SURF alumni

This page contains a list of the SURF students who have worked with me over the years. This list is not complete, so if you see a name that is missing, please let me know.

2021

• Victoria Chen (Caltech BE)
• Halle Holzbauer (Caltech BE)
• Joshua Ibrahim (U. Pennsylvania)
• Hannah Lim (Cornell)
• Pranay Satya (Caltech BE)
• Christian Stromberger (Caltech CS)
• Bridget Yang (Caltech BE)

2020

• Giovanna Amorim (U. Maryland)
• Tom Andersson (Lund U.)
• Albert Anis (Lund U.) - Synthetic Cell
• Peter Birmingham (U. South Carolina) - Synthetic Cell
• Victoria Chen (Caltech BE)
• Berlin Del Aguila (Humbolt State)
• Ayush Blindish (India) - Synthetic Cell
• Agrima Deedwania (India) - Synthetic Cell
• Bruno Freeman (Caltech CS/Ma)
• Joe Peterson (U. Minnesota)
• Ankita Roychoudhury (Caltech BE) - Synthetic Cell
• Nazmus Saadat (Oxford) - Synthetic Cell
• Jere Susas (Cal State Northridge) - Synthetic Cell
• Katherine Pan (BE)

2019

• Ann Caplin (Caltech)
• Victoria Chen (Caltech)
• Ludvig Doeser (Sweden)
• Leah Keiser (Northwestern)
• Filip Kronström (Sweden)
• Lillian Parr (William and Mary)
• James Walker (Caltech)

2018

• Emanuel Flores (Mexico) - Characterization of the lifetime of bacterial synthetic circuits
• Steve Guo (Caltech) - Contract-based design of control snystems
• Elin Larsson (Sweden) - Engineering metabolic cross-feeding relationships for robust microbial consortia
• Leah Keiser (Northwestern) - Designing a module for cell death
• Filip Claesson (Sweden) - Design and implementation of a controller to advance in multi-lane traffic similar to human behavior using control improvisation
• Sanjana Kulkarni (Caltech) - Building event recorder circuits in Bacillus subtilis that record sequence and magnitude of cell death by integrating DNA released by lysed Escherichia coli
• John Lee (Harvey Mudd, VURP) - River mapping with autonomous surface vehicles for flood hazard monitoring
• Harman Mehta (India) - Modeling the effect of intracellular signaling mechanisms on population dynamic behaviors in the context of paradoxical signaling
• Sannat Mengi (India) - Resource usage in TX-TL
• Rebecka Winqvist (Sweden) - Test design based on model mismatch for controlled systems

2017

• Swati Agrawal (IIT Delhi) - Synthetic modules for control of bacterial growth
• Rijad Alisic (Sweden) - Robust Synthesis from Temporal Logic Specifications
• Joy Doong (UC Davis) - Length and time scales of cell-cell signaling circuits in agar
• Miroslav Gasparek (United Kingdom) - Mathematical and computational modeling of simple artificial cell and development of general framework for rapid implementation of modularization of its subsystems
• Malin Jonsson (Sweden) - Engineering Communication Circuits for Synthetic Cells
• Kyle Martin - Toward a pH Sensor in Synthetic Circuit Design: Utilizing Acid Resistance Pathways in Enteric Bacteria for Novel Synthetic Gene Circuits
• Hubert Menou (France) - Temporal Logic Control with Integrated Experiment Design

2016

• Andrew Montequin - dCas9-Mediated Transcriptional Regulation in TX-TL
• Alex White - Functionalization of TX-TL Systems for Paper-Based Biosensor Arrays

2015

• Enrique Amaya - Rapid Prototyping of Moderate Complexity Biomolecular Circuits: Bistable Switch
• Divyansh Apurva - Designing Biomolecular Temperature Sensors
• Rafsan Chowdhury - Machine-readable protocols and rapid2 prototyping for synthetic biology research
• Nuno Duarte - Optimal Trajectory Generation under Environmental Uncertainties using Signal Temporal Logic Specifications
• Cody Dunn - Development of Criteria for the Analysis of Bimodal Distributions in Stochastic Biochemical Reaction Networks
• Charlie Erwall - Formal synthesis of switching protocols for estimation and control of aircraft electric power systems
• Marcus Greiff - Machine-readable protocols and rapid-prototyping for synthetic biology research: Implementation of a liquid handling robot
• Riashat Islam - Improved State Estimation for a Resilient Spacecraft Executive
• Sandra Liu - Integration of Behavioral Commands for Improved State Estimation and Control of Pioneer 3-DX for a Resilient Spacecraft
• Xianglin (Flora) Meng - Finding stationary solutions to the chemical master equation by gluing graphs at one or two vertices
• Phuc (Sam) Nguyen - Design Space Exploration of the Violacein Pathway in Escherichia coli Based Transcription Translation Cell-Free System (TX-TL)
• Anushka Rau - Estimating parameters of the TX-TL system to model a genetic bistable switch
• Yuening Zhang - Platform-Based Design for Robotics Applications

2014

• Monique Alkiewicz (iGEM), Implementation of Non-Endogenous Bacterial Quorum Sensing Systems in E. coli
• Anthony Chen (iGEM), Implementation of Non-Endogenous Bacterial Quorum Sensing Systems in E. coli
• Mattias Falt, Invariant Refinement for Receding Horizon Temporal Logic Planning
• Anton Frisk, Rapid prototyping of moderate complexity biomolecular circuits
• Joaquin Gabaldon, Symbolic Verification of Nonlinear Hybrid Systems using Theorem Provers
• Galen Gao (iGEM), Implementation of Non-Endogenous Bacterial Quorum Sensing Systems in E. coli
• Andrew Hou (iGEM), Implementation of Non-Endogenous Bacterial Quorum Sensing Systems in E. coli
• Joon Sik (David) Kim, Invariant Refinement for Receding Horizon Temporal Logic Planning
• Bianca Lepe (iGEM), Implementation of Non-Endogenous Bacterial Quorum Sensing Systems in E. coli
• Pulkit Malik, Rapid prototyping of moderate complexity biomolecular circuits
• Robert Mattila, Improved methods of discretization for temporal logic planning
• Linnea Persson, Switching control synthesis in the presence of uncertainty and general loads for an aircraft electric power system testbed
• Rohit Satija, Fabricating a Toolbox of RNA Thermometers
• Samriddhi Sharma, Symbolic Verification of Nonlinear Hybrid Systems using Theorem Provers
• Ben Wu, Applying Formal Methods to Improve Automated Security Systems
• Yuanyuan (Tina) Xu (iGEM), Implementation of Non-Endogenous Bacterial Quorum Sensing Systems in E. coli
• Tiffany Zhou, Rapid prototyping of moderate complexity biomolecular circuits

2013

• James Bern, Robot Motion Planning with Complex Tasks
• Mattias Falt (LTH), The role of delays in biological systems
• Aurelija Grigonyte (UCL), Characterizing gene expression for different extracts
• Monica Li, Investigating physical methods of protecting linear DNA fragments in cell free expression systems
• Oscar Mickelin (KTH), Synthesis of correct-by-construction control protocols for air management systems of aircraft
• Andrew Ng (WUSTL), Understanding and Quantifying the Effect of Compositional Context on Biocircuit Performance
• Juan Quijano (UANL), Synthetic logic circuits using RNA aptamers
• Rohit Sharma (IIT Dehli), Synthetic biological circuit design implementing protein degradation in-vitro
• Chris Zheng, Experiments with dynamic obstacles and correct-by-construction controllers
• Tiffany Zhou, The costs and benefits of various designs of biochemical 'decision engines'

2012

• Julia Brown (iGEM) - Isolation of Organisms to Degrade Biopolymers
• Giulia Giordano (Udine) - Biomolecular Rate–Regulator Circuits
• Alex Jose - On-the-Fly Task-Level Plan Correction for Planar Mobile Robots in Unknown Environments
• Shaunak Kar (IITG) - Regulation of an In Vitro Transcriptional Network with Target Molecules: A Modular Approach
• Ishan Khetarpal - Analysis and Design of Novel In Vitro Bistable Toggle Switches
• Kathryn Knister (iGEM) - Animated Bacteria and Biofuel Synthesis
• Daisy Lin (iGEM) - Increasing Ethanol Yields by Integrating Proteorhodopsin in Bacterial ATP Production Pathways
• Patrik Lundin (Lund) - Transcriptional Switches on a Biological Breadboard
• Paulo De Souza Motta (FGV, Brazil) - Gene Circuit Interference in Multiple Plasmid Layouts
• Adam Nilsson (Lund) - Diffeomorphism Based Motion Planning for Bootstrapping Vehicles and Robots
• R. Edward Pursifull (iGEM) - Engineering Proteorhodopsin into E. coli to increase Ethanol Production
• Chenxi Qiu (iGEM) - Maximizing Alcohol Production Using Ndh/Nuo Knockouts and Proteorhodopsin in E. coli
• Giulia Ripellino (KTH) - Evolution and Sporulation of Bacillus subtilis in the Presence of Antibiotics
• Robert Rogersten (KTH) - Aircraft Electric Power System Modeling
• Nicholas Spooner (Cambridge) - Evaluation and Benchmarking for Robot Motion Planning Problems Using TuLiP
• Ashley Su (CSULA; iGEM) - Engineering Escherichia coli to Animate in Response to Light
• Huey-Ru (Debra) Tsai (iGEM) - Metabolic Engineering and Construction of Expression Plasmids in Zymomonas mobilis
• Vinayak Viswanadham (UC Berkeley) - Understanding Feedback in Bacterial Toxin-Antitoxin Systems: An In Vitro Approach

2011

• Julia Brown (iGEM) - Bioremediation of Endocrine Disruptors: Isolation of an Endocrine-Disruptor-Degrading Bacterium
• Arjun Chandrasekhar - Simulac: A Stochastic Simulator for Modeling Biomolecular Circuits
• Puikei Cheng (iGEM) - Using E. coli to Bioremediate Endocrine Disrupting Chemicals
• Magnus Håkansson - Bootstrapping Robotic Systems: Implementation and Analysis
• Samuel Jones (Solar Decathlon) - Implementation of Home Planning and Automation Software for Solar Decathlon 2011
• Yuchen Lin - Simulation Interface for Receding Horizon Temporal Logic Planning
• Ishan Khetarpal - Design and Analysis of an in vitro Exact Adapter
• Paul Nguyen - Programmable Genetic Regulation by sRNA-mRNA Hybridization
• Petter Nilsson - State Space Partitioning Algorithm in TuLiP
• Keshav Sapatnekar - Design and Modeling of an Autoinhibiting Biomolecular Circuit Incorporating Scaffolding
• Amanda Shelton (iGEM) - Bioremediation of Endocrine Disrupting Compounds Using the Synthetic Biology BioBrick Standard
• Ka-Chuan Suen (Solar Decathlon) - Gesture Based Interface for Solar Decathlon House
• Nicole Thadani (iGEM) - Bioremediation of Endocrine Disruptors From Water Using Genetically Modified Escherichia coli
• Stephanie Tsuei - Implementation of a Distributed Camera Control Protocol

2010

• Alexandre Boulgakov - iGEM
• Arjun Ravikumar - Construction of an environmental stimulus receptive DNA circuit in a cell-free transcription/translation system
• Brian Ma - iGEM
• Lucas Hartsough - iGEM
• Melissa Xu - iGEM
• Oskar Hjartquist (LTH) - Origins of uncertainty in building synthetic genetic circuits
• Yuehan Huang - iGEM

2009

• Fei Chen (Caltech Bi/EE)
• Chris Sturk (Lund)

2008

• Mariette Annergren (KTH)
• Bjorn Heinbokel
• Karl Murray (KTH)
• Noele Norris (Caltech, EE) - Planning Under Sensing Uncertainty for a Mobile Autonomous Robot
• Ben Prindle (Caltech, ChE)
• Manuel Segura
• Stefan Skoog (Lund University)
• Glenn Wagner (Caltech, ME)
• Kevin Welch

2007

• Humberto Bento Ayres Pereira (U. Porto)
• Magnus Linderoth
• Christopher J. Schantz (Caltech)
• Kristian Soltesz (Lund) - Nonlinear Lateral Control Strategy for Nonholonomic Vehicles

2006

• Jessica N. Austin [Gonzalez] (Caltech)
• Morlan Liu (College of the Canyons)
• Joshua J. Feingold (Caltech)
• Bernardo Maciel (Portugal) - Attention and Awareness for Autonomous Driving
• Humberto Bento Ayres Pereira (Portugal)
• David M. Rosen (Caltech, Ma)
• Jing Shen (Caltech)
• Jose Torres (USC)
• Johan Ugander (Lund)

2005

• Ludo Antonov - Riegl LADAR Linux driver and Sensor Synchronization via Real-Time Kernel Extensions
• Tully Foote - Adrive: Autonomous Driving Software
• Jeremy Gillula - Data Fusion from Multiple Sensors: Real-Time Mapping on an Unmanned Ground Vehicle
• Marie Göransson (Lund) - Measuring Sensor Health in DARPA Grand Challenge
• Rob Grogan - Automotive Failures and Solutions for Autonomous Vehicle Development
• George Hines - Environmental Considerations in a Mobile Computing Facility
• Erik Johannesson (Lund) - Integrated Stereovision for an Autonomous Ground Vehicle
• Tony Kelman - Dynamical Modeling of an Autonomous Ground Vehicle
• Jeremy Leibs - Improvements in State Estimation
• Gustav Lindstrom (Lund) - Road following based on video and LADAR data
• Laura Lindzey - Trajectory Following in Off-Road Desert Terrain
• Lisa Nystrom (Lund) - Online terrain classification for the DARPA Grand Challenge
• Tami Reyda - Development of Gimbaled Sensor Platform and Gimbal Pointing Algorithm
• Dave Rosen - Hierarchical Path Planning in Autonomous Ground Vehicles
• Alex Stewart - Development of a Supervisory Control Architecture for Deterministic System Control of Alice
• Lusann Yang (Princeton) -
• Jason Yosinksi - Terrain Sensing through Analysis of Vehicle State Variables

2004

• Lyle J. Chamberlain
• Meghan R. Crowley
• Jeremy H. Gillula
• Haomiao Huang
• Andrew N. Kwok
• Alexander J. Sutherland
• Jin Xiong
• Henrik Kjellander (Lund)
• Brian Beck (Princeton)
• Jon Gibbs (MIT)
• Hans-Kristian Knudson (Lund)
• Roger Hsiao (UIUC),
• John McNamara
• Randall Ward

2003

• Claire Walton
• Burak Cendek
• Cesar Del Solar
• Michael Yeh
• Denny Chao

2002

• Lyle Chamberlain
• Megha Watagalu
• Japeck Tang

1995

• Gary Fay

1993

• Henry Choi
• Asif Khalak
• Steven Rhee

1992

• Nicky Impert - investigating shape memory alloys for use in biomedical equipment
• Matt Tucker