publications

preprints

1. A universal niche geometry governs the response of ecosystems to environmental perturbations

   Akshit Goyal, Jason W Rocks, and Pankaj Mehta (2024) [arXiv]
2. Engineering synthetic phosphorylation signaling networks in human cells

   Xiaoyu Yang, Jason W Rocks, Kaiyi Jiang, Andrew J Walters, Kshitij Rai, Jing Liu, Jason Nguyen, Scott D Olson, Pankaj Mehta, James J Collins, Nichole M Daringer, and Caleb J Bashor (2023) [bioRxiv]
3. Phase transition to chaos in complex ecosystems with non-reciprocal species-resource interactions

   Emmy Blumenthal, Jason W Rocks, and Pankaj Mehta (2023) [arXiv]
4. Ultra-high throughput mapping of genetic design space

   Ronan W O’Connell, Kshitij Rai, Trenton C Piepergerdes, Kian D Samra, Jack A Wilson, Shujian Lin, Thomas H Zhang, Eduardo Ramos, Andrew Sun, Bryce Kille, Kristen D Curry, Jason W Rocks, Todd J Treangen, Pankaj Mehta, and Caleb J Bashor (2023) [bioRxiv]
5. Integrating local energetics into Maxwell-Calladine constraint counting to design mechanical metamaterials

   Jason W Rocks, and Pankaj Mehta (2022) [arXiv]
6. Thermodynamic origins of topological protection in nonequilibrium stochastic systems

   Pankaj Mehta, and Jason Rocks (2022) [arXiv]
7. The Geometry of Over-parameterized Regression and Adversarial Perturbations

   Jason W Rocks, and Pankaj Mehta (2021) [arXiv]

published articles

1. An elementary mean-field approach to the spectral densities of random matrix ensembles

   Wenping Cui, Jason W Rocks, and Pankaj Mehta

   Physica A 637, 129608 (2024) [PDF] [arXiv] [URL]
2. Emergent competition shapes the ecological properties of multi-trophic ecosystems

   Zhijie Feng, Robert Marsland III, Jason W Rocks, and Pankaj Mehta

   PLOS Computational Biology 20, e1011675 (2024) [PDF] [arXiv] [URL]
3. Bias-variance decomposition of overparameterized regression with random linear features

   Jason W Rocks, and Pankaj Mehta

   Physical Review E 106, 025304 (2022) [PDF] [arXiv] [URL]
4. Correlation of plastic events with local structure in jammed packings across spatial dimensions

   Sean A Ridout, Jason W Rocks, and Andrea J Liu

   Proceedings of the National Academy of Sciences 119, e2119006119 (2022) [PDF] [arXiv] [URL]
5. Supervised learning in physical networks: From machine learning to learning machines

   Menachem Stern, Daniel Hexner, Jason W Rocks, and Andrea J Liu

   Physical Review X 11, 021045 (2021) [PDF] [arXiv] [URL]
6. Memorizing without overfitting: Bias, variance, and interpolation in overparameterized models

   Jason W Rocks, and Pankaj Mehta

   Physical Review Research 4, 013201 (2022) [PDF] [Supp] [arXiv] [URL]
7. Learning-based approach to plasticity in athermal sheared amorphous packings: Improving softness

   Jason W Rocks, Sean A Ridout, and Andrea J Liu

   APL Materials 9, 021107 (2021) [PDF] [arXiv] [URL]
8. Revealing structure-function relationships in functional flow networks via persistent homology

   Jason W Rocks, Andrea J Liu, and Eleni Katifori

   Physical Review Research 2, 033234 (2020) [PDF] [arXiv] [URL]
9. Hidden topological structure of flow network functionality

   Jason W Rocks, Andrea J Liu, and Eleni Katifori

   Physical Review Letters 126, 028102 (2021) [PDF] [arXiv] [URL]
10. Limits of multifunctionality in tunable networks

    Jason W Rocks, Henrik Ronellenfitsch, Andrea J Liu, Sidney R Nagel, and Eleni Katifori

    Proceedings of the National Academy of Sciences 116, 2506–2511 (2019) [PDF] [arXiv] [URL]
11. Designing allostery-inspired response in mechanical networks

    Jason W Rocks, Nidhi Pashine, Irmgard Bischofberger, Carl P Goodrich, Andrea J Liu, and Sidney R Nagel

    Proceedings of the National Academy of Sciences 114, 2520–2525 (2017) [PDF] [arXiv] [URL]
12. Mechanical signaling coordinates the embryonic heartbeat

    Kevin K Chiou, Jason W Rocks, Christina Yingxian Chen, Sangkyun Cho, Koen E Merkus, Anjali Rajaratnam, Patrick Robison, Manorama Tewari, Kenneth Vogel, Stephanie F Majkut, Benjamin L Prosser, Dennis E Discher, and Andrea J Liu

    Proceedings of the National Academy of Sciences 113, 8939–8944 (2016) [PDF] [URL]