Browse by Committee Member

2024

Pandey, Ayush (2024) Modeling Frameworks for Modular and Scalable Biological Circuit Design. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/qacp-dw76. https://resolver.caltech.edu/CaltechTHESIS:06062023-021337351

2023

Chen, Zhewei (2023) Engineering Conditional Guide RNAs for Cell-Selective Regulation of CRISPR/Cas9. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/cajs-d417. https://resolver.caltech.edu/CaltechTHESIS:12022022-010002116

Huang, Jining (2023) Applications of Dynamic Nucleic Acid Nanotechnology in Closed-Loop Genetic Circuits and Detection of Viral Pathogens. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/54tw-ym95. https://resolver.caltech.edu/CaltechTHESIS:01172023-195222304

Schulte, Samuel Jordan (2023) New HCR Technologies: 10-Plex Quantitative Spectral Imaging of RNAs and Proteins; Multiplexed Quantitative Imaging of Protein:Protein Complexes; and Sensitive, Instrument-Free, At-Home Pathogen Detection. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/nzk8-2d38. https://resolver.caltech.edu/CaltechTHESIS:06092023-193714022

2022

Cheng, Lixue (2022) Accurate and Transferable Molecular-Orbital-Based Machine Learning for Molecular Modeling. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/cjak-4x38. https://resolver.caltech.edu/CaltechThesis:04012022-153013173

Fornace, Mark Evan (2022) Computational Methods for Simulating and Parameterizing Nucleic Acid Secondary Structure Thermodynamics and Kinetics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/ayeg-at42. https://resolver.caltech.edu/CaltechTHESIS:12212021-202554260

Hoffmann, Magnus Adrian Gero (2022) Nanoparticle Technologies to Cure and Prevent Infectious Diseases. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/g0w1-rc77. https://resolver.caltech.edu/CaltechTHESIS:10302021-184745797

Savela, Emily Sue (2022) Nucleic Acid Measurements for Antibiotic Susceptibility Testing and Early Detection of SARS-CoV-2. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/vp9a-n206. https://resolver.caltech.edu/CaltechTHESIS:10072021-173853251

Shur, Andrey Sergeyvich (2022) Serine Integrase-Based Event Recording in E. coli. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/x4q0-nx18. https://resolver.caltech.edu/CaltechTHESIS:12212021-193826426

2021

McCardell, Reed Dillard (2021) Genetic Circuits for the Control of Multi-Strain Bacterial Populations. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/wgpp-vj97. https://resolver.caltech.edu/CaltechTHESIS:05082021-185615529

Ren, Xinying (Cindy) (2021) Principles for Designing Robust and Stable Synthetic Microbial Consortia. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/hc8x-3280. https://resolver.caltech.edu/CaltechTHESIS:05262021-072231177

2020

Hanewich-Hollatz, Mikhail Henning (2020) Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function via Dynamic RNA Nanotechnology. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/NS2B-DJ96. https://resolver.caltech.edu/CaltechTHESIS:11042019-135312842

Johnson, Robert Francis (2020) Formal Design and Analysis for DNA Implementations of Chemical Reaction Networks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/a74v-kv80. https://resolver.caltech.edu/CaltechTHESIS:04292020-052418975

Porubsky, Nicholas James (2020) Enhanced Algorithms for Analysis and Design of Nucleic Acid Reaction Pathways. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/M8CZ-MW98. https://resolver.caltech.edu/CaltechTHESIS:10062019-213347699

2018

Baetica, Ania-Ariadna (2018) Design, Analysis, And Computational Methods For Engineering Synthetic Biological Networks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/98qt-zv92. https://resolver.caltech.edu/CaltechTHESIS:06042018-171639726

Burke, Kelly Suzanne (2018) Visualizing mRNA Translation in situ in Single Cells. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z92B8W6R. https://resolver.caltech.edu/CaltechTHESIS:07292017-201142545

2016

Acharya, Aneesh (2016) Multiplexed Analysis of Diverse RNA Classes via Hybridization Chain Reaction. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z95M63N0. https://resolver.caltech.edu/CaltechTHESIS:06032016-143422651

Hsiao, Victoria (2016) Synthetic Circuits for Feedback and Detection in Bacteria. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9WD3XJW. https://resolver.caltech.edu/CaltechTHESIS:05082016-170628018

Husain, Naeem Shahab (2016) Mapping mRNA and Protein Expression with High Signal-to-Background in Diverse Organisms. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9DF6P73. https://resolver.caltech.edu/CaltechTHESIS:02252016-123239637

2015

Srinivas, Niranjan (2015) Programming Chemical Kinetics: Engineering Dynamic Reaction Networks with DNA Strand Displacement. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9KD1VVJ. https://resolver.caltech.edu/CaltechTHESIS:06012015-171243593

Trivedi, Vikas (2015) From Molecules to Organs : Microscopy and Multi-Scale Nature of Development. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9SX6B59. https://resolver.caltech.edu/CaltechTHESIS:05292015-080950114

Wannier, Timothy Milton (2015) Computationally Guided Monomerization of Red Fluorescent Proteins of the Class Anthozoa. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9571908. https://resolver.caltech.edu/CaltechTHESIS:01272015-110638252

2014

Evans, Constantine Glen (2014) Crystals that Count! Physical Principles and Experimental Investigations of DNA Tile Self-Assembly. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/7FMK-9403. https://resolver.caltech.edu/CaltechTHESIS:05132014-142306756

Hamdouche, Samy (2014) Engineered Antibody and Monobody Domains with T Cell Receptor-Like Selectivity for Tumor Associated Peptide-MHC Antigens. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9WH2N02. https://resolver.caltech.edu/CaltechTHESIS:06062014-175608943

Sun, Bing (2014) Mechanistic Studies of Reactions at the Single-Molecule Level using Microfluidics with Applications in Molecular Diagnostics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/BT81-YX06. https://resolver.caltech.edu/CaltechTHESIS:05052014-142031176

Wolfe, Brian Robert (2014) Design and Analysis of Nucleic Acid Reaction Pathways. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/G4XZ-ZF47. https://resolver.caltech.edu/CaltechTHESIS:03272014-193400848

2013

Dabby, Nadine L. (2013) Synthetic Molecular Machines for Active Self-Assembly: Prototype Algorithms, Designs, and Experimental Study. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/T0ZG-PA07. https://resolver.caltech.edu/CaltechTHESIS:05122013-221658522

Hochrein, Lisa Marie (2013) Towards Conditional RNAi : Shape and Sequence Transduction with Small Conditional RNAs. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/NTZT-8Q67. https://resolver.caltech.edu/CaltechTHESIS:06072013-160243112

Pahlevan, Niema Mohammed (2013) A Systems Approach to Cardiovascular Health and Disease with a Focus on Aortic Wave Dynamics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9DR2SFM. https://resolver.caltech.edu/CaltechTHESIS:05082013-152249157

Schaeffer, Joseph Malcolm (2013) Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/JEBY-6X69. https://resolver.caltech.edu/CaltechTHESIS:02042013-110332492

Schwarzkopf, Ma'ayan (2013) Engineering Nucleic Acid Mechanisms for Regulation and Readout of Gene Expression: Conditional Dicer Substrate Formation and Sensitive Multiplexed Northern Blots. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z94Q7S0V. https://resolver.caltech.edu/CaltechTHESIS:05212013-161536447

Sternberg, Jonathan Ben-Zion (2013) Signal Transduction with Hybridization Chain Reactions. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z90Z719Z. https://resolver.caltech.edu/CaltechTHESIS:06072013-170244348

Woo, Sungwook (2013) Beyond Watson and Crick: Programming the Self-Assembly and Reconfiguration of DNA Nanostructures Based on Stacking Interactions. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/4NZK-XK58. https://resolver.caltech.edu/CaltechTHESIS:05302013-123041371

2012

Johnson, Stephanie Lynn (2012) DNA Mechanics and Transcriptional Regulation in the E. coli lac Operon. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/W40T-PD39. https://resolver.caltech.edu/CaltechTHESIS:05112012-140027276

2010

Choi, Harry Ming Tak (2010) Programmable In Situ Amplification for Multiplexed Bioimaging. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/K4A3-1K41. https://resolver.caltech.edu/CaltechTHESIS:12292009-170615072

Wu, David Dah-wei (2010) Biomechanical Information Transfer: Maximum Caliber, λ Genome Ejection Dynamics, and the Formation of Otoliths in Zebrafish. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/X454-MV52. https://resolver.caltech.edu/CaltechTHESIS:05182010-213110299

Zadeh, Joseph N. (2010) Algorithms for Nucleic Acid Sequence Design. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/20DG-NF39. https://resolver.caltech.edu/CaltechTHESIS:05112010-205335518

Zhang, David Yu (2010) Dynamic DNA Strand Displacement Circuits. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Q4NR-CH87. https://resolver.caltech.edu/CaltechTHESIS:05262010-173410602

2009

Beisel, Chase Lawrence (2009) Engineering Ligand Control of RNA Interference. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/CBRX-PG36. https://resolver.caltech.edu/CaltechETD:etd-05212009-144705

Lyon, Mark Edward (2009) High-Order Unconditionally-Stable FC-AD PDE Solvers for General Domains. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/3FFW-GK56. https://resolver.caltech.edu/CaltechETD:etd-07312008-102751

Othmer, Jonathan Andrew (2009) Algorithms for Mapping Nucleic Acid Free Energy Landscapes. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/VJX1-6376. https://resolver.caltech.edu/CaltechETD:etd-12312008-153810

2008

McHale, Kevin L. (2008) Feedback Tracking and Correlation Spectroscopy of Fluorescent Nanoparticles and Biomolecules. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/6YYA-9T10. https://resolver.caltech.edu/CaltechETD:etd-05072008-204627

Monro, John Anderson (2008) A Super-Algebraically Convergent, Windowing-Based Approach to the Evaluation of Scattering from Periodic Rough Surfaces. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/F9VM-JP39. https://resolver.caltech.edu/CaltechETD:etd-01032008-222910

2007

Alvizo, Oscar (2007) Computational Protein Design Force Field Optimization: A Negative Design Approach. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/NYVY-7Z76. https://resolver.caltech.edu/CaltechETD:etd-05212007-164114

Bois, Justin S. (2007) Analysis of Interacting Nucleic Acids in Dilute Solutions. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/2JCJ-SX75. https://resolver.caltech.edu/CaltechETD:etd-05242007-211446

Latini, Marco (2007) Simulations and Analysis of Two- and Three-Dimensional Single-Mode Richtmyer-Meshkov Instability using Weighted Essentially Non-Oscillatory and Vortex Methods. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/1397-GZ04. https://resolver.caltech.edu/CaltechETD:etd-12082006-124547

2006

Forster, Robert Burke (2006) Population Dynamics in the Presence of Quasispecies Effects and Changing Environments. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/QHEA-NV73. https://resolver.caltech.edu/CaltechETD:etd-04262006-231415

Strinopoulos, Theofilos (2006) Upscaling Immiscible Two-Phase Flows in an Adaptive Frame. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/AP0P-8S11. https://resolver.caltech.edu/CaltechETD:etd-02192006-165348

Zollars, Eric Stafford (2006) Force Field Development in Protein Design. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/55br-9a21. https://resolver.caltech.edu/CaltechETD:etd-06052006-155305

2005

Dirks, Robert Michael (2005) Analysis, Design, and Construction of Nucleic Acid Devices. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/VZ43-FM66. https://resolver.caltech.edu/CaltechETD:etd-05242005-133116

Endelman, Jeffrey B. (2005) Design and Analysis of Combinatorial Protein Libraries Created by Site-Directed Recombination. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/GF35-Q269. https://resolver.caltech.edu/CaltechETD:etd-06022005-192548

Hom, Geoffrey Kai Tong (2005) Advances in Computational Protein Design: Development of More Efficient Search Algorithms and their Application to the Full-Sequence Design of Larger Proteins. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/M4R9-YM51. https://resolver.caltech.edu/CaltechETD:etd-05302005-223153

Shah, Premal S. (2005) Advances in Force Field Development and Sequence Optimization Methods for Computational Protein Design. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/mg9x-s593. https://resolver.caltech.edu/CaltechETD:etd-04042005-142719

Spakowitz, Andrew James (2005) Semiflexible Polymers: Fundamental Theory and Applications in DNA Packaging. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/GGY2-SZ67. https://resolver.caltech.edu/CaltechETD:etd-11162004-120143

Stredie, Valentin Gabriel (2005) Mathematical Modeling and Simulation of Aquatic and Aerial Animal Locomotion. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/8PWE-RK28. https://resolver.caltech.edu/CaltechETD:etd-05272005-004852

Westhead, Andrew Neil (2005) Upscaling for Two-Phase Flows in Porous Media. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/T7Q0-FG76. https://resolver.caltech.edu/CaltechETD:etd-05252005-085744

2004

Chaubell, Mario Julián (2004) Low-Coherence Interferometric Imaging: Solution of the One-Dimensional Inverse Scattering Problem. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/ED7Y-Q436. https://resolver.caltech.edu/CaltechETD:etd-09092003-212358

2003

Fetecau, Razvan Constantin (2003) Variational Methods for Nonsmooth Mechanics. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/VXBJ-R447. https://resolver.caltech.edu/CaltechETD:etd-05222003-110241

Greenberg, Andrei Yakovlevich (2003) Chebyshev Spectral Method for Singular Moving Boundary Problems with Application to Finance. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/J383-YX41. https://resolver.caltech.edu/CaltechETD:etd-09042002-131120

Hyde, Edward McKay (2003) Fast, High-Order Methods for Scattering by Inhomogeneous Media. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z0V0-KM52. https://resolver.caltech.edu/CaltechETD:etd-08142002-182101

Kastner, Jason Christopher (2003) Modeling a Hox Gene Network: Stochastic Simulation with Experimental Perturbation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/2TWD-EK72. https://resolver.caltech.edu/CaltechETD:etd-10042002-200303

2002

Craciun, Bogdan (2002) Phase Boundary Propagation in Heterogeneous Media. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/JXG6-W865. https://resolver.caltech.edu/CaltechTHESIS:10082010-142653040

Feldmann, Michael Todd (2002) Quantum Monte Carlo: Quest to Get Bigger, Faster, and Cheaper. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/4D4F-WZ34. https://resolver.caltech.edu/CaltechTHESIS:01252012-135136531

Ginis, Roman (2002) Automating Resource Management for Distributed Business Processes. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/9GXT-BD03. https://resolver.caltech.edu/CaltechETD:etd-11012005-093745