Pierce, Niles A.

Committee Member — 69 thesises

• Monro, John Anderson — A Super-Algebraically Convergent, Windowing-Based Approach to the Evaluation of Scattering from Periodic Rough Surfaces (2008, Dissertation (Ph.D.))
• Pahlevan, Niema Mohammed — A Systems Approach to Cardiovascular Health and Disease with a Focus on Aortic Wave Dynamics (2013, Dissertation (Ph.D.))
• Cheng, Lixue — Accurate and Transferable Molecular-Orbital-Based Machine Learning for Molecular Modeling (2022, Dissertation (Ph.D.))
• Hom, Geoffrey Kai Tong — Advances in Computational Protein Design: Development of More Efficient Search Algorithms and their Application to the Full-Sequence Design of Larger Proteins (2005, Dissertation (Ph.D.))
• Shah, Premal S. — Advances in Force Field Development and Sequence Optimization Methods for Computational Protein Design (2005, Dissertation (Ph.D.))
• Othmer, Jonathan Andrew — Algorithms for Mapping Nucleic Acid Free Energy Landscapes (2009, Dissertation (Ph.D.))
• Zadeh, Joseph N. — Algorithms for Nucleic Acid Sequence Design (2010, Dissertation (Ph.D.))
• Bois, Justin S. — Analysis of Interacting Nucleic Acids in Dilute Solutions (2007, Dissertation (Ph.D.))
• Dirks, Robert Michael — Analysis, Design, and Construction of Nucleic Acid Devices (2005, Dissertation (Ph.D.))
• Huang, Jining — Applications of Dynamic Nucleic Acid Nanotechnology in Closed-Loop Genetic Circuits and Detection of Viral Pathogens (2023, Dissertation (Ph.D.))
• Ginis, Roman — Automating Resource Management for Distributed Business Processes (2002, Dissertation (Ph.D.))
• Woo, Sungwook — Beyond Watson and Crick: Programming the Self-Assembly and Reconfiguration of DNA Nanostructures Based on Stacking Interactions (2013, Dissertation (Ph.D.))
• Wu, David Dah-wei — Biomechanical Information Transfer: Maximum Caliber, λ Genome Ejection Dynamics, and the Formation of Otoliths in Zebrafish (2010, Dissertation (Ph.D.))
• Greenberg, Andrei Yakovlevich — Chebyshev Spectral Method for Singular Moving Boundary Problems with Application to Finance (2003, Dissertation (Ph.D.))
• Ortiz-Muñoz, Andrés — Combinatorics and Stochasticity for Chemical Reaction Networks (2022, Dissertation (Ph.D.))
• Gonzalvo i Ulla, Marta — Computational Methods for Nucleic Acid Structure Prediction and G Protein-Coupled Receptor Mechanism Investigation (2025, Dissertation (Ph.D.))
• Fornace, Mark Evan — Computational Methods for Simulating and Parameterizing Nucleic Acid Secondary Structure Thermodynamics and Kinetics (2022, Dissertation (Ph.D.))
• Alvizo, Oscar — Computational Protein Design Force Field Optimization: A Negative Design Approach (2007, Dissertation (Ph.D.))
• Wannier, Timothy Milton — Computationally Guided Monomerization of Red Fluorescent Proteins of the Class Anthozoa (2015, Dissertation (Ph.D.))
• Hanewich-Hollatz, Mikhail Henning — Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function via Dynamic RNA Nanotechnology (2020, Dissertation (Ph.D.))
• Evans, Constantine Glen — Crystals that Count! Physical Principles and Experimental Investigations of DNA Tile Self-Assembly (2014, Dissertation (Ph.D.))
• Endelman, Jeffrey B. — Design and Analysis of Combinatorial Protein Libraries Created by Site-Directed Recombination (2005, Dissertation (Ph.D.))
• Wolfe, Brian Robert — Design and Analysis of Nucleic Acid Reaction Pathways (2014, Dissertation (Ph.D.))
• Baetica, Ania-Ariadna — Design, Analysis, And Computational Methods For Engineering Synthetic Biological Networks (2018, Dissertation (Ph.D.))
• Johnson, Stephanie Lynn — DNA Mechanics and Transcriptional Regulation in the E. coli lac Operon (2012, Dissertation (Ph.D.))
• Zhang, David Yu — Dynamic DNA Strand Displacement Circuits (2010, Dissertation (Ph.D.))
• Hamdouche, Samy — Engineered Antibody and Monobody Domains with T Cell Receptor-Like Selectivity for Tumor Associated Peptide-MHC Antigens (2014, Dissertation (Ph.D.))
• Chen, Zhewei — Engineering Conditional Guide RNAs for Cell-Selective Regulation of CRISPR/Cas9 (2023, Dissertation (Ph.D.))
• Zou, Olivia Aoli — Engineering DNA liquids Towards Macroscopic Separation of Biomolecules (2026, Dissertation (Ph.D.))
• Beisel, Chase Lawrence — Engineering Ligand Control of RNA Interference (2009, Dissertation (Ph.D.))
• Schwarzkopf, Ma'ayan — Engineering Nucleic Acid Mechanisms for Regulation and Readout of Gene Expression: Conditional Dicer Substrate Formation and Sensitive Multiplexed Northern Blots (2013, Dissertation (Ph.D.))
• Porubsky, Nicholas James — Enhanced Algorithms for Analysis and Design of Nucleic Acid Reaction Pathways (2020, Dissertation (Ph.D.))
• Guareschi, Matteo Michele — Enriching Architectures for Biosensing and Motor-Filament Systems Through the Programmability of DNA (2025, Dissertation (Ph.D.))
• Hyde, Edward McKay — Fast, High-Order Methods for Scattering by Inhomogeneous Media (2003, Dissertation (Ph.D.))
• McHale, Kevin L. — Feedback Tracking and Correlation Spectroscopy of Fluorescent Nanoparticles and Biomolecules (2008, Dissertation (Ph.D.))
• Zollars, Eric Stafford — Force Field Development in Protein Design (2006, Dissertation (Ph.D.))
• Johnson, Robert Francis — Formal Design and Analysis for DNA Implementations of Chemical Reaction Networks (2020, Dissertation (Ph.D.))
• Trivedi, Vikas — From Molecules to Organs : Microscopy and Multi-Scale Nature of Development (2015, Dissertation (Ph.D.))
• McCardell, Reed Dillard — Genetic Circuits for the Control of Multi-Strain Bacterial Populations (2021, Dissertation (Ph.D.))
• Lyon, Mark Edward — High-Order Unconditionally-Stable FC-AD PDE Solvers for General Domains (2009, Dissertation (Ph.D.))
• Davidson, Samuel Ryan — Localized Catalytic DNA Circuits for Integrated Information Processing in Molecular Machines (2025, Dissertation (Ph.D.))
• Chaubell, Mario Julián — Low-Coherence Interferometric Imaging: Solution of the One-Dimensional Inverse Scattering Problem (2004, Dissertation (Ph.D.))
• Husain, Naeem Shahab — Mapping mRNA and Protein Expression with High Signal-to-Background in Diverse Organisms (2016, Dissertation (Ph.D.))
• Stredie, Valentin Gabriel — Mathematical Modeling and Simulation of Aquatic and Aerial Animal Locomotion (2005, Dissertation (Ph.D.))
• Sun, Bing — Mechanistic Studies of Reactions at the Single-Molecule Level using Microfluidics with Applications in Molecular Diagnostics (2014, Dissertation (Ph.D.))
• Kastner, Jason Christopher — Modeling a Hox Gene Network: Stochastic Simulation with Experimental Perturbation (2003, Dissertation (Ph.D.))
• Pandey, Ayush — Modeling Frameworks for Modular and Scalable Biological Circuit Design (2024, Dissertation (Ph.D.))
• Acharya, Aneesh — Multiplexed Analysis of Diverse RNA Classes via Hybridization Chain Reaction (2016, Dissertation (Ph.D.))
• Hoffmann, Magnus Adrian Gero — Nanoparticle Technologies to Cure and Prevent Infectious Diseases (2022, Dissertation (Ph.D.))
• Schulte, Samuel Jordan — 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 (2023, Dissertation (Ph.D.))
• Savela, Emily Sue — Nucleic Acid Measurements for Antibiotic Susceptibility Testing and Early Detection of SARS-CoV-2 (2022, Dissertation (Ph.D.))
• Craciun, Bogdan — Phase Boundary Propagation in Heterogeneous Media (2002, Dissertation (Ph.D.))
• Forster, Robert Burke — Population Dynamics in the Presence of Quasispecies Effects and Changing Environments (2006, Dissertation (Ph.D.))
• Ren, Xinying (Cindy) — Principles for Designing Robust and Stable Synthetic Microbial Consortia (2021, Dissertation (Ph.D.))
• Choi, Harry Ming Tak — Programmable In Situ Amplification for Multiplexed Bioimaging (2010, Dissertation (Ph.D.))
• Srinivas, Niranjan — Programming Chemical Kinetics: Engineering Dynamic Reaction Networks with DNA Strand Displacement (2015, Dissertation (Ph.D.))
• Feldmann, Michael Todd — Quantum Monte Carlo: Quest to Get Bigger, Faster, and Cheaper (2002, Dissertation (Ph.D.))
• Spakowitz, Andrew James — Semiflexible Polymers: Fundamental Theory and Applications in DNA Packaging (2005, Dissertation (Ph.D.))
• Shur, Andrey Sergeyvich — Serine Integrase-Based Event Recording in E. coli (2022, Dissertation (Ph.D.))
• Sternberg, Jonathan Ben-Zion — Signal Transduction with Hybridization Chain Reactions (2013, Dissertation (Ph.D.))
• Latini, Marco — Simulations and Analysis of Two- and Three-Dimensional Single-Mode Richtmyer-Meshkov Instability using Weighted Essentially Non-Oscillatory and Vortex Methods (2007, Dissertation (Ph.D.))
• Schaeffer, Joseph Malcolm — Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands (2013, Dissertation (Ph.D.))
• Hsiao, Victoria — Synthetic Circuits for Feedback and Detection in Bacteria (2016, Dissertation (Ph.D.))
• Dabby, Nadine L. — Synthetic Molecular Machines for Active Self-Assembly: Prototype Algorithms, Designs, and Experimental Study (2013, Dissertation (Ph.D.))
• Hochrein, Lisa Marie — Towards Conditional RNAi : Shape and Sequence Transduction with Small Conditional RNAs (2013, Dissertation (Ph.D.))
• Westhead, Andrew Neil — Upscaling for Two-Phase Flows in Porous Media (2005, Dissertation (Ph.D.))
• Strinopoulos, Theofilos — Upscaling Immiscible Two-Phase Flows in an Adaptive Frame (2006, Dissertation (Ph.D.))
• Fetecau, Razvan Constantin — Variational Methods for Nonsmooth Mechanics (2003, Dissertation (Ph.D.))
• Burke, Kelly Suzanne — Visualizing mRNA Translation in situ in Single Cells (2018, Dissertation (Ph.D.))