Tissue Environment) modelling framework to develop a new agent-based model of macrophage infiltration into solid tumours. We first use our model to simulate in vitro experiments in which inert microbeads infiltrate into multicellular tumour spheroids (MCTSs). This study enables us to investigate the role of passive infiltration caused by spatial variation in cell proliferation and death rates across the MCTS. The interplay between cell proliferation and death drives an advective flow from nutrient-rich, proliferative, regions towards necrotic regions. Our agent-based framework reproduces results from previous continuum models of this process and provides new insight into the observed infiltration patterns that cannot be obtained without resolving the trajectories of individual particles in an agent-based framework. We subsequently extend this model to describe macrophage infiltration into MCTSs via a combination of passive infiltration and chemotaxis in response to colony stimulating factor-1 (CSF-1). This chemoattractant, which is expressed by hypoxic tumour cells, is implicated in metastasis and is a target for immunotherapy treatments currently in Phase I trials at Roche. Finally, we discuss methods of integrating whole slide imaging with our agent-based modelling approaches and compare simulated macrophage distributions with those from in vivo images analysed using our imaging pipeline.

Subjects/Keywords: Immunology; Mathematics; Mathematical Oncology; Biological systems – Mathematical models; Mathematical Biology

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APA (6^th Edition):

Bull, J. (2018). Characterisation of macrophage infiltration into solid tumours via image analysis and computational modelling. (Doctoral Dissertation). University of Oxford. Retrieved from http://ora.ox.ac.uk/objects/uuid:6319ffed-8db3-4e10-924b-cfa677923d34 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.780574

Chicago Manual of Style (16^th Edition):

Bull, Joshua. “Characterisation of macrophage infiltration into solid tumours via image analysis and computational modelling.” 2018. Doctoral Dissertation, University of Oxford. Accessed January 22, 2021. http://ora.ox.ac.uk/objects/uuid:6319ffed-8db3-4e10-924b-cfa677923d34 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.780574.

MLA Handbook (7^th Edition):

Bull, Joshua. “Characterisation of macrophage infiltration into solid tumours via image analysis and computational modelling.” 2018. Web. 22 Jan 2021.

Vancouver:

Bull J. Characterisation of macrophage infiltration into solid tumours via image analysis and computational modelling. [Internet] [Doctoral dissertation]. University of Oxford; 2018. [cited 2021 Jan 22]. Available from: http://ora.ox.ac.uk/objects/uuid:6319ffed-8db3-4e10-924b-cfa677923d34 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.780574.

Council of Science Editors:

Bull J. Characterisation of macrophage infiltration into solid tumours via image analysis and computational modelling. [Doctoral Dissertation]. University of Oxford; 2018. Available from: http://ora.ox.ac.uk/objects/uuid:6319ffed-8db3-4e10-924b-cfa677923d34 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.780574

Ryerson University

2. Teslya, Alexandra. Adaptive Methods For Stochastic Simulation Of Biochemical Systems.

Degree: 2011, Ryerson University

URL: https://digital.library.ryerson.ca/islandora/object/RULA%3A2081

► Computational and Systems Biology are recently experiencing a rapid development. Mathematical modeling is a key tool in analyzing critical biological processes in cells and living… (more)

Subjects/Keywords: Biological systems – Mathematical models; Stochastic models; Systems biology – Mathematical models; Simulation methods

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APA (6^th Edition):

Teslya, A. (2011). Adaptive Methods For Stochastic Simulation Of Biochemical Systems. (Thesis). Ryerson University. Retrieved from https://digital.library.ryerson.ca/islandora/object/RULA%3A2081

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Teslya, Alexandra. “Adaptive Methods For Stochastic Simulation Of Biochemical Systems.” 2011. Thesis, Ryerson University. Accessed January 22, 2021. https://digital.library.ryerson.ca/islandora/object/RULA%3A2081.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Teslya, Alexandra. “Adaptive Methods For Stochastic Simulation Of Biochemical Systems.” 2011. Web. 22 Jan 2021.

Vancouver:

Teslya A. Adaptive Methods For Stochastic Simulation Of Biochemical Systems. [Internet] [Thesis]. Ryerson University; 2011. [cited 2021 Jan 22]. Available from: https://digital.library.ryerson.ca/islandora/object/RULA%3A2081.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Teslya A. Adaptive Methods For Stochastic Simulation Of Biochemical Systems. [Thesis]. Ryerson University; 2011. Available from: https://digital.library.ryerson.ca/islandora/object/RULA%3A2081

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Ryerson University

3. Gassoumov, Farid. Accurate parametric sensitivity of stochastic biochemical systems.

Degree: 2015, Ryerson University

URL: https://digital.library.ryerson.ca/islandora/object/RULA%3A4673

► Computational and Systems Biology are experiencing a rapid development in recent years. Mathematical and computational modelling are critical tools for studying cellular dynamics. Molecular interactions… (more)

Subjects/Keywords: Stochastic models; Biological systems – Mathematical models; Systems biology – Mathematical models; Markov processes

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APA (6^th Edition):

Gassoumov, F. (2015). Accurate parametric sensitivity of stochastic biochemical systems. (Thesis). Ryerson University. Retrieved from https://digital.library.ryerson.ca/islandora/object/RULA%3A4673

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Gassoumov, Farid. “Accurate parametric sensitivity of stochastic biochemical systems.” 2015. Thesis, Ryerson University. Accessed January 22, 2021. https://digital.library.ryerson.ca/islandora/object/RULA%3A4673.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Gassoumov, Farid. “Accurate parametric sensitivity of stochastic biochemical systems.” 2015. Web. 22 Jan 2021.

Vancouver:

Gassoumov F. Accurate parametric sensitivity of stochastic biochemical systems. [Internet] [Thesis]. Ryerson University; 2015. [cited 2021 Jan 22]. Available from: https://digital.library.ryerson.ca/islandora/object/RULA%3A4673.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Gassoumov F. Accurate parametric sensitivity of stochastic biochemical systems. [Thesis]. Ryerson University; 2015. Available from: https://digital.library.ryerson.ca/islandora/object/RULA%3A4673

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

4. Saha, Sudipta. A comparative analysis on computational methods for fitting an ERGM to biological network data.

Degree: Thesis (M.S.), 2013, Ball State University

URL: http://cardinalscholar.bsu.edu/handle/123456789/197173

► Understanding of a global biological network structure by studying its simple local properties through the well-developed field of graph theory is of interest. In particular,… (more)

Subjects/Keywords: Biological systems – Mathematical models; Graph theory; Network analysis (Planning); Escherichia coli – Genetics – Mathematical models

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APA (6^th Edition):

Saha, S. (2013). A comparative analysis on computational methods for fitting an ERGM to biological network data. (Masters Thesis). Ball State University. Retrieved from http://cardinalscholar.bsu.edu/handle/123456789/197173

Chicago Manual of Style (16^th Edition):

Saha, Sudipta. “A comparative analysis on computational methods for fitting an ERGM to biological network data.” 2013. Masters Thesis, Ball State University. Accessed January 22, 2021. http://cardinalscholar.bsu.edu/handle/123456789/197173.

MLA Handbook (7^th Edition):

Saha, Sudipta. “A comparative analysis on computational methods for fitting an ERGM to biological network data.” 2013. Web. 22 Jan 2021.

Vancouver:

Saha S. A comparative analysis on computational methods for fitting an ERGM to biological network data. [Internet] [Masters thesis]. Ball State University; 2013. [cited 2021 Jan 22]. Available from: http://cardinalscholar.bsu.edu/handle/123456789/197173.

Council of Science Editors:

Saha S. A comparative analysis on computational methods for fitting an ERGM to biological network data. [Masters Thesis]. Ball State University; 2013. Available from: http://cardinalscholar.bsu.edu/handle/123456789/197173

Michigan State University

5. Du, Jun (Graduate of Michigan State University). Transition path theory and transition state.

Degree: 2019, Michigan State University

URL: http://etd.lib.msu.edu/islandora/object/etd:48327

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Thesis Ph. D. Michigan State University. Applied Mathematics 2019.

This thesis will mainly discuss the transition path theory and its extension to the transition state.… (more)

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Thesis Ph. D. Michigan State University. Applied Mathematics 2019.

This thesis will mainly discuss the transition path theory and its extension to the transition state. The framework of transition path theory (TPT) is developed in the context of continuous-time Markov chains on discrete state-spaces. Under the assumption of ergodicity,Transition path theory will first choose any two subsets (mostly metastable states) in the finite state-space based on the equilibrium distribution of the transition probability, and then it analyzes the statistical properties of those associated reactive trajectories, for instance,those trajectories by which the random walker transits from one subset to another. Transition path theory gives properties of these trajectories, such as their probability distribution, their probability current and flux, and their rate of occurrence and finally the dominantreaction pathways. In this thesis, we will first introduce the framework of transition path theory for Markov chains, and then briefly discuss its relation to the electric resistor network theory and Laplacian eigenmaps, and also diffusion maps is discussed as well.Based on Transition Path Theory (TPT) for Markov jump processes, this thesis develops a general approach for identifying and calculating Transition States (TS) of stochastic chemical reacting networks. The thesis first extend the concept of probability current, originally defined on edges connecting different nodes in the configuration space, to each sub-network. To locate sub-networks with maximal probability current on the separatrix between reactive and non-reactive events, which will give the Transition States of the reaction, constraint optimization is conducted. The thesis further introduce an alternative scheme to compute the transition pathways by topological sorting, which is shown to be highly efficient through analysis. Finally, the theory and algorithms are illustrated in several examples.

Description based on online resource;

Advisors/Committee Members: Liu, Di, Wei, Guowei, Zhan, Dapeng, Bates, Peter.

Subjects/Keywords: Probabilities; Markov processes; Biological systems – Mathematical models; Applied mathematics

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APA (6^th Edition):

Du, J. (. o. M. S. U. (2019). Transition path theory and transition state. (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:48327

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Du, Jun (Graduate of Michigan State University). “Transition path theory and transition state.” 2019. Thesis, Michigan State University. Accessed January 22, 2021. http://etd.lib.msu.edu/islandora/object/etd:48327.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Du, Jun (Graduate of Michigan State University). “Transition path theory and transition state.” 2019. Web. 22 Jan 2021.

Vancouver:

Du J(oMSU. Transition path theory and transition state. [Internet] [Thesis]. Michigan State University; 2019. [cited 2021 Jan 22]. Available from: http://etd.lib.msu.edu/islandora/object/etd:48327.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Du J(oMSU. Transition path theory and transition state. [Thesis]. Michigan State University; 2019. Available from: http://etd.lib.msu.edu/islandora/object/etd:48327

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Northeastern University

6. Ghiassian, Susan Dina. Network medicine: a network-based approach to human diseases.

Degree: PhD, Department of Physics, 2015, Northeastern University

URL: http://hdl.handle.net/2047/D20193648

► With the availability of large-scale data, it is now possible to systematically study the underlying interaction maps of many complex systems in multiple disciplines. Statistical… (more)

▼ With the availability of large-scale data, it is now possible to systematically study the underlying interaction maps of many complex systems in multiple disciplines. Statistical physics has a long and successful history in modeling and characterizing systems with a large number of interacting individuals. Indeed, numerous approaches that were first developed in the context of statistical physics, such as the notion of random walks and diffusion processes, have been applied successfully to study and characterize complex systems in the context of network science. Based on these tools, network science has made important contributions to our understanding of many real-world, self-organizing systems, for example in computer science, sociology and economics.; Biological systems are no exception. Indeed, recent studies reflect the necessity of applying statistical and network-based approaches in order to understand complex biological systems, such as cells. In these approaches, a cell is viewed as a complex network consisting of interactions among cellular components, such as genes and proteins. Given the cellular network as a platform, machinery, functionality and failure of a cell can be studied with network-based approaches, a field known as systems biology.; Here, we apply network-based approaches to explore human diseases and their associated genes within the cellular network. This dissertation is divided in three parts: (i) A systematic analysis of the connectivity patterns among disease proteins within the cellular network. The quantification of these patterns inspires the design of an algorithm which predicts a disease-specific subnetwork containing yet unknown disease associated proteins. (ii) We apply the introduced algorithm to explore the common underlying mechanism of many complex diseases. We detect a subnetwork from which inflammatory processes initiate and result in many autoimmune diseases. (iii) The last chapter of this dissertation describes the statistical methods, detailed data curation processes and additional analyses performed to accomplish the previous parts.

Subjects/Keywords: network medicine; network science; Systems biology; Mathematical models; Computational biology; Mathematical models; Biological systems; Mathematical models; Cells; Physiology; Proteins; Diseases; Self-organizing systems

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APA (6^th Edition):

Ghiassian, S. D. (2015). Network medicine: a network-based approach to human diseases. (Doctoral Dissertation). Northeastern University. Retrieved from http://hdl.handle.net/2047/D20193648

Chicago Manual of Style (16^th Edition):

Ghiassian, Susan Dina. “Network medicine: a network-based approach to human diseases.” 2015. Doctoral Dissertation, Northeastern University. Accessed January 22, 2021. http://hdl.handle.net/2047/D20193648.

MLA Handbook (7^th Edition):

Ghiassian, Susan Dina. “Network medicine: a network-based approach to human diseases.” 2015. Web. 22 Jan 2021.

Vancouver:

Ghiassian SD. Network medicine: a network-based approach to human diseases. [Internet] [Doctoral dissertation]. Northeastern University; 2015. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/2047/D20193648.

Council of Science Editors:

Ghiassian SD. Network medicine: a network-based approach to human diseases. [Doctoral Dissertation]. Northeastern University; 2015. Available from: http://hdl.handle.net/2047/D20193648

7. Rehm, Amanda. Proper orthogonal decomposition for parameter estimation in oscillating biological networks.

Degree: MS, 2011, University of Alabama – Birmingham

URL: http://contentdm.mhsl.uab.edu/u?/etd,985

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Proper orthogonal decomposition (POD) is frequently applied to estimate parameters of partial differential equations. This study examines the application of the POD method in estimating… (more)

Subjects/Keywords: Orthogonal decompositions <; br>; Parameter estimation <; br>; Biological systems – Mathematical models <; br>; Oscillations – Mathematical models

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APA (6^th Edition):

Rehm, A. (2011). Proper orthogonal decomposition for parameter estimation in oscillating biological networks. (Masters Thesis). University of Alabama – Birmingham. Retrieved from http://contentdm.mhsl.uab.edu/u?/etd,985

Chicago Manual of Style (16^th Edition):

Rehm, Amanda. “Proper orthogonal decomposition for parameter estimation in oscillating biological networks.” 2011. Masters Thesis, University of Alabama – Birmingham. Accessed January 22, 2021. http://contentdm.mhsl.uab.edu/u?/etd,985.

MLA Handbook (7^th Edition):

Rehm, Amanda. “Proper orthogonal decomposition for parameter estimation in oscillating biological networks.” 2011. Web. 22 Jan 2021.

Vancouver:

Rehm A. Proper orthogonal decomposition for parameter estimation in oscillating biological networks. [Internet] [Masters thesis]. University of Alabama – Birmingham; 2011. [cited 2021 Jan 22]. Available from: http://contentdm.mhsl.uab.edu/u?/etd,985.

Council of Science Editors:

Rehm A. Proper orthogonal decomposition for parameter estimation in oscillating biological networks. [Masters Thesis]. University of Alabama – Birmingham; 2011. Available from: http://contentdm.mhsl.uab.edu/u?/etd,985

Florida Atlantic University

8. Ippolito, Stephen Anthony. Kicks and Maps A different Approach to Modeling Biological Systems.

Degree: 2015, Florida Atlantic University

URL: http://purl.flvc.org/fau/fd/FA00004508 ; (URL) http://purl.flvc.org/fau/fd/FA00004508

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Summary: Modeling a biological systems, is a cyclic process which involves constructing a model from current theory and beliefs and then validating that model against… (more)

Subjects/Keywords: Artificial intellligence – Biological applications; Biology – Mathematical models; Computational intelligence; Differential dynamical systems; Nonliner mechanics – Mathematical models

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APA (6^th Edition):

Ippolito, S. A. (2015). Kicks and Maps A different Approach to Modeling Biological Systems. (Thesis). Florida Atlantic University. Retrieved from http://purl.flvc.org/fau/fd/FA00004508 ; (URL) http://purl.flvc.org/fau/fd/FA00004508

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ippolito, Stephen Anthony. “Kicks and Maps A different Approach to Modeling Biological Systems.” 2015. Thesis, Florida Atlantic University. Accessed January 22, 2021. http://purl.flvc.org/fau/fd/FA00004508 ; (URL) http://purl.flvc.org/fau/fd/FA00004508.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ippolito, Stephen Anthony. “Kicks and Maps A different Approach to Modeling Biological Systems.” 2015. Web. 22 Jan 2021.

Vancouver:

Ippolito SA. Kicks and Maps A different Approach to Modeling Biological Systems. [Internet] [Thesis]. Florida Atlantic University; 2015. [cited 2021 Jan 22]. Available from: http://purl.flvc.org/fau/fd/FA00004508 ; (URL) http://purl.flvc.org/fau/fd/FA00004508.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ippolito SA. Kicks and Maps A different Approach to Modeling Biological Systems. [Thesis]. Florida Atlantic University; 2015. Available from: http://purl.flvc.org/fau/fd/FA00004508 ; (URL) http://purl.flvc.org/fau/fd/FA00004508

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Missouri – Columbia

9. Iyoho, Anthony E., 1978-. Modeling and analysis of nonlinear biological systems.

Degree: PhD, 2007, University of Missouri – Columbia

URL: http://hdl.handle.net/10355/6012

► [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] This dissertation focuses on the modeling and analysis of a set of biological phenomenon… (more)

Subjects/Keywords: Biological systems – Mathematical models; Cytology – Mathematical models

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APA (6^th Edition):

Iyoho, Anthony E., 1. (2007). Modeling and analysis of nonlinear biological systems. (Doctoral Dissertation). University of Missouri – Columbia. Retrieved from http://hdl.handle.net/10355/6012

Chicago Manual of Style (16^th Edition):

Iyoho, Anthony E., 1978-. “Modeling and analysis of nonlinear biological systems.” 2007. Doctoral Dissertation, University of Missouri – Columbia. Accessed January 22, 2021. http://hdl.handle.net/10355/6012.

MLA Handbook (7^th Edition):

Iyoho, Anthony E., 1978-. “Modeling and analysis of nonlinear biological systems.” 2007. Web. 22 Jan 2021.

Vancouver:

Iyoho, Anthony E. 1. Modeling and analysis of nonlinear biological systems. [Internet] [Doctoral dissertation]. University of Missouri – Columbia; 2007. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10355/6012.

Council of Science Editors:

Iyoho, Anthony E. 1. Modeling and analysis of nonlinear biological systems. [Doctoral Dissertation]. University of Missouri – Columbia; 2007. Available from: http://hdl.handle.net/10355/6012

Texas Tech University

10. Sinha, Pradeep. Estimation of ventilation transients of respiratory control system.

Degree: Industrial and Systems Engineering, 1970, Texas Tech University

URL: http://hdl.handle.net/2346/10022

Subjects/Keywords: Biological control systems – Mathematical models; Respiration – Mathematical models

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APA (6^th Edition):

Sinha, P. (1970). Estimation of ventilation transients of respiratory control system. (Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/10022

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sinha, Pradeep. “Estimation of ventilation transients of respiratory control system.” 1970. Thesis, Texas Tech University. Accessed January 22, 2021. http://hdl.handle.net/2346/10022.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sinha, Pradeep. “Estimation of ventilation transients of respiratory control system.” 1970. Web. 22 Jan 2021.

Vancouver:

Sinha P. Estimation of ventilation transients of respiratory control system. [Internet] [Thesis]. Texas Tech University; 1970. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/2346/10022.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sinha P. Estimation of ventilation transients of respiratory control system. [Thesis]. Texas Tech University; 1970. Available from: http://hdl.handle.net/2346/10022

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

McGill University

11. Parrott, Lael. The EcoCyborg project : a model of an artificial ecosystem.

Degree: MS, Department of Agricultural Engineering, 1995, McGill University

URL: https://escholarship.mcgill.ca/downloads/ng451k657.pdf ; https://escholarship.mcgill.ca/concern/theses/05741t84s

► A model of an artificial ecosystem has been formulated for use as a tool to investigate the dynamics of autonomous biosystems. The model is part… (more)

Subjects/Keywords: Biotic communities – Mathematical models.; Biological systems – Mathematical models.

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APA (6^th Edition):

Parrott, L. (1995). The EcoCyborg project : a model of an artificial ecosystem. (Masters Thesis). McGill University. Retrieved from https://escholarship.mcgill.ca/downloads/ng451k657.pdf ; https://escholarship.mcgill.ca/concern/theses/05741t84s

Chicago Manual of Style (16^th Edition):

Parrott, Lael. “The EcoCyborg project : a model of an artificial ecosystem.” 1995. Masters Thesis, McGill University. Accessed January 22, 2021. https://escholarship.mcgill.ca/downloads/ng451k657.pdf ; https://escholarship.mcgill.ca/concern/theses/05741t84s.

MLA Handbook (7^th Edition):

Parrott, Lael. “The EcoCyborg project : a model of an artificial ecosystem.” 1995. Web. 22 Jan 2021.

Vancouver:

Parrott L. The EcoCyborg project : a model of an artificial ecosystem. [Internet] [Masters thesis]. McGill University; 1995. [cited 2021 Jan 22]. Available from: https://escholarship.mcgill.ca/downloads/ng451k657.pdf ; https://escholarship.mcgill.ca/concern/theses/05741t84s.

Council of Science Editors:

Parrott L. The EcoCyborg project : a model of an artificial ecosystem. [Masters Thesis]. McGill University; 1995. Available from: https://escholarship.mcgill.ca/downloads/ng451k657.pdf ; https://escholarship.mcgill.ca/concern/theses/05741t84s

University of Melbourne

12. Trewenack, Abbey Jane. Reaction-diffusion models for dispersing and settling populations in biology.

Degree: 2008, University of Melbourne

URL: http://hdl.handle.net/11343/35250

► We investigate reaction-diffusion models for populations whose members undergo two specific processes: dispersal and settling. Systems of this type occur throughout biological science, in contexts… (more)

▼ We investigate reaction-diffusion models for populations whose members undergo two specific processes: dispersal and settling. Systems of this type occur throughout biological science, in contexts ranging from ecology to cell biology.Here we consider three distinct applications, namely: • animal translocation, • the invasion of a domain by precursor and differentiated cells, and • the development of tissue-engineered cartilage. Mathematical modelling of these systems provides an understanding of the population-level patterns that emerge from the behaviour of individuals. A multi-species reaction-diffusion model is developed and analysed for each of the three applications. We present numerical results, which are illuminated through analytical results derived for simplified or limiting cases. For these special cases, results are obtained using analytical techniques including perturbation analysis, travelling wave analysis and phase plane methods. These analytic results provide a more complete understanding of system behaviour than numerical results alone. Emphasis is placed on connecting modelling results with experimental observations. The first application considered is animal translocations. Translocations are widely used to reintroduce threatened species to areas where they have disappeared. A variety of different dispersal and settling mechanisms are considered, and results compared. The model is applied to a case study of a double translocation of the Maud Island frog, Leiopelma pakeka. Results suggest that settling occurs at a constant rate, with repulsion playing a significantrole in dispersal. This research demonstrates that mathematical modelling of translocations is useful in suggesting design and monitoring strategies for future translocations, and as an aid in understanding observed behaviour. The second application we investigate is the invasion of a domain by cells that migrate, proliferate and differentiate. The model is applicable to neural crest cell invasion in the developing enteric (intestinal) nervous system, but is presented in general terms and is of broader applicability. Regions of the parameter space are characterised according to existence, shape and speed of travelling wave solutions. Our observations may be used in conjunction with experimental results to identify key parameters determining the invasion speed for a particular biological system. Furthermore, these results may assist experimentalists in identifying the resource that is limiting proliferation of precursor cells. As a third application, we propose a model for the development of cartilage around a single chondrocyte. The limited ability of cartilage to repair when damaged…

Subjects/Keywords: reaction-diffusion models; biological systems; mathematical models

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APA (6^th Edition):

Trewenack, A. J. (2008). Reaction-diffusion models for dispersing and settling populations in biology. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/35250

Chicago Manual of Style (16^th Edition):

Trewenack, Abbey Jane. “Reaction-diffusion models for dispersing and settling populations in biology.” 2008. Doctoral Dissertation, University of Melbourne. Accessed January 22, 2021. http://hdl.handle.net/11343/35250.

MLA Handbook (7^th Edition):

Trewenack, Abbey Jane. “Reaction-diffusion models for dispersing and settling populations in biology.” 2008. Web. 22 Jan 2021.

Vancouver:

Trewenack AJ. Reaction-diffusion models for dispersing and settling populations in biology. [Internet] [Doctoral dissertation]. University of Melbourne; 2008. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/11343/35250.

Council of Science Editors:

Trewenack AJ. Reaction-diffusion models for dispersing and settling populations in biology. [Doctoral Dissertation]. University of Melbourne; 2008. Available from: http://hdl.handle.net/11343/35250

Oregon State University

13. El Amrani, Samia. Computationally efficient block diagonalization for downlink multiuser MIMO-OFDM systems.

Degree: MS, Electrical and Computer Engineering, 2010, Oregon State University

URL: http://hdl.handle.net/1957/16857

► One of the key challenges in downlink multiuser multiple-input multiple-output (MIMO) orthogonal frequency division multiplexing (OFDM) systems is the mitigation of the multi-access interference when… (more)

Subjects/Keywords: downlink; MIMO systems – Mathematical models

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APA (6^th Edition):

El Amrani, S. (2010). Computationally efficient block diagonalization for downlink multiuser MIMO-OFDM systems. (Masters Thesis). Oregon State University. Retrieved from http://hdl.handle.net/1957/16857

Chicago Manual of Style (16^th Edition):

El Amrani, Samia. “Computationally efficient block diagonalization for downlink multiuser MIMO-OFDM systems.” 2010. Masters Thesis, Oregon State University. Accessed January 22, 2021. http://hdl.handle.net/1957/16857.

MLA Handbook (7^th Edition):

El Amrani, Samia. “Computationally efficient block diagonalization for downlink multiuser MIMO-OFDM systems.” 2010. Web. 22 Jan 2021.

Vancouver:

El Amrani S. Computationally efficient block diagonalization for downlink multiuser MIMO-OFDM systems. [Internet] [Masters thesis]. Oregon State University; 2010. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1957/16857.

Council of Science Editors:

El Amrani S. Computationally efficient block diagonalization for downlink multiuser MIMO-OFDM systems. [Masters Thesis]. Oregon State University; 2010. Available from: http://hdl.handle.net/1957/16857

Hong Kong University of Science and Technology

14. Dai, Dan. A systematic procedure for applying robot dynamics-based control.

Degree: 2016, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-86630 ; https://doi.org/10.14711/thesis-b1610749 ; http://repository.ust.hk/ir/bitstream/1783.1-86630/1/th_redirect.html

► Although dynamics-based control is a quite old topic and lots of companies, such as ABB, Fanuc and so on claim they have implemented it, there… (more)

▼ Although dynamics-based control is a quite old topic and lots of companies, such as ABB, Fanuc and so on claim they have implemented it, there have little literature about how well it works in practice and how to successfully implement it. This thesis systematically studies robot dynamics modelling, identification and control to comprehensively improve the capability of controller. Sufficient experimental results provide a guide for late researchers. Firstly, we employ geometric method to describe the dynamics in different forms, including recursive, matrix and regressive forms. We make a clear contribution to derive regressive formula which is suitable for dynamics identification and adaptive control. The accuracy of modelling has been validated by comparing with Simmechanics. Next, we identify dynamics model by experiment. We firstly find the minimal identifiable parameters set. The regrouping formula is the first time proposed using geometric method. Secondly, we optimize a identification trajectory in Fourier-Series form. Next, the modified weighted least square algorithm is adopted to estimate parameters. Finally, we do validation experiments for verification. Thirdly, different control schemes are thoroughly simulated in Matlab and implemented via dSpace. We deeply analyse rationality and drawbacks of Traditional PID controller. It only performs well locally due to varying motor inertias at different configurations. We firstly propose to simply add feed-forward torque to current loop. Furthermore, we select computed-torque type controllers designed by feedback linearisation or passivity-based techniques. Traditional PD, Modified PD and Augmented PD controllers are put forward. We add integral terms into PD type law after considering actual experimental performance. Finally, for counteracting effects of imperfect model, we apply adaptive control to on-line modifying model. Here we contribute to a modified adaptive control law for eliminating constraint relationship between position gain K_P and velocity gain K_D. We did thorough simulation to verify the stability, following performance and convergence. For real experiments, we introduce other two commercial controllers for comparison, i.e PDFF controller and HD controller. We study the tuning performance, trajectory accuracy and global stability. For testing adaptive control, we attach 8kg load to robot end. We explore how to successfully implement adaptive control in practice with conclusions that soft loop gain and small time delay are beneficial. Finally, we fulfil some applications based on dynamics model. One is robot teaching by dragging. The dynamics compensation provides assistance force for ease of dragging under a modified control scheme. Besides, we explore energy efficient trajectory planning for P2P movement by considering dynamics constraints. It can be simplified with B-spline parametrization of path which leads to only optimize control points.

Subjects/Keywords: Robots ; Control systems ; Mathematical models

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APA (6^th Edition):

Dai, D. (2016). A systematic procedure for applying robot dynamics-based control. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-86630 ; https://doi.org/10.14711/thesis-b1610749 ; http://repository.ust.hk/ir/bitstream/1783.1-86630/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Dai, Dan. “A systematic procedure for applying robot dynamics-based control.” 2016. Thesis, Hong Kong University of Science and Technology. Accessed January 22, 2021. http://repository.ust.hk/ir/Record/1783.1-86630 ; https://doi.org/10.14711/thesis-b1610749 ; http://repository.ust.hk/ir/bitstream/1783.1-86630/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Dai, Dan. “A systematic procedure for applying robot dynamics-based control.” 2016. Web. 22 Jan 2021.

Vancouver:

Dai D. A systematic procedure for applying robot dynamics-based control. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2016. [cited 2021 Jan 22]. Available from: http://repository.ust.hk/ir/Record/1783.1-86630 ; https://doi.org/10.14711/thesis-b1610749 ; http://repository.ust.hk/ir/bitstream/1783.1-86630/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Dai D. A systematic procedure for applying robot dynamics-based control. [Thesis]. Hong Kong University of Science and Technology; 2016. Available from: http://repository.ust.hk/ir/Record/1783.1-86630 ; https://doi.org/10.14711/thesis-b1610749 ; http://repository.ust.hk/ir/bitstream/1783.1-86630/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

15. Yeung, Chun Kit CSE. Improving deep knowledge tracing with prediction-consistent regularization.

Degree: 2018, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-95795 ; https://doi.org/10.14711/thesis-991012636367803412 ; http://repository.ust.hk/ir/bitstream/1783.1-95795/1/th_redirect.html

► Knowledge tracing is one of the key research areas for empowering personalized education. It is a task to model student’s knowledge state, that is, the… (more)

Subjects/Keywords: Intelligent tutoring systems ; Mathematical models

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APA (6^th Edition):

Yeung, C. K. C. (2018). Improving deep knowledge tracing with prediction-consistent regularization. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-95795 ; https://doi.org/10.14711/thesis-991012636367803412 ; http://repository.ust.hk/ir/bitstream/1783.1-95795/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Yeung, Chun Kit CSE. “Improving deep knowledge tracing with prediction-consistent regularization.” 2018. Thesis, Hong Kong University of Science and Technology. Accessed January 22, 2021. http://repository.ust.hk/ir/Record/1783.1-95795 ; https://doi.org/10.14711/thesis-991012636367803412 ; http://repository.ust.hk/ir/bitstream/1783.1-95795/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Yeung, Chun Kit CSE. “Improving deep knowledge tracing with prediction-consistent regularization.” 2018. Web. 22 Jan 2021.

Vancouver:

Yeung CKC. Improving deep knowledge tracing with prediction-consistent regularization. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2018. [cited 2021 Jan 22]. Available from: http://repository.ust.hk/ir/Record/1783.1-95795 ; https://doi.org/10.14711/thesis-991012636367803412 ; http://repository.ust.hk/ir/bitstream/1783.1-95795/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Yeung CKC. Improving deep knowledge tracing with prediction-consistent regularization. [Thesis]. Hong Kong University of Science and Technology; 2018. Available from: http://repository.ust.hk/ir/Record/1783.1-95795 ; https://doi.org/10.14711/thesis-991012636367803412 ; http://repository.ust.hk/ir/bitstream/1783.1-95795/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Hong Kong

16. Ren, Xiaojing. Modeling pattern formation of swimming E.coli.

Degree: 2010, University of Hong Kong

URL: http://hdl.handle.net/10722/57576

Subjects/Keywords: Pattern formation (Biology) - Mathematical models.; Escherichia coli - Genetics.; Biological systems - Mathematical models.

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ren, X. (2010). Modeling pattern formation of swimming E.coli. (Thesis). University of Hong Kong. Retrieved from http://hdl.handle.net/10722/57576

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ren, Xiaojing. “Modeling pattern formation of swimming E.coli.” 2010. Thesis, University of Hong Kong. Accessed January 22, 2021. http://hdl.handle.net/10722/57576.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ren, Xiaojing. “Modeling pattern formation of swimming E.coli.” 2010. Web. 22 Jan 2021.

Vancouver:

Ren X. Modeling pattern formation of swimming E.coli. [Internet] [Thesis]. University of Hong Kong; 2010. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10722/57576.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ren X. Modeling pattern formation of swimming E.coli. [Thesis]. University of Hong Kong; 2010. Available from: http://hdl.handle.net/10722/57576

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of New Mexico

17. Broilo, Frank Matt. Modeling of a gimbal azimuth drive and simulation of control techniques.

Degree: Electrical and Computer Engineering, 2011, University of New Mexico

URL: http://hdl.handle.net/1928/12024

► A common problem in developing new gimbal products is predicting performance. At the beginning of the design stage, typically the proposal writing stage, it is… (more)

▼ A common problem in developing new gimbal products is predicting performance. At the beginning of the design stage, typically the proposal writing stage, it is critical to be able to anticipate the performance of a design, which may still be very roughly defined. Static performance metrics such as pointing accuracy are easier to predict and can be related to position sensor resolution and compliance in the structure and drive. Dynamic performance metrics such as rate tracking and bandwidth are much more difficult to estimate. These dynamic parameters will serve as the results of this paper. A gimbal model is usually developed in this early stage of design. A model is built for each axis as cross-coupling is not usually significant. The development of each model is inherently dependent on the integrity of the parameters used. Some parameters may be easily accessible and clearly defined, such as manufacturer specifications for commercial-off-the-shelf (COTS) components. An example of these would be motors. A motor datasheet will usually include specifications such as winding resistance, torque constant, etc. Some parameters have to estimated such as drive friction, structural rigidity and drive parameters. There is also much less certainty in these estimates due to their dependence on the integrated, final system. Building an accurate and sufficient model of the system is a challenging task. This thesis developments and validates a single axis gimbal model. Following this is a recursion on the model parameters based upon empirical data. Finally, application of different control laws are evaluated in simulation on the model. First, a classical output feedback law is implemented. Secondly, a state observer is implemented with state feedback. State feedback coefficients are found using both pole placement (PP) algorithms and linear quadratic regulation (LQR) optimal control formulas. Advisors/Committee Members: Abdallah, Chaouki, Jayaweera, Sudharman, Fierro, Rafael.

Subjects/Keywords: Linear control systems – Mathematical models; Feedback control systems – Mathematical models; PID controllers – Mathematical models.

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APA (6^th Edition):

Broilo, F. M. (2011). Modeling of a gimbal azimuth drive and simulation of control techniques. (Masters Thesis). University of New Mexico. Retrieved from http://hdl.handle.net/1928/12024

Chicago Manual of Style (16^th Edition):

Broilo, Frank Matt. “Modeling of a gimbal azimuth drive and simulation of control techniques.” 2011. Masters Thesis, University of New Mexico. Accessed January 22, 2021. http://hdl.handle.net/1928/12024.

MLA Handbook (7^th Edition):

Broilo, Frank Matt. “Modeling of a gimbal azimuth drive and simulation of control techniques.” 2011. Web. 22 Jan 2021.

Vancouver:

Broilo FM. Modeling of a gimbal azimuth drive and simulation of control techniques. [Internet] [Masters thesis]. University of New Mexico; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1928/12024.

Council of Science Editors:

Broilo FM. Modeling of a gimbal azimuth drive and simulation of control techniques. [Masters Thesis]. University of New Mexico; 2011. Available from: http://hdl.handle.net/1928/12024

Stellenbosch University

18. Hanekom, Arno J. Generic kinetic equations for modelling multisubstrate reactions in computational systems biology.

Degree: Biochemistry, 2006, Stellenbosch University

URL: http://hdl.handle.net/10019.1/1659

►

Thesis (MSc (Biochemistry)) – University of Stellenbosch, 2006.

Systems biology is a rapidly developing field, studying biological systems by methodically perturbing them either chemically, genetically or… (more)

▼

Thesis (MSc (Biochemistry)) – University of Stellenbosch, 2006.

Systems biology is a rapidly developing field, studying biological systems by methodically perturbing them either chemically, genetically or biologically. The system response is observed and incorporated into mathematical models. These computational models describe the system structure, predicting its behaviour in response to individual perturbations. Metabolic networks are examples of such systems and are modelled in silico as kinetic models. These kinetic models consist of the constituent enzyme reactions that make up the different pathways of a metabolic network. Each enzyme reaction is represented as a mathematical equation. The main focus of a kinetic model is to portray as realistically as possible a view in silico of physiological behaviour. The equations used to describe model reactions therefore need to make accurate predictions of enzyme behaviour. Numerous enzymes in metabolic networks are cooperative enzymes and many equations have been put forward to describe these reactions. Examples of equations used to model cooperative enzymes are the Adair equation, the uni-reactant Monod, Wyman and Changeux model, Hill equation, and the recently derived reversible Hill equation. Hill equations fit the majority of experimental data very well and have many advantages over their uni-substrate counterparts. In contrast to the abovementioned equations, the majority of enzyme reactions in metabolism are of a multisubstrate nature. Moreover, these multisubstrate reactions should be modelled as reversible reactions, as the contribution of the reverse reaction rate on the net conversion rate can not be ignored [1]. To date, only the bi-substrate reversible MWC equation has been formulated to describe cooperativity for a reversible reaction of more than one substrate. It is, however, difficult to use as a result of numerous parameters, not all of which have clear operational meaning. Moreover, MWC equations do not predict realistic allosteric modifier behaviour [2, 3]. Hofmeyr & Cornish-Bowden [3] showed how the uni-reactant reversible Hill equation succeeds in predicting realistic allosteric inhibitor behaviour, compared to the uni-reactant MWC equation, which does not. The aim of this study was to therefore derive a reversible Hill equation that can describe multisubstrate cooperative reactions and predicts realistic allosteric modifier behaviour. In this work, we present a generalised multisubstrate reversible Hill (GRH) equation. The bi-substrate and three substrate cases of this equation were also extended to incorporate any number of independently binding allosteric modifiers. The derived GRH equation is evaluated against the above mentioned cooperative models and shows good correlation. Moreover, the predicted behaviour of the bi-substrate reversible Hill equation with one allosteric inhibitor is compared to the MWC equation with one allosteric inhibitor in silico. This showed how the bi-substrate reversible Hill equation…

Advisors/Committee Members: Rohwer, J. M., Hofmeyr, J-H. S., University of Stellenbosch. Faculty of Science. Dept. of Biochemistry..

Subjects/Keywords: Biochemistry; Biological systems – Computer simulation; Biological systems – Mathematical models; Biochemistry – Computer simulation

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APA (6^th Edition):

Hanekom, A. J. (2006). Generic kinetic equations for modelling multisubstrate reactions in computational systems biology. (Thesis). Stellenbosch University. Retrieved from http://hdl.handle.net/10019.1/1659

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Hanekom, Arno J. “Generic kinetic equations for modelling multisubstrate reactions in computational systems biology.” 2006. Thesis, Stellenbosch University. Accessed January 22, 2021. http://hdl.handle.net/10019.1/1659.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Hanekom, Arno J. “Generic kinetic equations for modelling multisubstrate reactions in computational systems biology.” 2006. Web. 22 Jan 2021.

Vancouver:

Hanekom AJ. Generic kinetic equations for modelling multisubstrate reactions in computational systems biology. [Internet] [Thesis]. Stellenbosch University; 2006. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10019.1/1659.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Hanekom AJ. Generic kinetic equations for modelling multisubstrate reactions in computational systems biology. [Thesis]. Stellenbosch University; 2006. Available from: http://hdl.handle.net/10019.1/1659

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Rutgers University

19. Wang, Liming, 1978-. Dynamics and asymptotic behaviors of biochemical networks.

Degree: PhD, Mathematics, 2008, Rutgers University

URL: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000050469

►

The purpose of this dissertation is to study the dynamics and asymptotic behaviors of biochemical networks using a "modular'' approach. New mathematics is motivated and… (more)

▼

The purpose of this dissertation is to study the dynamics and asymptotic behaviors of biochemical networks using a "modular'' approach. New mathematics is motivated and developed to analyze modules in terms of the number of steady states and the stability of the steady states. One of the main contributions of the thesis is to extend Hirsch's generic convergence result from monotone systems to systems "close'' to monotone using geometric singular perturbation theory. A monotone system is a dynamical system for which the comparison principle holds, that is, "bigger'' initial states lead to "bigger'' future states. In monotone systems, every net feedback loop is positive. On the other hand, negative feedback loops are important features of many systems, since they are required for adaptation and precision. We show that, provided that these negative loops act at a comparatively fast time scale, the generic convergence property still holds. This is an appealing result, which suggests that monotonicity has broader implications than previously thought. One particular application of great interest is that of double phosphorylation dephosphorylation cycles. Other recurring modules in biochemical networks are also analyzed in detail. For systems without time scale separation, we study the global stability of one special class of systems, called monotone tridiagonal systems with negative feedback. The key technique is to rule out periodic orbits using the theory of second compound matrices. We also investigate the effect of diffusion on the stability of a constant steady state for systems with more general structures represented by graphs. This work extends the passivity-based stability criterion developed by Arcak and Sontag to reaction diffusion equations. Upon assembling different modules, the dynamics of individual modules might be affected. One particular effect is called "retroactivity'' in the systems biology literature. We propose designs and conditions under which the retroactivity can be attenuated.

Advisors/Committee Members: Wang, Liming, 1978- (author), Sontag, Eduardo (chair), Mischaikow, Konstantin (internal member), Li, YanYan (internal member), Gajic, Zoran (outside member).

Subjects/Keywords: Biological systems – Mathematical models; Computational biology; Stochastic analysis

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APA (6^th Edition):

Wang, Liming, 1. (2008). Dynamics and asymptotic behaviors of biochemical networks. (Doctoral Dissertation). Rutgers University. Retrieved from http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000050469

Chicago Manual of Style (16^th Edition):

Wang, Liming, 1978-. “Dynamics and asymptotic behaviors of biochemical networks.” 2008. Doctoral Dissertation, Rutgers University. Accessed January 22, 2021. http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000050469.

MLA Handbook (7^th Edition):

Wang, Liming, 1978-. “Dynamics and asymptotic behaviors of biochemical networks.” 2008. Web. 22 Jan 2021.

Vancouver:

Wang, Liming 1. Dynamics and asymptotic behaviors of biochemical networks. [Internet] [Doctoral dissertation]. Rutgers University; 2008. [cited 2021 Jan 22]. Available from: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000050469.

Council of Science Editors:

Wang, Liming 1. Dynamics and asymptotic behaviors of biochemical networks. [Doctoral Dissertation]. Rutgers University; 2008. Available from: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000050469

Michigan State University

20. Pakanati, Anuraag R. Structure and evolutionary dynamics in fitness landscapes.

Degree: 2015, Michigan State University

URL: http://etd.lib.msu.edu/islandora/object/etd:2617

►

Thesis Ph. D. Michigan State University. Computer Science; Ecology, Evolutionary Biology, and Behavior 2015

Evolution can be conceptualized as an optimization algorithm that allows populations… (more)

Subjects/Keywords: Biological fitness – Mathematical models; Population genetics – Mathematical models; Evolution (Biology) – Mathematical models; Natural selection – Mathematical models; Computer science; Evolution & development

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APA (6^th Edition):

Pakanati, A. R. (2015). Structure and evolutionary dynamics in fitness landscapes. (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:2617

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Pakanati, Anuraag R. “Structure and evolutionary dynamics in fitness landscapes.” 2015. Thesis, Michigan State University. Accessed January 22, 2021. http://etd.lib.msu.edu/islandora/object/etd:2617.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Pakanati, Anuraag R. “Structure and evolutionary dynamics in fitness landscapes.” 2015. Web. 22 Jan 2021.

Vancouver:

Pakanati AR. Structure and evolutionary dynamics in fitness landscapes. [Internet] [Thesis]. Michigan State University; 2015. [cited 2021 Jan 22]. Available from: http://etd.lib.msu.edu/islandora/object/etd:2617.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Pakanati AR. Structure and evolutionary dynamics in fitness landscapes. [Thesis]. Michigan State University; 2015. Available from: http://etd.lib.msu.edu/islandora/object/etd:2617

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Stellenbosch University

21. Green, Kathleen. Whole body modelling of glucose metabolism in malaria patients.

Degree: MSc, 2017, Stellenbosch University

URL: http://hdl.handle.net/10019.1/101094

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ENGLISH ABSTRACT : Diagnosing a patient with a disease is typically done by considering a list of clinical symptoms. For severe malaria two of the… (more)

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ENGLISH ABSTRACT : Diagnosing a patient with a disease is typically done by considering a list of clinical symptoms. For severe malaria two of the key pathophysiological indicators for poor chances of survival are hypoglycemia (blood glucose < 2.2 mmol/L) and lactic acidosis (blood lactate > 5 mmol/L). These could be due to accelerated glycolytic flux (conversion of glucose to lactate) in parasite infected red blood cells, anaemia brought about by the parasites destroying the red blood cells, or reduced perfusion resulting from coagulation of red blood cells (parasites change the red blood cell shape) in the bloodstream. To date, no mathematical models exist that can quantify the relative contribution of increased glycolytic flux to hypoglycemia and lactic acidosis. In this study we constructed a physiologically relevant model of human glucose metabolism that contains the molecular mechanisms of erythrocyte and Plasmodium glycolysis. This allows for the investigation of the extent to which hypoglycaemia and lactic acidosis can be explained by the increased metabolic burden of the parasite. This was accomplished by combining three independent models of glucose metabolism in the parasite, red blood cell and the whole body to form a model of glucose metabolism at the level of the whole body that now contained mechanistic detail of reactions at the level of the red blood cell and malaria parasite (the green1 model). Predictions from the green1 model were compared to clinical data which showed that the increased glycolytic flux caused by the presence of the parasites could be sufficient to explain clinical symptoms of hypoglycemia and lactic acidosis seen in malaria patients. It was seen that for the strength of this modelling technique to be tested, better quality data are needed to validate the model predictions. Furthermore with local and global sensitivity analysis it was observed that there are reactions and parameters in the Plasmodium glycolysis pathway that could guide the development of possible drug targets that could lead to a reversal of hypoglycemia and lactic acidosis.

AFRIKAANSE OPSOMMING : Diagnose van ’n pasiënt met ’n siekte word tipies gedoen deur die oorweging van ’n lys kliniese simptome. Vir ernstige malaria is twee van die belangrikste patofisiologiese aanwysers vir swak kanse op oorlewing hipoglukemie (bloedglukose <2.2 mmol/L) en laktaatversuring (bloed laktaat> 5 mmol/L). Dit kan wees as gevolg van versnelde glikolitiese fluksie (omskakeling van glukose na laktaat) in parasietgeinfekteerde rooibloedselle, bloedarmoede teweeg gebring word deur die vernieteging van rooibloedselle deur parasiete, verminderde perfusie as gevolg van koagulasie van rooibloedselle (parasiete verander die rooibloedselle se vorm) in die bloedstroom. Tot op datum, bestaan geen wiskundige modelle wat die relatiewe bydrae van verhoogde glikolitiese vloed te hipoglukemie en laktaatversuring kan kwantifiseer. In hierdie studie het ons ’n fisiologies relevante model van menslike glukose…

Advisors/Committee Members: Snoep, Jacky L., Van Niekerk, David, Stellenbosch University. Faculty of Science. Dept. o fMathematical Sciences.

Subjects/Keywords: Malaria – Prevention; Glucose metabolism – Mathematical models; Systems biology – Mathematical models; Biology – Mathematical models; UCTD

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APA (6^th Edition):

Green, K. (2017). Whole body modelling of glucose metabolism in malaria patients. (Masters Thesis). Stellenbosch University. Retrieved from http://hdl.handle.net/10019.1/101094

Chicago Manual of Style (16^th Edition):

Green, Kathleen. “Whole body modelling of glucose metabolism in malaria patients.” 2017. Masters Thesis, Stellenbosch University. Accessed January 22, 2021. http://hdl.handle.net/10019.1/101094.

MLA Handbook (7^th Edition):

Green, Kathleen. “Whole body modelling of glucose metabolism in malaria patients.” 2017. Web. 22 Jan 2021.

Vancouver:

Green K. Whole body modelling of glucose metabolism in malaria patients. [Internet] [Masters thesis]. Stellenbosch University; 2017. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10019.1/101094.

Council of Science Editors:

Green K. Whole body modelling of glucose metabolism in malaria patients. [Masters Thesis]. Stellenbosch University; 2017. Available from: http://hdl.handle.net/10019.1/101094

Ryerson University

22. Chang, John Shih-Hua. Measurement of the properties of MetalMUMPS® thin films.

Degree: 2009, Ryerson University

URL: https://digital.library.ryerson.ca/islandora/object/RULA%3A1184

► The metal multi-user micro-electro-mechanical-systems (MEMS) processes (MetalMUMPs®) micro-machining process includes two silicon nitride films, one polysilicon film, and one nickel film for constructing various MEMS… (more)

Subjects/Keywords: Thin films – Mathematical models; Thin films; Microelectromechanical systems – Mathematical models

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APA (6^th Edition):

Chang, J. S. (2009). Measurement of the properties of MetalMUMPS® thin films. (Thesis). Ryerson University. Retrieved from https://digital.library.ryerson.ca/islandora/object/RULA%3A1184

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chang, John Shih-Hua. “Measurement of the properties of MetalMUMPS® thin films.” 2009. Thesis, Ryerson University. Accessed January 22, 2021. https://digital.library.ryerson.ca/islandora/object/RULA%3A1184.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chang, John Shih-Hua. “Measurement of the properties of MetalMUMPS® thin films.” 2009. Web. 22 Jan 2021.

Vancouver:

Chang JS. Measurement of the properties of MetalMUMPS® thin films. [Internet] [Thesis]. Ryerson University; 2009. [cited 2021 Jan 22]. Available from: https://digital.library.ryerson.ca/islandora/object/RULA%3A1184.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chang JS. Measurement of the properties of MetalMUMPS® thin films. [Thesis]. Ryerson University; 2009. Available from: https://digital.library.ryerson.ca/islandora/object/RULA%3A1184

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Ryerson University

23. Sehgal, Summit. Performance driven design space exploration for multi-objective optimization using stability in competition.

Degree: 2011, Ryerson University

URL: https://digital.library.ryerson.ca/islandora/object/RULA%3A6079

► Multi Parametric Design Space Exploration (DSE) for optimal micro-architecture synthesis is an extremely complex yet crucial stage in embedded systems development. Often it is very… (more)

Subjects/Keywords: Computer architecture – Mathematical models; Systems on a chip – Mathematical models

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APA (6^th Edition):

Sehgal, S. (2011). Performance driven design space exploration for multi-objective optimization using stability in competition. (Thesis). Ryerson University. Retrieved from https://digital.library.ryerson.ca/islandora/object/RULA%3A6079

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sehgal, Summit. “Performance driven design space exploration for multi-objective optimization using stability in competition.” 2011. Thesis, Ryerson University. Accessed January 22, 2021. https://digital.library.ryerson.ca/islandora/object/RULA%3A6079.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sehgal, Summit. “Performance driven design space exploration for multi-objective optimization using stability in competition.” 2011. Web. 22 Jan 2021.

Vancouver:

Sehgal S. Performance driven design space exploration for multi-objective optimization using stability in competition. [Internet] [Thesis]. Ryerson University; 2011. [cited 2021 Jan 22]. Available from: https://digital.library.ryerson.ca/islandora/object/RULA%3A6079.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sehgal S. Performance driven design space exploration for multi-objective optimization using stability in competition. [Thesis]. Ryerson University; 2011. Available from: https://digital.library.ryerson.ca/islandora/object/RULA%3A6079

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Ryerson University

24. Sengupta, Anirban. A fast Design Space Exploration Based On Priority Factor For A Multi Parametric Optimized High Level Synthesis Design Flow.

Degree: 2010, Ryerson University

URL: https://digital.library.ryerson.ca/islandora/object/RULA%3A2212

► This thesis introduces a novel approach to rapid Design Space Exploration (DSE) and presents a formalized High Level Synthesis (HLS) design flow with multi parametric… (more)

Subjects/Keywords: Computer architecture – Mathematical models Systems on a chip – Mathematical models

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APA (6^th Edition):

Sengupta, A. (2010). A fast Design Space Exploration Based On Priority Factor For A Multi Parametric Optimized High Level Synthesis Design Flow. (Thesis). Ryerson University. Retrieved from https://digital.library.ryerson.ca/islandora/object/RULA%3A2212

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sengupta, Anirban. “A fast Design Space Exploration Based On Priority Factor For A Multi Parametric Optimized High Level Synthesis Design Flow.” 2010. Thesis, Ryerson University. Accessed January 22, 2021. https://digital.library.ryerson.ca/islandora/object/RULA%3A2212.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sengupta, Anirban. “A fast Design Space Exploration Based On Priority Factor For A Multi Parametric Optimized High Level Synthesis Design Flow.” 2010. Web. 22 Jan 2021.

Vancouver:

Sengupta A. A fast Design Space Exploration Based On Priority Factor For A Multi Parametric Optimized High Level Synthesis Design Flow. [Internet] [Thesis]. Ryerson University; 2010. [cited 2021 Jan 22]. Available from: https://digital.library.ryerson.ca/islandora/object/RULA%3A2212.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sengupta A. A fast Design Space Exploration Based On Priority Factor For A Multi Parametric Optimized High Level Synthesis Design Flow. [Thesis]. Ryerson University; 2010. Available from: https://digital.library.ryerson.ca/islandora/object/RULA%3A2212

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

25. Radke, Andreas Martin. An inventory planning methodology based on the value of inventory in high-mix low-volume production.

Degree: 2012, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-7815 ; https://doi.org/10.14711/thesis-b1207863 ; http://repository.ust.hk/ir/bitstream/1783.1-7815/1/th_redirect.html

► The transition of manufacturing systems towards high responsiveness and flexibility in order to address customer needs in dynamic markets allows a rephrasing of the inventory… (more)

▼ The transition of manufacturing systems towards high responsiveness and flexibility in order to address customer needs in dynamic markets allows a rephrasing of the inventory management problem towards models treating inventory budgets as independent variables. This research builds a foundation towards such inventory management approaches in manufacturing, which is characterized by multiple production stages. The proposed methodology allows planning inventory by considering the product structure, supply chain structure, and available inventory budget without requiring forecasts. Any available forecast can instead be used to evaluate the probability of being met by a given inventory budget. For discrete-item high-mix low-volume production companies, a methodology is proposed to determine which items to stock, and how much to stock of each under a limited inventory budget, based on a theory to value inventory items at each stocking point by their ability to hedge against uncertainty, decouple operations, and buffer lead time. The value of each inventory item is analytically determined according to the purposes of holding inventory considering the characteristics of bills of materials, the ability to recover from shortage, and the stocking position in the supply chain. Each inventory item’s distinct risk profile is evaluated relative to each other item to ensure continuity of production flow, so that uncertain input parameters like demand and throughput no longer unduly influence the derivation of target inventory levels. The valuation of all items can be interpreted as a map of the company’s inventory stocking risk, enabling the efficient allocation of a given inventory budget to maximize the system’s customer responsiveness. The behavior of this methodology is simulated by sensitivity analyses of the available inventory budget and selected stocking item parameters. Two pilot studies in the industries of acoustic electronics and industrial hydraulic equipment support the viability of the approach in practice.

Subjects/Keywords: Flexible manufacturing systems – Mathematical models ; Production management – Mathematical models

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APA (6^th Edition):

Radke, A. M. (2012). An inventory planning methodology based on the value of inventory in high-mix low-volume production. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-7815 ; https://doi.org/10.14711/thesis-b1207863 ; http://repository.ust.hk/ir/bitstream/1783.1-7815/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Radke, Andreas Martin. “An inventory planning methodology based on the value of inventory in high-mix low-volume production.” 2012. Thesis, Hong Kong University of Science and Technology. Accessed January 22, 2021. http://repository.ust.hk/ir/Record/1783.1-7815 ; https://doi.org/10.14711/thesis-b1207863 ; http://repository.ust.hk/ir/bitstream/1783.1-7815/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Radke, Andreas Martin. “An inventory planning methodology based on the value of inventory in high-mix low-volume production.” 2012. Web. 22 Jan 2021.

Vancouver:

Radke AM. An inventory planning methodology based on the value of inventory in high-mix low-volume production. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2012. [cited 2021 Jan 22]. Available from: http://repository.ust.hk/ir/Record/1783.1-7815 ; https://doi.org/10.14711/thesis-b1207863 ; http://repository.ust.hk/ir/bitstream/1783.1-7815/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Radke AM. An inventory planning methodology based on the value of inventory in high-mix low-volume production. [Thesis]. Hong Kong University of Science and Technology; 2012. Available from: http://repository.ust.hk/ir/Record/1783.1-7815 ; https://doi.org/10.14711/thesis-b1207863 ; http://repository.ust.hk/ir/bitstream/1783.1-7815/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Michigan State University

26. Zhang, Xu. Statistical properties of some almost Anosov systems.

Degree: 2016, Michigan State University

URL: http://etd.lib.msu.edu/islandora/object/etd:3797

►

Thesis Ph. D. Michigan State University. Mathematics 2016.

We investigate the polynomial lower and upper bounds for decay of correlations of a class of two-dimensional… (more)

Subjects/Keywords: Anosov diffeomorphisms – Mathematical models; Differentiable dynamical systems – Mathematical models; Mathematics

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APA (6^th Edition):

Zhang, X. (2016). Statistical properties of some almost Anosov systems. (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:3797

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zhang, Xu. “Statistical properties of some almost Anosov systems.” 2016. Thesis, Michigan State University. Accessed January 22, 2021. http://etd.lib.msu.edu/islandora/object/etd:3797.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zhang, Xu. “Statistical properties of some almost Anosov systems.” 2016. Web. 22 Jan 2021.

Vancouver:

Zhang X. Statistical properties of some almost Anosov systems. [Internet] [Thesis]. Michigan State University; 2016. [cited 2021 Jan 22]. Available from: http://etd.lib.msu.edu/islandora/object/etd:3797.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zhang X. Statistical properties of some almost Anosov systems. [Thesis]. Michigan State University; 2016. Available from: http://etd.lib.msu.edu/islandora/object/etd:3797

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Oregon State University

27. Yildirim, Ferhat (Ahmet Ferhat). Directional 60 GHz communication networks.

Degree: PhD, Electical and Computer Engineering, 2009, Oregon State University

URL: http://hdl.handle.net/1957/12844

► It is well known that multipath effects cause inter-symbol interference (ISI) for high-speed signaling and ultimately limit the achievable data rate at any frequency band.… (more)

Subjects/Keywords: Wireless communications; Wireless communication systems – Mathematical models

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APA (6^th Edition):

Yildirim, F. (. F. (2009). Directional 60 GHz communication networks. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/12844

Chicago Manual of Style (16^th Edition):

Yildirim, Ferhat (Ahmet Ferhat). “Directional 60 GHz communication networks.” 2009. Doctoral Dissertation, Oregon State University. Accessed January 22, 2021. http://hdl.handle.net/1957/12844.

MLA Handbook (7^th Edition):

Yildirim, Ferhat (Ahmet Ferhat). “Directional 60 GHz communication networks.” 2009. Web. 22 Jan 2021.

Vancouver:

Yildirim F(F. Directional 60 GHz communication networks. [Internet] [Doctoral dissertation]. Oregon State University; 2009. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1957/12844.

Council of Science Editors:

Yildirim F(F. Directional 60 GHz communication networks. [Doctoral Dissertation]. Oregon State University; 2009. Available from: http://hdl.handle.net/1957/12844

Oregon State University

28. Xu, Tao. Feedback in multiple antenna wireless communication systems.

Degree: PhD, Electrical and Computer Engineering, 2010, Oregon State University

URL: http://hdl.handle.net/1957/16210

► Multiple-input multiple-output wireless systems promise significant capacity gain and/or diversity gain over single antenna systems. If channel state information (CSI) is available at both the… (more)

▼ Multiple-input multiple-output wireless systems promise significant capacity gain and/or diversity gain over single antenna systems. If channel state information (CSI) is available at both the transmitter and the receiver, the performance can be further improved. In this thesis, first, we study binary index feedback problem in beamforming systems when the feedback channel is not error free. Feedback errors lead to incorrect beamforming vectors to be applied at the transmitter and thus degrade beamforming performance. Index-assignment algorithms that minimize the impact of feedback errors are proposed. Second, in the limited feedback beamforming scheme the receiver has to determine the best codeword from the beamforming codebook. Exhaustive codeword search for large-size codebooks becomes a burden when the receiver is a mobile device with limited computational power. We propose an algorithm to drastically reduce codeword selection complexity with negligible performance loss. Third, we compare angle feedback scheme and transmit antenna shuffling feedback scheme for double space-time transmit diversity systems. We show that the 1-bit angle feedback scheme does not provide a better performance than the 1-bit antenna shuffling feedback scheme. Fourth, we consider training power allocation for a closed-loop MIMO system in i.i.d. Rayleigh flat-fading channels with power constraint. We derive the optimal solution and asymptotic optimal solution of training power allocation for spatial power control and spatial and fading power control. Lastly, we analyze the optimal diversity-multiplexing tradeoff of multiple beamforming systems and compare it with the well known result for MIMO channels with channel state information at the receiver (CSIR) only and with the optimal diversity-multiplexing tradeoff of spatial multiplexing system with channel state information at the transmitter (CSIT), but without coding over space and time. Advisors/Committee Members: Hamdaoui, Bechir (committee member).

Subjects/Keywords: Multiple antennas; MIMO systems – Mathematical models

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APA (6^th Edition):

Xu, T. (2010). Feedback in multiple antenna wireless communication systems. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/16210

Chicago Manual of Style (16^th Edition):

Xu, Tao. “Feedback in multiple antenna wireless communication systems.” 2010. Doctoral Dissertation, Oregon State University. Accessed January 22, 2021. http://hdl.handle.net/1957/16210.

MLA Handbook (7^th Edition):

Xu, Tao. “Feedback in multiple antenna wireless communication systems.” 2010. Web. 22 Jan 2021.

Vancouver:

Xu T. Feedback in multiple antenna wireless communication systems. [Internet] [Doctoral dissertation]. Oregon State University; 2010. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1957/16210.

Council of Science Editors:

Xu T. Feedback in multiple antenna wireless communication systems. [Doctoral Dissertation]. Oregon State University; 2010. Available from: http://hdl.handle.net/1957/16210

University of Delaware

29. Feng, Hao. Overhead, uncertainty, and interference in wireless networks.

Degree: PhD, University of Delaware, Department of Electrical and Computer Engineering, 2014, University of Delaware

URL: http://udspace.udel.edu/handle/19716/16805

► In general, the performance of many wireless systems is approaching the fundamental limits on transmission capacity. For example, current commercial wireless standards such as 3GPP… (more)

▼ In general, the performance of many wireless systems is approaching the fundamental limits on transmission capacity. For example, current commercial wireless standards such as 3GPP LTE-A and IEEE 802.11ac have a near-optimal physical layer. In order to meet the ever growing demand for capacity, other directions for improving network performance must be found. In most existing research on wireless networks, overhead, the "non-data'' portion including coordination, control signaling and other costs of serving different purposes, is assumed to be negligible. However, the final application throughput could be much lower than the theoretical bounds as a result of overhead, especially in large and dynamic networks. Therefore, it is critical to quantitatively analyze the overhead in wireless networks, which could provide clear insights on the performance in practical systems and could help to identify opportunities for improvements in their designs. Surprisingly, the fundamental limits on overhead are largely unknown, and the framework needed to design overhead-aware systems has not been adequately investigated. In addition, interference is one of the main performance-limiting factors in most future wireless applications. Conventional "interference avoidance'' techniques might not be feasible because the degrees of freedom (for example, bandwidth, number of orthogonal codes, and time) might be limited. Although the interference can be mitigated quite efficiently with centralized control, existing approaches are usually very sensitive to channel uncertainties; if the knowledge of the channel state information is imperfect, the system performance could be severely degraded. Also, collecting accurate information incurs a significant amount of overhead due to the time-varying nature of the wireless medium. Thus, it is imperative to jointly consider overhead, uncertainty, and interference. In this dissertation, we investigate practical and overhead-aware designs that can achieve better performance in a realistic networking context. We start with a simple, single-user, two-hop cooperative relaying network model. For this model, we first prove that M -group cooperation is the optimal distributed space-time block coding strategy when neither central control nor inter-relay communications is permitted. Then, we consider the relay selection problem where a small and acceptable amount of overhead is allowed. The tradeoff between the feedback overhead and the performance is investigated via rate distortion theory. Compared to existing research, which is usually highly dependent on the specific implementation approaches, the analysis presented here addresses the fundamental tradeoff of a general network. Using our theoretical results, we also compare practical centralized and decentralized relay selection schemes in terms of spectral efficiency. Then, interference-limited networks with multiple concurrent transmissions are studied. We analyze and compare the performance of cooperative and non-cooperative schemes. Although cooperation… Advisors/Committee Members: Cimini, Leonard J..

Subjects/Keywords: Wireless communication systems.; Uncertainty – Mathematical models.

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APA (6^th Edition):

Feng, H. (2014). Overhead, uncertainty, and interference in wireless networks. (Doctoral Dissertation). University of Delaware. Retrieved from http://udspace.udel.edu/handle/19716/16805

Chicago Manual of Style (16^th Edition):

Feng, Hao. “Overhead, uncertainty, and interference in wireless networks.” 2014. Doctoral Dissertation, University of Delaware. Accessed January 22, 2021. http://udspace.udel.edu/handle/19716/16805.

MLA Handbook (7^th Edition):

Feng, Hao. “Overhead, uncertainty, and interference in wireless networks.” 2014. Web. 22 Jan 2021.

Vancouver:

Feng H. Overhead, uncertainty, and interference in wireless networks. [Internet] [Doctoral dissertation]. University of Delaware; 2014. [cited 2021 Jan 22]. Available from: http://udspace.udel.edu/handle/19716/16805.

Council of Science Editors:

Feng H. Overhead, uncertainty, and interference in wireless networks. [Doctoral Dissertation]. University of Delaware; 2014. Available from: http://udspace.udel.edu/handle/19716/16805

Hong Kong University of Science and Technology

30. Chen, Tianwen CSE. Session-based recommendation with local invariance.

Degree: 2019, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-102332 ; https://doi.org/10.14711/thesis-991012757569403412 ; http://repository.ust.hk/ir/bitstream/1783.1-102332/1/th_redirect.html

► Session-based recommendation is a task to predict users’ next actions given a sequence of previous actions in the same session. Existing methods either encode the… (more)

Subjects/Keywords: Recommender systems (Information filtering) ; Mathematical models

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APA (6^th Edition):

Chen, T. C. (2019). Session-based recommendation with local invariance. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-102332 ; https://doi.org/10.14711/thesis-991012757569403412 ; http://repository.ust.hk/ir/bitstream/1783.1-102332/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chen, Tianwen CSE. “Session-based recommendation with local invariance.” 2019. Thesis, Hong Kong University of Science and Technology. Accessed January 22, 2021. http://repository.ust.hk/ir/Record/1783.1-102332 ; https://doi.org/10.14711/thesis-991012757569403412 ; http://repository.ust.hk/ir/bitstream/1783.1-102332/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chen, Tianwen CSE. “Session-based recommendation with local invariance.” 2019. Web. 22 Jan 2021.

Vancouver:

Chen TC. Session-based recommendation with local invariance. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2019. [cited 2021 Jan 22]. Available from: http://repository.ust.hk/ir/Record/1783.1-102332 ; https://doi.org/10.14711/thesis-991012757569403412 ; http://repository.ust.hk/ir/bitstream/1783.1-102332/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chen TC. Session-based recommendation with local invariance. [Thesis]. Hong Kong University of Science and Technology; 2019. Available from: http://repository.ust.hk/ir/Record/1783.1-102332 ; https://doi.org/10.14711/thesis-991012757569403412 ; http://repository.ust.hk/ir/bitstream/1783.1-102332/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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Open Access Theses and Dissertations