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1.
Fox, Neal P.
Top-Down Effects on Speech Perception: An Integrated
Computational and Behavioral Approach.
Degree: PhD, Cognitive Sciences, 2016, Brown University
URL: https://repository.library.brown.edu/studio/item/bdr:674171/
► During auditory language comprehension, bottom-up acoustic cues in the sensory signal are critical to the recognition of spoken words. However, listeners are also sensitive to…
(more)
▼ During auditory language comprehension, bottom-up
acoustic cues in the sensory signal are critical to the recognition
of spoken words. However, listeners are also sensitive to
higher-level processing; in general, identification of ambiguous
targets is biased by prior expectations (e.g., words over
non-words, contextually consistent words over inconsistent words).
Although it is clear that such top-down cues influence word
recognition, how they do so is less clear. The present work
examines several questions about the
computational principles
underlying top-down effects on speech perception, focusing
primarily on the influence of a preceding sentential context (e.g.,
Valerie hated the... vs. Brett hated to...) on the identification
of phonetically ambiguous targets from voice-onset time continua
(e.g., between bay and pay). Chapter 1 considers a longstanding
debate: do top-down effects result from interactive modulation of
perceptual processing or from entirely autonomous, decision-level
processing? Some research has suggested that the time course of
top-down effects is incompatible with interactive models. However,
two experiments illustrate that, with appropriate controls, the
predictions of interactive models are supported. Ultimately,
though, two weaknesses of existing spoken word recognition models
(whether interactive or autonomous) are that they ignore the role
of sentential context and that they ignore the enormous variability
in the size of top-down effects. To address these gaps, Chapter 2
introduces BIASES (short for Bayesian Integration of Acoustic and
Sentential Evidence in Speech), a newly developed
computational
model of speech perception. Chapter 3 demonstrates BIASES’ ability
to predict and explain fine-grained variability and asymmetries in
both novel experimental data and in previously published work.
Finally, Chapter 4 employs BIASES to examine top-down processing in
patients with aphasia. Model-based analysis of previously published
data and new data utilizing stimuli from Chapter 1 suggest that
patients experience both bottom-up processing deficits and lexical
processing deficits. Importantly, those impairments differ as a
function of patients’ clinical diagnoses. In sum, this work offers
new insights into the computations occurring at the interface
between the perceptual processing of speech and the cognitive and
linguistic processing of language.
Advisors/Committee Members: Blumstein, Sheila (Director), Frank, Michael (Reader), Morgan, James (Reader).
Subjects/Keywords: computational modeling
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APA (6th Edition):
Fox, N. P. (2016). Top-Down Effects on Speech Perception: An Integrated
Computational and Behavioral Approach. (Doctoral Dissertation). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:674171/
Chicago Manual of Style (16th Edition):
Fox, Neal P. “Top-Down Effects on Speech Perception: An Integrated
Computational and Behavioral Approach.” 2016. Doctoral Dissertation, Brown University. Accessed April 16, 2021.
https://repository.library.brown.edu/studio/item/bdr:674171/.
MLA Handbook (7th Edition):
Fox, Neal P. “Top-Down Effects on Speech Perception: An Integrated
Computational and Behavioral Approach.” 2016. Web. 16 Apr 2021.
Vancouver:
Fox NP. Top-Down Effects on Speech Perception: An Integrated
Computational and Behavioral Approach. [Internet] [Doctoral dissertation]. Brown University; 2016. [cited 2021 Apr 16].
Available from: https://repository.library.brown.edu/studio/item/bdr:674171/.
Council of Science Editors:
Fox NP. Top-Down Effects on Speech Perception: An Integrated
Computational and Behavioral Approach. [Doctoral Dissertation]. Brown University; 2016. Available from: https://repository.library.brown.edu/studio/item/bdr:674171/

Wake Forest University
2.
Decker, William.
Modular Use of Human Body Models of Various Complexities in the Head and Thoraco-Abdominal Regions.
Degree: 2018, Wake Forest University
URL: http://hdl.handle.net/10339/90702
► The field of injury biomechanics is constantly evolving, and with it, the tools available for researchers. Computational modeling is one of these tools, specifically finite…
(more)
▼ The field of injury biomechanics is constantly evolving, and with it, the tools available for researchers. Computational modeling is one of these tools, specifically finite element human body models (HBMs). Finite element human body models can be used to investigate the mechanism and injury tolerance of various regions of the human body during blunt impact trauma through the use of computer simulation. These models can be used as a supplement to traditional crash test dummies for crash safety evaluation due to their affordability, ease of use, and increased available data points. As part of the Global Human Body Models Consortium (GHBMC) project, HBMs have developed and become more complex and biofidelic. They have also become more computationally expensive which may restrict usage from individuals with limited computational power. This motivated the development of faster running simplified HBMs similar to the detailed models, but restricted to analysis of kinematics and kinetics. In order to use the benefits from both types of models, we have developed an approach to modularly incorporate detailed components into the simplified models which allows the ability to obtain organ level response much faster than the full detailed model. The method has been implemented with the brain and thoracoabdominal cavity with comparable results to the detailed model, but with a time savings up to 90%. This thesis describes the implementation and evaluation of this modular method within the GHBMC 50th percentile male model.
Subjects/Keywords: computational modeling
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Decker, W. (2018). Modular Use of Human Body Models of Various Complexities in the Head and Thoraco-Abdominal Regions. (Thesis). Wake Forest University. Retrieved from http://hdl.handle.net/10339/90702
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):
Decker, William. “Modular Use of Human Body Models of Various Complexities in the Head and Thoraco-Abdominal Regions.” 2018. Thesis, Wake Forest University. Accessed April 16, 2021.
http://hdl.handle.net/10339/90702.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Decker, William. “Modular Use of Human Body Models of Various Complexities in the Head and Thoraco-Abdominal Regions.” 2018. Web. 16 Apr 2021.
Vancouver:
Decker W. Modular Use of Human Body Models of Various Complexities in the Head and Thoraco-Abdominal Regions. [Internet] [Thesis]. Wake Forest University; 2018. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/10339/90702.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Decker W. Modular Use of Human Body Models of Various Complexities in the Head and Thoraco-Abdominal Regions. [Thesis]. Wake Forest University; 2018. Available from: http://hdl.handle.net/10339/90702
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Georgia Tech
3.
Faraji Mosalman, Mozhdeh Sadat.
From experimental observations to a functional model of the lignin pathway: Computational modeling reveals new insights.
Degree: PhD, Mechanical Engineering, 2018, Georgia Tech
URL: http://hdl.handle.net/1853/59881
► Lignin is a natural polymer that is interwoven with cellulose and hemicellulose within plant cell walls. Due to this molecular arrangement, lignin is a major…
(more)
▼ Lignin is a natural polymer that is interwoven with cellulose and hemicellulose within plant cell walls. Due to this molecular arrangement, lignin is a major contributor to the recalcitrance of plant materials with respect to the extraction of sugars and their fermentation into ethanol, butanol, and other potential bioenergy crops. The lignin biosynthetic pathway is similar, but not identical in different plant species. It is in each case comprised of a moderate number of enzymatic steps, but its responses to manipulations, such as gene knock-downs, are complicated by the fact that several of the key enzymes are involved in several reaction steps. This feature poses a challenge to bioenergy production, as it renders it difficult to select the most promising combinations of genetic manipulations for the optimization of lignin composition and amount. Moreover, species specific regulatory features and distinct spatial and topological characteristics hinder accuracy of a unified lignin pathway model. In this dissertation a systems biology approach is used to address these challenges by means of
computational modeling. Novel mathematical techniques are employed on different types of experimental data in situ, and shed light on complexities of lignin biosynthesis pathway. The developed methods are nevertheless general enough to be used in a wide range of metabolic
modeling applications.
Advisors/Committee Members: Voit, Eberhard O. (advisor), Bommarius, Andreas S. (committee member), Leamy, Michael J. (committee member), Peralta-Yahya, Pamela (committee member), Qiu, Peng (committee member).
Subjects/Keywords: Lignin; Computational modeling
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Faraji Mosalman, M. S. (2018). From experimental observations to a functional model of the lignin pathway: Computational modeling reveals new insights. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/59881
Chicago Manual of Style (16th Edition):
Faraji Mosalman, Mozhdeh Sadat. “From experimental observations to a functional model of the lignin pathway: Computational modeling reveals new insights.” 2018. Doctoral Dissertation, Georgia Tech. Accessed April 16, 2021.
http://hdl.handle.net/1853/59881.
MLA Handbook (7th Edition):
Faraji Mosalman, Mozhdeh Sadat. “From experimental observations to a functional model of the lignin pathway: Computational modeling reveals new insights.” 2018. Web. 16 Apr 2021.
Vancouver:
Faraji Mosalman MS. From experimental observations to a functional model of the lignin pathway: Computational modeling reveals new insights. [Internet] [Doctoral dissertation]. Georgia Tech; 2018. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1853/59881.
Council of Science Editors:
Faraji Mosalman MS. From experimental observations to a functional model of the lignin pathway: Computational modeling reveals new insights. [Doctoral Dissertation]. Georgia Tech; 2018. Available from: http://hdl.handle.net/1853/59881

University of Texas – Austin
4.
-8909-3631.
Multi-physics computational modeling of electromagnetic acceleration devices.
Degree: PhD, Aerospace Engineering, 2018, University of Texas – Austin
URL: http://hdl.handle.net/2152/71466
► A multi-physics computational framework is developed to simulate dense, high-ionization fraction plasmas in electromagnetic acceleration devices. The primary motivation for this research is the simulation…
(more)
▼ A multi-physics
computational framework is developed to simulate dense, high-ionization fraction plasmas in electromagnetic acceleration devices. The primary motivation for this research is the simulation of extreme conditions generated by the impingement of hypervelocity plasma jets, emerging from the accelerator, onto fixed target surfaces. By directing these jets on material surfaces, experiments carried out at the Stanford Plasma Gun (SPG) facility use the accelerator as a platform to mimic the extreme conditions on confining walls of nuclear fusion reactors, generated by disruption events. The simulations are performed in close collaboration with the experiments at Stanford. From a
computational modeling perspective the plasma accelerator presents an interesting problem because different regions of the device sustain different types of plasma discharges that require their own characteristic numerical treatment. As the neutral gas enters the device and encounters the charged electrodes, it breaks down to form a high number density non-equilibrium discharge. However, due to the high electron number densities and high pressure operating conditions, the non-equilibrium plasma transitions to a single temperature arc discharge as it is transported further down the length of the accelerator. Due to an associated increase in plasma conductivity, the non-equilibrium (glow) to equilibrium (arc) transition is also accompanied by a substantial increase in the conduction current. This results in the generation of strong magnetic fields and a large self-induced Lorentz force that accelerates the thermal plasma, forming a hypervelocity plasma jet that emerges from the device. The impingement of the jet on a fixed target surface then generates the extreme material conditions that are the focus of this research. The coupled nature of the problem leads to a scenario where the non-equilibrium physics affects properties of the thermal plasma which in turn determines the jet velocities and stagnation conditions generated on the target upon impact. Hence, accurately resolving the plasma-surface interactions requires
modeling the non-equilibrium as well as the equilibrium plasma sustaining regions that precede the target interaction zone. Accordingly, the
computational modeling efforts have been divided into three main parts. In the first part, a multi-species self-consistent plasma model is used to simulate the plasma breakdown, ionization and thermalization processes in the inlet region of the device. This is an important step in the multi-physics framework because it provides an estimate of the length fraction of the accelerator that is in thermal non-equilibrium and the temperature/pressure at the location where the thermal plasma is formed. In the second part of this study, these conditions are taken as inflow boundary conditions for the MHD model that predicts the plasma jet formed due to the current discharged through the device. The vacuum conditions that surround the accelerating plasma jet lead to the generation of an…
Advisors/Committee Members: Raja, Laxminarayan L. (advisor), Goldstein, David B (committee member), Dawson, Clint N (committee member), Varghese, Philip L (committee member), Ezekoye, Ofodike A (committee member).
Subjects/Keywords: Multiphysics; Computational modeling
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
-8909-3631. (2018). Multi-physics computational modeling of electromagnetic acceleration devices. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/71466
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Chicago Manual of Style (16th Edition):
-8909-3631. “Multi-physics computational modeling of electromagnetic acceleration devices.” 2018. Doctoral Dissertation, University of Texas – Austin. Accessed April 16, 2021.
http://hdl.handle.net/2152/71466.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
MLA Handbook (7th Edition):
-8909-3631. “Multi-physics computational modeling of electromagnetic acceleration devices.” 2018. Web. 16 Apr 2021.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Vancouver:
-8909-3631. Multi-physics computational modeling of electromagnetic acceleration devices. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2018. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/2152/71466.
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Council of Science Editors:
-8909-3631. Multi-physics computational modeling of electromagnetic acceleration devices. [Doctoral Dissertation]. University of Texas – Austin; 2018. Available from: http://hdl.handle.net/2152/71466
Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Mississippi State University
5.
Taylor, Benjamin Hugh.
Predictive capabilities of advanced turbulence models in the wake region of a wall mounted cube.
Degree: MS, Mechanical Engineering, 2016, Mississippi State University
URL: http://sun.library.msstate.edu/ETD-db/theses/available/etd-10282016-135510/
;
► This thesis seeks to investigate the predictive capabilities of Advanced turbulence models in the wake region of a wall-mounted cube. Dynamic Hybrid RANS/LES (DHRL), Hybrid…
(more)
▼ This thesis seeks to investigate the predictive capabilities of Advanced turbulence models in the wake region of a wall-mounted cube. Dynamic Hybrid RANS/LES (DHRL), Hybrid RANS/LES (HRL) models, Nonlinear Explicit Algebraic Reynolds Stress Model (NEARSM), One- and Two-equation models, and numerical flux schemes will be compared against Direct Numerical Simulation (DNS) results to determine which model, or combination of models, produce the closest replication. The simulations were ran in Loci-Chem using both built-in features and modular code additions. The simulation results show the Shear Stress Transport (SST) model ran with NEARSM and Optimized Gradient REconstruction (OGRE) scheme gives better results than all other RANS and HRL models investigated herein. This result is matched only by SST with DHRL and OGRE. The best results were achieved using SST with NEARSM, DHRL, and OGRE. Thus, the NEARSM model shows potential to improve simulation results compared to simpler linear eddy-viscosity models.
Advisors/Committee Members: David Thompson (committee member), Scott Thompson (committee member), Keith Walters (chair).
Subjects/Keywords: computational fluid dynamics; turbulence modeling
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Taylor, B. H. (2016). Predictive capabilities of advanced turbulence models in the wake region of a wall mounted cube. (Masters Thesis). Mississippi State University. Retrieved from http://sun.library.msstate.edu/ETD-db/theses/available/etd-10282016-135510/ ;
Chicago Manual of Style (16th Edition):
Taylor, Benjamin Hugh. “Predictive capabilities of advanced turbulence models in the wake region of a wall mounted cube.” 2016. Masters Thesis, Mississippi State University. Accessed April 16, 2021.
http://sun.library.msstate.edu/ETD-db/theses/available/etd-10282016-135510/ ;.
MLA Handbook (7th Edition):
Taylor, Benjamin Hugh. “Predictive capabilities of advanced turbulence models in the wake region of a wall mounted cube.” 2016. Web. 16 Apr 2021.
Vancouver:
Taylor BH. Predictive capabilities of advanced turbulence models in the wake region of a wall mounted cube. [Internet] [Masters thesis]. Mississippi State University; 2016. [cited 2021 Apr 16].
Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-10282016-135510/ ;.
Council of Science Editors:
Taylor BH. Predictive capabilities of advanced turbulence models in the wake region of a wall mounted cube. [Masters Thesis]. Mississippi State University; 2016. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-10282016-135510/ ;

Penn State University
6.
Husain, Taha Murtuza.
Computational Modeling of Lava Domes using Particle Dynamics to investigate the effect of conduit flow mechanics on flow patterns.
Degree: 2015, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/25682
► Large (1 – 4 x 106 m3) to major (> 4 x 106 m3) dome collapses for andesitic lava domes such as Soufriere Hills Volcano,…
(more)
▼ Large (1 – 4 x 106 m3) to major (> 4 x 106 m3) dome collapses for andesitic lava domes such as Soufriere Hills Volcano, Montserrat are observed for elevated magma discharge rates (6 – 13 m3/s). The gas rich magma pulses lead to pressure build up in the lava dome that result in structural failure of the over steepened canyon-like walls which may lead to rockfall or pyroclastic flow. This indicates that dome collapse at Soufriere Hills Volcano, Montserrat is intimately related to magma extrusion rate. Variation in magma extrusion rate for open-system magma chambers is observed to follow alternating periods of high and low activity. Periodic behavior of magma exhibits a rich diversity in the nature of its eruptive history due to variation in magma chamber size, total crystal content, linear crystal growth rate and magma replenishment rate. Distinguished patterns of growth were observed at different magma flow rates ranging from endogenous to exogenous dome growth for magma with varying strengths.
Determining the key parameters that control the transition in flow pattern of the magma during its lava dome building eruption is the main focus of this work. This dissertation examines the mechanical effects on the morphology of the evolving lava dome on the extrusion of magma from a central vent using a 2D particle dynamics model. The particle dynamics model is coupled with a conduit flow model that incorporates the kinetics of crystallization and rheological stiffening to investigate important mechanisms during lava dome building eruptions.
Chapter I of this dissertation explores lava dome growth and failure mechanics using a two-dimensional particle-dynamics model. The model follows the evolution of fractured lava, with solidification driven by degassing induced crystallization of magma. The particle-dynamics model emulates the natural development of dome growth and rearrangement of the lava dome which is difficult in mesh-based analyses due to mesh entanglement effects. The deformable talus evolves naturally as a frictional carapace that caps a ductile magma core. Extrusion rate and magma rheology together with crystallization temperature and volatile content govern the distribution of strength in the composite structure. This new model is calibrated against existing observational models of lava dome growth. Results show that the shape and extent of the ductile core and the overall structure of the lava dome are strongly controlled by the infusion rate. The effects of extrusion rate on magma rheology are sensitive to material stiffness, which in turn is a function of volatile content and crystallinity. Material stiffness and material strength are key model parameters which govern magma rheology and subsequently the morphological character of the lava dome and in turn stability. Degassing induced crystallization causes material stiffening and enhances material strength reflected in non-Newtonian magma behavior. The increase in stiffness and strength of the injected magma causes a transition in the style of dome growth,…
Advisors/Committee Members: Derek Elsworth, Dissertation Advisor/Co-Advisor, Derek Elsworth, Committee Chair/Co-Chair, Barry Voight, Committee Member, Tong Qiu, Committee Member, Zuleima T Karpyn, Committee Member, Jamal Rostami, Committee Member, Glen Mattioli, Special Member.
Subjects/Keywords: computational modeling; lava domes
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Husain, T. M. (2015). Computational Modeling of Lava Domes using Particle Dynamics to investigate the effect of conduit flow mechanics on flow patterns. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/25682
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):
Husain, Taha Murtuza. “Computational Modeling of Lava Domes using Particle Dynamics to investigate the effect of conduit flow mechanics on flow patterns.” 2015. Thesis, Penn State University. Accessed April 16, 2021.
https://submit-etda.libraries.psu.edu/catalog/25682.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Husain, Taha Murtuza. “Computational Modeling of Lava Domes using Particle Dynamics to investigate the effect of conduit flow mechanics on flow patterns.” 2015. Web. 16 Apr 2021.
Vancouver:
Husain TM. Computational Modeling of Lava Domes using Particle Dynamics to investigate the effect of conduit flow mechanics on flow patterns. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Apr 16].
Available from: https://submit-etda.libraries.psu.edu/catalog/25682.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Husain TM. Computational Modeling of Lava Domes using Particle Dynamics to investigate the effect of conduit flow mechanics on flow patterns. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/25682
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Vermont
7.
Stanton, Suzanne Louise.
Homology Modeling and Molecular Docking of Antagonists to Class B G-Protein Coupled Receptor Pituitary Adenylate Cyclase Type 1 (PAC1R).
Degree: MS, Chemistry, 2016, University of Vermont
URL: https://scholarworks.uvm.edu/graddis/624
► Recent studies have identified the Class B g-protein coupled receptor (GPCR) pituitary adenylate cyclase activating polypeptide type 1 (PAC1R) as a key component in…
(more)
▼ Recent studies have identified the Class B g-protein coupled receptor (GPCR) pituitary adenylate cyclase activating polypeptide type 1 (PAC1R) as a key component in physiological stress management. Over-activity of neurological stress response systems due to prolonged or extreme exposure to traumatic events has led researchers to investigate PAC1R inhibition as a possible treatment for anxiety disorders such as post-traumatic stress disorder (PTSD). In 2008, Beebe and coworkers identified two such small molecule hydrazide antagonists and a general pharmacaphore for PAC1R inhibition. However, a relative dearth of information about Class B GPCRs in general, and PAC1R in specific, has significantly hindered progress toward the development of small molecule antagonists of PAC1R. The recent crystallization of the homologically similar glucagon receptor (GCGR) by Siu and coworkers in 2013, also a Class B receptor, has provided an experimentally resolved template from which to base computationally derived models of PAC1R.
Initially, this research was focused towards synthesizing small molecule antagonists for PAC1R which were to be biologically screened via a qualitative western blot assay followed by a radioisotope binding assay for those hydrazides exhibiting down-stream signaling inhibitory capabilities. However, the resolution of the GCGR crystal structure shifted research objectives towards developing a homology model of PAC1R and evaluating that computationally created model with Beebe's known small molecule antagonists. Created using academic versions of on-line resources including UniProtKB, Swiss-Model and Maestro, a homology model for PAC1R is presented here. The model is validated and evaluated for the presence of conserved Class B GPCR residues and motifs, including expected disulfide bridges, a conserved tyrosine residue, a GWGxP motif, a conserved glutamic acid residue and the extension of the transmembrane helix 1 (TM1) into the extra-cellular domain.
Having determined this virtual PAC1R an acceptable model, ligand docking studies of known antagonists to the receptor were undertaken using AutoDock Vina in conjunction with AutoDock Tools and PyMol.
Computational docking results were evaluated via comparison of theoretical binding affinity results to Beebe's experimental data. Based on hydrogen bonding capabilities, several residues possibly key to the ligand-receptor binding complex are identified and include ASN 240, TYR 241 and HIST 365. Although the docking software does not identify non-bonding interactions other than hydrogen-bonding, the roles of additional proposed binding pocket residues are discussed in terms of hydrophobic interactions, π-π interactions and halogen bonding. These residues include TYR 161, PHE 196, VAL 203, PHE 204, ILE 209, LEU 210, VAL 237, TRP 297, PHE 362 and LEU 386. Although theoretical in nature, this reported homology
modeling and docking exercise details a proposed binding site that may potentially further the development of drugs designed…
Advisors/Committee Members: Matthias Brewer.
Subjects/Keywords: Computational; Homology; Modeling; Chemistry
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Stanton, S. L. (2016). Homology Modeling and Molecular Docking of Antagonists to Class B G-Protein Coupled Receptor Pituitary Adenylate Cyclase Type 1 (PAC1R). (Thesis). University of Vermont. Retrieved from https://scholarworks.uvm.edu/graddis/624
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):
Stanton, Suzanne Louise. “Homology Modeling and Molecular Docking of Antagonists to Class B G-Protein Coupled Receptor Pituitary Adenylate Cyclase Type 1 (PAC1R).” 2016. Thesis, University of Vermont. Accessed April 16, 2021.
https://scholarworks.uvm.edu/graddis/624.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Stanton, Suzanne Louise. “Homology Modeling and Molecular Docking of Antagonists to Class B G-Protein Coupled Receptor Pituitary Adenylate Cyclase Type 1 (PAC1R).” 2016. Web. 16 Apr 2021.
Vancouver:
Stanton SL. Homology Modeling and Molecular Docking of Antagonists to Class B G-Protein Coupled Receptor Pituitary Adenylate Cyclase Type 1 (PAC1R). [Internet] [Thesis]. University of Vermont; 2016. [cited 2021 Apr 16].
Available from: https://scholarworks.uvm.edu/graddis/624.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Stanton SL. Homology Modeling and Molecular Docking of Antagonists to Class B G-Protein Coupled Receptor Pituitary Adenylate Cyclase Type 1 (PAC1R). [Thesis]. University of Vermont; 2016. Available from: https://scholarworks.uvm.edu/graddis/624
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Manitoba
8.
Curtis, Evan.
Reinterpreting selective impairments in memory: computational and empirical simulations of dissociations in amnesia.
Degree: Psychology, 2017, University of Manitoba
URL: http://hdl.handle.net/1993/32111
► By a dominant account, memory is composed of multiple storage systems, each operating according to unique principles. By an alternative account, memory is a single…
(more)
▼ By a dominant account, memory is composed of multiple storage systems, each operating according to unique principles. By an alternative account, memory is a single storage system and operates according to a single set of principles. Selective memory impairments in amnesia serve as the primary evidence for the multiple-system perspective. This thesis reports a critical appraisal of the multiple-system perspective using a combination of
computational and empirical methods. In the
computational analysis, I adopt the Holographic Exemplar Model, a single-system model of memory based on Hintzman’s (1986) classic MINERVA2 model. I simulate amnesia by manipulating the quality with which items are encoded in memory. In the empirical analysis, I simulate amnesia by manipulating peoples’ quality of encoding by limiting the time given to study stimuli. Simulations 1-2 and Experiments 1-2 simulate a dissociation between classification and recognition. All four analyses are consistent with the original results. Simulation 3 and Experiment 3 simulate single and double dissociations between tachistoscopic identification and recognition. The analyses were consistent with the single but not double dissociation. Simulation 4 and Experiment 4 simulate a dissociation among word-stem completion, cued recall, and recognition. Both analyses were only partially consistent with the original results, representing a failure overall. Simulation 5 and Experiment 5 derived a novel prediction from artificial grammar learning, predicting a non-dissociation between string completion and recognition. The mixed results provide some support for a single-system account of memory and opens opportunities for future work. I argue that the analysis is best considered in convergence with previous work moving toward a more integrated account of memory
Advisors/Committee Members: Jamieson, Randall (Psychology) (supervisor), Mondor, Todd (Psychology) .
Subjects/Keywords: Memory; Dissociation; Amnesia; Computational modeling
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APA (6th Edition):
Curtis, E. (2017). Reinterpreting selective impairments in memory: computational and empirical simulations of dissociations in amnesia. (Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/32111
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):
Curtis, Evan. “Reinterpreting selective impairments in memory: computational and empirical simulations of dissociations in amnesia.” 2017. Thesis, University of Manitoba. Accessed April 16, 2021.
http://hdl.handle.net/1993/32111.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Curtis, Evan. “Reinterpreting selective impairments in memory: computational and empirical simulations of dissociations in amnesia.” 2017. Web. 16 Apr 2021.
Vancouver:
Curtis E. Reinterpreting selective impairments in memory: computational and empirical simulations of dissociations in amnesia. [Internet] [Thesis]. University of Manitoba; 2017. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1993/32111.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Curtis E. Reinterpreting selective impairments in memory: computational and empirical simulations of dissociations in amnesia. [Thesis]. University of Manitoba; 2017. Available from: http://hdl.handle.net/1993/32111
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Virginia Tech
9.
Meyer, Kevin Joseph.
Improved Prediction of Glass Fiber Orientation in Basic Injection Molding Geometries.
Degree: PhD, Chemical Engineering, 2013, Virginia Tech
URL: http://hdl.handle.net/10919/24762
► This work is concerned with the prediction of short (SGF) and long glass fiber (LGF) orientation in a center-gated disk and end-gated plaque injection molding…
(more)
▼ This work is concerned with the prediction of short (SGF) and long glass fiber (LGF) orientation in a center-gated disk and end-gated plaque injection molding test geometry using a simulation method that has not been attempted previously. Previous work has used assumptions to simplify the fiber orientation geometry (assuming a thin cavity) or flow field (neglecting fountain flow and entry regions). LGF orientation is predicted in a center-gated disk injection molding geometry including the advancing front and simulating the sprue and gate region (SGM method) so that no assumption about fiber orientation at the mold entrance has to be made. Using a semi-flexible fiber model and orientation parameters obtained through rheology, increased agreement was found between predicted and experimentally obtained values of orientation using the SGM method and a semi-flexible fiber model than was found using a Hele-Shaw approximation. The SGM method was applied to the end-gated plaque to predict SGF orientation both along and away from the centerline using an objective (reduced strain closure model) and non-objective (strain reduction factor model) orientation model. The predicted values of the strain reduction factor model showed reasonable agreement with experimentally obtained values of orientation throughout the three-dimensional cavity when using orientation parameters fit to experimental orientation data. Furthermore it was found that the objective model predicted results very similar to the non-objective model suggesting that objectivity may not play a role in predicting orientation in more complex geometries such as an end-gated plaque. Finally, the SGM method was applied to the end-gated plaque geometry to predict LGF orientation using a rigid and semi-flexible fiber model. It was found that the SGM method and the semi-flexible fiber model provides orientation predictions that are similar to experimentally obtained values of orientation.
Advisors/Committee Members: Baird, Donald G. (committeechair), Achenie, Luke E. K. (committee member), Wapperom, Peter (committee member), Martin, Stephen Michael (committee member).
Subjects/Keywords: Injection Molding; Composites; Computational Modeling
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Meyer, K. J. (2013). Improved Prediction of Glass Fiber Orientation in Basic Injection Molding Geometries. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/24762
Chicago Manual of Style (16th Edition):
Meyer, Kevin Joseph. “Improved Prediction of Glass Fiber Orientation in Basic Injection Molding Geometries.” 2013. Doctoral Dissertation, Virginia Tech. Accessed April 16, 2021.
http://hdl.handle.net/10919/24762.
MLA Handbook (7th Edition):
Meyer, Kevin Joseph. “Improved Prediction of Glass Fiber Orientation in Basic Injection Molding Geometries.” 2013. Web. 16 Apr 2021.
Vancouver:
Meyer KJ. Improved Prediction of Glass Fiber Orientation in Basic Injection Molding Geometries. [Internet] [Doctoral dissertation]. Virginia Tech; 2013. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/10919/24762.
Council of Science Editors:
Meyer KJ. Improved Prediction of Glass Fiber Orientation in Basic Injection Molding Geometries. [Doctoral Dissertation]. Virginia Tech; 2013. Available from: http://hdl.handle.net/10919/24762

University of Notre Dame
10.
Cameron Wade Harvey.
Collective Movement in Myxobacteria: Modeling and
Experiments with Myxococcus
xanthus</h1>.
Degree: Physics, 2013, University of Notre Dame
URL: https://curate.nd.edu/show/sx61dj55b1t
► A remarkable example of how patterns of movement and organization in populations of bacterial cells emerge from individual level interactions is seen with Myxobacteria.…
(more)
▼ A remarkable example of how patterns of
movement and organization in populations of bacterial cells emerge
from individual level interactions is seen with Myxobacteria. How
cells coordinate movement is fundamental to many important areas of
study from development biology where cells must form patterns and
differentiate with precise timing to topics like infectious
diseases where bacterial cells can colonize surfaces and infect
tissue. In this thesis, I will present a study on the biophysical
mechanisms that drive pattern formation in both phases of the
Myxococcus xanthus life cycle. In this study
that combines experiments with
computational modeling and
simulation, I will present novel techniques for imaging the
patterns of movement and cellular organization that reveal unique
patterns of clustering. The experimental observations helped to
inform the development of a cell-based biophysical model that
account for the adhesive forces between cells and the elastic
properties of the cells. Simulations with this model were used to
study how the physical and behavioral properties impact the ability
of cells to form and move as organized clusters of cells. My
findings provide new insight into the three-dimensional structure
of myxo fruiting bodies as well as the demonstrate the importance
of both physical and behavioral properties in the role of
multi-cellular coordination.
Advisors/Committee Members: Anthony Hyder, Committee Member, Mark Alber, Committee Member, Zoltan Toroczkai, Committee Member, Joshua Shrout, Committee Member.
Subjects/Keywords: biophysics; myxobacteria; simulation; computational modeling
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Harvey, C. W. (2013). Collective Movement in Myxobacteria: Modeling and
Experiments with Myxococcus
xanthus</h1>. (Thesis). University of Notre Dame. Retrieved from https://curate.nd.edu/show/sx61dj55b1t
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):
Harvey, Cameron Wade. “Collective Movement in Myxobacteria: Modeling and
Experiments with Myxococcus
xanthus</h1>.” 2013. Thesis, University of Notre Dame. Accessed April 16, 2021.
https://curate.nd.edu/show/sx61dj55b1t.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Harvey, Cameron Wade. “Collective Movement in Myxobacteria: Modeling and
Experiments with Myxococcus
xanthus</h1>.” 2013. Web. 16 Apr 2021.
Vancouver:
Harvey CW. Collective Movement in Myxobacteria: Modeling and
Experiments with Myxococcus
xanthus</h1>. [Internet] [Thesis]. University of Notre Dame; 2013. [cited 2021 Apr 16].
Available from: https://curate.nd.edu/show/sx61dj55b1t.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Harvey CW. Collective Movement in Myxobacteria: Modeling and
Experiments with Myxococcus
xanthus</h1>. [Thesis]. University of Notre Dame; 2013. Available from: https://curate.nd.edu/show/sx61dj55b1t
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Georgia State University
11.
Aiken, John M.
Transforming High School Physics With Modeling And Computation.
Degree: MS, Physics and Astronomy, 2013, Georgia State University
URL: https://scholarworks.gsu.edu/phy_astr_theses/18
► The Engage to Excel (PCAST) report, the National Research Council's Framework for K-12 Science Education, and the Next Generation Science Standards all call for…
(more)
▼ The Engage to Excel (PCAST) report, the National Research Council's Framework for K-12 Science Education, and the Next Generation Science Standards all call for transforming the physics classroom into an environment that teaches students real scientific practices. This work describes the early stages of one such attempt to transform a high school physics classroom. Specifically, a series of model-building and
computational modeling exercises were piloted in a ninth grade Physics First classroom. Student use of computation was assessed using a proctored programming assignment, where the students produced and discussed a
computational model of a baseball in motion via a high-level programming environment (VPython). Student views on computation and its link to mechanics was assessed with a written essay and a series of think-aloud interviews. This pilot study shows computation's ability for connecting scientific practice to the high school science classroom.
Advisors/Committee Members: Brian D. Thoms, Michael F. Schatz, Rajshekhar Sunderraman, Marcos D. Caballero.
Subjects/Keywords: Computational Modeling; Physics; Education
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Aiken, J. M. (2013). Transforming High School Physics With Modeling And Computation. (Thesis). Georgia State University. Retrieved from https://scholarworks.gsu.edu/phy_astr_theses/18
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):
Aiken, John M. “Transforming High School Physics With Modeling And Computation.” 2013. Thesis, Georgia State University. Accessed April 16, 2021.
https://scholarworks.gsu.edu/phy_astr_theses/18.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Aiken, John M. “Transforming High School Physics With Modeling And Computation.” 2013. Web. 16 Apr 2021.
Vancouver:
Aiken JM. Transforming High School Physics With Modeling And Computation. [Internet] [Thesis]. Georgia State University; 2013. [cited 2021 Apr 16].
Available from: https://scholarworks.gsu.edu/phy_astr_theses/18.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Aiken JM. Transforming High School Physics With Modeling And Computation. [Thesis]. Georgia State University; 2013. Available from: https://scholarworks.gsu.edu/phy_astr_theses/18
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas – Austin
12.
Lee, Yongjin.
First principles-based molecular modeling of thermal transport in silicon-based nanomaterials.
Degree: PhD, Chemical Engineering, 2014, University of Texas – Austin
URL: http://hdl.handle.net/2152/69263
► In today’s nanotechnology, a critical issue is to gain the ability to control the structure and function of matter with a deeper understanding of the…
(more)
▼ In today’s nanotechnology, a critical issue is to gain the ability to control the structure and function of matter with a deeper understanding of the quantitative and qualitative relationship among their synthesis conditions, structures, and properties. Experiments may provide information regarding the behavior of nanomaterials, but their interpretations are often controversial due largely to the difficulty of direct measurement. Hereupon, with the amazing advance in computer technology since the late 20th century,
computational modeling in science and engineering is increasingly important particularly in the fields of nanoscience and nanotechnology while it can provide researchers with significant insights into atomic-level interactions in various materials systems and underlying fundamental theories. The ability of engineering thermal conductivity of materials on the nanoscale has become extremely important in various applications including electronics and energy storage/conversion technologies. Due to technical difficulties in experimentally measuring the thermal conductivity of disordered and complex nanostructures, there has been much interest in use of theoretical and
computational methods to investigate thermal transport properties nanostructured materials. One
computational method that can perform an accurate analysis for the thermal conductivity of new or complex systems is molecular dynamics (MD), due to its capability of predicting the behaviors of atoms in large systems. In this work, we have developed a comprehensive MD-based
computational platform capable of predicting and explaining thermal transport in disordered and complex nanostructured materials. The unique features include construction of realistic nanostructures, determination of reliable force fields, and direct simulation of large systems, which are allowed by coupling various state-of-the-art
computational methods including quantum mechanics, molecular mechanics, statistical theories, and massively parallel computing. The
computational scheme was applied to describe thermal transport in various silicon and carbon-based disordered and nanostructures. First, the effects of defects including vacancy clusters, substitutional dopants, and dopant-defect complexes on the thermal conductivity of bulk crystalline silicon were investigated. Next, we analyzed the factors affecting heat transport in silicon-germanium and ternary silicon-germanium-tin alloys. Lastly, we performed the analysis of heat transport in silicon-based nanostructures such as nanowires and polycrystalline structures.
Advisors/Committee Members: Hwang, Gyeong S. (advisor), Ekerdt, John (committee member), Shi, Li (committee member), Mullins, Charles (committee member), Sanchez, Isaac (committee member).
Subjects/Keywords: Heat transport; Computational modeling; Nanomaterials
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Lee, Y. (2014). First principles-based molecular modeling of thermal transport in silicon-based nanomaterials. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/69263
Chicago Manual of Style (16th Edition):
Lee, Yongjin. “First principles-based molecular modeling of thermal transport in silicon-based nanomaterials.” 2014. Doctoral Dissertation, University of Texas – Austin. Accessed April 16, 2021.
http://hdl.handle.net/2152/69263.
MLA Handbook (7th Edition):
Lee, Yongjin. “First principles-based molecular modeling of thermal transport in silicon-based nanomaterials.” 2014. Web. 16 Apr 2021.
Vancouver:
Lee Y. First principles-based molecular modeling of thermal transport in silicon-based nanomaterials. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2014. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/2152/69263.
Council of Science Editors:
Lee Y. First principles-based molecular modeling of thermal transport in silicon-based nanomaterials. [Doctoral Dissertation]. University of Texas – Austin; 2014. Available from: http://hdl.handle.net/2152/69263

University of Utah
13.
DeMille, Robert Curtis.
Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail.
Degree: PhD, Chemistry, 2012, University of Utah
URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/2028/rec/1656
► A theoretical study of a chemical system is focused on representing the systemproperly with a model and using it to accurately represent and predict physical…
(more)
▼ A theoretical study of a chemical system is focused on representing the systemproperly with a model and using it to accurately represent and predict physical anddynamical properties of interest. The trade off between accuracy of simulations using atheoretical model and its computational expense is an important consideration inchoosing and implementing the model and accompanying force field. My research hassampled the two extremes of this balance. In developing the mW-Ion and mW/3SPNDNAmodels, a coarse-grained technique was used to simplify the interactions andsignificantly increase the efficiency of the calculations with respect to atomisticsimulations. These models have limited transferability to other studies due to theircoarseness, but reproduce properties such as solvation structure and ion dynamics quitewell, and this with the ability to extend the simulation studies to timescales intractable fortheir atomistic counterparts. In later work, while investigating potential improvements tosolid polymer electrolytes used in lithium battery technologies, an atomistic model with apolarizable force field was used in order to correctly capture the mobility of lithiumcations. This involved a considerably larger computational expense, but was necessary toretain fidelity to experimental data. The advantages and disadvantages of the two sidesof this balance is explored here, with detailed examination of the models and force fieldsused, their applicability, and broader impact in the simulation and scientific community.
Subjects/Keywords: Computational efficiency; DNA; Modeling; Molecular Dynamics
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
DeMille, R. C. (2012). Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail. (Doctoral Dissertation). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/2028/rec/1656
Chicago Manual of Style (16th Edition):
DeMille, Robert Curtis. “Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail.” 2012. Doctoral Dissertation, University of Utah. Accessed April 16, 2021.
http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/2028/rec/1656.
MLA Handbook (7th Edition):
DeMille, Robert Curtis. “Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail.” 2012. Web. 16 Apr 2021.
Vancouver:
DeMille RC. Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail. [Internet] [Doctoral dissertation]. University of Utah; 2012. [cited 2021 Apr 16].
Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/2028/rec/1656.
Council of Science Editors:
DeMille RC. Multiple disciplinary modeling and reproduction of physical phenomena with computer simulations at high and low atomic detail. [Doctoral Dissertation]. University of Utah; 2012. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd3/id/2028/rec/1656

Carnegie Mellon University
14.
MacLellan, Christopher J.
Computational Models of Human Learning: Applications for Tutor Development, Behavior Prediction, and Theory Testing.
Degree: 2017, Carnegie Mellon University
URL: http://repository.cmu.edu/dissertations/1054
► Intelligent tutoring systems are effective for improving students’ learning outcomes (Bowen et al., 2013; Koedinger & Anderson, 1997; Pane et al., 2013). However, constructing tutoring…
(more)
▼ Intelligent tutoring systems are effective for improving students’ learning outcomes (Bowen et al., 2013; Koedinger & Anderson, 1997; Pane et al., 2013). However, constructing tutoring systems that are pedagogically effective has been widely recognized as a challenging problem (Murray, 1999, 2003). In this thesis, I explore the use of computational models of apprentice learning, or computer models that learn interactively from examples and feedback, to support tutor development. In particular, I investigate their use for authoring expert-models via demonstrations and feedback (Matsuda et al., 2014), predicting student behavior within tutors (VanLehn et al., 1994), and for testing alternative learning theories (MacLellan, Harpstead, Patel, & Koedinger, 2016). To support these investigations, I present the Apprentice Learner Architecture, which posits the types of knowledge, performance, and learning components needed for apprentice learning and enables the generation and testing of alternative models. I use this architecture to create two models: the DECISION TREE model, which non- incrementally learns when to apply its skills, and the TRESTLE model, which instead learns incrementally. Both models both draw on the same small set of prior knowledge for all simulations (six operators and three types of relational knowledge). Despite their limited prior knowledge, I demonstrate their use for efficiently authoring a novel experimental design tutor and show that they are capable of achieving human-level performance in seven additional tutoring systems that teach a wide range of knowledge types (associations, categories, and skills) across multiple domains (language, math, engineering, and science). I show that the models are capable of predicting which versions of a fraction arithmetic and box and arrows tutors are more effective for human students’ learning. Further, I use a mixedeffects regression analysis to evaluate the fit of the models to the available human data and show that across all seven domains the TRESTLE model better fits the human data than the DECISION TREE model, supporting the theory that humans learn the conditions under which skills apply incrementally, rather than non-incrementally as prior work has suggested (Li, 2013; Matsuda et al., 2009). This work lays the foundation for the development of a Model Human Learner— similar to Card, Moran, and Newell’s (1986) Model Human Processor—that encapsulates psychological and learning science findings in a format that researchers and instructional designers can use to create effective tutoring systems.
Subjects/Keywords: Computational Modeling; Science of Learning; Educational Technology
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
MacLellan, C. J. (2017). Computational Models of Human Learning: Applications for Tutor Development, Behavior Prediction, and Theory Testing. (Thesis). Carnegie Mellon University. Retrieved from http://repository.cmu.edu/dissertations/1054
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):
MacLellan, Christopher J. “Computational Models of Human Learning: Applications for Tutor Development, Behavior Prediction, and Theory Testing.” 2017. Thesis, Carnegie Mellon University. Accessed April 16, 2021.
http://repository.cmu.edu/dissertations/1054.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
MacLellan, Christopher J. “Computational Models of Human Learning: Applications for Tutor Development, Behavior Prediction, and Theory Testing.” 2017. Web. 16 Apr 2021.
Vancouver:
MacLellan CJ. Computational Models of Human Learning: Applications for Tutor Development, Behavior Prediction, and Theory Testing. [Internet] [Thesis]. Carnegie Mellon University; 2017. [cited 2021 Apr 16].
Available from: http://repository.cmu.edu/dissertations/1054.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
MacLellan CJ. Computational Models of Human Learning: Applications for Tutor Development, Behavior Prediction, and Theory Testing. [Thesis]. Carnegie Mellon University; 2017. Available from: http://repository.cmu.edu/dissertations/1054
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
15.
Vedula, Vijay.
Image based computational modeling of intracardiac flows.
Degree: 2015, Johns Hopkins University
URL: http://jhir.library.jhu.edu/handle/1774.2/37858
► With continuous advancements in four-dimensional medical imaging technologies, increasing computational speeds, and widespread availability of high performance computing facilities, computational modeling of intracardiac flows is…
(more)
▼ With continuous advancements in four-dimensional medical imaging technologies, increasing
computational speeds, and widespread availability of high performance computing facilities,
computational modeling of intracardiac flows is becoming increasingly viable and has the potential to become a powerful non-invasive diagnostic tool for the diagnosis and treatment of cardiovascular disease. The motive of the current study is to develop a
modeling framework that facilitates image-based analysis of intracardiac flows in health as well as disease and to use this framework to gain fundamental insights into intracardiac hemodynamics. A procedure is developed for constructing
computational fluid dynamics (CFD) – ready models from in vivo imaging data. The key components of this procedure are the registration and segmentation of the 4D data for several (~20) key frames, template based mapping to ensure surface grid conformality and high-fidelity simulations using a
sharp-interface immersed boundary solver. A physiologically representative, kinematic model of the mitral valve is also developed for use in these simulations. As a precursor, a comprehensive quantitative validation of the flow solver is performed using experimental data in a simple model of the left ventricle. A quantitative comparison of the phase-averaged velocity and vorticity fields between the simulation and the experiment shows a reasonable agreement. The detailed assessment of this comparison is used to identify and discuss the key challenges and uncertainties associated in conducting such a validation study. The vast majority of
computational investigations of intracardiac flows have focused either on the left or the right ventricles while the corresponding atria were modeled in highly simplistic ways. However, the impact of this simplification on the hemodynamics of the ventricular filling has not been clearly understood. Additionally, the surface of the ventricle has been
assumed to be smooth although it is well known that the left ventricle is highly corrugated with surface protrusions or trabeculae and papillary muscles extending deep into the ventricular cavity. Hence, separate studies were conducted to understand the effect of complex atrial flows on the intraventricular flow development and also to understand and quantify the impact of the trabeculae and papillary muscles on ventricular hemodynamics Results indicate that the trabeculae and papillary muscles significantly impact ventricular flow resulting in a deeper penetration of the mitral jet into the ventricle during filling. These anatomical features are also found to produce a “squeezing” effect that enhances apical washout. It is also demonstrated that the complex flow dynamics developed inside the left atrium have minimal influence on the flow inside the left ventricle, which is primarily governed by the mitral valve leaflets configuration. The complex vortical structures inside the left
atrium are rapidly dissipated due to the complex interaction of multiple vortex rings leading to breakup,…
Advisors/Committee Members: Mittal, Rajat (advisor).
Subjects/Keywords: Cardiac hemodynamics; computational modeling; immersed boundary methods
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Vedula, V. (2015). Image based computational modeling of intracardiac flows. (Thesis). Johns Hopkins University. Retrieved from http://jhir.library.jhu.edu/handle/1774.2/37858
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):
Vedula, Vijay. “Image based computational modeling of intracardiac flows.” 2015. Thesis, Johns Hopkins University. Accessed April 16, 2021.
http://jhir.library.jhu.edu/handle/1774.2/37858.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Vedula, Vijay. “Image based computational modeling of intracardiac flows.” 2015. Web. 16 Apr 2021.
Vancouver:
Vedula V. Image based computational modeling of intracardiac flows. [Internet] [Thesis]. Johns Hopkins University; 2015. [cited 2021 Apr 16].
Available from: http://jhir.library.jhu.edu/handle/1774.2/37858.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Vedula V. Image based computational modeling of intracardiac flows. [Thesis]. Johns Hopkins University; 2015. Available from: http://jhir.library.jhu.edu/handle/1774.2/37858
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Cornell University
16.
Boston, Marisa.
A Computational Model Of Cognitive Constraints In Syntactic Locality.
Degree: PhD, Linguistics, 2012, Cornell University
URL: http://hdl.handle.net/1813/29156
► This dissertation is broadly concerned with the question: how do human cognitive limitations influence difficult sentences? The focus is a class of grammatical restrictions, locality…
(more)
▼ This dissertation is broadly concerned with the question: how do human cognitive limitations influence difficult sentences? The focus is a class of grammatical restrictions, locality constraints. The majority of relations between words are local; the relations between question words and their governors are not. Locality constraints restrict the formation of these non-local dependencies. Though necessary, the origin, operation, and scope of locality constraints is a controversial topic in the literature. The dissertation describes the implementation of a
computational model that clarifies these issues. The model tests, against behavioral data, a series of cognitive constraints argued to account for locality. The result is an explanatory model predictive of a variety of cross-linguistic locality data. The model distinguishes those cognitive limitations that affect locality processing, and addresses the competence-performance debate by determining how and when cognitive constraints explain human behavior. The results provide insight into the nature of locality constraints, and promote language models sensitive to human cognitive limitations.
Advisors/Committee Members: Hale, John T. (chair), Rooth, Mats (committee member), Cardie, Claire T (committee member).
Subjects/Keywords: Computational modeling; Syntactic locality; Cognitive constraints
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APA (6th Edition):
Boston, M. (2012). A Computational Model Of Cognitive Constraints In Syntactic Locality. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/29156
Chicago Manual of Style (16th Edition):
Boston, Marisa. “A Computational Model Of Cognitive Constraints In Syntactic Locality.” 2012. Doctoral Dissertation, Cornell University. Accessed April 16, 2021.
http://hdl.handle.net/1813/29156.
MLA Handbook (7th Edition):
Boston, Marisa. “A Computational Model Of Cognitive Constraints In Syntactic Locality.” 2012. Web. 16 Apr 2021.
Vancouver:
Boston M. A Computational Model Of Cognitive Constraints In Syntactic Locality. [Internet] [Doctoral dissertation]. Cornell University; 2012. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1813/29156.
Council of Science Editors:
Boston M. A Computational Model Of Cognitive Constraints In Syntactic Locality. [Doctoral Dissertation]. Cornell University; 2012. Available from: http://hdl.handle.net/1813/29156

Vanderbilt University
17.
Kragel, James Edward.
The functional neuroanatomy of episodic retrieval: using neuroimaging to understand the computational processes underlying human memory.
Degree: PhD, Neuroscience, 2015, Vanderbilt University
URL: http://hdl.handle.net/1803/12347
► The medial temporal lobe (MTL) is essential to episodic memory through its role in the reactivation of past experience. Cortical networks provide top-down influence on…
(more)
▼ The medial temporal lobe (MTL) is essential to episodic memory
through its role in the reactivation of past experience.
Cortical networks provide top-down influence on the
MTL, influencing the manner in which information can be
retrieved. While neuroimaging investigations of human memory
have characterized the functional correlates of episodic
retrieval, the coordination of MTL systems during
self-guided memory search is poorly understood. Using
functional neuroimaging to estimate neural activation during
variants of the free-recall paradigm, this dissertation
demonstrates that the posterior MTL is critically involved in
internally-directed memory search, through its interactions with
distributed cortical systems. First, I characterize the
engagement of a cortico-hippocampal network during memory
search. I then demonstrate increased functional connectivity
between this network and multiple frontoparietal systems,
identifying neural mechanisms that may potentially reflect
top-down control of memory search. Next, I relate activation of
the posterior MTL to the process of episodic recollection
through comparison of activity during free recall and source
recognition tasks. I additionally demonstrate common activation
in dorsal frontoparietal networks during free recall and
processing of item familiarity. To characterize the computations
mediated by the MTL, I develop a neuro-cognitive model of free
recall. Retrieved-context theories propose that temporal
context, a slowly integrating representation of the recent past,
cues the hippocampus during retrieval. I link activation of the
MTL to the process of temporal reinstatement, predicting the
temporal organization of recall. Next, I use a variant of the
free-recall paradigm in which memory is disrupted prior to
retrieval, to test the capacity of large-scale cortical networks
to control episodic memory. I show that a frontoparietal control
network (FPCN) functionally couples with the MTL when memory is
disrupted. Using a neurally informed
computational model of
recall, I demonstrate that activation of the FPCN and posterior
MTL predict when individuals will overcome distraction by
reinstating contextual information to guide memory search. Taken
together, these findings demonstrate how the MTL supports memory
search through the reinstatement of contextual information, a
process that is coordinated through top-down signals from
frontoparietal networks.
Advisors/Committee Members: Sean M. Polyn (committee member), René Marois (committee member), Thomas J. Palmeri (committee member), Frank Tong (Committee Chair).
Subjects/Keywords: computational modeling; fMRI; free recall; episodic memory
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Kragel, J. E. (2015). The functional neuroanatomy of episodic retrieval: using neuroimaging to understand the computational processes underlying human memory. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/12347
Chicago Manual of Style (16th Edition):
Kragel, James Edward. “The functional neuroanatomy of episodic retrieval: using neuroimaging to understand the computational processes underlying human memory.” 2015. Doctoral Dissertation, Vanderbilt University. Accessed April 16, 2021.
http://hdl.handle.net/1803/12347.
MLA Handbook (7th Edition):
Kragel, James Edward. “The functional neuroanatomy of episodic retrieval: using neuroimaging to understand the computational processes underlying human memory.” 2015. Web. 16 Apr 2021.
Vancouver:
Kragel JE. The functional neuroanatomy of episodic retrieval: using neuroimaging to understand the computational processes underlying human memory. [Internet] [Doctoral dissertation]. Vanderbilt University; 2015. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1803/12347.
Council of Science Editors:
Kragel JE. The functional neuroanatomy of episodic retrieval: using neuroimaging to understand the computational processes underlying human memory. [Doctoral Dissertation]. Vanderbilt University; 2015. Available from: http://hdl.handle.net/1803/12347

Vanderbilt University
18.
Lemmon, Gordon Howard.
Development of methods for docking and designing small molecules within the Rosetta code framework.
Degree: PhD, Chemical and Physical Biology, 2012, Vanderbilt University
URL: http://hdl.handle.net/1803/14316
► Structure-based drug design is a key challenge for pharmaceutical chemists. By studying the structure of proteins bound to natural substrates, researchers can design small molecules…
(more)
▼ Structure-based drug design is a key challenge for pharmaceutical chemists. By studying the structure of proteins bound to natural substrates, researchers can design small molecules which they predict will bind in a similar fashion. Ligand docking software such as RosettaLigand plays a key role in structure-based drug design by predicting how a small molecule and a protein will interact. In this body of research I present improvements to the RosettaLigand docking algorithm. I first demonstrate a strategy for achieving accurate predictions of HIV-1 protease/protease inhibitor binding affinity. Next I present a tutorial for using a new version of RosettaLigand docking code which I wrote. This new version allows simultaneous docking of multiple ligands, docking with interface design, and uses an XML-script interface. The XML interface allows fully customizable ligand docking protocols. Finally I demonstrate simultaneous docking of waters along with small molecule inhibitors within protein interfaces. Water docking improves Rosetta’s ability to predict the structure of the protein/inhibitor interface.
Advisors/Committee Members: Brian Bachmann (committee member), Jarrod Smith (committee member), Richard D'Aquila (committee member), David Tabb (Committee Chair).
Subjects/Keywords: macromolecular modeling; computational biology; strutural biology
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Lemmon, G. H. (2012). Development of methods for docking and designing small molecules within the Rosetta code framework. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/14316
Chicago Manual of Style (16th Edition):
Lemmon, Gordon Howard. “Development of methods for docking and designing small molecules within the Rosetta code framework.” 2012. Doctoral Dissertation, Vanderbilt University. Accessed April 16, 2021.
http://hdl.handle.net/1803/14316.
MLA Handbook (7th Edition):
Lemmon, Gordon Howard. “Development of methods for docking and designing small molecules within the Rosetta code framework.” 2012. Web. 16 Apr 2021.
Vancouver:
Lemmon GH. Development of methods for docking and designing small molecules within the Rosetta code framework. [Internet] [Doctoral dissertation]. Vanderbilt University; 2012. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1803/14316.
Council of Science Editors:
Lemmon GH. Development of methods for docking and designing small molecules within the Rosetta code framework. [Doctoral Dissertation]. Vanderbilt University; 2012. Available from: http://hdl.handle.net/1803/14316

Vanderbilt University
19.
McKenna, Matthew Thomas.
Development and Validation of a Predictive Model of Chemotherapy in Triple Negative Breast Cancer.
Degree: PhD, Biomedical Engineering, 2017, Vanderbilt University
URL: http://hdl.handle.net/1803/14399
► Precision medicine is the concept of incorporating patient-specific variability into prevention and treatment strategies. Precision medicine initiatives in oncology have primarily focused on the use…
(more)
▼ Precision medicine is the concept of incorporating patient-specific variability into prevention and treatment strategies. Precision medicine initiatives in oncology have primarily focused on the use of genetics to classify and pharmaceutically target cancers. While the genetic-centric approach to precision cancer therapy has merit in selecting therapy, an expanded effort is required to guide optimal dosing of those therapies. Fundamentally, treatment response is driven by patient‑, tumor‑, and cell‑specific pharmacologic properties. We posit that mathematical models that explicitly incorporate such processes will improve the ability to deliver precision therapy. In this Dissertation, we develop a combined experimental-mathematical
modeling framework to establish a mechanistic mathematical model of doxorubicin treatment response in triple negative breast cancer (TNBC). TNBC is a subgroup of invasive cancers that lack significant expression of the estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Lacking specific pharmaceutical targets, the current approach to neoadjuvant therapy for locally advanced disease employs a combination of cytotoxic drugs, including doxorubicin. We present a coupled pharmacokinetic/pharmacodynamic (PK/PD) model that describes how the concentration and duration of doxorubicin therapy shape subsequent cell population dynamics in vitro. The proposed model accurately captures doxorubicin uptake and treatment response dynamics in a panel of cell lines, and the model can be leveraged to predict response to a wide range of doxorubicin treatment timecourses. We propose the equivalent dose metric, a value derived from the mechanistic PK/PD model, to explicitly account for variable cell line pharmacological properties. We demonstrate that the equivalent dose is a more precise means of quantifying combination therapies and comparing cell line response to therapy relative to current approaches. Finally, we extend the model to describe treatment response in heterogeneous populations. We demonstrate that the biological composition of the population significantly impacts treatment response dynamics, and we propose a PK-based mechanism to explain the behavior. By studying various experimental perturbations within a single mechanistic, mathematical framework, this approach provides a means for more efficient discovery of predictive biomarkers and translation of those discoveries into patient care.
Advisors/Committee Members: Vandana G. Abramson (committee member), Vito Quaranta (committee member), William A. Grissom (committee member), Michael I. Miga (Committee Chair), Thomas E. Yankeelov (Committee Chair).
Subjects/Keywords: doxorubicin; pharmacology; mathematical modeling; computational oncology
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
McKenna, M. T. (2017). Development and Validation of a Predictive Model of Chemotherapy in Triple Negative Breast Cancer. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/14399
Chicago Manual of Style (16th Edition):
McKenna, Matthew Thomas. “Development and Validation of a Predictive Model of Chemotherapy in Triple Negative Breast Cancer.” 2017. Doctoral Dissertation, Vanderbilt University. Accessed April 16, 2021.
http://hdl.handle.net/1803/14399.
MLA Handbook (7th Edition):
McKenna, Matthew Thomas. “Development and Validation of a Predictive Model of Chemotherapy in Triple Negative Breast Cancer.” 2017. Web. 16 Apr 2021.
Vancouver:
McKenna MT. Development and Validation of a Predictive Model of Chemotherapy in Triple Negative Breast Cancer. [Internet] [Doctoral dissertation]. Vanderbilt University; 2017. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1803/14399.
Council of Science Editors:
McKenna MT. Development and Validation of a Predictive Model of Chemotherapy in Triple Negative Breast Cancer. [Doctoral Dissertation]. Vanderbilt University; 2017. Available from: http://hdl.handle.net/1803/14399

University of Edinburgh
20.
Warren, Mariah.
Modeling Allophonic Rule Learning with Distributional and Phonetic Factors.
Degree: 2012, University of Edinburgh
URL: http://hdl.handle.net/1842/8496
► A fundamental task faced by infants during language acquisition is acquiring the phonological structure of the native language, including the abstract phonemic categories and the…
(more)
▼ A fundamental task faced by infants during language acquisition is acquiring the phonological structure of the native language, including the abstract phonemic categories and the phonological rules relating the underlying categories to phonetic surface forms. Allophones are phonetic variants of phonemes which appear in select, non-overlapping phonetic contexts. Acquiring allophonic rules is necessary for infants to fully construct their phonological inventory. Statistical learning, including a sensitivity to the distribution of phonetic segments and their contexts, may play a role in infant acquisition of allophones. Two
computational models of allophonic rule induction were explored. First, a statistical algorithm by Peperkamp et al (2006) was re-implemented. It detects allophones by searching for segments in complementary distribution using the Kullback-Leibler measure. The model was tested with an artificial language and a corpus of phonemically-transcribed speech, and linguistic filters were used to discard falsely identified allophones. The model successful detected allophones in noise and with varying numbers of rules and contexts, but did not scale well. A novel phonetic distance filter was applied with superior results. Secondly, a novel model was developed which represents segments as vectors in a context space, and identifies allophonic pairs based on contextual non-overlap, segment frequency, and sonority. The model detected 5 (out of 7) allophones with very high accuracy from a corpus of phonemically-transcribed speech. The results from both models indicate that both distributional and phonetic information are required for allophonic rule learning, and that segment frequency, corpus size, and context size interact to affect the performance of both models. Finally, the limitations and assumptions of the models are discussed.
Advisors/Committee Members: Kirby, James.
Subjects/Keywords: Allophone; Phonological Rules; Statistical Learning; Computational Modeling
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Warren, M. (2012). Modeling Allophonic Rule Learning with Distributional and Phonetic Factors. (Thesis). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/8496
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):
Warren, Mariah. “Modeling Allophonic Rule Learning with Distributional and Phonetic Factors.” 2012. Thesis, University of Edinburgh. Accessed April 16, 2021.
http://hdl.handle.net/1842/8496.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Warren, Mariah. “Modeling Allophonic Rule Learning with Distributional and Phonetic Factors.” 2012. Web. 16 Apr 2021.
Vancouver:
Warren M. Modeling Allophonic Rule Learning with Distributional and Phonetic Factors. [Internet] [Thesis]. University of Edinburgh; 2012. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1842/8496.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Warren M. Modeling Allophonic Rule Learning with Distributional and Phonetic Factors. [Thesis]. University of Edinburgh; 2012. Available from: http://hdl.handle.net/1842/8496
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Jawaharlal Nehru University
21.
Patil, Kiran Suresh.
Computational modeling and simulation of Neuronal
dynamics : effects of Stochastic Perturbations; -.
Degree: Computer Science, 2007, Jawaharlal Nehru University
URL: http://shodhganga.inflibnet.ac.in/handle/10603/32306
none
References, Tables, Figures vip.
118p.
Advisors/Committee Members: Karmeshu.
Subjects/Keywords: Neurons; computational; modeling
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Patil, K. S. (2007). Computational modeling and simulation of Neuronal
dynamics : effects of Stochastic Perturbations; -. (Thesis). Jawaharlal Nehru University. Retrieved from http://shodhganga.inflibnet.ac.in/handle/10603/32306
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):
Patil, Kiran Suresh. “Computational modeling and simulation of Neuronal
dynamics : effects of Stochastic Perturbations; -.” 2007. Thesis, Jawaharlal Nehru University. Accessed April 16, 2021.
http://shodhganga.inflibnet.ac.in/handle/10603/32306.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Patil, Kiran Suresh. “Computational modeling and simulation of Neuronal
dynamics : effects of Stochastic Perturbations; -.” 2007. Web. 16 Apr 2021.
Vancouver:
Patil KS. Computational modeling and simulation of Neuronal
dynamics : effects of Stochastic Perturbations; -. [Internet] [Thesis]. Jawaharlal Nehru University; 2007. [cited 2021 Apr 16].
Available from: http://shodhganga.inflibnet.ac.in/handle/10603/32306.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Patil KS. Computational modeling and simulation of Neuronal
dynamics : effects of Stochastic Perturbations; -. [Thesis]. Jawaharlal Nehru University; 2007. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/32306
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Texas A&M University
22.
Knight, Jason Matthew.
Optimal Model-Based Approaches for Predictive Inference in Biology.
Degree: PhD, Electrical Engineering, 2015, Texas A&M University
URL: http://hdl.handle.net/1969.1/155131
► Predictive modeling of the dynamic, multivariate, non-linear, stochastic systems of biology is a difficult enterprise. High throughput measurement techniques are enabling new approaches to computational…
(more)
▼ Predictive
modeling of the dynamic, multivariate, non-linear, stochastic systems of biology is a difficult enterprise. High throughput measurement techniques are enabling new approaches to
computational biology, but the small number of samples typically available relative to the number of features measured make additional sources of information critical for accurate predictions. In this dissertation, we offer an approach to incorporate biological pathway knowledge into a predictive stochastic model for genetic regulatory networks. In addition, we propose a statistical model for shotgun sequencing and use
computational approximation strategies to derive optimal estimators for classification.
We perform comparisons of classifiers trained using this framework to other existing classification rules including non-linear support vector machines. Using both synthetic and real sequencing data, our classifiers delivered lower classification error rates than existing classification techniques. In addition, we demonstrate using prior knowledge to construct the classifier through properly constructed prior distributions and several scenarios where this increases classification performance. This research establishes a flexible framework to generate optimal estimators with respect to statistical biological models. By demonstrating the role and power of computation in unlocking these estimators, we point future research efforts towards this computationally intensive approach for the
computational biology field.
Advisors/Committee Members: Dougherty, Edward R (advisor), Ivanov, Ivan (advisor), Chamberland, Jean-Francois (committee member), Chapkin, Robert S (committee member).
Subjects/Keywords: computational biology; predictive inference; statistical modeling; bioinformatics
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Knight, J. M. (2015). Optimal Model-Based Approaches for Predictive Inference in Biology. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/155131
Chicago Manual of Style (16th Edition):
Knight, Jason Matthew. “Optimal Model-Based Approaches for Predictive Inference in Biology.” 2015. Doctoral Dissertation, Texas A&M University. Accessed April 16, 2021.
http://hdl.handle.net/1969.1/155131.
MLA Handbook (7th Edition):
Knight, Jason Matthew. “Optimal Model-Based Approaches for Predictive Inference in Biology.” 2015. Web. 16 Apr 2021.
Vancouver:
Knight JM. Optimal Model-Based Approaches for Predictive Inference in Biology. [Internet] [Doctoral dissertation]. Texas A&M University; 2015. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1969.1/155131.
Council of Science Editors:
Knight JM. Optimal Model-Based Approaches for Predictive Inference in Biology. [Doctoral Dissertation]. Texas A&M University; 2015. Available from: http://hdl.handle.net/1969.1/155131

Texas A&M University
23.
Martin, Michael.
Modeling of Transport in Lithium Ion Battery Electrodes.
Degree: MS, Mechanical Engineering, 2012, Texas A&M University
URL: http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11178
► Lithium ion battery systems are promising solutions to current energy storage needs due to their high operating voltage and capacity. Numerous efforts have been conducted…
(more)
▼ Lithium ion battery systems are promising solutions to current energy storage needs due to their high operating voltage and capacity. Numerous efforts have been conducted to model these systems in order to aid the design process and avoid expensive and time consuming prototypical experiments. Of the numerous processes occurring in these systems, solid state transport in particular has drawn a large amount of attention from the research community, as it tends to be one of the rate limiting steps in lithium ion battery performance. Recent studies have additionally indicated that purposeful design of battery electrodes using 3D microstructures offers new freedoms in design, better use of available cell area, and increased battery performance.
The following study is meant to serve as a first principles investigation into the behaviors of 3D electrode architectures by monitoring concentration and cycle behaviors under realistic operating conditions. This was accomplished using
computational tools to model the solid state diffusion behavior in several generated electrode morphologies. Developed
computational codes were used to generate targeted structures under prescribed conditions of particle shape, size, and overall morphology. The diffusion processes in these morphologies were simulated under conditions prescribed from literature.
Primary results indicate that parameters usually employed to describe electrode geometry, such as volume to surface area ratio, cannot be solely relied upon to predict or characterize performance. Additionally, the interaction between particle shapes implies some design aspects that may be exploited to improve morphology behavior. Of major importance is the degree of particle isolation and overlap in 3D architectures, as these govern gradient development and lithium depletion within the electrode structures. The results of this study indicate that there are optimum levels of these parameters, and so purposeful design must make use of these behaviors.
Advisors/Committee Members: Mukherjee, Partha P. (advisor), Ranjan, Devesh (advisor), Annamalai, Kalyan (committee member), Lazarov, Raytcho (committee member).
Subjects/Keywords: Lithium Ion Battery; 3D Electrode; Computational Modeling
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Martin, M. (2012). Modeling of Transport in Lithium Ion Battery Electrodes. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11178
Chicago Manual of Style (16th Edition):
Martin, Michael. “Modeling of Transport in Lithium Ion Battery Electrodes.” 2012. Masters Thesis, Texas A&M University. Accessed April 16, 2021.
http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11178.
MLA Handbook (7th Edition):
Martin, Michael. “Modeling of Transport in Lithium Ion Battery Electrodes.” 2012. Web. 16 Apr 2021.
Vancouver:
Martin M. Modeling of Transport in Lithium Ion Battery Electrodes. [Internet] [Masters thesis]. Texas A&M University; 2012. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11178.
Council of Science Editors:
Martin M. Modeling of Transport in Lithium Ion Battery Electrodes. [Masters Thesis]. Texas A&M University; 2012. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11178

Boston College
24.
Zhang, Lu.
Analysis and Interpretation of Complex Lipidomic Data Using
Bioinformatic Approaches.
Degree: PhD, Biology, 2012, Boston College
URL: http://dlib.bc.edu/islandora/object/bc-ir:101631
► The field of lipidomics has rapidly progressed since its inception only a decade ago. Technological revolutions in mass spectrometry, chromatography, and computational biology now enables…
(more)
▼ The field of lipidomics has rapidly progressed since
its inception only a decade ago. Technological revolutions in mass
spectrometry, chromatography, and
computational biology now enables
high-throughput high-accuracy quantification of the cellular
lipidome. One significant improvement of these technologies is that
lipids can now be identified and quantified as individual molecular
species. Lipidomics provides an additional layer of information to
genomics and proteomics and opens a new opportunity for furthering
our understanding of cellular signaling networks and physiology,
which have broad therapeutic values. As with other 'omics sciences,
these new technologies are producing vast amounts of lipidomic
data, which require sophisticated statistical and
computational
approaches for analysis and interpretation. However,
computational
tools for utilizing such data are sparse. The complexity of lipid
metabolic systems and the fact that lipid enzymes remain poorly
understood also present challenges to
computational lipidomics. The
focus of my dissertation has been the development of novel
computational methods for systematic study of lipid metabolism in
cellular function and human diseases using lipidomic data. In this
dissertation, I first present a mathematical model describing
cardiolipin molecular species distribution in steady state and its
relationship with fatty acid chain compositions. Knowledge of this
relationship facilitates determination of isomeric species for
complex lipids, providing more detailed information beyond current
limits of mass spectrometry technology. I also correlate lipid
species profiles with diseases and predict potential therapeutics.
Second, I present statistical studies of mechanisms influencing
phosphatidylcholine and phosphatidylethanolamine molecular
architectures, respectively. I describe a statistical approach to
examine dependence of sn1 and sn2 acyl chain regulatory mechanisms.
Third, I describe a novel network inference approach and illustrate
a dynamic model of ethanolamine glycerophospholipid acyl chain
remodeling. The model is the first that accurately and robustly
describes lipid species changes in pulse-chase experiments. A key
outcome is that the deacylation and reacylation rates of individual
acyl chains can be determined, and the resulting rates explain the
well-known prevalence of sn1 saturated chains and sn2 unsaturated
chains. Lastly, I summarize and remark on future studies for
lipidomics.
Advisors/Committee Members: Jeffrey H. Chuang (Thesis advisor).
Subjects/Keywords: bioinformatic; computational; dynamics; lipidomics; modeling; statistical
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Zhang, L. (2012). Analysis and Interpretation of Complex Lipidomic Data Using
Bioinformatic Approaches. (Doctoral Dissertation). Boston College. Retrieved from http://dlib.bc.edu/islandora/object/bc-ir:101631
Chicago Manual of Style (16th Edition):
Zhang, Lu. “Analysis and Interpretation of Complex Lipidomic Data Using
Bioinformatic Approaches.” 2012. Doctoral Dissertation, Boston College. Accessed April 16, 2021.
http://dlib.bc.edu/islandora/object/bc-ir:101631.
MLA Handbook (7th Edition):
Zhang, Lu. “Analysis and Interpretation of Complex Lipidomic Data Using
Bioinformatic Approaches.” 2012. Web. 16 Apr 2021.
Vancouver:
Zhang L. Analysis and Interpretation of Complex Lipidomic Data Using
Bioinformatic Approaches. [Internet] [Doctoral dissertation]. Boston College; 2012. [cited 2021 Apr 16].
Available from: http://dlib.bc.edu/islandora/object/bc-ir:101631.
Council of Science Editors:
Zhang L. Analysis and Interpretation of Complex Lipidomic Data Using
Bioinformatic Approaches. [Doctoral Dissertation]. Boston College; 2012. Available from: http://dlib.bc.edu/islandora/object/bc-ir:101631

Uppsala University
25.
Holmgren, Hanna.
Computational Ice Dynamics and Hydraulics : Towards a Coupling in the Ice Sheet Code ARCTIC-TARAH.
Degree: Information Technology, 2012, Uppsala University
URL: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-179861
► Numerical ice sheet modeling is a rather young discipline: it started in the 1950s. The "first generation" models developed at that time are currently…
(more)
▼ Numerical ice sheet modeling is a rather young discipline: it started in the 1950s. The "first generation" models developed at that time are currently being replaced by "new generations" ones, such as e.g. ARCTIC-TARAH. ARCTIC-TARAH is a Bert Bolin Center for Climate Research spin-off from the Pennsylvania State University Ice sheet model (PSUI). When the Bolin Center received PSUI for subsequent independent development and adaption of the code to Arctic settings in 2010, an initial inspection of the source code suggested that PSUI also contained a module that allows for the treatment of glacial hydraulics. A numerical ice sheet model including coupling of ice dynamics and hydraulics is an extremely important tool in testing new hypotheses of former geological events. E.g., based on the recent finding that Arctic Ocean sediments contain a very distinct signature, it has been suggested that ice dammed lakes at the south-eastern margin of the late Weichselian Eurasian ice sheet drained into the Arctic Ocean in a catastrophic event around 55.000 years ago. The aim of this thesis is to perform a reconnaissance analysis of the glacio-hydraulic algorithms in ARCTIC-TARAH, as "inherited" (but never with published record of functionality) from PSUI. The work is carried out in two steps: first the routines and algorithms describing the hydraulics are located and explored, and then these routines are tested and verified by performing experiment simulations. The investigation of the program code reveals the presence of two hydraulics related modules in ARCTIC-TARAH. The main tasks of the module Water are to initiate lakes and oceans and to adjust hydrostatic pressure in each lake. Further, with the module Move Water activated, transportation of water (e.g. in rivers) is possible. Results from idealized experiment simulations verify the functionality of the routines in the module Water. An in-depth analysis of the module Move Water suggests that there is a mismatch in time units when solving the equations describing flow of water. Experiment simulations also support this flaw detected in the flow model. Preliminary adjustments were made to the source code of the module Move Water, which made it possible to simulate the transportation of water both under an ice sheet and in rivers on land. However, these adjustments do not solve the problem of mismatching time scales, and the numerical solutions obtained from the experiments were observed to be unstable and, therefore, possibly incorrect. To be able to perform more advanced simulations in support of the above mentioned hypothesis, the flow model in the module Move Water needs to be improved or replaced. One solution to the problem with mismatching time scales, could be to use a so called multiscale solution in time.
Subjects/Keywords: ice dynamics; ice sheet modeling; computational hydraulics
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APA ·
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MLA ·
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APA (6th Edition):
Holmgren, H. (2012). Computational Ice Dynamics and Hydraulics : Towards a Coupling in the Ice Sheet Code ARCTIC-TARAH. (Thesis). Uppsala University. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-179861
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):
Holmgren, Hanna. “Computational Ice Dynamics and Hydraulics : Towards a Coupling in the Ice Sheet Code ARCTIC-TARAH.” 2012. Thesis, Uppsala University. Accessed April 16, 2021.
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-179861.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Holmgren, Hanna. “Computational Ice Dynamics and Hydraulics : Towards a Coupling in the Ice Sheet Code ARCTIC-TARAH.” 2012. Web. 16 Apr 2021.
Vancouver:
Holmgren H. Computational Ice Dynamics and Hydraulics : Towards a Coupling in the Ice Sheet Code ARCTIC-TARAH. [Internet] [Thesis]. Uppsala University; 2012. [cited 2021 Apr 16].
Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-179861.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Holmgren H. Computational Ice Dynamics and Hydraulics : Towards a Coupling in the Ice Sheet Code ARCTIC-TARAH. [Thesis]. Uppsala University; 2012. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-179861
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Rice University
26.
Huang, Bin.
Decoding biological gene regulatory networks by quantitative modeling.
Degree: PhD, Computational Biology, 2017, Rice University
URL: http://hdl.handle.net/1911/96073
► Gene regulatory network is essential to regulate the biological functions of cells. With the rapid development of “omics” technologies, the network can be inferred for…
(more)
▼ Gene regulatory network is essential to regulate the biological functions of cells.
With the rapid development of “omics” technologies, the network can be inferred for a
certain biological function. However, it still remains a challenge to understand the
complex network at a systematic level. In this thesis, we utilized quantitative
modeling
approaches to study the nonlinear dynamics and the design principles of these biological
gene regulatory networks. We aim to explain the existing experimental observations with
the model, and further propose reasonable hypothesis for future experimental designs.
More importantly, the understanding of the circuit’s regulatory mechanism would benefit
the design of a de novo gene circuit for a new biological function.
We first studied the plasticity of cell migration phenotypes during cancer
metastasis, which contains two key cellular plasticity mechanisms - epithelial-tomesenchymal
transition (EMT) and mesenchymal-to-amoeboid transition (MAT). In this
study, we quantitatively modeled the core Rac1/RhoA gene regulatory circuit for MAT
and later connected it with the core regulatory circuit for EMT. We found four different
stable states, consistent with the amoeboid (A), mesenchymal (M), the hybrid
amoeboid/mesenchymal (A/M), and the hybrid epithelial/mesenchymal (E/M)
phenotypes that are observed in the experiment. We also explored the effects of
microRNAs and EMT-inducing signals like Hepatocyte Growth Factor (HGF), and
provided a new insight for the transitions among these phenotypes.
To improve the traditional
modeling approaches, we developed a new
computational modeling method called Random Circuit Perturbation (RACIPE) to
explore the dynamic behavior of gene regulatory circuits without the requirement of
detailed kinetic parameters. We applied RACIPE on several gene circuits, and found the
existence of robust gene expression patterns even though the model parameters are wildly
perturbed. We also showed the powerful aspect of RACIPE to decipher the operating
principles of the circuits.
This kind of quantitative models not only works for gene regulatory network, but
also is capable to be extended to study the cell-cell interactions among cancer and
immune cells. The results shown the co-occurrence of three cancer states: low risk
cancer with intermediate immunity (L), intermediate risk cancer with high immunity (I) and high risk cancer with low immunity state (H). We further used the model to assess the different combinations of cancer therapies.
Advisors/Committee Members: Onuchic, Jose (advisor).
Subjects/Keywords: Computational biology; System biology; Gene network; Modeling
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Huang, B. (2017). Decoding biological gene regulatory networks by quantitative modeling. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/96073
Chicago Manual of Style (16th Edition):
Huang, Bin. “Decoding biological gene regulatory networks by quantitative modeling.” 2017. Doctoral Dissertation, Rice University. Accessed April 16, 2021.
http://hdl.handle.net/1911/96073.
MLA Handbook (7th Edition):
Huang, Bin. “Decoding biological gene regulatory networks by quantitative modeling.” 2017. Web. 16 Apr 2021.
Vancouver:
Huang B. Decoding biological gene regulatory networks by quantitative modeling. [Internet] [Doctoral dissertation]. Rice University; 2017. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1911/96073.
Council of Science Editors:
Huang B. Decoding biological gene regulatory networks by quantitative modeling. [Doctoral Dissertation]. Rice University; 2017. Available from: http://hdl.handle.net/1911/96073

Rice University
27.
Lin, Ka Wai.
Insulin Signaling & Hypoxic Response in Brain Cancer.
Degree: PhD, Engineering, 2015, Rice University
URL: http://hdl.handle.net/1911/108004
► Glioblastoma patient survival rate has stagnated for the past 30 years, with median survival time less than 1 year. Only 20% of the young (0-19…
(more)
▼ Glioblastoma patient survival rate has stagnated for the past 30 years, with median survival time less than 1 year. Only 20% of the young (0-19 years old) glioblastoma patients survive past 5 years, and this number drops to just less than 5% for patients above 40 years old. Due to poor survival rate of glioblastoma patients, there is a pressing need to develop more effective treatment methods.
In this project, we investigated the effects of the insulin signaling pathway on the glioblastoma growth. Glioblastoma growth has been shown to be promoted by three key molecular signaling factors: IGFI, IGFBP2 and HIF1α. We used both the current literature data and our own experimental data to understand the interactions between these molecular factors on glioblastoma growth via a mathematical model. The model predicted that the activation of HIF1α by IGFBP2 is a crucial driver in the glioblastoma growth. We then used in vitro experiments to validate the findings of the model, and to further explore the response of glioblastoma progression by the stimulation of IGFBP2 and IGFI.
This research demonstrates how IGFI and IGFBP2 influence glioblastoma growth, and suggest that future research should investigate the effects of both IGFI and IGFBP2 to control the glioblastoma progression system as a whole.
Advisors/Committee Members: Qutub, Amina A (advisor).
Subjects/Keywords: Glioblastoma; Computational Modeling; Insulin Signaling; Hypoxic Response
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Lin, K. W. (2015). Insulin Signaling & Hypoxic Response in Brain Cancer. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/108004
Chicago Manual of Style (16th Edition):
Lin, Ka Wai. “Insulin Signaling & Hypoxic Response in Brain Cancer.” 2015. Doctoral Dissertation, Rice University. Accessed April 16, 2021.
http://hdl.handle.net/1911/108004.
MLA Handbook (7th Edition):
Lin, Ka Wai. “Insulin Signaling & Hypoxic Response in Brain Cancer.” 2015. Web. 16 Apr 2021.
Vancouver:
Lin KW. Insulin Signaling & Hypoxic Response in Brain Cancer. [Internet] [Doctoral dissertation]. Rice University; 2015. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1911/108004.
Council of Science Editors:
Lin KW. Insulin Signaling & Hypoxic Response in Brain Cancer. [Doctoral Dissertation]. Rice University; 2015. Available from: http://hdl.handle.net/1911/108004

Boston University
28.
Vogel, Adam Tyler.
A tool for the in vivo gating of gene expression in neurons using the co-occurrence of neural activity and light.
Degree: PhD, Computational Neuroscience, 2020, Boston University
URL: http://hdl.handle.net/2144/41105
► Advancements in genetically based technologies have begun to allow us to better understand the relationships between underlying neural activity and the patterns of measurable behavior…
(more)
▼ Advancements in genetically based technologies have begun to allow us to better understand the relationships between underlying neural activity and the patterns of measurable behavior that can be reproducibly studied in the laboratory. As this field develops, there are key limitations to the currently available technologies hindering their full potential to deliver meaningful datasets. The limitations which are most critical to advancement of these technologies in behavioral neuroscience are: the temporal resolution at which physiological events can be windowed, the divergent molecular pathways in signal transduction that introduce ambiguity into the output of activity sensors, and the impractical size of the tool’s genetic material—requiring 3-4 separate AAV vectors to deliver a fully functional system into a cell. To address these limitations and help bring the potential of these types of technologies into better realization, we have engineered a nucleus localized light-sensitive Ca2+-dependent gene expression system based on AsLOV2 and the downstream responsive element antagonist modulator (DREAM). The design and engineering of each component was performed in such a way to: 1) preserve behaviorally relevant temporal dynamics, 2) preserve signal fidelity appropriate for studying experience-driven neural activity patterns and their relationship to specific animal responses, and 3) have full delivery of the system’s genetic material via a single AAV vector. The system was tested in vitro and subsequently in vivo with neural activity induced by Channelrhodopsin, and could be used in the future with behaviorally-driven neural activity. To our knowledge this is the first optogenetic tool for the practical use of linking activity-dependent gene activation in response to direct nuclear calcium transduction.
Advisors/Committee Members: Russek, Shelley J. (advisor), Hasselmo, Michael (advisor).
Subjects/Keywords: Neurosciences; Biotechnology; Computational modeling; Genetic engineering; Neuroscience
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Vogel, A. T. (2020). A tool for the in vivo gating of gene expression in neurons using the co-occurrence of neural activity and light. (Doctoral Dissertation). Boston University. Retrieved from http://hdl.handle.net/2144/41105
Chicago Manual of Style (16th Edition):
Vogel, Adam Tyler. “A tool for the in vivo gating of gene expression in neurons using the co-occurrence of neural activity and light.” 2020. Doctoral Dissertation, Boston University. Accessed April 16, 2021.
http://hdl.handle.net/2144/41105.
MLA Handbook (7th Edition):
Vogel, Adam Tyler. “A tool for the in vivo gating of gene expression in neurons using the co-occurrence of neural activity and light.” 2020. Web. 16 Apr 2021.
Vancouver:
Vogel AT. A tool for the in vivo gating of gene expression in neurons using the co-occurrence of neural activity and light. [Internet] [Doctoral dissertation]. Boston University; 2020. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/2144/41105.
Council of Science Editors:
Vogel AT. A tool for the in vivo gating of gene expression in neurons using the co-occurrence of neural activity and light. [Doctoral Dissertation]. Boston University; 2020. Available from: http://hdl.handle.net/2144/41105
29.
Stafford, William Tucker.
Geospatial Assessment of Port Infrastructure and Computational Modeling of Coastal Disasters.
Degree: M.S. in Engineering Science, Civil Engineering, 2017, University of Mississippi
URL: https://egrove.olemiss.edu/etd/1296
► The research began with a review of recent natural disasters in the U.S. that showed there was an average of 121 federally declared disasters per…
(more)
▼ The research began with a review of recent natural disasters in the U.S. that showed there was an average of 121 federally declared disasters per year. Ports are critical to every country because they allow for the transport of commodities through that country and even internationally. If a natural disaster were to strike a port that was not properly prepared, the port would not only suffer, but the commodities that transported through there would be affected as well. The major motivation for this thesis was to address the risk of coastal disasters posed to people and critical infrastructure for port cities. The primary objective is to use remote sensing data and geospatial analysis to simulate coastal disasters for mapping risks to communities and infrastructure assets. The research included computer simulations of 2 m sea level rise (SLR) and 2 m tsunami wave surge using the Center for Advanced Infrastructure Technology (CAIT) methodologies, as well as an extreme rainfall simulation. Case studies involved geospatial mapping of infrastructure planimetrics of selected areas. The planimetric method using the Landsat-8 multispectral satellite imagery, the L-BANS surface classification, and the 2011 National Land Cover Database (NLCD) were implemented to determine an efficient method for identifying and mapping the built infrastructure, land use features and non-built areas. The study sites included the greater metropolitan area of Los Angeles, the Port of Miami and surrounding areas, and the Port of Gwadar and surrounding areas. The result showed that spatial mapping using L-BANS is more efficient than the manual creation of planimetrics using geospatial analysis for mapping and identifying the critical infrastructure of coastal cities and ports. However, by the NLCD (2011) for Los Angeles which was available through the United States Geological Survey (USGS), it was determined to be more efficient and faster to generate the land use and land cover features. Spatial maps of digital elevation models (DEM) for the three study sites were obtained to create elevation maps that were used for performing the two simulations methods of 2 m SLR, and 2 m tsunamis wave peak height (WPH). An analysis of variance (ANOVA) was conducted to determine if three periods (1900 – 1970, 1971 – 2000, 2001 -2015) seen in record occurrences of natural disasters were statistically significant. The ANOVA found that the three periods were statistically significantly different and a rate of change analysis was performed. The investigation found that the period of 2001 to 2015 had a 45.8% rate of decrease from the previous period of 1971 to 2000. The ANOVA was also performed to determine if there were any statistically significant difference between the means of the two simulation methods and the means from the three study sites. The results showed that statistically significant differences exist among the study sites and there is no statistically significant difference between the two simulation methods. Further simulations, for…
Advisors/Committee Members: Waheed Uddin.
Subjects/Keywords: Coastal Disasters; Computational Modeling; Geospatial; Infrastructure; Engineering
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Stafford, W. T. (2017). Geospatial Assessment of Port Infrastructure and Computational Modeling of Coastal Disasters. (Thesis). University of Mississippi. Retrieved from https://egrove.olemiss.edu/etd/1296
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):
Stafford, William Tucker. “Geospatial Assessment of Port Infrastructure and Computational Modeling of Coastal Disasters.” 2017. Thesis, University of Mississippi. Accessed April 16, 2021.
https://egrove.olemiss.edu/etd/1296.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Stafford, William Tucker. “Geospatial Assessment of Port Infrastructure and Computational Modeling of Coastal Disasters.” 2017. Web. 16 Apr 2021.
Vancouver:
Stafford WT. Geospatial Assessment of Port Infrastructure and Computational Modeling of Coastal Disasters. [Internet] [Thesis]. University of Mississippi; 2017. [cited 2021 Apr 16].
Available from: https://egrove.olemiss.edu/etd/1296.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Stafford WT. Geospatial Assessment of Port Infrastructure and Computational Modeling of Coastal Disasters. [Thesis]. University of Mississippi; 2017. Available from: https://egrove.olemiss.edu/etd/1296
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Missouri – Columbia
30.
Pendyam, Sandeep.
Computational models of neuronal fear and addiction circuits.
Degree: 2011, University of Missouri – Columbia
URL: https://doi.org/10.32469/10355/14516
► [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Computational Neuroscience provides tools to abstract and generalize principles of neuronal functions using mathematics,…
(more)
▼ [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.]
Computational Neuroscience provides tools to abstract and generalize principles of neuronal functions using mathematics, with applicability to the entire neuroscience spectrum. Subcircuits related to fear and addiction are considered at three levels, network, cellular and intracellular levels. In the area of fear learning, we developed biophysically realistic network models for two regions of the fear circuit. We first developed a
computational network model of the lateral amygdala (LA) region, and investigated how two different types of cell populations formed in LAd after auditory fear conditioning. Next, we developed a
computational model of another critical element of the fear circuit, the prelimbic cortex and linked it with a model of the basal amygdala, to investigate how these two structures worked together to modulate fear expression. Since malfunction in the fear circuit is thought to underlie the pathology of post traumatic stress (PTSD) and other anxiety disorders, such models could potentially provide ideas and approaches for the development of new medications. For cocaine addiction, we developed a cellular level model of neurotransmitter homeostasis around a cortico-accumbal synapse which undergoes enduring changes after drug abuse. We then propose ideas for the development of the associated intracellular pathways for such synapses. Understanding the mechanisms involved in neurotransmitter homeostasis and in LTP/LTD can shed light on the specific targets for potential development of effective pharmacotherapy for cocaine addiction.
Advisors/Committee Members: Nair, Satish S., 1960- (advisor).
Subjects/Keywords: neuronal functions; subcircuits; computational modeling; anxiety disorder
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Pendyam, S. (2011). Computational models of neuronal fear and addiction circuits. (Thesis). University of Missouri – Columbia. Retrieved from https://doi.org/10.32469/10355/14516
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):
Pendyam, Sandeep. “Computational models of neuronal fear and addiction circuits.” 2011. Thesis, University of Missouri – Columbia. Accessed April 16, 2021.
https://doi.org/10.32469/10355/14516.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Pendyam, Sandeep. “Computational models of neuronal fear and addiction circuits.” 2011. Web. 16 Apr 2021.
Vancouver:
Pendyam S. Computational models of neuronal fear and addiction circuits. [Internet] [Thesis]. University of Missouri – Columbia; 2011. [cited 2021 Apr 16].
Available from: https://doi.org/10.32469/10355/14516.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Pendyam S. Computational models of neuronal fear and addiction circuits. [Thesis]. University of Missouri – Columbia; 2011. Available from: https://doi.org/10.32469/10355/14516
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
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