An NSF Expedition in Computing
Mind in Vitro

Publications

Preprints

  1. Upadhyay, Kazemi, Kim, Zhang, Yuan, Dou, Kang, Saif, Kong, Beggs, Gritton, Gazzola, Living Neurosheets: Engineering readily deployable neural architectures, bioRxiv.

  2. Naughton, Tekinalp, Shivam, Kim, Kindratenko, Gazzola, Neural reservoir control of a soft bio-hybrid arm, arXiv.

  3. Ghavasieh, Vila-Minana, Khurd, Beggs, Ortiz, Fortunato, Toward a Physics of Deep Learning and Brains, arXiv.

  4. LaGrange, Varley, O’Shea, Fitzpatrick, Cummings, Beggs, Effect of acute elevated magnesium on bursting activity and information-processing dynamics in cortical cultures, bioRxiv.

  5. Lee, Saif, Tension shapes memory: Computational insights into neural plasticity, bioRxiv.

  6. Lee, Motes, Ngui, Morales, Amato, Lazy-DaSH: Lazy Approach for Hypergraph-based Multi-robot Task and Motion Planning, arXiv.

  7. Anderson, Varshney, Hemmatian, Robles-Granda, Nayak, Wilcox, Zwilling, Kim, Barbey, Human Intelligence and the Connectome are Driven by Structural Brain Network Control, bioRxiv.

  8. Pagan-Diaz, Kilacarslan, Wester, Rahman, Aydin, Gapinske, Kim, Buoros, Saif, Bashir, Engineering 3D neuronal networks with directional endogenous neuronal plasticity pathways, bioRxiv.

Published

Journal Articles

 

  1. Drennan, Aydin, Emon, Li, Joy, Barishman, Kim, Wei, Denham, Carrillo, Saif, A forward-engineered, muscle-driven soft robotic swimmer, Science Advances, 2025. 

  2. Kang, Kim, Burgeson, Han, Rogers, Kong, Interrogating functional connectivity of in vitro neural glia tissue model modulated through integrative control of matrix stiffness and a neurotrophic factor, Biomaterials, 2025.

  3. Ellis-Mohr, Nayak, Varshney, A Theory of Inference Compute Scaling: Reasoning through Directed Stochastic Skill Search, Philosophical Transactions of the Royal Society A, 2025.

  4. Min, Wang, Wang, Li, Kim, Aydin, Kang, You, Lim, Wolhaupter, Xu, Zhu, Gu, Li, Kim, Rao, Kong, Saif, Huang, Rogers, Bashir. Optogenetic neuromuscular actuation of a miniature electronic biohybrid robot, Science Robotics, 2025.

  5. Rahman, Joy, Saif, Optogenetic neural spheroids excite primary neural network, Journal of Neural Engineering, 2025.

  6. Dou, Hong, Cui, Li, Chan, Bhosale, Aydin, Juarez, Saif, Chamorro, Gazzola, An in-vitro living system for streaming flow rectification. Physical Review Research, 2025.

  7. Akcal, Raikov, Gribkova, Choudhuri, Kim, Gazzola, Gillette, Soltesz, Chowdhary, LoCS-Net: Localizing convolutional spiking neural network for fast visual place recognition, Frontiers in Neurorobotics, 2025.

  8. Huang, Chung, Kong, Reply to Caruso Bavisotto et al.: Toward exploring the potential of muscle-secreting exosomes in the muscle–brain axis, PNAS, 2025.

  9. Hemmatian, Varshney, Pi, Barbey, The Utilitarian Brain: Moving Beyond the Free Energy Principle, Cortex, 2024.

  10. You, Karaman, Reyes-Ordonez, Lee, Kim, Bashir, Chen, Leucyl-tRNA Synthetase Contributes to Muscle Weakness through Mammalian Target of Rapamycin Complex 1 Activation and Autophagy Suppression in a Mouse Model of Duchenne Muscular Dystrophy, The American Journal of Pathology, 2024.

  11. Min, Kim, Bashir, A miniature humanoid biorobot on the run, Device, 2024.

  12. Aydin, Hirashima, Saif, Incorporating Geometric Nonlinearity in Theoretical Modeling of Muscle-Powered Soft Robotic Bio-Actuators, Journal of Applied Mechanics, 2024.

  13. Bosch, Chan, Davis, Gutierrez, Karahalios, Koyejo, Loui, Mendenhall, Sanfilippo, Tong, Varshney, Wang, Artificial Intelligence, Social Responsibility, and the Roles of the University, Communications of the ACM, 2024.

  14. Huang, Upadhyay, Ahn, Sakakura, Pagan-Diaz, Cho, Weiss, Huang, Mitchell, Li, Tan, Deng, Ellis-Mohr, Dou, Zhang, Kang, Chen, Sweedler, Im, Bashir, Chung, Popescu, Gillette, Gazzola, Kong, Neuronal innervation regulates the secretion of neurotrophic myokines and exosomes from skeletal muscle, PNAS, 2024.

  15. Tekinalp, Naughton, Kim, Halder, Gillette, Mehta, Kier, Gazzola, Topology, dynamics, and control of a muscle-architected soft arm, PNAS, 2024.

  16. Zhao, Gribkova, Shen, Cui, Naughton, Liu, Seo, Tong, Gazzola, Gillette, Zhao, Highly stretchable and customizable microneedle electrode arrays for intramuscular electromyography, Science Advances, 2024.

  17. Mestre, Astobizaf, Webster-Wood, Ryan, Saif, Ethics and responsibility in biohybrid robotics research, PNAS, 2024.

  18. Joya, Nall, Emon, Lee, Barishman, Ahmed, Rahman, Selvin, Saif, Synapses without tension fail to fire in an in vitro network of hippocampal neurons, PNAS, 2024.

  19. Varley, Havert, Fosque, Alipour, Weerawongphrom, Naganobori, O’Shea, Pope, Beggs, The serotonergic psychedelic N,N-dipropyltryptamine alters information-processing dynamics in in vitro cortical neural circuits, Network Neuroscience, 2024.

  20. Salners, Dahmen, Beggs, Simple model for the prediction of seizure durations, Physical Review E, 2024.

  21. Zhang, Dou, Kim, Upadhyay, Havert, Kang, Kazemi, Huang, Aydin, Huang, Rahman, Ellis-Mohr, Noblet, Lim, Chung, Gritton, Saif, Kong, Beggs, Gazzola, 'Mind in Vitro' platforms:  Versatile, scalable, robust, and open solutions to interfacing with living neurons, Advanced Science, 2024.

  22. Salners, Avila, Nicholson, Myers, Beggs, Dahmen.  Recurrent activity in neuronal avalanches, Scientific Reports, 2023.

  23. Kim, Yang, Zhang, Li, Vazquez-Guardado, Park, Wang, Efimov, Dou, Wang, Park, Luan, Ni, Kim, Baek, Xie, Zhao, Gazzola, Rogers, Bashir, Remote control of miniature robots integrating biological muscles and battery-free wireless optoelectronics, Science Robotics, 2023.

  24. Joy, Nall, Emon, Lee, Barishman, Ahmed, Rahman, Selvin, Saif, Synapses without tension fail to fire in an in vitro network of hippocampal neurons, PNAS, 2023.

  25. Lee, Rhodes, Saif, Astrocyte-mediated Transduction of Muscle Fiber Contractions Synchronizes Hippocampal Neuronal Network Development, Neuroscience, 2023.

 

Conference / Workshop Proceedings

 

  1. Gressmann, Chen, Xie, Amato, Rauchwerger, Position: It Is Time We Test Neural Computation In Vitro, Proceedings of the 42nd International Conference on Machine Learning, 2025.

  2. Coats, Varshney, Neural Network Memory Criticality: from Echo State to HiPPO and Beyond, Proceedings of the New York Scientific Data Summit, 2025.

  3. Pattanaik, Varshney, Online Reinforcement Learning with Passive Memory, Proceedings of the American Control Conference, 2025.

  4. Ellis-Mohr, Gazzola, Varshney, Synthetic Neurocomputers: Advancing Scientific Research through Computing with Living Neurons, DOE Analog Computing for Science Workshop, Bethesda, Maryland, 2024.

  5. Ellis-Mohr, Varshney, Directed Information Flow in Computing Systems with Living Neurons, Proceedings of the IEEE International Symposium on Information Theory Workshops, 2024.

  6. Naik, Arnold, Varshney, Modeling Clinical Symptoms of Cognitive Decline in Neurodegenerative Disease as Faulty Computing, Proceedings of the IEEE International Symposium on Information Theory Workshops, 2024.

  7. Gressmann, Chen, Xie, Dowden, Amato, Rauchwerger, A primer on in-vitro biological neural networks, Workshop on Machine Learning with new Compute Paradigms, NeurIPS, 2024.

  8. Gressmann, Rauchwerger, Learning to harness in-vitro biological neural networks, ACM SIGPLAN International Conference on Systems, Programming, Languages and Applications: Software for Humanity (SPLASH), 2024.

  9. Varshney, Schutt-Aine, Rakheja, Ghose, Co-Design Methodologies for Integrating Small Organism-Inspired Chiplets, DOE Neuromorphic Computing for Science Workshop, 2024.

Books

 

  1. Beggs, The Cortex and the Critical Point, MIT Press, 2022.