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<title> Ayush Pandey </title>
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<p>Visit my <a href="https://scholar.google.com/citations?user=dl98f5UAAAAJ&hl=en">Google Scholar</a> profile here for a list of papers and citations.</p>
<h2 id="papers">Publications (including preprints)</h2>
*denotes equal contribution
<ul>
<li>S. Shailja, Satish Kumar, Arthur Caetano, Ayush Pandey. "Scaffolding AI research projects increases self-efficacy of high school students in learning neural networks (Fundamental)" American Society for Engineering Education (ASEE), 2024. <a href = "documents/author_copy_ASEE_2024_PCEE_final_paper.pdf">PDF</a></li>
<li>Ayush Pandey. "Modeling Frameworks for Modular and Scalable Biological Circuit Design" PhD Thesis, California Institute of Technology, June 2023. <a href = "https://thesis.library.caltech.edu/16087/">DOI:10.7907/qacp-dw76</a></li>
<li>Zoila Jurado, Ayush Pandey, Richard M Murray. "A chemical reaction network model of PURE" bioRxiv 2024. <a href = "https://www.biorxiv.org/content/10.1101/2023.08.14.553301v1.abstract">DOI:10.1101/2023.08.14.553301</a></li>
<li>Inigo Incer, Apurva Badithela, Josefine Graebener, Piergiuseppe Mallozzi, Ayush Pandey, Sheng-Jung Yu, Albert Benveniste, Benoit Caillaud, Richard M Murray, Alberto Sangiovanni-Vincentelli, Sanjit A Seshia. "Pacti: Scaling Assume-Guarantee Reasoning for System Analysis and Design" ACM Transactions on Cyber-Physical Systems (minor revisions). <a href = "https://arxiv.org/abs/2303.17751">arXiv:2303.17751</a></li>
<li>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. <a href = "https://joss.theoj.org/papers/10.21105/joss.05057.pdf">DOI: 10.21105.joss.05057</a>, <a href = "https://www.biorxiv.org/content/10.1101/121152v3">bioRxiv preprint</a></li>
<li>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). <a href="https://doi.org/10.1021/acssynbio.2c00534">DOI:10.1021/acssynbio.2c00534</a></li>
<li>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. <a href="https://www.biorxiv.org/content/10.1101/2022.04.08.487709v1">DOI:10.1101/2022.04.08.487709</a></li>
<li>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). <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009987">DOI:10.1371/journal.pcbi.100997S</a>
<li>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). <a href = "https://onlinelibrary.wiley.com/doi/full/10.1002/rnc.6013">URL</a>, <a href="/documents/IJRNC_2022_paper.pdf">PDF</a>.</li>
<li>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. <a href = "/documents/cdc_2021.pdf">PDF</a>.</li>
<li>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). <a href = "https://authors.library.caltech.edu/106610/1/2020.11.10.377085v1.full.pdf">PDF</a>.</li>
<li>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. <a href = "/documents/acc_2020.pdf">PDF</a>.</li>
<li>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). <a href = "https://www.biorxiv.org/content/10.1101/2020.11.25.399287v1.full.pdf+html">PDF</a>.</li>
<li>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). <a href = "https://www.biorxiv.org/content/10.1101/2020.08.02.233478v2.full.pdf+html">PDF</a>.</li>
<li>Ayush Pandey and Richard M. Murray. "Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits." bioRxiv (2020): <a href = "https://www.biorxiv.org/content/10.1101/2020.02.15.950840v2.abstract">PDF</a>.</li>
<li>Ayush Pandey and Richard M. Murray. "An automated model reduction tool to guide the design and analysis of synthetic biological circuits." bioRxiv (2019): <a href="https://www.biorxiv.org/content/10.1101/640276v1">PDF</a>.</li>
<li>Reed D. McCardell, Ayush Pandey, and Richard M. Murray. "Control of density and composition in an engineered two-member bacterial community." bioRxiv (2019): <a href="https://www.biorxiv.org/content/10.1101/632174v1">PDF</a>.</li>
<li>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). <a href="https://ieeexplore.ieee.org/abstract/document/7926529">IEEE</a>, 2017.</li>
<li>Ayush Pandey "Information Performance Tradeoffs in Control." arXiv preprint arXiv:1611.01827 (2016).</li>
<li>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). <a href="https://ieeexplore.ieee.org/abstract/document/7386938/">IEEE</a>, 2015.</li>
<li>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. <a href="https://dcc.ligo.org/LIGO-T1500351/public">LIGO DCC</a></li>
</ul>
<h2 id="conference-publication-and-talks">Posters and Talks</h2>
<ul>
<li>Oral talk on "Scaffolding AI research projects increases self-efficacy of high school students in learning neural networks (Fundamental)" at the 2024 American Society for Engineering Education (ASEE) Annual Symposium & Exposition. Slides: <a href="documents/asee_slides.pptx">Can high school students learn neural networks?</a>.
<li>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: <a href="http://tiny.cc/iwbda-autoreduce">On Model Reduction</a>, <a href="http://tiny.cc/iwbda-bioscrape">On Parameter Inference</a>.</li>
<li>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. <a href="/documents/iwbda22_contracts.pptx">Slides</a></li>
<li>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. <a href="/documents/iwbda22_pipeline.pptx">Slides</a></li>
<li>Poster at the Build-A-Cell workshop #8 at Caltech on "Full Stack Modeling and Analysis Pipeline for Biological Circuit Design". <a href="/documents/q-bio_slides.pptx">Poster PDF</a></li>
<li>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".</li>
<li>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).</li>
<li>Seminar talk at the Build-A-Cell seminar series on sensing in synthetic biological systems (June 2020).</li>
<li>Talk on : "Auto-Reduce : Python based model reduction tools for synthetic biology." In: "8th Annual Winter q-bio conference", Big Island, Hawaii, US, 2020. <a href = "/documents/q-bio_slides.pptx">Slides</a>.</li>
<li>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. <a href="/documents/poster_iwbda.pdf">PDF</a></li>
<li>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. <a href="/documents/iwbda_slides.pptx">Slides</a>.</li>
<li>Poster on: "Software tools for the design and analysis of synthetic biological circuits.". In: "Caltech Alumni Day 2018". <a href="/documents/software_poster.pdf">PDF</a>.</li>
<li>Talk on: “Sub-SBML : A subsystem interaction modeling toolbox for SBML models”. In: “Computational Modeling in Biology” Network (COMBINE 2018), Boston, MA. <a href="https://ayush-pandey.github.io/projects#subsbml">Abstract</a>. <a href="/~apandeydocuments/subsbml_slides.pdf">Slides</a></li>
<li>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. <a href="http://ieeexplore.ieee.org/document/7926529/">IEEE Xplore</a>.</li>
<li>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. <a href="http://ieeexplore.ieee.org/document/7386938/">IEEE Xplore</a>.</li>
</ul>
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All original material on this website is free-to-use and can be shared with proper attribution. You can view the <a href="/LICENSE">LICENSE</a> here.
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