SURF alumni

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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.


  • 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)


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


  • 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


  • 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


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


  • 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


  • 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


  • 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'


  • 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


  • 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


  • 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


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


  • 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


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


  • 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)


  • 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


  • 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


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


  • Lyle Chamberlain
  • Megha Watagalu
  • Japeck Tang


  • Gary Fay


  • Henry Choi
  • Asif Khalak
  • Steven Rhee


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