Ayush Pandey

Visit my Google Scholar profile here for a list of papers and citations.

Publications (including preprints)

*denotes equal contribution

Ayush Pandey*, William Poole*, Anandh Swaminathan*, Victoria Hsiao, and Richard M. Murray. "Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape." Journal of Open Source Software (JOSS), 2023. DOI: 10.21105.joss.05057, bioRxiv preprint
Ayush Pandey, Makena L. Rodriguez, William Poole, and Richard M. Murray. "Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline." ACS Synthetic Biology (2023). DOI:10.1021/acssynbio.2c00534
Ayush Pandey*, Inigo Incer*, Alberto Sangiovanni-Vincentelli, and Richard M. Murray. "From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology." International Workshop on Bio-Design Automation (2022). Accepted as a talk. DOI:10.1101/2022.04.08.487709
William Poole, Ayush Pandey, Zoltan Tuza, Andrey Shur, and Richard M. Murray. "BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts." PLoS Computational Biology (2022). DOI:10.1371/journal.pcbi.100997S
Ayush Pandey and Richard M. Murray. "Robustness guarantees for structured model reduction of dynamical systems with applications to biomolecular models." International Journal of Robust and Nonlinear Control (2022). URL, PDF.
Ayush Pandey and Richard M. Murray. "Robustness Guarantees for Structured Model Reduction of Dynamical Systems." 2021 60th IEEE Conference on Decision and Control (CDC). IEEE, 2021. PDF.
Liana N. Merk, Andrey S. Shur, Ayush Pandey, Richard M. Murray, and Leopold N. Green. "Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions." bioRxiv (2020). PDF.
Ayush Pandey and Aaron D. Ames. "On a Converse theorem for Finite-time Lyapunov Functions to Estimate Domains of Attraction." 2020 American Control Conference (ACC). IEEE, 2020. PDF.
Ayush Pandey and Richard M. Murray. "A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression." bioRxiv (2020). PDF.
William Poole, Ayush Pandey, Zoltan Tuza, Andrey Shur, and Richard M. Murray. "BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts." bioRxiv (2020). PDF.
Ayush Pandey and Richard M. Murray. "Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits." bioRxiv (2020): PDF.
Ayush Pandey and Richard M. Murray. "An automated model reduction tool to guide the design and analysis of synthetic biological circuits." bioRxiv (2019): PDF.
Reed D. McCardell, Ayush Pandey, and Richard M. Murray. "Control of density and composition in an engineered two-member bacterial community." bioRxiv (2019): PDF.
Ayush Pandey, Siddharth Jha, and Debashish Chakravarty. "Modeling and control of an autonomous three wheeled mobile robot with front steer." 2017 First IEEE International Conference on Robotic Computing (IRC). IEEE, 2017.
Ayush Pandey "Information Performance Tradeoffs in Control." arXiv preprint arXiv:1611.01827 (2016).
Ayush Pandey et al. "Low cost autonomous navigation and control of a mechanically balanced bicycle with dual locomotion mode." 2015 IEEE International Transportation Electrification Conference (ITEC). IEEE, 2015.
Ayush Pandey, Chirstopher Wipf, et al. (2015). “Quantization Noise Anlysis in Advanced LIGO Digital Control System”. In: LIGO DCC, Presented at LIGO Livingston Laboratory, Louisiana, USA. LIGO DCC

Posters and Talks

Workshop on "Learning Parameters from Experimental Data using Bayesian Inference and Model Reduction" at the iGEM Grand Jamboree and at the 14th International Workshop on Bio-Design Automation (IWBDA), 2022. Jupyter Notebooks: On Model Reduction, On Parameter Inference.
Talk on "From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology" at the 14th International Workshop on Bio-Design Automation in Paris, France held alongside iGEM Grand Jamboree. Slides
Talk on "Characterization of integrase and excisionase activity in cell-free protein expression system using a modeling and analysis pipeline" at the 14th International Workshop on Bio-Design Automation in Paris, France held alongside iGEM Grand Jamboree. Slides
Poster at the Build-A-Cell workshop #8 at Caltech on "Full Stack Modeling and Analysis Pipeline for Biological Circuit Design". Poster PDF
Contributed talk at the 1st International Bio-Design Research Conference, 2020, on our preprint: "A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression".
Lightning talk at the American Control Conference 2020 on "On a Converse theorem for Finite-time Lyapunov Functions to Estimate Domains of Attraction" (held virtually).
Seminar talk at the Build-A-Cell seminar series on sensing in synthetic biological systems (June 2020).
Talk on : "Auto-Reduce : Python based model reduction tools for synthetic biology." In: "8th Annual Winter q-bio conference", Big Island, Hawaii, US, 2020. Slides.
Poster on: "An automated model reduction tool to guide the design and analysis of synthetic biological circuits." In: "International Workshop on Control Engineering and Synthetic Biology", Oxford, UK, 2019. PDF
Talk on: "An automated model reduction tool to guide the design and analysis of synthetic biological circuits." In: "11th International Workshop on Bio-Design Automation", Cambridge, UK, 2019. Slides.
Poster on: "Software tools for the design and analysis of synthetic biological circuits.". In: "Caltech Alumni Day 2018". PDF.
Talk on: “Sub-SBML : A subsystem interaction modeling toolbox for SBML models”. In: “Computational Modeling in Biology” Network (COMBINE 2018), Boston, MA. Abstract. Slides
Talk on: “Modeling and control of an autonomous three wheeled mobile robot with front steer”. In: "IEEE International Conference on Robotic Computing (IRC 2017)", Taichung, Taiwan. IEEE Xplore.
Talk on: “Low cost autonomous navigation and control of a mechanically balanced bicycle with dual locomotion mode”. In: "IEEE International Conference on Transportation Electrification (ITEC 2015)", Chennai, India. IEEE Xplore.

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