You searched for subject:(Protein Side chain Networks PScN ).
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Indian Institute of Science
1.
Dighe, Anasuya.
Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins.
Degree: PhD, Faculty of Science, 2019, Indian Institute of Science
URL: http://etd.iisc.ac.in/handle/2005/4236 
► Molecular recognition between proteins and their associated ligands constitutes ligand-induced protein rewiring thereby enabling the formation of a stable protein-ligand complex. The studies presented in…
(more)
▼ Molecular recognition between proteins and their associated ligands constitutes ligand-induced
protein rewiring thereby enabling the formation of a stable
protein-ligand complex. The studies presented in this thesis address the conformational plasticity inherent to proteins by virtue of which they adapt to diverse ligands and orchestrate complex biological processes like signal transduction, transcription and
protein-protein interaction. Adopting network theory based formalisms for understanding
protein-ligand associations involve deconstructing the three-dimensional structure of a
protein in terms of nodes and edges. With this view,
Protein Structure
Networks (PSNs) of ligand-bound complexes are studied by considering their
side-
chain non-covalent interactions. Agonist and antagonist-bound G-
Protein Coupled Receptors (GPCRs) are investigated to gain mechanistic insights into allostery and its role in signal transduction. The degree of similarity between PSNs of these complexes is quantified by means of Network Similarity Score (NSS). The physical nature of these
networks is inspected by subjecting them to perturbations and major players in maintaining the stability of such
networks are identified. Residue-wise groupings (at backbone and
side-
chain level) are obtained by applying graph spectral methods.
All-atom Molecular Dynamics (MD) simulations are carried out to gain a better understanding of
protein-ligand binding by analysing conformational ensembles of these complexes. In this scenario, two members from a highly versatile ligand-inducible transcription factor superfamily, i.e., Nuclear Receptors (NR) are studied, that are known to exhibit extremes of ligand binding behavior ranging from promiscuity to specificity.
Diverse ligands are known to bind to proteins and the overall nature of their binding site is investigated. In particular, similarities among binding sites of diverse proteins are analysed by using PocketMatch. Percolation of these similarities to regions surrounding the binding site is reported and examples depicting this extended similarity are discussed.
Overall, studies presented in this thesis provide a structural perspective into the adaptability of proteins for recognizing diverse ligands and undergoing local or global re-organizations in their framework to regulate complex biological processes.
Advisors/Committee Members: Vishveshwara, Saraswathi (advisor), Chandra, Nagasuma (advisor).
Subjects/Keywords: Protein-ligand Interactions; Protein Ligand Interactions; Protein Structure Networks (PSNs); Graph Theory; Protein Side-chain Networks (PScN); Muscarinic Acetylcholine Receptors; Muscarinic Receptor Cmplexes; Protein-Protein Interactions; Pregnane X Receptor; G-Protein Coupled Receptors (GPCRs); Network Similarity Score (NSS); Biochemistry
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APA (6th Edition):
Dighe, A. (2019). Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/4236
Chicago Manual of Style (16th Edition):
Dighe, Anasuya. “Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins.” 2019. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021.
http://etd.iisc.ac.in/handle/2005/4236.
MLA Handbook (7th Edition):
Dighe, Anasuya. “Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins.” 2019. Web. 18 Jan 2021.
Vancouver:
Dighe A. Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2019. [cited 2021 Jan 18].
Available from: http://etd.iisc.ac.in/handle/2005/4236.
Council of Science Editors:
Dighe A. Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins. [Doctoral Dissertation]. Indian Institute of Science; 2019. Available from: http://etd.iisc.ac.in/handle/2005/4236
Indian Institute of Science
2.
Vijayabaskar, M S.
Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks.
Degree: PhD, Faculty of Science, 2013, Indian Institute of Science
URL: http://etd.iisc.ac.in/handle/2005/1904
► Proteins orchestrate a number of cellular processes either alone or in concert with other biomolecules like nucleic acids, carbohydrates, and lipids. They exhibit an intrinsic…
(more)
▼ Proteins orchestrate a number of cellular processes either alone or in concert with other biomolecules like nucleic acids, carbohydrates, and lipids. They exhibit an intrinsic ability to fold de novo to their functional states. The three–dimensional structure of a
protein, dependent on its amino acid sequence, is important for its function. Understanding this sequence– structure–function relationship has become one of the primary goals in biophysics. Various experimental techniques like X–ray crystallography, Nuclear Magnetic Resonance (NMR), and site–directed mutagenesis have been used extensively towards this goal. Computational studies include mainly sequence based, and structure based approaches. The sequence based approaches such as sequence alignments, phylogenetic analysis, domain identification, statistical coupling analysis etc., aim at deriving meaningful information from the primary sequence of the
protein. The structure based approaches, on the other hand, use structures of folded proteins. Recent advances in structure determination and efforts by various structural consortia have resulted in an enormous amount of structures available for analysis. Innumerable observations such as the allowed and disallowed regions in the conformations of a peptide unit, hydrophobic core in globular proteins, existence of regular secondary structures like helices, sheets, and turns and a limited fold space have been landmarks in understanding the characteristics of
protein structures.
The uniqueness of
protein structure is attained through non–covalent interactions among the constituent amino acids. Analyses of
protein structures show that different types of non–covalent interactions like hydrophobic interactions, hydrogen bonding, salt bridges, aromatic stacking, cation–π interactions, and solvent interactions hold
protein structures together. Although such structure analyses have provided a wealth of information, they have largely been performed at a pair–wise level and an investigation involving such pair–wise interactions alone is not sufficient to capture all the determinants of
protein structures, since they happen at a global level. This consideration has led to the development of graphs/
networks for proteins.
Graphs or
Networks are a collection of nodes connected by edges.
Protein Structure
Networks (PSNs) can be constructed using various definitions of nodes and edges. Nodes may vary from atoms to secondary structures in Synopsis proteins, and the edges can range from simple atom–atom distances to distance between secondary structures. To study the interplay of amino acids in structure formation, the most commonly used PSNs consider amino acids as nodes. The criterion for edge definition, however, varies. PSNs can be constructed at a course grain level by considering the distances between Cα/Cβ atoms, any side–
chain atoms, or the centroids of the amino acids. At a finer level, PSNs can be constructed using atomic details by considering the interaction types or by computing the extent of interaction between…
Advisors/Committee Members: Vishveshwara, Saraswathi (advisor).
Subjects/Keywords: Proteins-DNA Graphs (PDGs); Protein Structures; Protein Side–chain Networks (PScNs); Protein–DNA Graphs (PDGs); Protein Energy Networks (PENs); Dps; Mycobacterium smegmatis; Structure Network Analysis; Protein Structure Networks; GraProStr; Structure Networks; Biochemistry
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APA (6th Edition):
Vijayabaskar, M. S. (2013). Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/1904
Chicago Manual of Style (16th Edition):
Vijayabaskar, M S. “Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks.” 2013. Doctoral Dissertation, Indian Institute of Science. Accessed January 18, 2021.
http://etd.iisc.ac.in/handle/2005/1904.
MLA Handbook (7th Edition):
Vijayabaskar, M S. “Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks.” 2013. Web. 18 Jan 2021.
Vancouver:
Vijayabaskar MS. Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2013. [cited 2021 Jan 18].
Available from: http://etd.iisc.ac.in/handle/2005/1904.
Council of Science Editors:
Vijayabaskar MS. Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks. [Doctoral Dissertation]. Indian Institute of Science; 2013. Available from: http://etd.iisc.ac.in/handle/2005/1904
Rice University
3.
Ma, Tianqi.
OPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing.
Degree: MS, Natural Sciences, 2018, Rice University
URL: http://hdl.handle.net/1911/105797
► In this thesis, we report a new distance- and orientation-dependent, all-atom statistical potential derived from side-chain packing, named OPUS-DOSP, for protein structure modeling. The framework…
(more)
▼ In this thesis, we report a new distance- and orientation-dependent, all-atom statistical potential derived from
side-
chain packing, named OPUS-DOSP, for
protein structure modeling. The framework of OPUS DOSP is based on OPUS-PSP, with refinement and new features. In particular, distance or orientation contribution is considered depending on the range of contact distance. A new auxiliary function in energy function is also introduced, in addition to the traditional Boltzmann term, in
order to adjust the contributions of extreme cases. OPUS-DOSP was tested on 11 decoy sets commonly used for statistical potential benchmarking. Among 278 native structures, 239 and 249 native structures were recognized by OPUS DOSP without and with the auxiliary function respectively. The results show that OPUS-DOSP has an increased decoy recognition capability comparing with those of other relevant potentials to date.
Advisors/Committee Members: Ma, Jianpeng (advisor).
Subjects/Keywords: protein structure prediction; empirical potential function; decoy recognition; side-chain packing
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APA (6th Edition):
Ma, T. (2018). OPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing. (Masters Thesis). Rice University. Retrieved from http://hdl.handle.net/1911/105797
Chicago Manual of Style (16th Edition):
Ma, Tianqi. “OPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing.” 2018. Masters Thesis, Rice University. Accessed January 18, 2021.
http://hdl.handle.net/1911/105797.
MLA Handbook (7th Edition):
Ma, Tianqi. “OPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing.” 2018. Web. 18 Jan 2021.
Vancouver:
Ma T. OPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing. [Internet] [Masters thesis]. Rice University; 2018. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/1911/105797.
Council of Science Editors:
Ma T. OPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing. [Masters Thesis]. Rice University; 2018. Available from: http://hdl.handle.net/1911/105797
NSYSU
4.
Hsin, Jing-Liang.
An Ant Colony Optimization Approach for the Protein Side Chain Packing Problem.
Degree: Master, Computer Science and Engineering, 2006, NSYSU
URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0830106-191348
► The protein side chain prediction is an essential issue, in protein structure prediction, protein design, and protein docking problems. The protein side chain packing problem…
(more)
▼ The
protein side chain prediction is an essential issue, in
protein structure prediction,
protein design, and
protein docking problems. The
protein side chain packing problem has been proved to be NP-hard. Our method for solving this problem is first to reduce it to the clique finding problem, and then we can apply the Ant Colony Optimization (ACO) algorithm to solve it. In knowledge-based methods, the rotamers are chosen from the rotamer library, which are
based on the pair of dihedral angles, Ï and Ï, of backbones. We take the coordinate rotamer library as the template, so we do not need the complicated energy function to calculate the bond length and bond angle. We use a simple score function to evaluate the goodness of a solution of the ACO algorithm. The score function combines some factors, such as charge-charge interaction, intermolecular hydrogen bonds, disulfide bonds and van der Waals interactions. The experimental results show that our score function is biologically sensible. We compare our computational results with the results of SCWRL 3.0 and the
residue-rotamer-reduction (R3) algorithm. The accuracy
of our method outperforms both SCWRL 3.0 and R3 methods.
Advisors/Committee Members: Bang-ye Wu (chair), Chung-Lung Cho (chair), Chia-ning Yang (chair), Yow-ling Shiue (chair), Chang-biau Yang (committee member).
Subjects/Keywords: protein; ACO; side chain; structure prediction
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APA (6th Edition):
Hsin, J. (2006). An Ant Colony Optimization Approach for the Protein Side Chain Packing Problem. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0830106-191348
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Hsin, Jing-Liang. “An Ant Colony Optimization Approach for the Protein Side Chain Packing Problem.” 2006. Thesis, NSYSU. Accessed January 18, 2021.
http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0830106-191348.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Hsin, Jing-Liang. “An Ant Colony Optimization Approach for the Protein Side Chain Packing Problem.” 2006. Web. 18 Jan 2021.
Vancouver:
Hsin J. An Ant Colony Optimization Approach for the Protein Side Chain Packing Problem. [Internet] [Thesis]. NSYSU; 2006. [cited 2021 Jan 18].
Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0830106-191348.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Hsin J. An Ant Colony Optimization Approach for the Protein Side Chain Packing Problem. [Thesis]. NSYSU; 2006. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0830106-191348
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – Irvine
5.
Nagata, Ken.
Novel Machine Learning Approach for Protein Structure Prediction.
Degree: Computer Science, 2014, University of California – Irvine
URL: http://www.escholarship.org/uc/item/1336f301
► The side-chain prediction and residue-residue contact prediction are sub-problems in the protein structure prediction. Both predictions are important for protein prediction and other applications.We have…
(more)
▼ The side-chain prediction and residue-residue contact prediction are sub-problems in the protein structure prediction. Both predictions are important for protein prediction and other applications.We have developed a new algorithm, SIDEpro, for the side-chain prediction where an energy function for each rotamer in a structure is computed additively over pairs of contacting atoms. A family of 156 neural networks indexed by amino acids and contacting atom types is used to compute these rotamer energies as a function of atomic contact distances. Although direct energy targets are not available for training, the neural networks can still be optimized by converting the energies to probabilities and optimizing these probabilities using Markov Chain Monte Carlo methods. The resulting predictor SIDEpro makes predictions by initially setting the rotamer probabilities for each residue from a backbone-dependent rotamer library, then iteratively updating these probabilities using the trained neural networks. After convergences of the probabilities, the side-chains are set to the highest probability rotamer. Finally, a post processing clash reduction step is applied to the models. SIDEpro represents a significant improvement in speed and a modest, but statistically significant, improvement in accuracy when compared with the state-of-the-art for rapid side-chain prediction method SCWRL4 on the 379 protein test set of SCWRL4. Using the SCWRL4 test set, SIDEpro's accuracy (χ1 86.14%, χ1+2 74.15%) is slightly better than SCWRL4-FRM (χ1 85.43%, χ1+2 73.47%) and it is 7.0 times faster. SIDEpro can also predict the side chains of proteins containing non-standard amino acids, including 15 of the most frequently observed PTMs in the Protein Data Bank and all types of phosphorylation. For PTMs, the χ1 and χ1+2 accuracies are comparable with those obtained for the precursor amino acid, and so are the RMSD values for the atoms shared with the precursor amino acid. In addition, SIDEpro can accommodate any PTM or unnatural amino acid, thus providing a flexible prediction system for high-throughput modeling of proteins beyond the standard amino acids.We have also developed a novel machine learning approach for contact map prediction using three steps of increasing resolution. First, we use 2D recursive neural networks to predict coarse contacts and orientations between secondary structure elements. Second, we use an energy-based method to align secondary structure elements and predict contact probabilities between residues in contacting alpha-helices or strands. Third, we use a deep neural network architecture to organize and progressively refine the prediction of contacts, integrating information over both space and time. We train the architecture on a large set of non-redundant proteins and test it on a large set of non-homologous domains, as well as on the set of protein domains used for contact prediction in the two most recent CASP8 and CASP9…
Subjects/Keywords: Bioinformatics; Artificial intelligence; contact map; deep architecture; neural network; protein structure; side-chain prediction; SIDEpro
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APA (6th Edition):
Nagata, K. (2014). Novel Machine Learning Approach for Protein Structure Prediction. (Thesis). University of California – Irvine. Retrieved from http://www.escholarship.org/uc/item/1336f301
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Nagata, Ken. “Novel Machine Learning Approach for Protein Structure Prediction.” 2014. Thesis, University of California – Irvine. Accessed January 18, 2021.
http://www.escholarship.org/uc/item/1336f301.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Nagata, Ken. “Novel Machine Learning Approach for Protein Structure Prediction.” 2014. Web. 18 Jan 2021.
Vancouver:
Nagata K. Novel Machine Learning Approach for Protein Structure Prediction. [Internet] [Thesis]. University of California – Irvine; 2014. [cited 2021 Jan 18].
Available from: http://www.escholarship.org/uc/item/1336f301.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Nagata K. Novel Machine Learning Approach for Protein Structure Prediction. [Thesis]. University of California – Irvine; 2014. Available from: http://www.escholarship.org/uc/item/1336f301
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Boston University
6.
Moghadasi, Mohammad.
Optimization methods for side-chain positioning and macromolecular docking.
Degree: PhD, Systems Engineering, 2015, Boston University
URL: http://hdl.handle.net/2144/16091
► This dissertation proposes new optimization algorithms targeting protein-protein docking which is an important class of problems in computational structural biology. The ultimate goal of docking…
(more)
▼ This dissertation proposes new optimization algorithms targeting protein-protein docking which is an important class of problems in computational structural biology. The ultimate goal of docking methods is to predict the 3-dimensional structure of a stable protein-protein complex. We study two specific problems encountered in predictive docking of proteins. The first problem is Side-Chain Positioning (SCP), a central component of homology modeling and computational protein docking methods. We formulate SCP as a Maximum Weighted Independent Set (MWIS) problem on an appropriately constructed graph. Our formulation also considers the significant special structure of proteins that SCP exhibits for docking. We develop an approximate algorithm that solves a relaxation of MWIS and employ randomized estimation heuristics to obtain high-quality feasible solutions to the problem. The algorithm is fully distributed and can be implemented on multi-processor architectures. Our computational results on a benchmark set of protein complexes show that the accuracy of our approximate MWIS-based algorithm predictions is comparable with the results achieved by a state-of-the-art method that finds an exact solution to SCP.
The second problem we target in this work is protein docking refinement. We propose two different methods to solve the refinement problem. The first approach is based on a Monte Carlo-Minimization (MCM) search to optimize rigid-body and side-chain conformations for binding. In particular, we study the impact of optimally positioning the side-chains in the interface region between two proteins in the process of binding. We report computational results showing that incorporating side-chain flexibility in docking provides substantial improvement in the quality of docked predictions compared to the rigid-body approaches. Further, we demonstrate that the inclusion of unbound side-chain conformers in the side-chain search introduces significant improvement in the performance of the docking refinement protocols. In the second approach, we propose a novel stochastic optimization algorithm based on Subspace Semi-Definite programming-based Underestimation (SSDU), which aims to solve protein docking and protein structure prediction. SSDU is based on underestimating the binding energy function in a permissive subspace of the space of rigid-body motions. We apply Principal Component Analysis (PCA) to determine the permissive subspace and reduce the dimensionality of the conformational search space. We consider the general class of convex polynomial underestimators, and formulate the problem of finding such underestimators as a Semi-Definite Programming (SDP) problem. Using these underestimators, we perform a biased sampling in the vicinity of the conformational regions where the energy function is at its global minimum.
Moreover, we develop an exploration procedure based on density-based clustering to detect the near-native regions even when there are many local minima residing far from each other. We also incorporate a Model…
Subjects/Keywords: Bioinformatics; Message-passing; Monte Carlo-minimization; Optimization; Protein docking; Semi-definite programming; Side-chain positioning
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APA ·
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APA (6th Edition):
Moghadasi, M. (2015). Optimization methods for side-chain positioning and macromolecular docking. (Doctoral Dissertation). Boston University. Retrieved from http://hdl.handle.net/2144/16091
Chicago Manual of Style (16th Edition):
Moghadasi, Mohammad. “Optimization methods for side-chain positioning and macromolecular docking.” 2015. Doctoral Dissertation, Boston University. Accessed January 18, 2021.
http://hdl.handle.net/2144/16091.
MLA Handbook (7th Edition):
Moghadasi, Mohammad. “Optimization methods for side-chain positioning and macromolecular docking.” 2015. Web. 18 Jan 2021.
Vancouver:
Moghadasi M. Optimization methods for side-chain positioning and macromolecular docking. [Internet] [Doctoral dissertation]. Boston University; 2015. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/2144/16091.
Council of Science Editors:
Moghadasi M. Optimization methods for side-chain positioning and macromolecular docking. [Doctoral Dissertation]. Boston University; 2015. Available from: http://hdl.handle.net/2144/16091
7.
ZHANG LEI.
DEVELOPING SOFTWARE TOOLS FOR STRUCTURE DETERMINATION OF LARGE PROTEINS BY NMR SPECTROSCOPY.
Degree: 2007, National University of Singapore
URL: http://scholarbank.nus.edu.sg/handle/10635/15673
Subjects/Keywords: NMR; Resonance Assignment; Software; Large Protein; Side-chain
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APA ·
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APA (6th Edition):
LEI, Z. (2007). DEVELOPING SOFTWARE TOOLS FOR STRUCTURE DETERMINATION OF LARGE PROTEINS BY NMR SPECTROSCOPY. (Thesis). National University of Singapore. Retrieved from http://scholarbank.nus.edu.sg/handle/10635/15673
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
LEI, ZHANG. “DEVELOPING SOFTWARE TOOLS FOR STRUCTURE DETERMINATION OF LARGE PROTEINS BY NMR SPECTROSCOPY.” 2007. Thesis, National University of Singapore. Accessed January 18, 2021.
http://scholarbank.nus.edu.sg/handle/10635/15673.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
LEI, ZHANG. “DEVELOPING SOFTWARE TOOLS FOR STRUCTURE DETERMINATION OF LARGE PROTEINS BY NMR SPECTROSCOPY.” 2007. Web. 18 Jan 2021.
Vancouver:
LEI Z. DEVELOPING SOFTWARE TOOLS FOR STRUCTURE DETERMINATION OF LARGE PROTEINS BY NMR SPECTROSCOPY. [Internet] [Thesis]. National University of Singapore; 2007. [cited 2021 Jan 18].
Available from: http://scholarbank.nus.edu.sg/handle/10635/15673.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
LEI Z. DEVELOPING SOFTWARE TOOLS FOR STRUCTURE DETERMINATION OF LARGE PROTEINS BY NMR SPECTROSCOPY. [Thesis]. National University of Singapore; 2007. Available from: http://scholarbank.nus.edu.sg/handle/10635/15673
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Virginia Commonwealth University
8.
Ahmed, Mostafa H.
Hydropathic Interactions and Protein Structure: Utilizing the HINT Force Field in Structure Prediction and Protein‐Protein Docking.
Degree: PhD, Pharmaceutical Sciences, 2014, Virginia Commonwealth University
URL: https://doi.org/10.25772/XZA0-X283
;
https://scholarscompass.vcu.edu/etd/3581
► Protein structure predication is a field of computational molecular modeling with an enormous potential for improvement. Side-chain geometry prediction is a critical component of…
(more)
▼ Protein structure predication is a field of computational molecular modeling with an enormous potential for improvement.
Side-
chain geometry prediction is a critical component of this process that is crucial for computational
protein structure predication as well as crystallographers in refining experimentally determined
protein crystal structures. The cornerstone of
side-
chain geometry prediction are
side-
chain rotamer libraries, usually obtained through exhaustive statistical analysis of existing
protein structures. Little is known, however, about the driving forces leading to the preference or suitability of one rotamer over another. Construction of 3D hydropathic interaction maps for nearly 30,000 tyrosines extracted from the PDB reveals their environments, in terms of hydrophobic and polar (collectively “hydropathic”) interactions. Using a unique 3D similarity metric, these environments were clustered with k-means. In the ϕ, ψ region (–200° < ϕ < –155°; –205° < ψ < –160°) representing 631 tyrosines, clustering reduced the set to 14 unique hydropathic environments, with most diversity arising from favorable hydrophobic interactions. Polar interactions for tyrosine include ubiquitous hydrogen bonding with the phenolic OH and a handful of unique environments surrounding the backbone. The memberships of all but one of the 14 environments are dominated by a single χ
1/χ
2 rotamer. Each tyrosine residue attempts to fulfill its hydropathic valence. Structural water molecules are thus used in a variety of roles throughout
protein structure. A second project involves elucidating the 3D structure of CRIP1a, a cannabinoid 1 receptor (CB
1R) binding
protein that could provide information for designing small molecules targeting the CRIP1a-CB
1R interaction. The CRIP1a
protein was produced in high purity. Crystallization experiments failed, both with and without the last 9 or 12 amino acid peptide of the CB
1R C-terminus. Attempts were made to use NMR for structure determination; however, the
protein precipitated out during data acquisition. A model was thus built computationally to which the CB
1R C-terminus peptide was docked. HINT was used in selecting optimum models and analyzing interactions involved in the CRIP1a-CB
1R complex. The final model demonstrated key putative interactions between CRIP1a and CB
1R while also predicting highly flexible areas of the CRIP1a possibly contributing to the difficulties faced during crystallization.
Advisors/Committee Members: Glen E. Kellogg, Ph.D., Martin K. Safo, Ph.D..
Subjects/Keywords: HINT; Hydropathic Interactions; Protein Structure; Protein-protein docking; Sidechain Geometry; Side-chain Geometry; CRIP1a; Cannabinoid Receptor; Amino Acids, Peptides, and Proteins; Medicinal and Pharmaceutical Chemistry; Pharmacy and Pharmaceutical Sciences
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Manager
APA (6th Edition):
Ahmed, M. H. (2014). Hydropathic Interactions and Protein Structure: Utilizing the HINT Force Field in Structure Prediction and Protein‐Protein Docking. (Doctoral Dissertation). Virginia Commonwealth University. Retrieved from https://doi.org/10.25772/XZA0-X283 ; https://scholarscompass.vcu.edu/etd/3581
Chicago Manual of Style (16th Edition):
Ahmed, Mostafa H. “Hydropathic Interactions and Protein Structure: Utilizing the HINT Force Field in Structure Prediction and Protein‐Protein Docking.” 2014. Doctoral Dissertation, Virginia Commonwealth University. Accessed January 18, 2021.
https://doi.org/10.25772/XZA0-X283 ; https://scholarscompass.vcu.edu/etd/3581.
MLA Handbook (7th Edition):
Ahmed, Mostafa H. “Hydropathic Interactions and Protein Structure: Utilizing the HINT Force Field in Structure Prediction and Protein‐Protein Docking.” 2014. Web. 18 Jan 2021.
Vancouver:
Ahmed MH. Hydropathic Interactions and Protein Structure: Utilizing the HINT Force Field in Structure Prediction and Protein‐Protein Docking. [Internet] [Doctoral dissertation]. Virginia Commonwealth University; 2014. [cited 2021 Jan 18].
Available from: https://doi.org/10.25772/XZA0-X283 ; https://scholarscompass.vcu.edu/etd/3581.
Council of Science Editors:
Ahmed MH. Hydropathic Interactions and Protein Structure: Utilizing the HINT Force Field in Structure Prediction and Protein‐Protein Docking. [Doctoral Dissertation]. Virginia Commonwealth University; 2014. Available from: https://doi.org/10.25772/XZA0-X283 ; https://scholarscompass.vcu.edu/etd/3581
University of Notre Dame
9.
Andrew Tayanjana Namanja.
Molecular Basis for Signal Transduction in the Bimodular
Cell-Cycle Enzyme Pin1</h1>.
Degree: Chemistry and Biochemistry, 2009, University of Notre Dame
URL: https://curate.nd.edu/show/73666397v54
► It has become more evident that many proteins experience activity regulation via binding of small molecules or other proteins to sites that are distal…
(more)
▼ It has become more evident that many proteins
experience activity regulation via binding of small molecules or
other proteins to sites that are distal from the active site. This
phenomenon, commonly referred to as allostery, plays an important
role as a mechanism for signal transduction within and between
proteins to make up the complex cellular information
networks.
Proteins of modular design represent a unique class of proteins
that construct such information systems whereby a docking module
and a loosely connected module of catalytic function operate in
concert to achieve optimal activity for the viability of the cell.
In this case, inter-domain signal transduction is carried out by
the process known as modular allostery. Unlike the classic
intra-domain allosteric mechanism, modular allostery is also
associated with large inter-domain structural transitions to
regulate activity. For instance, ligand binding at one domain may
control access of substrate to the active site of another domain by
directly blocking the active site or indirectly via a distal
allosteric site. Pin1 is a model system of an allosteric
protein of
modular design which consists of the binding WW domain that is
flexibly tethered to a peptidyl-prolyl cis-trans isomerase (PPIase)
domain. Pin1 recognizes and catalyses the cis-trans conversion of
the peptidyl pSer/pThr-Pro bond of many targets. Variations in the
substrate ‘input’ sequence induces differential processing by Pin1,
thereby modulating the resultant ‘output’ activities for binding
and/or catalysis. The isolated domains only hold part of the full
activity that is observed when they are linked. Although the WW
domain has no catalytic activity, its absence has deleterious
consequences on the catalytic activity of Pin1. In addition, ligand
interaction results in inter-domain coupling. Therefore, a mode of
information transformation exists that qualifies the WW as an
allosteric modulator of the activity of Pin1-PPIase. The underlying
molecular processes for site to site communication in proteins are
thought to involve conformational transitions that are propagated
between the active site and the allosteric site. The time scales
for such motions can be in the order of slow
(Ì
ås-ms) displacements to fast (ps-ns)
fluctuating motions. Nuclear Magnetic Resonance (NMR) is a
versatile non-invasive technique that probes such molecular
dynamics in solution and at multiple sites. This dissertation
reports the research on the discovery of a novel internal dynamic
conduit of modular allosteric communication between the catalytic
site of Pin1-PPIase and the allosteric WW interaction site located
about 12 angstroms away. In particular, deuterium (2D) NMR
relaxation experiments were used to probe the internal flexibility
of methyl
side chains of Pin1-PPIase upon ligand interaction.
Ligands of different chemical compositions, configurations and
flexibilities induced varying rigidification magnitudes of Pin1’s
internal fast (ps-ns) fluctuating motions. The greatest flexibility
loss was observed…
Advisors/Committee Members: Dr. Jeffrey W. Peng, Committee Chair, Dr. Holly Goodson , Committee Member, Dr. Olaf Wiest , Committee Member, Dr. Brian M. Baker, Committee Member.
Subjects/Keywords: Pin1; natural abundance; networks; Modular Alostery; side chain; NMR; deuterium; Dynamics-driven
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MLA ·
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CSE |
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Namanja, A. T. (2009). Molecular Basis for Signal Transduction in the Bimodular
Cell-Cycle Enzyme Pin1</h1>. (Thesis). University of Notre Dame. Retrieved from https://curate.nd.edu/show/73666397v54
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Namanja, Andrew Tayanjana. “Molecular Basis for Signal Transduction in the Bimodular
Cell-Cycle Enzyme Pin1</h1>.” 2009. Thesis, University of Notre Dame. Accessed January 18, 2021.
https://curate.nd.edu/show/73666397v54.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Namanja, Andrew Tayanjana. “Molecular Basis for Signal Transduction in the Bimodular
Cell-Cycle Enzyme Pin1</h1>.” 2009. Web. 18 Jan 2021.
Vancouver:
Namanja AT. Molecular Basis for Signal Transduction in the Bimodular
Cell-Cycle Enzyme Pin1</h1>. [Internet] [Thesis]. University of Notre Dame; 2009. [cited 2021 Jan 18].
Available from: https://curate.nd.edu/show/73666397v54.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Namanja AT. Molecular Basis for Signal Transduction in the Bimodular
Cell-Cycle Enzyme Pin1</h1>. [Thesis]. University of Notre Dame; 2009. Available from: https://curate.nd.edu/show/73666397v54
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
10.
Muley, Vijaykumar Yogesh.
Improved computational prediction and analysis of protein
- protein interaction networks.
Degree: 2012, Manipal University
URL: http://shodhganga.inflibnet.ac.in/handle/10603/5399
► Recent progress in computational methods for predicting physical and functional protein-protein interactions has provided new insights into the complexity of biological processes. Most of these…
(more)
▼ Recent progress in computational methods for
predicting physical and functional protein-protein interactions has
provided new insights into the complexity of biological processes.
Most of these methods assume that functionally interacting proteins
are likely to have a shared evolutionary history. These methods
include phylogenetic profiling (PP),gene neighborhood (GN), gene
cluster (GC), and the mirrortree. Expression similarity in various
physiological conditions also has been used an indicator of
functional linkages between genes. Comprehensive newlinecomparison
of these methods has not been frequently reported in literature. In
this work, I have shown that the higher performance for predicting
protein-protein interactions was achievable even with 100?150
bacterial genomes out of 565 genomes. I find that variants of PP
and GN are robust against reference genome selection. This study
also reveals that the prediction of metabolic pathway protein
interactions continues to be a challenging task for all methods
which possibly reflect flexible/independent evolutionary histories
of these proteins. On the contrary, genetic information processing
pathways are predicted with comparable accuracy. I have also shown
that the effective use of a particular prediction method depends on
the pathway under investigation. The topological properties of
network predicted by each method differ significantly. This study
suggests that organization of proteins in the predicted networks
ensure the local perturbations in the metabolic pathways and
protein complexes should communicate with quickly to other cellular
proteins. A set of seven machine learning classifiers also used to
predict genome-scale interactome. It is observed that probabilistic
classifiers such as naïve bayes are best suitable for PPI
prediction task. Finally, I have predicted functions for number of
uncharacterized proteins and some of them tested experimentally. A
high quality PPIs can be accessible through user friendly interface
at http://www.cdfd.org.in/ecofunppi
References p. 138-150, Appendix p.
151-157
Advisors/Committee Members: Ranjan, Akash.
Subjects/Keywords: Protein interaction networks; Protein
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APA ·
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APA (6th Edition):
Muley, V. Y. (2012). Improved computational prediction and analysis of protein
- protein interaction networks. (Thesis). Manipal University. Retrieved from http://shodhganga.inflibnet.ac.in/handle/10603/5399
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Muley, Vijaykumar Yogesh. “Improved computational prediction and analysis of protein
- protein interaction networks.” 2012. Thesis, Manipal University. Accessed January 18, 2021.
http://shodhganga.inflibnet.ac.in/handle/10603/5399.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Muley, Vijaykumar Yogesh. “Improved computational prediction and analysis of protein
- protein interaction networks.” 2012. Web. 18 Jan 2021.
Vancouver:
Muley VY. Improved computational prediction and analysis of protein
- protein interaction networks. [Internet] [Thesis]. Manipal University; 2012. [cited 2021 Jan 18].
Available from: http://shodhganga.inflibnet.ac.in/handle/10603/5399.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Muley VY. Improved computational prediction and analysis of protein
- protein interaction networks. [Thesis]. Manipal University; 2012. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/5399
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Maryland
11.
Lapizco Encinas, Grecia del Carmen.
Cooperative Particle Swarm Optimization for Combinatorial Problems.
Degree: Computer Science, 2009, University of Maryland
URL: http://hdl.handle.net/1903/9901
► A particularly successful line of research for numerical optimization is the well-known computational paradigm particle swarm optimization (PSO). In the PSO framework, candidate solutions are…
(more)
▼ A particularly successful line of research for numerical optimization is the well-known computational paradigm particle swarm optimization (PSO). In the PSO framework, candidate solutions are represented as particles that have a position and a velocity in a multidimensional search space. The direct representation of a candidate solution as a point that flies through hyperspace (i.e., R
n) seems to strongly predispose the PSO toward continuous optimization. However, while some attempts have been made towards developing PSO algorithms for combinatorial problems, these techniques usually encode candidate solutions as permutations instead of points in search space and rely on additional local search algorithms.
In this dissertation, I present extensions to PSO that by, incorporating a cooperative strategy, allow the PSO to solve combinatorial problems. The central hypothesis is that by allowing a set of particles, rather than one single particle, to represent a candidate solution, combinatorial problems can be solved by collectively constructing solutions. The cooperative strategy partitions the problem into components where each component is optimized by an individual particle. Particles move in continuous space and communicate through a feedback mechanism. This feedback mechanism guides them in the assessment of their individual contribution to the overall solution.
Three new PSO-based algorithms are proposed. Shared-space CCPSO and multispace CCPSO provide two new cooperative strategies to split the combinatorial problem, and both models are tested on proven NP-hard problems. Multimodal CCPSO extends these combinatorial PSO algorithms to efficiently sample the search space in problems with multiple global optima. Shared-space CCPSO was evaluated on an abductive problem-solving task: the construction of parsimonious set of independent hypothesis in diagnostic problems with direct causal links between disorders and manifestations. Multi-space CCPSO was used to solve a
protein structure prediction subproblem, sidechain packing. Both models are evaluated against the provable optimal solutions and results show that both proposed PSO algorithms are able to find optimal or near-optimal solutions. The exploratory ability of multimodal CCPSO is assessed by evaluating both the quality and diversity of the solutions obtained in a
protein sequence design problem, a highly multimodal problem. These results provide evidence that extended PSO algorithms are capable of dealing with combinatorial problems without having to hybridize the PSO with other local search techniques or sacrifice the concept of particles moving throughout a continuous search space.
Advisors/Committee Members: Reggia, James A (advisor), Kingsford, Carl L (advisor).
Subjects/Keywords: Artificial Intelligence; Computer Science; combinatorial heuristics; particle swarm optimization; protein side chain packing; protein structure prediction; swarm intelligence
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APA (6th Edition):
Lapizco Encinas, G. d. C. (2009). Cooperative Particle Swarm Optimization for Combinatorial Problems. (Thesis). University of Maryland. Retrieved from http://hdl.handle.net/1903/9901
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Lapizco Encinas, Grecia del Carmen. “Cooperative Particle Swarm Optimization for Combinatorial Problems.” 2009. Thesis, University of Maryland. Accessed January 18, 2021.
http://hdl.handle.net/1903/9901.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Lapizco Encinas, Grecia del Carmen. “Cooperative Particle Swarm Optimization for Combinatorial Problems.” 2009. Web. 18 Jan 2021.
Vancouver:
Lapizco Encinas GdC. Cooperative Particle Swarm Optimization for Combinatorial Problems. [Internet] [Thesis]. University of Maryland; 2009. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/1903/9901.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Lapizco Encinas GdC. Cooperative Particle Swarm Optimization for Combinatorial Problems. [Thesis]. University of Maryland; 2009. Available from: http://hdl.handle.net/1903/9901
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Queens University
12.
Vyner, Moira.
The Effect of Polymer Chain Mobility on Protein Adsorption and Subsequent Cell Behavior
.
Degree: Chemical Engineering, 2015, Queens University
URL: http://hdl.handle.net/1974/13854
► Many cell types are known to respond to the stiffness of polymeric biomaterial substrates. However, the mechanism by which cells sense this stiffness is still…
(more)
▼ Many cell types are known to respond to the stiffness of polymeric biomaterial substrates. However, the mechanism by which cells sense this stiffness is still under investigation. Cell response to a material is believed to be mediated by the composition and/or configuration of the protein layers that adsorb to the biomaterial surfaces prior to cell contact. It is, therefore, hypothesized that polymer stiffness, and specifically, the flexibility of the polymer chains at the polymer aqueous interface, affects the composition and configuration of the adsorbed protein layer, which is responsible for influencing cell response. In this thesis, two biomaterials known to induce stiffness dependent cell responses are used as model systems to determine whether polymer chain flexibility influences cell behavior via differences in the protein adsorption. The first is an elastomer formed from an acrylated star-poly(D,L-lactide-co-ϵ-caprolactone) (ELAS) which has been shown to support higher NIH3T3 fibroblast proliferation on a less stiff version of the elastomer despite minimal differences in surface chemistry. The second is poly(trimethylene carbonate) (PTMC) which has been shown to degrade in vivo via macrophage mediated erosion at molecular weights higher than 100 kg/mol, but does not degrade at molecular weights of less than 70 kg/mol, despite no difference in surface chemistry. Quantity and viscoelastic properties of protein layers adsorbed from individual solutions of albumin, immunoglobulin G, fibronectin and vitronectin, as well as fetal serum and adult plasma supplemented environments were compared on different stiffnesses of these materials to determine whether polymer chain flexibility affects protein adsorption. Polymer stiffness was found to affect quantity and conformation of individually adsorbed protein layers as well as the composition of protein layers adsorbed from serum and plasma supplemented media. Surface adsorbed fetuin A and vitronectin were identified and proposed to be responsible for influencing fibroblast proliferation and macrophage behavior, respectively. It was concluded that the flexibility of the polymer chains at the polymer-aqueous interface affects the arrangement of water molecules at the interface and alters the entropic gain associated with protein adsorption, thus favoring the adsorption of different types and adsorbed conformation of proteins which influences the subsequent cell response to the biomaterial.
Subjects/Keywords: Protein Adsorption
;
Polymer Chain Mobility
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APA ·
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MLA ·
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CSE |
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Vyner, M. (2015). The Effect of Polymer Chain Mobility on Protein Adsorption and Subsequent Cell Behavior
. (Thesis). Queens University. Retrieved from http://hdl.handle.net/1974/13854
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Vyner, Moira. “The Effect of Polymer Chain Mobility on Protein Adsorption and Subsequent Cell Behavior
.” 2015. Thesis, Queens University. Accessed January 18, 2021.
http://hdl.handle.net/1974/13854.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Vyner, Moira. “The Effect of Polymer Chain Mobility on Protein Adsorption and Subsequent Cell Behavior
.” 2015. Web. 18 Jan 2021.
Vancouver:
Vyner M. The Effect of Polymer Chain Mobility on Protein Adsorption and Subsequent Cell Behavior
. [Internet] [Thesis]. Queens University; 2015. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/1974/13854.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Vyner M. The Effect of Polymer Chain Mobility on Protein Adsorption and Subsequent Cell Behavior
. [Thesis]. Queens University; 2015. Available from: http://hdl.handle.net/1974/13854
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Georgia Tech
13.
Bellamy, Marcus A.
Leveraging supply network relationships to drive performance.
Degree: PhD, Business, 2015, Georgia Tech
URL: http://hdl.handle.net/1853/55521
► Effective supply chain management requires focal firms to develop capabilities to manage a myriad of multi-tier, interconnected relationships often spanning multiple industries. Conventional assessments of…
(more)
▼ Effective supply
chain management requires focal firms to develop capabilities to manage a myriad of multi-tier, interconnected relationships often spanning multiple industries. Conventional assessments of supply
chain relationships as linear or dyadic structures, rather than as a network, limit academician and managerial approaches to overcome challenges to effectively manage supply chains. Further, empirical research on innovation and performance implications of supply network structure and its corresponding relationship dynamics is still fairly nascent. My research focuses on leveraging supply network relationships to drive performance. Specifically, in my dissertation I examine how the structural, knowledge, and dependency differences in a firm’s supply network can affect knowledge and information flow, and ultimately the firm’s innovative, operational, and financial performance. My first study (CH. 2) contributes to current research at the interface of supply
chain management and innovation. My second (CH. 3) and third paper (CH. 4) incorporate the intensity of each supply network link, reflective of focal firms as customers (suppliers) that may rely heavier on a supplier (customer) based on their percentage of cost (revenue) that goes to (is generated from) that supplier (customer). All three papers extend current research findings by bringing a more holistic assessment of firms that are embedded in a supply network, addressing the need for deeper structural analysis.
Advisors/Committee Members: Ghosh, Soumen (advisor), Hora, Manpreet (advisor), Gaimon, Cheryl (committee member), Forman, Chris (committee member), Basole, Rahul (committee member).
Subjects/Keywords: Supply networks; Supply chain management
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APA (6th Edition):
Bellamy, M. A. (2015). Leveraging supply network relationships to drive performance. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/55521
Chicago Manual of Style (16th Edition):
Bellamy, Marcus A. “Leveraging supply network relationships to drive performance.” 2015. Doctoral Dissertation, Georgia Tech. Accessed January 18, 2021.
http://hdl.handle.net/1853/55521.
MLA Handbook (7th Edition):
Bellamy, Marcus A. “Leveraging supply network relationships to drive performance.” 2015. Web. 18 Jan 2021.
Vancouver:
Bellamy MA. Leveraging supply network relationships to drive performance. [Internet] [Doctoral dissertation]. Georgia Tech; 2015. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/1853/55521.
Council of Science Editors:
Bellamy MA. Leveraging supply network relationships to drive performance. [Doctoral Dissertation]. Georgia Tech; 2015. Available from: http://hdl.handle.net/1853/55521
NSYSU
14.
Wang, Shin-guo.
The Crystallization of Side Chain Effect on the Performances of Poly(3-dodecylthiophene)/fullerene âBulk Heterojunctionâ Solar Cells.
Degree: Master, Electro-Optical Engineering, 2009, NSYSU
URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0721109-170403
► P3DDT (3-dodecylthiophene-2,5-diyl) and PCBM( [6,6]-phenyl C61-butyric acid methyl ester) were fabricated to the active layer of Bulk Heterojunction Organic Solar Cells .We obtained the device…
(more)
▼ P3DDT (3-dodecylthiophene-2,5-diyl) and PCBM( [6,6]-phenyl C61-butyric acid methyl ester) were fabricated to the active layer of Bulk Heterojunction Organic Solar Cells .We obtained the device efficiency was 0.64 % by evaporating solvent at room temperature. We measured Thermal decomposition Temperature (Td) of P3DDT was 487â. But operational temperature was over 90â, it could affect the roughness of thin film and make efficiency to be 4Ã10-3(%). For results of experiments, we know that roughness changed by the crystallization of
side chain and exciton dissociation modified by the morphology between P3DDT and PCBM.
Thin film solar cell has a large effect on the formation of active layer, such as heat treatment, choices of solvents, composition ratio, and speed of spin coating. The efficiency of solar cell has been shown to be highly sensitive to the size, composition and crystallization of the formed domains. We studied two kinds of conjugated polythiophenes with the same main
chain but different
side chain. When the number of carbon atoms of alkyl
side chains is more than 10, some orderly arrangements will occur for
side chains between the layers. We tried to explain the crystallization caused by long alkyl
side chains determined which intrinsic phenomena are the most evident for altering the PCE of solar cell. After recrystallization, the layered structures of P3DDT can be improved, but those orderly degrees of the arrangements with PCBM are further aggregated.
The main point for low PEC and Jsc by heat treatment is the unfavorable and roughened morphology. Charge transfer only occurs at the boundary ,which is interfacial area between donor and acceptor materials, hence, the low Jsc could be caused by poor charge transfer between P3DDT and PCBM. The redistributed arrangement of P3DDT domains exclude PCBM from original space, and it makes PCBM to aggregate large particles, from nanophase to mesophase scales, which reduce mutual solubility to be the source of PCE and Jsc reduction.
Advisors/Committee Members: Hsin-Lung Chen (chair), Yu-Kai Han (chair), Ping-Tsung Huang (chair), Mei-Ying Chang (chair), Wen-Yao Huang (committee member).
Subjects/Keywords: Solar Cell; Crystallization; Side Chain; Poly(3-dodecylthiophene)
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APA ·
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APA (6th Edition):
Wang, S. (2009). The Crystallization of Side Chain Effect on the Performances of Poly(3-dodecylthiophene)/fullerene âBulk Heterojunctionâ Solar Cells. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0721109-170403
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wang, Shin-guo. “The Crystallization of Side Chain Effect on the Performances of Poly(3-dodecylthiophene)/fullerene âBulk Heterojunctionâ Solar Cells.” 2009. Thesis, NSYSU. Accessed January 18, 2021.
http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0721109-170403.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wang, Shin-guo. “The Crystallization of Side Chain Effect on the Performances of Poly(3-dodecylthiophene)/fullerene âBulk Heterojunctionâ Solar Cells.” 2009. Web. 18 Jan 2021.
Vancouver:
Wang S. The Crystallization of Side Chain Effect on the Performances of Poly(3-dodecylthiophene)/fullerene âBulk Heterojunctionâ Solar Cells. [Internet] [Thesis]. NSYSU; 2009. [cited 2021 Jan 18].
Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0721109-170403.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wang S. The Crystallization of Side Chain Effect on the Performances of Poly(3-dodecylthiophene)/fullerene âBulk Heterojunctionâ Solar Cells. [Thesis]. NSYSU; 2009. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0721109-170403
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Delft University of Technology
15.
Tubbing, Rico (author).
An Analysis of Deep Learning Based Profiled Side-channel Attacks: Custom Deep Learning Layer, CNN Hyperparameters for Countermeasures, and Portability Settings.
Degree: 2019, Delft University of Technology
URL: http://resolver.tudelft.nl/uuid:a2179003-b00b-495e-8f2f-225562e65232
► A side-channel attack (SCA) recovers secret data from a device by exploiting unintended physical leakages such as power consumption. In a profiled SCA, we assume…
(more)
▼ A side-channel attack (SCA) recovers secret data from a device by exploiting unintended physical leakages such as power consumption. In a profiled SCA, we assume an adversary has control over a target and copy device. Using the copy device the adversary learns a profile of the device. With the profile, the adversary exploits the measurements from a target device and recovers the secret key. As SCAs have shown to be a realistic attack vector, countermeasures have been invented to harden these kinds of attacks. In the last few years, deep learning has been applied in a wide variety of domains. For example, convolutional neural networks have shown to be effective for object recognition in images and recurrent neural networks for text generation. In the side-channel analysis domain, deep learning has shown to be successful. Up until recently, no deep learning layer existed that was specifically designed for SCAs. In this work, we analyze this layer, called the spread layer, and demonstrate the flaws of this layer. We improve the flaws and show the spread layer does not enhance the performance of SCAs. Additionally, we show there is no need to develop a deep learning layer specifically for SCAs on unprotected implementations. For implementations where countermeasures are present, literature demonstrated that convolutional neural networks are the most successful. However, for both the masking and random delay countermeasure, little is known about the influence of the kernel size and depth of the network. In this work, we illustrate that increasing the kernel size and depth of the network both increase the attack efficiency for the random delay countermeasure. For the masking countermeasure, we demonstrate that higher kernel sizes and shallow networks perform the best. Additionally, in this work, we consider a portability setting where the probe position has been changed in between the measurements of the profiling and attack measurements. Here, we show that the probe position causes a typical deep learning SCA to be ineffective. We introduce a normalization method such that the attack becomes effective, and show this method enables the attack to perform as expected.
Computer Science
Advisors/Committee Members: Picek, Stjepan (mentor), Doerr, Christian (graduation committee), Murukannaiah, Pradeep (graduation committee), Delft University of Technology (degree granting institution).
Subjects/Keywords: Side-Channel Attacks; Deep Learning; Profiled Side-channel Attack; Convolutional Neural Networks; Spread; Portability
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APA (6th Edition):
Tubbing, R. (. (2019). An Analysis of Deep Learning Based Profiled Side-channel Attacks: Custom Deep Learning Layer, CNN Hyperparameters for Countermeasures, and Portability Settings. (Masters Thesis). Delft University of Technology. Retrieved from http://resolver.tudelft.nl/uuid:a2179003-b00b-495e-8f2f-225562e65232
Chicago Manual of Style (16th Edition):
Tubbing, Rico (author). “An Analysis of Deep Learning Based Profiled Side-channel Attacks: Custom Deep Learning Layer, CNN Hyperparameters for Countermeasures, and Portability Settings.” 2019. Masters Thesis, Delft University of Technology. Accessed January 18, 2021.
http://resolver.tudelft.nl/uuid:a2179003-b00b-495e-8f2f-225562e65232.
MLA Handbook (7th Edition):
Tubbing, Rico (author). “An Analysis of Deep Learning Based Profiled Side-channel Attacks: Custom Deep Learning Layer, CNN Hyperparameters for Countermeasures, and Portability Settings.” 2019. Web. 18 Jan 2021.
Vancouver:
Tubbing R(. An Analysis of Deep Learning Based Profiled Side-channel Attacks: Custom Deep Learning Layer, CNN Hyperparameters for Countermeasures, and Portability Settings. [Internet] [Masters thesis]. Delft University of Technology; 2019. [cited 2021 Jan 18].
Available from: http://resolver.tudelft.nl/uuid:a2179003-b00b-495e-8f2f-225562e65232.
Council of Science Editors:
Tubbing R(. An Analysis of Deep Learning Based Profiled Side-channel Attacks: Custom Deep Learning Layer, CNN Hyperparameters for Countermeasures, and Portability Settings. [Masters Thesis]. Delft University of Technology; 2019. Available from: http://resolver.tudelft.nl/uuid:a2179003-b00b-495e-8f2f-225562e65232
16.
Cheung, Yuen-Lam.
Preprocessing and Reduction for Semidefinite Programming via Facial Reduction: Theory and Practice.
Degree: 2013, University of Waterloo
URL: http://hdl.handle.net/10012/8045
► Semidefinite programming is a powerful modeling tool for a wide range of optimization and feasibility problems. Its prevalent use in practice relies on the fact…
(more)
▼ Semidefinite programming is a powerful modeling tool for a wide range of optimization and feasibility problems. Its prevalent use in practice relies on the fact that a (nearly) optimal solution of a semidefinite program can be obtained efficiently in both theory and practice, provided that the semidefinite program and its dual satisfy the Slater condition.
This thesis focuses on the situation where the Slater condition (i.e., the existence of positive definite feasible solutions) does not hold for a given semidefinite program; the failure of the Slater condition often occurs in structured semidefinite programs derived from various applications. In this thesis, we study the use of the facial reduction technique, originally proposed as a theoretical procedure by Borwein and Wolkowicz, as a preprocessing technique for semidefinite programs. Facial reduction can be used either in an algorithmic or a theoretical sense, depending on whether the structure of the semidefinite program is known a priori.
The main contribution of this thesis is threefold. First, we study the numerical issues in the implementation of the facial reduction as an algorithm on semidefinite programs, and argue that each step of the facial reduction algorithm is backward stable. Second, we illustrate the theoretical importance of the facial reduction procedure in the topic of sensitivity analysis for semidefinite programs. Finally, we illustrate the use of facial reduction technique on several classes of structured semidefinite programs, in particular the side chain positioning problem in protein folding.
Subjects/Keywords: semidefinite programming; preprocessing; backward stability; numerical optimization; sensitvity analysis; perturbation theory; side chain positioning; protein structures
…130
9.1.1
9.1.2
9.2
Protein folding: the biology behind the side chain positioning problem… …programs, in particular the side chain positioning problem in
protein folding. We obtain a stable… …9 Side chain positioning problem
9.1
129
Introduction to the side chain positioning… …relaxation of the side chain positioning problem . . . . . . . . . . . . . . . 134
9.2.1
9.2.2
9.3… …Valid constraints for the side chain positioning problem . . . . . . . . . . . 135
SDP…
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MLA ·
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APA (6th Edition):
Cheung, Y. (2013). Preprocessing and Reduction for Semidefinite Programming via Facial Reduction: Theory and Practice. (Thesis). University of Waterloo. Retrieved from http://hdl.handle.net/10012/8045
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Cheung, Yuen-Lam. “Preprocessing and Reduction for Semidefinite Programming via Facial Reduction: Theory and Practice.” 2013. Thesis, University of Waterloo. Accessed January 18, 2021.
http://hdl.handle.net/10012/8045.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Cheung, Yuen-Lam. “Preprocessing and Reduction for Semidefinite Programming via Facial Reduction: Theory and Practice.” 2013. Web. 18 Jan 2021.
Vancouver:
Cheung Y. Preprocessing and Reduction for Semidefinite Programming via Facial Reduction: Theory and Practice. [Internet] [Thesis]. University of Waterloo; 2013. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/10012/8045.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Cheung Y. Preprocessing and Reduction for Semidefinite Programming via Facial Reduction: Theory and Practice. [Thesis]. University of Waterloo; 2013. Available from: http://hdl.handle.net/10012/8045
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Miami University
17.
Abu-Baker, Shadi.
Solid-State NMR Spectroscopic Studies on Phospholamban and
Saposin C Proteins in Phospholipid Membranes.
Degree: PhD, Chemistry, 2007, Miami University
URL: http://rave.ohiolink.edu/etdc/view?acc_num=miami1185851259
► Solid-state NMR spectroscopic techniques were used to investigate two significant membrane proteins, phospholamban (PLB) and Saposin C (Sap C). For the first protein, analysis of…
(more)
▼ Solid-state NMR spectroscopic techniques were used to
investigate two significant membrane proteins, phospholamban (PLB)
and Saposin C (Sap C). For the first
protein, analysis of the 2H
and 31P solid-state NMR data of chemically synthesized WT-PLB and
its phophorylated form (P-PLB) in
1-palmitoyl-2-oleoyl-sn-glycero-phosphocholine (POPC) multilamellar
vesicles (MLVs) indicates that the interaction of P-PLB with POPC
bilayers was less significant when compared to PLB. Moreover, the
secondary structure using 13C=O site-specific isotopically labeled
Ala15-PLB and Ala15-P-PLB in POPC bilayers suggests that this
residue, located in the cytoplasmic domain, is a part of an
?-helical structure for both PLB and P-PLB. Also, 2H NMR spectra of
site-specific CD3-labeled WT-PLB and P-PLB at Ala15 exhibit one
strong isotropic spectral component indicating the presence of
additional motions as well as faster
side-
chain reorientations when
compared with Leu51 and Ala24 representing the transmembrane
domain. Conversely, the 15N Ala11 NMR spectrum of WT-PLB located on
the cytoplasmic domain yields two dynamic components (powder
pattern component and isotropic component) implying that the
backbone dynamics of this residue exists in two populations: one
that is immobile, and another which is motionally averaged on the
NMR timescale. Upon phosphorylation, the 15N mobile component
contribution increases. The POPC 15N NMR spectra indicate that the
transmembrane domain has a tilt angle of 13 ± 6° with respect to
the mechanically oriented POPC bilayer normal and that the
cytoplasmic domain of WT-PLB lies on the surface of the
phospholipid bilayers. For the second
protein, 2H and 31P
solid-state NMR data of Sap C in dioleoylphosphatidylglycerol
(DOPG) and dioleoylphosphatidylserine (DOPS) mixed bilayers
indicates that Sap C is not inserting deep into the bilayers and
that it has no preference to DOPS over DOPG. Finally, several other
solid-state NMR spectroscopic experiments indicate that protonated
Sap C disturbs 1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-L-serine]
(POPS) lipid bilayers and not the neutral POPC
lipids.
Advisors/Committee Members: Dr. Gary, Lorigan (Advisor).
Subjects/Keywords: Phospholamban; Saposin C; Solid-state NMR spectroscopy; Solid-phase peptide synthesis; Protein-membrane interaction; multilamellar vesicles; Protein side-chain and backbone dynamics; Structural topology.
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APA ·
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Manager
APA (6th Edition):
Abu-Baker, S. (2007). Solid-State NMR Spectroscopic Studies on Phospholamban and
Saposin C Proteins in Phospholipid Membranes. (Doctoral Dissertation). Miami University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=miami1185851259
Chicago Manual of Style (16th Edition):
Abu-Baker, Shadi. “Solid-State NMR Spectroscopic Studies on Phospholamban and
Saposin C Proteins in Phospholipid Membranes.” 2007. Doctoral Dissertation, Miami University. Accessed January 18, 2021.
http://rave.ohiolink.edu/etdc/view?acc_num=miami1185851259.
MLA Handbook (7th Edition):
Abu-Baker, Shadi. “Solid-State NMR Spectroscopic Studies on Phospholamban and
Saposin C Proteins in Phospholipid Membranes.” 2007. Web. 18 Jan 2021.
Vancouver:
Abu-Baker S. Solid-State NMR Spectroscopic Studies on Phospholamban and
Saposin C Proteins in Phospholipid Membranes. [Internet] [Doctoral dissertation]. Miami University; 2007. [cited 2021 Jan 18].
Available from: http://rave.ohiolink.edu/etdc/view?acc_num=miami1185851259.
Council of Science Editors:
Abu-Baker S. Solid-State NMR Spectroscopic Studies on Phospholamban and
Saposin C Proteins in Phospholipid Membranes. [Doctoral Dissertation]. Miami University; 2007. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=miami1185851259
University of Manchester
18.
Schachter, Jonathan.
A Real Options Approach to Valuing Flexibility in
Demand-Side Response Operations and Investments under
Uncertainty.
Degree: 2016, University of Manchester
URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:300927
► This thesis investigates methodologies for valuing the flexibility of demand-side response (DSR) in its ability to respond to future uncertainties. The ability to quantify this…
(more)
▼ This thesis investigates methodologies for valuing
the flexibility of demand-
side response (DSR) in its ability to
respond to future uncertainties. The ability to quantify this
flexibility is especially important for energy systems investments
given their large and irreversible capital costs. The consideration
of uncertainty in electricity markets and energy
networks requires
solutions that allow decision makers to quickly respond to
unexpected events, such as extreme short-term electricity price
variations in an operational setting, or incorrect long-term demand
projections in planning. This uncertainty, coupled with the
irreversibility of energy network investments, results in the need
for viable 'wait-and-see' investment strategies that can help hedge
electicity price risk in the short-term while hedging planning risk
in the long-term, until at least some, if not all, uncertainty is
resolved. In both cases, this leads to an added value in the case
of temporary flexible investment options like DSR, which may
otherwise be considered unattractive under a deterministic analysis
setting. A number of significant contributions to power systems
research are offered in this work, focusing on valuation methods
for quantifying the flexibility value of DSR under both short-term
and long-term uncertainty. The first outcome of this research is an
extensive review of current real options (RO) methods that
clarifies the assumptions and utilization of RO for decision-making
in engineering applications. It suggests that many of the
assumptions used contribute to a misuse of the models when applied
to physical systems. A framework for investing under uncertainty is
proposed, where the methodologies, steps, inputs, assumptions,
limitations and advantages of different RO models are described so
as to offer a practical guide to decision makers for selecting the
most appropriate RO model for their valuation purposes. The second
outcome is the design of a probabilistic RO framework and
operational model for DSR that quantifies its benefits as an energy
service for hedging different market price risks. A mathematical
formulation for applying “real options thinking” is presented that
provides decision makers with a means of quantifying the value of
DSR when both operational and planning decisions are
subject to
uncertainty. In particular, DSR contracts can have tremendous value
as an arbitrage or portfolio-balancing tool, helping hedge almost
entirely electricity price risk in day-ahead and real-time markets,
especially when prices are highly volatile. This value is
quantified using a novel RO framework that frees the decision maker
from the assumptions needed in financial option models. A new load
forecasting and price simulation model is also developed to
forecast load profiles and simulate new price series with different
average values, higher volatilities and extreme price spikes to
represent potential future market scenarios and to determine under
which conditions DSR has the most value. The valuation of a DSR
investment is then…
Advisors/Committee Members: JOHNSON, PAUL PV, Johnson, Paul, Mancarella, Pierluigi.
Subjects/Keywords: real options; uncertainty; investment planning; distribution networks; demand side response
Record Details
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Schachter, J. (2016). A Real Options Approach to Valuing Flexibility in
Demand-Side Response Operations and Investments under
Uncertainty. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:300927
Chicago Manual of Style (16th Edition):
Schachter, Jonathan. “A Real Options Approach to Valuing Flexibility in
Demand-Side Response Operations and Investments under
Uncertainty.” 2016. Doctoral Dissertation, University of Manchester. Accessed January 18, 2021.
http://www.manchester.ac.uk/escholar/uk-ac-man-scw:300927.
MLA Handbook (7th Edition):
Schachter, Jonathan. “A Real Options Approach to Valuing Flexibility in
Demand-Side Response Operations and Investments under
Uncertainty.” 2016. Web. 18 Jan 2021.
Vancouver:
Schachter J. A Real Options Approach to Valuing Flexibility in
Demand-Side Response Operations and Investments under
Uncertainty. [Internet] [Doctoral dissertation]. University of Manchester; 2016. [cited 2021 Jan 18].
Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:300927.
Council of Science Editors:
Schachter J. A Real Options Approach to Valuing Flexibility in
Demand-Side Response Operations and Investments under
Uncertainty. [Doctoral Dissertation]. University of Manchester; 2016. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:300927
University of Manchester
19.
Schachter, Jonathan.
A real options approach to valuing flexibility in demand-side response operations and investments under uncertainty.
Degree: PhD, 2016, University of Manchester
URL: https://www.research.manchester.ac.uk/portal/en/theses/a-real-options-approach-to-valuing-flexibility-in-demandside-response-operations-and-investments-under-uncertainty(ecde4f40-5e42-4223-b347-fc05ea3ce4f4).html
;
http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686765
► This thesis investigates methodologies for valuing the flexibility of demand-side response (DSR) in its ability to respond to future uncertainties. The ability to quantify this…
(more)
▼ This thesis investigates methodologies for valuing the flexibility of demand-side response (DSR) in its ability to respond to future uncertainties. The ability to quantify this flexibility is especially important for energy systems investments given their large and irreversible capital costs. The consideration of uncertainty in electricity markets and energy networks requires solutions that allow decision makers to quickly respond to unexpected events, such as extreme short-term electricity price variations in an operational setting, or incorrect long-term demand projections in planning. This uncertainty, coupled with the irreversibility of energy network investments, results in the need for viable 'wait-and-see' investment strategies that can help hedge electicity price risk in the short-term while hedging planning risk in the long-term, until at least some, if not all, uncertainty is resolved. In both cases, this leads to an added value in the case of temporary flexible investment options like DSR, which may otherwise be considered unattractive under a deterministic analysis setting. A number of significant contributions to power systems research are offered in this work, focusing on valuation methods for quantifying the flexibility value of DSR under both short-term and long-term uncertainty. The first outcome of this research is an extensive review of current real options (RO) methods that clarifies the assumptions and utilization of RO for decision-making in engineering applications. It suggests that many of the assumptions used contribute to a misuse of the models when applied to physical systems. A framework for investing under uncertainty is proposed, where the methodologies, steps, inputs, assumptions, limitations and advantages of different RO models are described so as to offer a practical guide to decision makers for selecting the most appropriate RO model for their valuation purposes. The second outcome is the design of a probabilistic RO framework and operational model for DSR that quantifies its benefits as an energy service for hedging different market price risks. A mathematical formulation for applying “real options thinking” is presented that provides decision makers with a means of quantifying the value of DSR when both operational and planning decisions are subject to uncertainty. In particular, DSR contracts can have tremendous value as an arbitrage or portfolio-balancing tool, helping hedge almost entirely electricity price risk in day-ahead and real-time markets, especially when prices are highly volatile. This value is quantified using a novel RO framework that frees the decision maker from the assumptions needed in financial option models. A new load forecasting and price simulation model is also developed to forecast load profiles and simulate new price series with different average values, higher volatilities and extreme price spikes to represent potential future market scenarios and to determine under which conditions DSR has the most value. The valuation of a DSR investment is then…
Subjects/Keywords: 621.3; real options; uncertainty; investment planning; distribution networks; demand side response
Record Details
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Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Schachter, J. (2016). A real options approach to valuing flexibility in demand-side response operations and investments under uncertainty. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/a-real-options-approach-to-valuing-flexibility-in-demandside-response-operations-and-investments-under-uncertainty(ecde4f40-5e42-4223-b347-fc05ea3ce4f4).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686765
Chicago Manual of Style (16th Edition):
Schachter, Jonathan. “A real options approach to valuing flexibility in demand-side response operations and investments under uncertainty.” 2016. Doctoral Dissertation, University of Manchester. Accessed January 18, 2021.
https://www.research.manchester.ac.uk/portal/en/theses/a-real-options-approach-to-valuing-flexibility-in-demandside-response-operations-and-investments-under-uncertainty(ecde4f40-5e42-4223-b347-fc05ea3ce4f4).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686765.
MLA Handbook (7th Edition):
Schachter, Jonathan. “A real options approach to valuing flexibility in demand-side response operations and investments under uncertainty.” 2016. Web. 18 Jan 2021.
Vancouver:
Schachter J. A real options approach to valuing flexibility in demand-side response operations and investments under uncertainty. [Internet] [Doctoral dissertation]. University of Manchester; 2016. [cited 2021 Jan 18].
Available from: https://www.research.manchester.ac.uk/portal/en/theses/a-real-options-approach-to-valuing-flexibility-in-demandside-response-operations-and-investments-under-uncertainty(ecde4f40-5e42-4223-b347-fc05ea3ce4f4).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686765.
Council of Science Editors:
Schachter J. A real options approach to valuing flexibility in demand-side response operations and investments under uncertainty. [Doctoral Dissertation]. University of Manchester; 2016. Available from: https://www.research.manchester.ac.uk/portal/en/theses/a-real-options-approach-to-valuing-flexibility-in-demandside-response-operations-and-investments-under-uncertainty(ecde4f40-5e42-4223-b347-fc05ea3ce4f4).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686765
Rice University
20.
Bai, Jingwen.
Wireless Side-Channels in MIMO Full-Duplex Systems.
Degree: PhD, Engineering, 2016, Rice University
URL: http://hdl.handle.net/1911/96607
► In this thesis, we propose a new approach for enhanced interference management via wireless side-channels in advanced wireless systems such as MIMO full-duplex systems. The…
(more)
▼ In this thesis, we propose a new approach for enhanced interference management via wireless
side-channels in advanced wireless systems such as MIMO full-duplex systems. The rise of multiple radio interfaces, such as WiFi (operating in unlicensed ISM bands) and cellular (operating in licensed bands), with near-default inclusion in smartphones, allows for a new use of the ISM bands to manage interference in cellular bands, by creating wireless “
side-channels” between mobile users. In a multi-user MIMO full-duplex system, an in-band full-duplex base station (BS) with multiple antennas communicates with multiple up- and downlink users in the same time-frequency slot. We characterize the impact of
side- channels in managing interference from uplink users to downlink users in such MIMO full-duplex system.
First, we experimentally quantify the likelihood of establishing ISM
side-channels between smartphones in WiFi-free areas such as highways. Next, we study a
side-channel assisted two-user MIMO full-duplex sys- tem and characterize its generalized degrees-of-freedom and diversity- multiplexing tradeoff. For such a system, we show that the optimal perfor- mance is achieved by our proposed vector bin-and-cancel strategy which leverages Han-Kobayashi message splitting.
Then, we study a
side-channel assisted multi-user MIMO full-duplex system from a cross-layer protocol design perspective. Our protocol design integrates automatic repeat request (ARQ) at the medium access control (MAC) layer with enhanced interference management via
side-channels at the physical layer (PHY). Our proposed joint PHY-MAC protocols exploit the ARQ information offered by the MAC layer to reduce the data retransmission time and improve system goodput.
Finally, we study a multi-cell multi-user MIMO full-duplex system, where new forms of intra- and inter-cell interference appear due to the full-duplex operation. We characterize the up- and downlink ergodic achievable rates for the case of linear precoders and receivers. The rate analysis includes practical constraints such as imperfect full-duplex radio chains, channel estimation error, training overhead and pilot contamination. We show that with large antenna arrays at base-stations, the gains from full-duplex are available at the network level despite the increased interference in the full-duplex
networks. Moreover, full-duplex
networks can use fewer antennas to achieve spectral efficiency gain over the half-duplex counterparts. We also demonstrate that under realistic multi-cell MIMO full-duplex network scenarios,
side-channels are effective in significantly improving the spectral efficiency of cell-edge users.
Advisors/Committee Members: Sabharwal, Ashutosh (advisor).
Subjects/Keywords: MIMO; Wireless side-channels; Full-duplex; Multi-cell networks
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APA ·
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MLA ·
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Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Bai, J. (2016). Wireless Side-Channels in MIMO Full-Duplex Systems. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/96607
Chicago Manual of Style (16th Edition):
Bai, Jingwen. “Wireless Side-Channels in MIMO Full-Duplex Systems.” 2016. Doctoral Dissertation, Rice University. Accessed January 18, 2021.
http://hdl.handle.net/1911/96607.
MLA Handbook (7th Edition):
Bai, Jingwen. “Wireless Side-Channels in MIMO Full-Duplex Systems.” 2016. Web. 18 Jan 2021.
Vancouver:
Bai J. Wireless Side-Channels in MIMO Full-Duplex Systems. [Internet] [Doctoral dissertation]. Rice University; 2016. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/1911/96607.
Council of Science Editors:
Bai J. Wireless Side-Channels in MIMO Full-Duplex Systems. [Doctoral Dissertation]. Rice University; 2016. Available from: http://hdl.handle.net/1911/96607
University of New Mexico
21.
Zhang, Xu.
Next Generation TCP/IP Side Channels.
Degree: Department of Computer Science, 2018, University of New Mexico
URL: https://digitalrepository.unm.edu/cs_etds/91
► Side channel techniques have been developed in recent years to fulfill various tasks in modern computer network measurements. However, due to their nature, these…
(more)
▼ Side channel techniques have been developed in recent years to fulfill various tasks in modern computer network measurements. However, due to their nature, these techniques are typically limited in terms of both fidelity and their ability to be used on the real Internet without raising ethical concerns because of packet rates. I propose the next generation of TCP/IP
side channel techniques that exploit information flow in modern systems’ network stacks to overcome weaknesses in previous techniques. The proposed work is novel, non-intrusive, and can carry out measurements with high fidelity. I achieved this by deeply understanding the behaviors of modern systems’ network stacks and balancing the trade-offs (e.g. packet rate and fidelity) by applying suitable mathematical models. My work comprises three novel tools which each solve different challenges in current network measurement.
Firstly, I propose an Internet measurement technique for finding machines that are hidden behind firewalls. That is, if a firewall prevents outside IP addresses from sending packets to an internal protected machine that is only accessible on the local network, the technique can still find the machine. Secondly, I present an improved off-path round-trip time (RTT) measurement technique based on [11] that can, with high fidelity, measure the RTT between essentially any two machines (A and B) on the Internet without having special access to A or B or having any presence in the path between A and B. Finally, I proposed a new scanning technique that can perform network measurements such as: inferring TCP/IP-based trust relationships off-path, stealthily port scanning a target without using the scanner’s IP address, or detecting off-path packet drops between two international hosts. The thesis statement of my dissertation is: Previous
side channel techniques can be improved and used to solve new challenges in current network measurement based on deeply understanding the modern systems’ network stack behavior and building corresponding mathematical models to balance trade-offs between fidelity and ethical concerns related to packet rates.
Advisors/Committee Members: Jedidiah Crandall, Patrick Bridges, James Plusquellic, Benjamin Edwards.
Subjects/Keywords: TCP/IP; side channel; network measurement; OS and Networks
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APA ·
Chicago ·
MLA ·
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Export
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Manager
APA (6th Edition):
Zhang, X. (2018). Next Generation TCP/IP Side Channels. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/cs_etds/91
Chicago Manual of Style (16th Edition):
Zhang, Xu. “Next Generation TCP/IP Side Channels.” 2018. Doctoral Dissertation, University of New Mexico. Accessed January 18, 2021.
https://digitalrepository.unm.edu/cs_etds/91.
MLA Handbook (7th Edition):
Zhang, Xu. “Next Generation TCP/IP Side Channels.” 2018. Web. 18 Jan 2021.
Vancouver:
Zhang X. Next Generation TCP/IP Side Channels. [Internet] [Doctoral dissertation]. University of New Mexico; 2018. [cited 2021 Jan 18].
Available from: https://digitalrepository.unm.edu/cs_etds/91.
Council of Science Editors:
Zhang X. Next Generation TCP/IP Side Channels. [Doctoral Dissertation]. University of New Mexico; 2018. Available from: https://digitalrepository.unm.edu/cs_etds/91
NSYSU
22.
Wu, Yun-Sheng.
Morphology and Phase Behavior in Poly(n-alkyl methacrylate) and Poly(n-alkyl acrylate).
Degree: Master, Materials Science and Engineering, 2000, NSYSU
URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0716100-172602
► In this research,we observed PAMA(poly(n-alkyl methacrylate)) and PAA(poly(n-alkyl acrylate)ï¼side chain crystalline.We find side chain is longer and crystalize more easily,melting point is higher.In the result…
(more)
▼ In this research,we observed PAMA(poly(n-alkyl methacrylate)) and PAA(poly(n-alkyl acrylate)ï¼
side chain crystalline.We find
side chain is longer and crystalize more easily,melting point
is higher.In the result of DSC thermograms,the length of
side chain is 6 carbons,we can't find any thermal transition.But the length of
side chain is 12ã18 carbons,we only found Tm.In PLM observation,we only get
side chain crystalline's picture,and can't see any liquid crystalline yet.
Although in X-ray's illustrative can find layer structure's diffraction peak,but i think this evidence can't prove the system that is liquid crystalline.It just can be said that the layed structure was formed by
side chain crystallization.
Advisors/Committee Members: Ming Chen (chair), Jin Long Hong (chair), Shou An Chen (chair), An Chung Su (committee member).
Subjects/Keywords: phase behavior; side chain crystalline; morphology
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APA (6th Edition):
Wu, Y. (2000). Morphology and Phase Behavior in Poly(n-alkyl methacrylate) and Poly(n-alkyl acrylate). (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0716100-172602
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wu, Yun-Sheng. “Morphology and Phase Behavior in Poly(n-alkyl methacrylate) and Poly(n-alkyl acrylate).” 2000. Thesis, NSYSU. Accessed January 18, 2021.
http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0716100-172602.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wu, Yun-Sheng. “Morphology and Phase Behavior in Poly(n-alkyl methacrylate) and Poly(n-alkyl acrylate).” 2000. Web. 18 Jan 2021.
Vancouver:
Wu Y. Morphology and Phase Behavior in Poly(n-alkyl methacrylate) and Poly(n-alkyl acrylate). [Internet] [Thesis]. NSYSU; 2000. [cited 2021 Jan 18].
Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0716100-172602.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wu Y. Morphology and Phase Behavior in Poly(n-alkyl methacrylate) and Poly(n-alkyl acrylate). [Thesis]. NSYSU; 2000. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0716100-172602
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Guelph
23.
Ruprecht, Amanda.
The Investigation of Novel Acyl-CoA Dehydrogenases Involved in Bacterial Steroid Degradation.
Degree: MS, Department of Molecular and Cellular Biology, 2014, University of Guelph
URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8204
► FadE28-FadE29 is a heterotetrameric acyl-CoA dehydrogenase (ACAD) that catalyzes the dehydrogenation of the 3-carbon side chained 3-oxo-23,24-bisnorchol-4-en-22-oyl-CoA. FadE34 and CasC are also steroid degrading ACADs,…
(more)
▼ FadE28-FadE29 is a heterotetrameric acyl-CoA dehydrogenase (ACAD) that catalyzes the dehydrogenation of the 3-carbon
side chained 3-oxo-23,24-bisnorchol-4-en-22-oyl-CoA. FadE34 and CasC are also steroid degrading ACADs, however, they are a fusion of two ACAD domains encoded within one gene. FadE34 and CasC form homodimers and contain only two FAD molecules. Steady-state kinetic assays show that both CasC and FadE34 can utilize the 5- carbon
side chained cholyl-CoA, deoxycholyl-CoA, and 3β-hydroxy-5-cholen-24-oyl-CoA as substrates, with varying catalytic efficiencies. This suggests these ACADs recognize both the
side chain length and steroid ring structure. Replacement of a catalytic glutamic acid residue to a glutamine (FadE28-FadE29E241Q, FadE34E581Q, CasCE598Q) resulted in inactive variants, and replacement of an arginine residue to an alanine (FadE28R227A, FadE34R236A, CasCR239A) resulted in the decreased ability to bind FAD. These novel ACADs that utilize steroid substrates have half of the number of active sites compared to the previously characterized ACADs that utilize aliphatic substrates.
Advisors/Committee Members: Seah, Stephen (advisor).
Subjects/Keywords: Acyl-CoA dehydrogenase; Mycobacterium tuberculosis; Rhodococcus jostii RHA1; Side chain degradation; Cholesterol; Cholate
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APA (6th Edition):
Ruprecht, A. (2014). The Investigation of Novel Acyl-CoA Dehydrogenases Involved in Bacterial Steroid Degradation. (Masters Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8204
Chicago Manual of Style (16th Edition):
Ruprecht, Amanda. “The Investigation of Novel Acyl-CoA Dehydrogenases Involved in Bacterial Steroid Degradation.” 2014. Masters Thesis, University of Guelph. Accessed January 18, 2021.
https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8204.
MLA Handbook (7th Edition):
Ruprecht, Amanda. “The Investigation of Novel Acyl-CoA Dehydrogenases Involved in Bacterial Steroid Degradation.” 2014. Web. 18 Jan 2021.
Vancouver:
Ruprecht A. The Investigation of Novel Acyl-CoA Dehydrogenases Involved in Bacterial Steroid Degradation. [Internet] [Masters thesis]. University of Guelph; 2014. [cited 2021 Jan 18].
Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8204.
Council of Science Editors:
Ruprecht A. The Investigation of Novel Acyl-CoA Dehydrogenases Involved in Bacterial Steroid Degradation. [Masters Thesis]. University of Guelph; 2014. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8204
Université de Sherbrooke
24.
Fu, Shangyi.
L'orientation et la propriété de mémoire de forme des polymères cristallins liquides à chaînes latérales covalents et supramoléculaires.
Degree: 2016, Université de Sherbrooke
URL: http://hdl.handle.net/11143/9453
► In many studies of the side-chain liquid crystalline polymers (SCLCPs) bearing azobenzene mesogens as pendant groups, obtaining the orientation of azobenzene mesogens at a macroscopic…
(more)
▼ In many studies of the
side-
chain liquid crystalline polymers (SCLCPs) bearing azobenzene mesogens as pendant groups, obtaining the orientation of azobenzene mesogens at a macroscopic scale as well as its control is important, because it impacts many properties related to the cooperative motion characteristic of liquid crystals and the trans-cis photoisomerization of the azobenzene molecules. Various means can be used to align the mesogens in the polymers, including rubbed surface, mechanical stretching or shearing, and electric or magnetic field. In the case of azobenzene-containing SCLCPs, another method consists in using linearly polarized light (LPL) to induce orientation of azobenzene mesogens perpendicular to the polarization direction of the excitation light, and such photoinduced orientation has been the
subject of numerous studies. In the first study realized in this thesis (Chapter 1), we carried out the first systematic investigation on the interplay of the mechanically and optically induced orientation of azobenzene mesogens as well as the effect of thermal annealing in a SCLCP and a diblock copolymer comprising two SCLCPs bearing azobenzene and biphenyl mesogens, respectively. Using a supporting-film approach previously developed by our group, a given polymer film can be first stretched in either the nematic or smectic phase to yield orientation of azobenzene mesogens either parallel or perpendicular to the strain direction, then exposed to unpolarized UV light to erase the mechanically induced orientation upon the trans–cis isomerization, followed by linearly polarized visible light for photoinduced reorientation as a result of the cis–trans backisomerization, and finally heated to different LC phases for thermal annealing. Using infrared dichroism to monitor the change in orientation degree, the results of this study have unveiled complex and different orientational behavior and coupling effects for the homopolymer of poly{6-[4-(4-methoxyphenylazo)phenoxy]hexyl methacrylate} (PAzMA) and the diblock copolymer of PAzMA-block- poly{6-[4-(4-cyanophenyl) phenoxy]hexyl methacrylate} (PAzMA-PBiPh). Most notably for the homopolymer, the stretching-induced orientation exerts no memory effect on the photoinduced reorientation, the direction of which is determined by the polarization of the visible light regardless of the mechanically induced orientation direction in the stretched film. Moreover, subsequent thermal annealing in the nematic phase leads to parallel orientation independently of the initial mechanically or photoinduced orientation direction. By contrast, the diblock copolymer displays a strong orientation memory effect. Regardless of the condition used, either for photoinduced reorientation or thermal annealing in the liquid crystalline phase, only the initial stretching-induced perpendicular orientation of azobenzene mesogens can be recovered. The reported findings provide new insight into the different orientation mechanisms, and help understand the important issue of orientation induction and…
Advisors/Committee Members: Zhao, Yue (advisor).
Subjects/Keywords: Side-chain liquid crystalline polymers; Supramolecular polymers; Shape memory polymers; Azobenzene; Orientation of mesogens; Photoisomerization
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APA (6th Edition):
Fu, S. (2016). L'orientation et la propriété de mémoire de forme des polymères cristallins liquides à chaînes latérales covalents et supramoléculaires. (Doctoral Dissertation). Université de Sherbrooke. Retrieved from http://hdl.handle.net/11143/9453
Chicago Manual of Style (16th Edition):
Fu, Shangyi. “L'orientation et la propriété de mémoire de forme des polymères cristallins liquides à chaînes latérales covalents et supramoléculaires.” 2016. Doctoral Dissertation, Université de Sherbrooke. Accessed January 18, 2021.
http://hdl.handle.net/11143/9453.
MLA Handbook (7th Edition):
Fu, Shangyi. “L'orientation et la propriété de mémoire de forme des polymères cristallins liquides à chaînes latérales covalents et supramoléculaires.” 2016. Web. 18 Jan 2021.
Vancouver:
Fu S. L'orientation et la propriété de mémoire de forme des polymères cristallins liquides à chaînes latérales covalents et supramoléculaires. [Internet] [Doctoral dissertation]. Université de Sherbrooke; 2016. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/11143/9453.
Council of Science Editors:
Fu S. L'orientation et la propriété de mémoire de forme des polymères cristallins liquides à chaînes latérales covalents et supramoléculaires. [Doctoral Dissertation]. Université de Sherbrooke; 2016. Available from: http://hdl.handle.net/11143/9453
Virginia Tech
25.
Zhong, Yongliang.
Development of Controlled Ring-Opening Polymerization of O-Carboxyanhydrides.
Degree: PhD, Chemical Engineering, 2020, Virginia Tech
URL: http://hdl.handle.net/10919/100736
► Polyesters are widely used in everyday applications ranging from clothing and packaging to agriculture and biomedicine. Different from conventional unrecyclable plastics, polyesters are usually biocompatible…
(more)
▼ Polyesters are widely used in everyday applications ranging from clothing and packaging to agriculture and biomedicine. Different from conventional unrecyclable plastics, polyesters are usually biocompatible and biodegradable, and can be synthesized from renewable resources. A few commercially available polyesters have been approved by FDA and widely used for medical applications. However, their utility for applications that demand various mechanical and chemical properties is greatly limited by the lack of
side-
chain functional groups in polyesters and in their monomers—lactones. Increasing efforts have been devoted to the introduction of pendant groups along the polymer
chain in order to modify and modulate the desired properties of polyesters and thereby to expand their applications.
Over the last decade, O-carboxyanhydrides (OCAs) have emerged as an alternative class of highly active monomers for polyester polymerization. OCAs can be prepared from renewable source amino acids and thus have a richer range of
side chain functional groups. Like lactones, OCAs can undergo ring-opening polymerization (ROP). Unfortunately, current ROP methods usually result in uncontrolled polymerization of OCAs including loss of stereoregularity, unpredictable molecular weights, or slow polymerization rate.
To address the above-described polymer chemistry and materials challenges, I have been motivated to develop a new polymer chemistry knowledge base when starting my Ph.D. program. I was first involved in the development of a controlled photoredox polymerization of OCAs produces polyesters with various
side chain functional groups. By using photoredox Ni/Zn/Ir catalysts, stereoregular high molecular weight polyesters can be synthesized from racemic OCAs in a rapid, controlled manner.
IV
However, this catalytic system has to be used at -20 °C despite so successful in preparing stereoblock polyesters.
Encouraged by our recent success in this area, I started to work on the discovery of other transition metal complexes such as the Co complexes used in N-carboxyanhydride polymerization. Ultimately, innovative photoredox Co/Zn catalysts has been successfully developed, and applied to our protocol to achieve the controlled ROP of enantiopure OCAs under mild reaction condition (Chapter 2). The Co catalyst can replace both Ni and Ir in aforementioned photoredox system. Meanwhile, the combination of Co catalysts and various Zn/Hf complexes has also been developed to undergo photoredox ROP of racemic OCAs to efficiently produce polyesters with different microstructures (Chapter 3).
Although photoredox ROP is an efficient method for synthesizing degradable polyesters, great decrease in photonic flux with the depth of the reaction medium makes it less energy efficient compared to electricity. Therefore, we then extended our protocol to electrochemical reaction, which is one of the most energy-efficient chemical reactions. The newly identified Co/Zn catalytic system can be activated by electric current to mediate rapid electrochemical ROP (eROP)…
Advisors/Committee Members: Tong, Rong (committeechair), Lu, Chang (committee member), Goldstein, Aaron S. (committee member), Liu, Guoliang (committee member).
Subjects/Keywords: ring-opening polymerization; polyester; O-carboxyanydrides; photoredox; electrochemical; stereoselective; photocatalyst; side-chain functionalities; and mechanism.
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APA ·
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APA (6th Edition):
Zhong, Y. (2020). Development of Controlled Ring-Opening Polymerization of O-Carboxyanhydrides. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/100736
Chicago Manual of Style (16th Edition):
Zhong, Yongliang. “Development of Controlled Ring-Opening Polymerization of O-Carboxyanhydrides.” 2020. Doctoral Dissertation, Virginia Tech. Accessed January 18, 2021.
http://hdl.handle.net/10919/100736.
MLA Handbook (7th Edition):
Zhong, Yongliang. “Development of Controlled Ring-Opening Polymerization of O-Carboxyanhydrides.” 2020. Web. 18 Jan 2021.
Vancouver:
Zhong Y. Development of Controlled Ring-Opening Polymerization of O-Carboxyanhydrides. [Internet] [Doctoral dissertation]. Virginia Tech; 2020. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/10919/100736.
Council of Science Editors:
Zhong Y. Development of Controlled Ring-Opening Polymerization of O-Carboxyanhydrides. [Doctoral Dissertation]. Virginia Tech; 2020. Available from: http://hdl.handle.net/10919/100736
Macquarie University
26.
Pournader, Mehrdokht.
Identification and analysis of operational and behavioural risks emerging and propagating in supply chains: a multi-method approach.
Degree: 2017, Macquarie University
URL: http://hdl.handle.net/1959.14/1275939
► Thesis by publication.
Bibliography: pages 221-271.
Chapter One. Introduction – Chapter Two. Operational risks and resilience in supply chains – Chapter Three. Behavioural risks in…
(more)
▼ Thesis by publication.
Bibliography: pages 221-271.
Chapter One. Introduction – Chapter Two. Operational risks and resilience in supply chains – Chapter Three. Behavioural risks in supply chains – Chapter Four. Risk and vulnerability in service triads – Chapter Five. Conclusion and discussions – References – Appendices.
The study of supply chain risks can be conducted from various perspectives, including types of risks and supply chain structure. First, from the aspect of the types of supply chain risks, the thesis investigates operational and behavioural risks both separately and in tandem. For operational risks, the proposed research model tackles a critical research problem in supply chain risk literature, which revolves around making a link between supply chain resilience and risk assessment. Outsourcing malfunctions and risks associated with them are analysed as a specific type of operational risk that is prevalent in modern supply chains. For behavioural risks, the risk attitudes of decision makers and their impact on inventory decisions are investigated. Another study, conducted at the intersection of behavioural and operational risks, shows the importance of considering both types of the aforementioned risks while assessing vulnerabilities in supply chains. Second, the research adopts the viewpoint of supply chain structure, investigating supply chains and their vulnerability to risks in forms of service supply networks, in particular in service triads.
Most of the studies adopt a multi-method approach, proposing analytical models to assess supply chain vulnerability to risks and testing these models using surveys, interviews, archival data or behavioural experiments.
1 online resource (xv, 288 pages) diagrams, graphs, tables
Subjects/Keywords: Operational risk; Supply-side economics; Production (Economic theory); supply chain; behavioural operation; risk
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APA ·
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MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Pournader, M. (2017). Identification and analysis of operational and behavioural risks emerging and propagating in supply chains: a multi-method approach. (Doctoral Dissertation). Macquarie University. Retrieved from http://hdl.handle.net/1959.14/1275939
Chicago Manual of Style (16th Edition):
Pournader, Mehrdokht. “Identification and analysis of operational and behavioural risks emerging and propagating in supply chains: a multi-method approach.” 2017. Doctoral Dissertation, Macquarie University. Accessed January 18, 2021.
http://hdl.handle.net/1959.14/1275939.
MLA Handbook (7th Edition):
Pournader, Mehrdokht. “Identification and analysis of operational and behavioural risks emerging and propagating in supply chains: a multi-method approach.” 2017. Web. 18 Jan 2021.
Vancouver:
Pournader M. Identification and analysis of operational and behavioural risks emerging and propagating in supply chains: a multi-method approach. [Internet] [Doctoral dissertation]. Macquarie University; 2017. [cited 2021 Jan 18].
Available from: http://hdl.handle.net/1959.14/1275939.
Council of Science Editors:
Pournader M. Identification and analysis of operational and behavioural risks emerging and propagating in supply chains: a multi-method approach. [Doctoral Dissertation]. Macquarie University; 2017. Available from: http://hdl.handle.net/1959.14/1275939
University of Cincinnati
27.
Thapa, Mahendra B.
Molecular Dynamics Simulation of Calbindin D-9k in apo,
Singly and Doubly Loaded States in Various Side-chains.
Degree: PhD, Arts and Sciences: Physics, 2016, University of Cincinnati
URL: http://rave.ohiolink.edu/etdc/view?acc_num=ucin1470044265
► Calbindin D9k (CAB) is a single domain calcium-binding protein and is the smallest members of the calmodulin superfamily, possessing a pair of calcium-binding EF-hands, and…
(more)
▼ Calbindin D9k (CAB) is a single domain calcium-binding
protein and is the smallest members of the calmodulin superfamily,
possessing a pair of calcium-binding EF-hands, and structures for
all four states have been determined and extensively characterized
experimentally. Because of the tremendous advancement in hardware
and software computer technologies in recent years, longer and more
realistic molecular dynamics (MD) simulations of a
protein are
possible now in reasonable periods of time. These advances were
exploited to generate multiple, all-atom MD simulations of CAB via
the AMBER software package, and the resulting trajectories were
employed to calculate backbone order parameters of the apo, the
singly and the doubly loaded states of calcium in CAB. The results
are in very good agreement with corresponding experimental
NMR-based (Nuclear Magnetic Resonance spectroscopy) results, and
are improved in comparison to those calculated over a decade ago;
use of modified force fields played a key role in the observed
improvements. The apo state is the most flexible, and the singly
loaded and the doubly loaded states are similar, thus supporting
positive cooperativity in line with the experimental results.
Further, B-factor calculations of backbone atoms for these
calcium-binding states of calbindin D9k also support such
cooperativity.Although changes in
side-
chain motions are not
necessarily correlated to changes in
protein backbone mobility,
past studies on the comparison of experimental and simulated methyl
side-
chain NMR relaxation parameters of CAB for the doubly-loaded
state reported significant improvements in the quantitative
representation of
side-
chain motion by MD simulation. In this
project, the order parameters for various
side chains in apo,
singly loaded and doubly loaded states of CAB were calculated. The
primary goal of this work was to determine whether or not the
allosteric effect of calcium binding, as observed via the backbone
order parameters, also extended to the amino acid
side chains, and
if so, to what extent. Such information could be useful in better
understanding the physical basis of cooperative calcium binding in
CAB. Most of the residues which provide ligands to bind calcium at
the binding sites support positive cooperativity, as observed when
Ca-Cß, Cß-C?, C-C bond and C-O bonds of COO groups of aspartic and
glutamic acid residues, the C-N bond of the
side-
chain amide group
in asparagine and glutamine residues, and the N-H bonds of amide
(NH2) group order parameters were studied. There are only a few
residues containing methyl groups that are involved in providing
ligands to the calcium, and the studies of order parameters of C-C
bond and C-H bond of these methyl groups did not exhibit the
cooperativity effect upon calcium binding; the simulated C-C bond
order parameter of the methyl group symmetry axis did correlate
well with the experimental results for the fully loaded state of
CAB (4ICB). Analysis of the MD trajectories using GSATools and
MutInf, provided valuable insights into…
Advisors/Committee Members: Rance, Mark (Committee Chair).
Subjects/Keywords: Physics; Calbindin D-9k; Side-chain dynamics; Molecular Dynamics; 4ICB; AMBER; NMR
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APA (6th Edition):
Thapa, M. B. (2016). Molecular Dynamics Simulation of Calbindin D-9k in apo,
Singly and Doubly Loaded States in Various Side-chains. (Doctoral Dissertation). University of Cincinnati. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=ucin1470044265
Chicago Manual of Style (16th Edition):
Thapa, Mahendra B. “Molecular Dynamics Simulation of Calbindin D-9k in apo,
Singly and Doubly Loaded States in Various Side-chains.” 2016. Doctoral Dissertation, University of Cincinnati. Accessed January 18, 2021.
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1470044265.
MLA Handbook (7th Edition):
Thapa, Mahendra B. “Molecular Dynamics Simulation of Calbindin D-9k in apo,
Singly and Doubly Loaded States in Various Side-chains.” 2016. Web. 18 Jan 2021.
Vancouver:
Thapa MB. Molecular Dynamics Simulation of Calbindin D-9k in apo,
Singly and Doubly Loaded States in Various Side-chains. [Internet] [Doctoral dissertation]. University of Cincinnati; 2016. [cited 2021 Jan 18].
Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ucin1470044265.
Council of Science Editors:
Thapa MB. Molecular Dynamics Simulation of Calbindin D-9k in apo,
Singly and Doubly Loaded States in Various Side-chains. [Doctoral Dissertation]. University of Cincinnati; 2016. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ucin1470044265
University of Tennessee – Knoxville
28.
foutch, david.
Network Analysis of Protein Structure Networks Upon Ligand Binding.
Degree: MS, Life Sciences, 2020, University of Tennessee – Knoxville
URL: https://trace.tennessee.edu/utk_gradthes/5598
► Network analysis is a computational approach used to describe the structure and dynamics of complex systems.Residue-residue contacts that are made over the course of MD…
(more)
▼ Network analysis is a computational approach used to describe the structure and dynamics of complex systems.Residue-residue contacts that are made over the course of MD simulations were used to create
protein structure
networks (PSNs). As a case study, PSNs were generated for two
protein systems: the transcription factor constitutive androstane receptor and the enzyme ribonucleotide reductase. In order to understand the changes in residue-residue contacts induced upon ligand-binding in proteins, we performed topological analyses of three CAR systems and four RNR systems under different binding conditions.Four measures of centrality were used to evaluate structural changes between ligand-free and ligand-bound systems: betweenness, closeness, degree, and eigenvector centralities. Although ligand-binding induced contact rearrangements resulting in substantial changes in centrality values for many residues, the distributions of centrality values were generally very similar for all systems. Results obtained here suggested that closeness centrality primarily identifies residues that are physically central to the three-dimensional structure of the
protein. Previous reports suggested that closeness centrality identifies important residues in enzyme active sites. However, this may only be true for enzymes whose active site is centrally located. Moreover, the distributions for degree centrality are not power-law distributed, which also raises the question of whether the power-law degree distribution should be assumed for all ”real-world”
networks. In summary, this work demonstrated that the centrality distributions for the two representative proteins are remarkably invariant to ligand binding, despite substantial changes in centrality values for residues.
Advisors/Committee Members: Albrecht von Arnim, Tongye Shen, Rachel McCord.
Subjects/Keywords: Graph theory; protein structure networks; protein dynamic networks; network analysis
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APA (6th Edition):
foutch, d. (2020). Network Analysis of Protein Structure Networks Upon Ligand Binding. (Thesis). University of Tennessee – Knoxville. Retrieved from https://trace.tennessee.edu/utk_gradthes/5598
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
foutch, david. “Network Analysis of Protein Structure Networks Upon Ligand Binding.” 2020. Thesis, University of Tennessee – Knoxville. Accessed January 18, 2021.
https://trace.tennessee.edu/utk_gradthes/5598.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
foutch, david. “Network Analysis of Protein Structure Networks Upon Ligand Binding.” 2020. Web. 18 Jan 2021.
Vancouver:
foutch d. Network Analysis of Protein Structure Networks Upon Ligand Binding. [Internet] [Thesis]. University of Tennessee – Knoxville; 2020. [cited 2021 Jan 18].
Available from: https://trace.tennessee.edu/utk_gradthes/5598.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
foutch d. Network Analysis of Protein Structure Networks Upon Ligand Binding. [Thesis]. University of Tennessee – Knoxville; 2020. Available from: https://trace.tennessee.edu/utk_gradthes/5598
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Rochester Institute of Technology
29.
Duke, Jamie.
Structural analysis of the EGR family of transcription factors: Templates for predicitng protein - DNA internations.
Degree: Biomedical Sciences (CHST), 2006, Rochester Institute of Technology
URL: https://scholarworks.rit.edu/theses/2736
► The EGR family of transcription factors is known to be activated in cells exposed to growth factors in a variety of tissues. The overall structure…
(more)
▼ The EGR family of transcription factors is known to be activated in cells exposed to growth
factors in a variety of tissues. The overall structure of the family is highly conserved while the
amino acid sequence can be quite diverse allowing for a wide array of DNA recognition
sequences. Through homology modeling it is possible to reproduce the structure of the DNA
binding domain of EGR proteins, which consists of three zinc fingers. It has also been
determined through molecular dynamic simulations that most
side chains within the domain reach
an equilibrium state. However, residues that are essential for DNA binding are seen throughout
the simulation as not reaching an equilibrium state, but constantly sampling available
conformational space. Furthermore, through cluster analysis the three recognition residues in
each zinc finger are found to have
side chain conformations that are optimal for DNA
recognition. These studies help to show a possible mechanism for zinc finger recognition of
DNA and create homology modeled proteins that are able to be used in
protein – DNA interaction
prediction.
Advisors/Committee Members: Skuse, Gary - Chair.
Subjects/Keywords: Amino acid; Cluster analysis; Clustering; Conserved residues; DNA binding; Early growth response factor; EGR; Homology modeling; MD simulation; Molecular dynamic simulation; Protein - DNA interactions; Protein domain; Side chain conformation; Transcriptio
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APA (6th Edition):
Duke, J. (2006). Structural analysis of the EGR family of transcription factors: Templates for predicitng protein - DNA internations. (Thesis). Rochester Institute of Technology. Retrieved from https://scholarworks.rit.edu/theses/2736
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Duke, Jamie. “Structural analysis of the EGR family of transcription factors: Templates for predicitng protein - DNA internations.” 2006. Thesis, Rochester Institute of Technology. Accessed January 18, 2021.
https://scholarworks.rit.edu/theses/2736.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Duke, Jamie. “Structural analysis of the EGR family of transcription factors: Templates for predicitng protein - DNA internations.” 2006. Web. 18 Jan 2021.
Vancouver:
Duke J. Structural analysis of the EGR family of transcription factors: Templates for predicitng protein - DNA internations. [Internet] [Thesis]. Rochester Institute of Technology; 2006. [cited 2021 Jan 18].
Available from: https://scholarworks.rit.edu/theses/2736.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Duke J. Structural analysis of the EGR family of transcription factors: Templates for predicitng protein - DNA internations. [Thesis]. Rochester Institute of Technology; 2006. Available from: https://scholarworks.rit.edu/theses/2736
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Penn State University
30.
Zhao, Kang.
A multi-level analysis of information and supply flows in social and business networks.
Degree: 2012, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/14614
► Networks are ubiquitous in both the physical world and the cyberspace. They enable the flow of information, materials, services, etc. The common thread running through…
(more)
▼ Networks are ubiquitous in both the physical world and the cyberspace. They enable the flow of information, materials, services, etc. The common thread running through my dissertation is the macro-level and micro-level analysis of information and supply flows in social and business
networks. The overarching research question is "How do network flows relate to network structures and individual entities' behaviors in
networks?"
My dissertation approaches this question in the context of supply-
chain networks, online social
networks, and inter-organizational
networks. Specifically, I explore how changes in supply-
chain network topologies affect supply flows, and propose strategies to improve supply-
chain networks' robustness against disruptions. I analyze how the flow of information through individuals' interactions influences their sentiment in online health communities, and utilize the sentimental influence to identify influential users. I model how the flow of information via organizations' interactions impacts the structure of their collaboration network, and provide suggestions on how to promote collaboration. To support the research, the dissertation uses various computational and quantitative methodologies, such as network analysis and modeling, data and text mining, agent-based simulation, and statistical analysis.
The goal of my dissertation research is to achieve a deeper understanding of network flows, better prediction of network performance and individual behaviors, as well as new insights into ways to improve the design, management, and utilization of
networks. Specifically, the outcome of this dissertation has implications for network disruption management, health care, online community building, humanitarian relief, and so on.
Advisors/Committee Members: John Yen, Dissertation Advisor/Co-Advisor, Reka Z Albert, Committee Member, C Lee Giles, Committee Member, Akhil Kumar, Committee Member.
Subjects/Keywords: Social networks; supply-chain networks; inter-organizational networks; information flow; influence; online health community.
Record Details
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Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Zhao, K. (2012). A multi-level analysis of information and supply flows in social and business networks. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/14614
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Zhao, Kang. “A multi-level analysis of information and supply flows in social and business networks.” 2012. Thesis, Penn State University. Accessed January 18, 2021.
https://submit-etda.libraries.psu.edu/catalog/14614.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Zhao, Kang. “A multi-level analysis of information and supply flows in social and business networks.” 2012. Web. 18 Jan 2021.
Vancouver:
Zhao K. A multi-level analysis of information and supply flows in social and business networks. [Internet] [Thesis]. Penn State University; 2012. [cited 2021 Jan 18].
Available from: https://submit-etda.libraries.psu.edu/catalog/14614.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Zhao K. A multi-level analysis of information and supply flows in social and business networks. [Thesis]. Penn State University; 2012. Available from: https://submit-etda.libraries.psu.edu/catalog/14614
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
