News from the Lab

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    Michael Gerten at ASE

    Michael Gerten presented the paper "ChemTest: An Automated Software Testing Framework for an Emerging Paradigm," by Michael C. Gerten, James I. Lathrop, Myra Cohen, and Titus H. Klinge, on September 23, 2020, at the Thirty-fifth IEEE/ACM International Conference on Automated Software Engineering.

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    Posters at DNA

    LAMP had the following two posters at the Twenty-sixth International Conference on DNA Computing and Molecular Programming. 1. Willem Fletcher, a LAMP collaborator at Carleton College) and Matt Rayman presented "New Insights on Real-Time CRN-Computable Numbers," by Willem Fletcher, Titus H. Klinge, James I. Lathrop, and Matthew Rayman. 2. Michael Gerten presented "A Software Testing Framework for Stochastic Chemical Reaction Network Programs," by Michael C. Gerten, James I. Lathrop, Myra B Cohen, and Titus H. Klinge.

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    Hugh Potter Encore at DNA

    Hugh Potter presented the paper "Population-Induced Phase Transitions and the Verification of Chemical Reaction Networks," by James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Hugh D. Potter, and Matthew R. Riley, on September 17, 2020, at the Twenty-sixth International Conference on DNA Computing and Molecular Programming.

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    Hugh Potter at DNA

    Hugh Potter presented the paper "ALCH: An Imperative Language for Chemical Reaction Network-Controlled Tile Assembly," by Titus H. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, and Matthew R. Riley, on September 16, 2020, at the Twenty-sixth International Conference on DNA Computing and Molecular Programming.

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    ALCH Software Posted

    Titus H. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, and Matthew R. Riley released ALCH beta software binaries via this LAMP website.  This software helps users compile and simulate programs on the network-controlled tile assembly model.

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    Distinguished Paper Award at ASE

    The paper "ChemTest: An Automated Software Testing Framework for an Emerging Paradigm," by Michael C. Gerten, James I. Lathrop, Myra Cohen, and Titus H. Klinge, won an ACM SIGSOFT Distinguished Paper Award for the 35th IEEE/ACM International Conference on Automated Software Engineering (September 21-25, 2020).

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    Xiang Huang, Ph.D.

    Xiang Huang successfully defended his Ph.D. thesis, "Chemical Reaction Networks: Computability, Complexity, and Randomness," on August 19, 2020.  Dr. Huang was advised by Jack Lutz and has accepted a position as Assistant Professor of Computer Science at the University of Illinois Springfield.  Congratulations, Xiang!

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    Mikaela Cashman, Ph.D.

    Mikaela Cashman successfully defended her Ph.D. thesis, "Interpretability of Configurable Software in the Biosciences," on May 6, 2020.  Dr. Cashman was advised by Myra Cohen and has accepted a position as a Postdoctoral Researcher at the Oak Ridge National Laboratory.  Congratulations, Mikaela!

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    Sabbatical at Caltech

    Jack Lutz and Robyn Lutz spent the first half of their Spring, 2020, sabbatical visiting Erik Winfree and his molecular programming group at Caltech.  Jack and Robyn planned to spend the second half of the sabbatical at the University of Texas, but the COVID-19 crisis forced them to work from home in Ames instead.

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    Talk at IFIP

    Robyn Lutz gave the talk “Behavioral Modeling of Molecular Programs at Scale”, at the Annual meeting of IFIP (International Federation of Information Processing) 2.9, Working Group on Requirements Engineering, Panama City, Panama, Feb. 9-14, 2020.

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    Paper in TCS

    The paper "Robust Biomolecular Finite Automata," by Titus H. Klinge, James I. Lathrop, and Jack H. Lutz, appeared in the May 16, 2020, issue of Theoretical Computer Science.

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    Talk at JMM

    Jack Lutz gave an invited talk, "Passing Hilbert's Final Test," in the AMS-ASL Special Session on Logic Facing Outward at the Joint Mathematics Meetings, January 15-18, 2020, in Denver, CO.

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    CPS PI Meeting

    Robyn Lutz and Jack Lutz attended the NSF Cyber-Physical Systems Principal Investigators’ Meeting in Arlington, VA, Nov. 21-22, 2019. They presented the poster, James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Hugh D. Potter, and Matthew R. Riley, “Quorum Sensing and Verification in Chemical Reaction Networks.”

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    Talk at UF

    Robyn Lutz visited Tuba Yavuz and gave the talk “Designing Safe Programmed Molecular Systems,” in the ECE Seminar, University of Florida, Nov. 4, 2019.

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    Andrei Migunov at Allerton

    Andrei Migunov presented the paper "Algorithmic Randomness in Continuous-time Markov Chains," by Xiang Huang, Jack H. Lutz, and Andrei N. Migunov, on September 26, 2019, at the Fifty-seventh Annual Allerton Conference on Communication, Control, and Computing.

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    Best Student Paper Award at SPLC

    Mikaela Cashman presented the paper "DNA as Features: Organic Software Product Lines," by Mikaela Cashman, Justin Firestone, Myra B. Cohen, Thammasak Thianniwet, and Wei Niu, at the 23rd International Systems and Software Product Line Conference (SPLC 2019, Paris, France, September 9-13, 2019).  The paper won the Best Student Paper Award at the conference.  Congratulations, Mikaela!

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    Poster at DNA

    Sonia Moreno, Hugh Potter, and Narun Raman presented the poster "ALCH: An Imperative Language for the Chemical Reaction Network-Controlled Tile Assembly Model," by Titus H. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, and Matthew R. Riley, at the Twenty-fifth International Conference on DNA Computing and Molecular Programming in Seattle, WA, August 5-9, 2019.

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    Best Student Presentation at DNA

    Xiang Huang won the ISNSCE Best Presentation Award for his presentation of the paper "Real-Time Equivalence of Chemical Reaction Networks and Analog Computers," by Xiang Huang, Titus H. Klinge, and James I. Lathrop, at the Twenty-fifth International Conference on DNA Computing and Molecular Programming in Seattle, WA, August 5-9, 2019.  Congratulations, Xiang!

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    Talk at ICSE

    Robyn Lutz presented the paper "Robustness and Games Against Nature in Molecular Programming," by Jack H. Lutz, Neil Lutz, Robyn R. Lutz, and Matthew R. Riley, in the New Ideas and Emerging Results track at the Forty-first ACM/IEEE International Conference on Software Engineering in Montréal, CA, May 25-31, 2019.

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    ASL Tutorial

    Jack Lutz gave a two-hour invited tutorial, "Finite-State Information and Randomness," at the North American Annual Meeting of the Association for Symbolic Logic in New York, NY, May 20-23, 2019.

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    Singapore Visit

    Jack and Robyn Lutz visited the National University of Singapore May 5-16, 2019.  Jack gave an invited talk, "Quantifying equidistribution: a survey of finite-state dimensions," as part of his two-week participation in the program, Equidistribution: Arithmetic, Computational and Probabilistic Aspects, hosted by the Institute of Mathematical Sciences at NUS.  Robyn visited David Rosenblum and gave the talk, “Designing Safe Programmed Molecular Systems,” in the NUS School of Computing Computer Science Seminar, May 8, 2019.

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    NSF CAREER Award to David Doty

    LAMP alum David Doty, now at the University of California-Davis, has received a National Science Foundation CAREER Award (2019-2024) for research on "Error-Free, Uniform and Composable Chemical Computation." Congratulations, Dave!

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    Paper in ToSEM

    The paper "Runtime fault detection in programmed molecular systems," by Sam Ellis, Titus Klinge, Jim Lathrop, Jack Lutz, Robyn Lutz, Andy Miner, and Hugh Potter, appeared in ACM Transactions on Software Engineering and Methodology 28 (2019).

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    Georgia Tech Visit

    Robyn Lutz visited Georgia Tech Feb. 26, 2019 to discuss recent work by R. Mangal, Aditya Nori and Alex Orso on probabilistic robustness for neural networks.

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    Talk at IFIP 2.9

    Robyn Lutz gave a talk, "Describing 'Safe & Secure' for Programmed Molecular Systems," at the IFIP 2.9, Requirements Engineering meeting, Feb. 18-22, 2019.

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    USF Visit

    Jack and Robyn Lutz visited Natasha Jonoska at the University of South Florida and discussed molecular programming research February 14-15, 2019. Robyn gave the talk "Describing 'Safe & Secure' for Programmed Molecular Systems" to the Jonoska research group.

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    Paper in Natural Computing

    The paper "Real-time Computability of Real Numbers by Chemical Reaction Networks," by Xiang Huang, Titus Klinge, Jim Lathrop, Xiaoyuan Li, and Jack Lutz, has appeared in Natural Computing 18(2019).

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    Midwest Verification Days

    The group was well represented at the Midwest Verification Days workshop, held this year (its tenth) at the University of Iowa, September 28-29, 2018.   Hugh Potter gave the talk "Runtime fault detection in programmed molecular systems," reporting joint work with Sam Ellis, Titus Klinge, Jim Lathrop, Jack Lutz, Robyn Lutz, and Andy Miner.   Mikaela Cashman gave the talk "BioSIMP: using software testing techniques for sampling and inference in biological organisms," reporting joint work with Jennie Catlett, Myra Cohen, Nicole Buan, Zahmeeth Sakkaff, Max Pierobon, and Christine Kelley.   Josh Wallin gave the talk "Generating system-agnostic runtime verification benchmarks from MLTL formulas," reporting joint work with Kristin Rozier.

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    Keynote at SafeComp

    Robyn Lutz gave a keynote, "Software Engineering for Safety in Programmed Molecular Systems," at the 37th Int'l Conference on Computer Safety, Reliability, and Security, in Västerås, Sweden, Sept. 19, 2018.

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    Tutorial at RE 2018

    Jack Lutz and Robyn Lutz gave a half-­day tutorial, "On Tap: Writing Requirements for Molecular Programs," at the 26th IEEE Int’l Conference on Requirements Engineering, in Banff, Canada, Aug. 21, 2018.

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    CCA conference

    Jack Lutz gave the talk, "Algorithmic Randomness in Chemical Reaction Networks," at the 15th Int'l Conference on Computability and Complexity in Analysis, Lake Kochel, Germany, Aug. 5­-8, 2018. This is joint work with Ph.D. students Xiang Huang and Andrei Migunov.

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    Fields Institute workshop

    Jack Lutz attended the workshop Computability Theory and its Applications at the Fields Institute, Waterloo, Ontario, CA, June 4­-8, 2018.

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    Paper in Natural Computing

    Adam Case, Jack Lutz, and Don Stull's paper, "Reachability Problems for Continuous Chemical Reaction Networks," appeared in Natural Computing 17 (2018).

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    ASL Annual Meeting

    Jack Lutz participated in the Association for Symbolic Logic North American Annual Meeting in Macomb, IL, May 16-­19, 2018.

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    Caltech visit

    Robyn Lutz and Jack Lutz visited the Caltech Rothemund and Winfree Labs April 7-­14, 2018, and attended their joint group meeting with the Qian Lab to discuss new advances in molecular programming.

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    Oberwolfach lecture

    Jack Lutz gave the talk, "Who Asked Us? How the Theory of Computing Answers Questions that Weren't About Computing," at the invitation-only Computability Theory Workshop at the Oberwolfach Research Institute for Mathematics, Oberwolfach-­Walke, Germany, Jan. 7-­13, 2018.

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    NSF CPS PI Meeting

    Robyn Lutz and Jack Lutz attended the NSF Cyber­Physical Systems Principal Investigators' Meeting Nov. 13-14, 2017, in Alexandria, VA. They presented the poster “Logging of States in Deterministic Chemical Reaction Networks” describing work by Samuel Ellis, James Lathrop and Robyn Lutz.

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    Paper at TPNC 2017

    LAMP alum Titus Klinge presented the paper “Robust Combinatorial Circuits in Chemical Reaction Networks”, co-authored with Jim Lathrop and Sam Ellis, at the Sixth International Conference on the Theory and Practice of Natural Computing (TPNC 2017) at Charles University in Prague, December 18-20, 2017.

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    Don Stull, Ph.D.

    Don Stull successfully defended his Ph.D. thesis, “Algorithmic Randomness and Analysis”, on November 17, 2017. Don is now a Postdoctoral Research Fellow at INRIA in Nancy, France.

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    Sam Ellis, Ph.D.

    Sam Ellis successfully defended his Ph.D. thesis, “Devices for Safety-Critical Molecular Programmed Systems”, on November 17, 2017.

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    DNA 23 in Austin

    Xiang Huang, Andrei Migunov, Don Nye, Hugh Potter, Don Stull, Josh Wallin, and Jack Lutz attended the 23rd International Conference on DNA Computing and Molecular Programming (DNA23) at the University of Texas, September 24-28, 2017.

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    Continuous Time in Lisbon

    Jack Lutz visited Félix Costa at the IST University of Lisbon to discuss chemical reaction networks and other continuous-time models of computation.

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    Quantum Dots in Cages

    LAMP alum Divita Mathur (Ph.D. 2016, now a postdoctoral scholar at the U.S. Naval Research Laboratory) is the lead author with A. Samanta, E. Oh, S.A. Díaz, K. Susumu, M.G. Ancona, and I.L. Medintz of the paper "Quantum Dot Encapsulation Using a Peptide-Modified Tetrahedral Cage,"  published in the journal Chemistry of Materials.

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    Paper at RE 2017

    Robyn Lutz presented the paper, “RE at 50, with a focus on the last 25 years,” at the 25th IEEE International Conference on Requirements Engineering (RE’17) in Lisbon, Portugal, September 4-­8, 2017.

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    Paper at NanoCom 2017

    Sam Ellis presented the paper, “State Logging in Chemical Reaction Networks,” by Sam Ellis, Jim Lathrop and Robyn Lutz at the 4th ACM International Conference on Nanoscale Computing and Communication (NanoCom 2017), Washington, DC, September 27­-29, 2017.

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    Workshop CCC 2017

    Jack Lutz presented the paper, “Computing Absolutely Normal Numbers in Nearly Linear Time,” by Jack H. Lutz and Elvira Mayordomo at Continuity, Computability, Constructivity -- ­From Logic to Algorithms (CCC workshop 2017) at Loria in Nancy, France, June 26-30, 2017.  He also discussed chemical reaction networks and analog computation with other scientists at the workshop.

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    Paper at UCNC 2017

    Ph.D. student Xiang Huang presented the paper, "Real­-time computability of real numbers by chemical reaction networks,” by Xiang Huang, Xiaoyuan Li, Titus H. Klinge, James I. Lathrop, and Jack H. Lutz at the 16th International Conference on Unconventional Computation and Natural Computation (UCNC 2017) in Fayetteville, AR, June 5-9, 2017.

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    Santa Fe Institute talk

    Eric Henderson gave the talk, “Little Machines That Make Themselves,” at the Santa Fe Institute on June 29, 2017.

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    Teaching Excellence Award

    Ph.D. student Samuel Ellis was awarded a Teaching Excellence Award for Spring, 2017, by the Iowa State University Graduate College.

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    University of Zaragoza talk

    Robyn Lutz gave the talk, “Programming Molecules in the Age of Nanotechnology,” Dept. de Informaìtica e Ingenieriìa de Sistemas, Universidad de Zaragoza, May 8, 2017.