Browse by Committee Member

Cherry, Kevin Matthew (2024) Molecular Pattern Recognition and Supervised Learning in DNA-Based Neural Networks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/529f-kf62. https://resolver.caltech.edu/CaltechTHESIS:04292024-172707491

Kiliç, Kordağ Mehmet (2024) On the Complexity of Neural Network Representations. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/trse-ff38. https://resolver.caltech.edu/CaltechTHESIS:06032024-055145735

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

Raghavan, Guruprasad (2023) Engineering Artificial Systems with Natural Intelligence. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/374f-1202. https://resolver.caltech.edu/CaltechTHESIS:03172023-050019811

Clamons, Samuel Eric (2022) Three Problems in the Design and Specification of Biomolecular Circuits. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/9b4h-8f95. https://resolver.caltech.edu/CaltechTHESIS:09262021-022402778

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

Galstyan, Vahe (2022) Studies in Physical Biology: Exploring Allosteric Regulation, Enzymatic Error Correction, and Cytoskeletal Self-Organization Using Theory and Modeling. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/1fzr-1240. https://resolver.caltech.edu/CaltechTHESIS:08242021-212959886

Ortiz-Muñoz, Andrés (2022) Combinatorics and Stochasticity for Chemical Reaction Networks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/s9mc-3d59. https://resolver.caltech.edu/CaltechTHESIS:04182022-222416729

Poole, William (2022) Compilation and Inference with Chemical Reaction Networks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/x3qc-je74. https://resolver.caltech.edu/CaltechTHESIS:11102021-210013472

Xiao, Fangzhou (2022) Biocontrol of Biomolecular Systems: Polyhedral Constraints on Binding's Regulation of Catalysis from Biocircuits to Metabolism. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/rtwq-v497. https://resolver.caltech.edu/CaltechTHESIS:05302022-235732314

Parkin, James Michael (2021) Signal Amplification in Synthetic Bacterial Communication. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/50p8-bd89. https://resolver.caltech.edu/CaltechTHESIS:03262021-160841703

Ross, Tyler David (2021) Guiding Self-Organization in Active Matter with Spatiotemporal Boundary Conditions. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/q85h-j730. https://resolver.caltech.edu/CaltechTHESIS:07082020-113341068

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

Jain, Siddharth (2019) Decoding the Past. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/K286-5N63. https://resolver.caltech.edu/CaltechTHESIS:04032019-102853075

Singhal, Vipul (2019) Modeling, Computation, and Characterization to Accelerate the Development of Synthetic Gene Circuits in Cell-Free Extracts. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/g31j-ch52. https://resolver.caltech.edu/CaltechTHESIS:08262018-213846283

Petersen, Philip Fai (2018) Engineering Molecular Self-assembly and Reconfiguration in DNA Nanostructures. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/7FXP-8402. https://resolver.caltech.edu/CaltechTHESIS:05312018-112853523

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

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

Jones, Daniel Lawson III (2014) Sequence-Function Relationships in E. coli Transcriptional Regulation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/4J7V-WD59. https://resolver.caltech.edu/CaltechTHESIS:06022014-165211576

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

Chandra, Fiona Adriani (2013) Limits and Tradeoffs in the Control of Autocatalytic Systems. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z1BQ-ZX85. https://resolver.caltech.edu/CaltechTHESIS:06032013-143158080

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

Wang, Zhiying (2013) Coding for Information Storage. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/TFHZ-RW88. https://resolver.caltech.edu/CaltechTHESIS:05312013-123819501

Weir, Peter Thomas (2013) Polarization-Based Navigation in Drosophila. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/3VXQ-TE73. https://resolver.caltech.edu/CaltechTHESIS:07242012-154851161

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

Zhou, Hongchao (2013) Randomness and Noise in Information Systems. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/82KV-2H11. https://resolver.caltech.edu/CaltechTHESIS:07122012-141803264

Franco, Elisa (2012) Analysis, Design, and in vitro Implementation of Robust Biochemical Networks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/1C3S-FA59. https://resolver.caltech.edu/CaltechTHESIS:10192011-161454857

Levine, Joseph H. (2012) Genetic Regulatory Circuit Dynamics: Analysis and Synthesis. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/35A7-K421. https://resolver.caltech.edu/CaltechTHESIS:06052012-121432503

Liang, Joe Chih Yao (2012) High-Throughput Strategies for the Scalable Generation of RNA Component Functions. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/FQHC-EW36. https://resolver.caltech.edu/CaltechTHESIS:01312012-154032563

Rolfe, Jason Tyler (2012) Intrinsic Gradient Networks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/YCB7-7X24. https://resolver.caltech.edu/CaltechTHESIS:04202012-133210844

Stetson, Robert Chess Abernathy (2012) Interaction of Planning Regions in Cortex. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/VGS7-PZ20. https://resolver.caltech.edu/CaltechTHESIS:05262012-075609487

Hariadi, Rizal Fajar (2011) Non-Equilibrium Dynamics of DNA Nanotubes. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/6GQW-YG26. https://resolver.caltech.edu/CaltechTHESIS:06062011-122322347

Pascal, Tod Augustin (2010) New Approaches to Accurate Predictions of Free Energies: From Proteins to Organic Nanostructures. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/P0JH-QM60. https://resolver.caltech.edu/CaltechTHESIS:10262009-204842274

Shen, Kai (2010) Neural Encoding of Mixtures and Stimulus Generation in the Insect Brain. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/MDZC-0J48. https://resolver.caltech.edu/CaltechTHESIS:09122010-130333994

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

Cohen, Justin Delgado (2009) Programming Protein Patterns on DNA Nanostructures with Pyrrole-Imidazole Polyamides. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/CZ2K-MJ03. https://resolver.caltech.edu/CaltechETD:etd-11232008-171327

Cox, Robert Sidney, III (2008) Transcriptional Regulation and Combinatorial Genetic Logic in Synthetic Bacterial Circuits. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/KRW6-DH88. https://resolver.caltech.edu/CaltechETD:etd-03042008-130011

Dunlop, Mary Julia (2008) Dynamics and Correlated Noise in Gene Regulation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/AC8V-6S05. https://resolver.caltech.edu/CaltechETD:etd-05302008-141602

Soloveichik, David (2008) Molecules Computing: Self-Assembled Nanostructures, Molecular Automata,and Chemical Reaction Networks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/ZGE0-AF38. https://resolver.caltech.edu/CaltechETD:etd-05292008-142339

Beierholm, Ulrik Ravnsborg (2007) Bayesian Modeling of Sensory Cue Combinations. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/K89B-XW75. https://resolver.caltech.edu/CaltechETD:etd-05212007-172639

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

Jayaraman, Vivek (2007) Neural Circuit Dynamics and Ensemble Coding in the Locust and Fruit Fly Olfactory System. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/A4VB-6C23. https://resolver.caltech.edu/CaltechETD:etd-05192007-195030

Kim, Jongmin (2007) In Vitro Synthetic Transcriptional Networks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Q9YA-N192. https://resolver.caltech.edu/CaltechETD:etd-12182006-115817

Schulman, Rebecca Beth (2007) The Self-Replication and Evolution of DNA Crystals. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/3F8C-9D50. https://resolver.caltech.edu/CaltechETD:etd-04302007-164103

Teal, Tracy Kristin (2007) Studies of the Spatial Organization of Metabolism in Shewanella oneidensis and Pseudomonas aeruginosa Biofilms. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/2gdf-yh13. https://resolver.caltech.edu/CaltechETD:etd-05312007-190155

Christianson, Gestur Björn (2006) Information Processing in the Interaural Time Difference Pathway of the Barn Owl. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/3WJJ-7294. https://resolver.caltech.edu/CaltechETD:etd-11212005-110457

Drummond, David Allan (2006) Misfolding Dominates Protein Evolution. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/DH8E-2N10. https://resolver.caltech.edu/CaltechETD:etd-06022006-154329

Mihalas, Stefan (2006) Quantitative Model of Calcium/Calmodulin- Dependent Protein Kinase II Activation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/d0zv-g984. https://resolver.caltech.edu/CaltechETD:etd-06052006-142955

Papadantonakis, Karl Spyros (2006) Rigorous Analog Verification of Asynchronous Circuits. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/4R8F-WF03. https://resolver.caltech.edu/CaltechETD:etd-01132006-152609

Cook, Matthew M. (2005) Networks of Relations. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/CVKM-D684. https://resolver.caltech.edu/CaltechETD:etd-06032005-140944

Hart, Christopher Edward (2005) Inferring Genetic Regulatory Network Structure: Integrative Analysis of Genome-Scale Data. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/2JXP-3G71. https://resolver.caltech.edu/CaltechETD:etd-03152005-110423

Riedel, Marcus D. (2004) Cyclic Combinational Circuits. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/410B-XR25. https://resolver.caltech.edu/CaltechETD:etd-05032004-153842

Schkolne, Steven (2004) 3-D Interfaces for Spatial Construction. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/8VWJ-TX38. https://resolver.caltech.edu/CaltechETD:etd-05272004-003252