subject:(computational modeling)

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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: computational modeling

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APA (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: Lignin; Computational modeling

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APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: computational fluid dynamics; turbulence modeling

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APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: Memory; Dissociation; Amnesia; Computational modeling

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APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: biophysics; myxobacteria; simulation; computational modeling

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APA (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: Computational Modeling; Physics; Education

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APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: Computational efficiency; DNA; Modeling; Molecular Dynamics

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APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: Computational modeling; Syntactic locality; Cognitive constraints

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APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: macromolecular modeling; computational biology; strutural biology

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APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: Allophone; Phonological Rules; Statistical Learning; Computational Modeling

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APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: computational biology; predictive inference; statistical modeling; bioinformatics

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APA (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: Glioblastoma; Computational Modeling; Insulin Signaling; Hypoxic Response

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APA (6^th 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 (16^th 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 (7^th 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)

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 (6^th 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 (16^th 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 (7^th 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 (6^th 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 (16^th 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 (7^th 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)

Subjects/Keywords: neuronal functions; subcircuits; computational modeling; anxiety disorder

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APA (6^th 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 (16^th 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 (7^th 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

Open Access Theses and Dissertations