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The earth’s biosphere is incredibly information-rich, with estimated information transmission rates exceeding those of the technosphere by 9 orders of magnitude. Here, we present classical and quantum nanophotonic methods that may enable unprecedented data about biochemical systems, at rates previously unattainable. First, we describe our lab’s Si-photonic “Very-large-scale Integrated high-Q Nanophotonic Pixels” (VINPix). These photonic resonators achieve high-Q factors, subwavelength mode volumes, and controlled dipole-like radiation, with Q-factors from the thousands to millions, and resonator densities exceeding 10M/cm2. By combining VINPix arrays with acoustic bioprinting for local chemical functionalization, we develop Si-chip microsystems and the associated AI framework to detect multi-omic signatures on the same platform. As a first application, we describe integration of these sensors with autonomous underwater robots from Monterey Bay Aquarium Research Institute for targeted gene, protein, and metabolite detection. Then, we describe how these chips can be used for peptide and glycoconjugate sequencing. We tether peptides from major histocompatibility complex to each resonator, and use dynamic Raman spectroscopy to monitor the cleavage of each amino acid from the distal terminus. We also show how these resonators, combined with computational metadynamics, can be used to identify previously unseen molecular species. Finally, we show how these resonators enable subcellular differentiation and functional state characterization of cells in the tumor immune microenvironment (TIME), including the ability to predict drug resistance, macrophage polarization, and T-cell activation state. Collectively, we anticipate that these nanophotonic platforms can provide completely new data on the biosphere – from improved understanding of molecular communication systems, to optimization of novel biochemical sensing platforms for health and sustainability.

Bio: Jennifer (Jen) Dionne is a Professor of Materials Science and, by courtesy, of Radiology at Stanford. She is also deputy director of Q-NEXT (a DOE-funded National Quantum Information Science Research Center), a Chan Zuckerberg Biohub Investigator, and co-founder of Pumpkinseed. Jen received her B.S. degrees in Physics and Systems Science and Mathematics from Washington University in St. Louis, her Ph.D. in Applied Physics at Caltech, and her postdoctoral training in Chemistry at Berkeley. As a pioneer of nanophotonics, she is passionate about developing novel methods to detect and direct biochemical transformations, emphasizing critical challenges in global health and sustainability. Her lab has demonstrated how AI-enabled Raman spectroscopy can be used to identify pathogens and predict their antibiotic resistance; and to monitor drug susceptibility of melanoma. She also forged new ground in developing in vivo tools for mechanobiology. Finally, she has pioneered environmental transmission electron microscopy, providing atomic-scale insights that enable catalysts for sustainable chemical manufacturing. Her work has been recognized with the NSF Waterman Award, a NIH Director’s New Innovator Award, a Moore Inventor Fellowship, and the Presidential Early Career Award for Scientists and Engineers, and was featured on Oprah’s list of “50 Things that will make you say ‘Wow’!”.