Browsing by Author "Lu, Yi"

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    The energetics and evolution of oxidoreductases in deep time
    (Wiley, 2024) McGuinness, Kenneth N.; Fehon, Nolan; Feehan, Ryan; Miller, Michelle; Mutter, Andrew C.; Rybak, Laryssa A.; Nam, Justin; AbuSalim, Jenna E.; Atkinson, Joshua T.; Heidari, Hirbod; Losada, Natalie; Kim, J. Dongun; Koder, Ronald L.; Lu, Yi; Silberg, Jonathan J.; Slusky, Joanna S. G.; Falkowski, Paul G.; Nanda, Vikas; Chemical and Biomolecular Engineering
    The core metabolic reactions of life drive electrons through a class of redox protein enzymes, the oxidoreductases. The energetics of electron flow is determined by the redox potentials of organic and inorganic cofactors as tuned by the protein environment. Understanding how protein structure affects oxidation–reduction energetics is crucial for studying metabolism, creating bioelectronic systems, and tracing the history of biological energy utilization on Earth. We constructed ProtReDox (https://protein-redox-potential.web.app), a manually curated database of experimentally determined redox potentials. With over 500 measurements, we can begin to identify how proteins modulate oxidation–reduction energetics across the tree of life. By mapping redox potentials onto networks of oxidoreductase fold evolution, we can infer the evolution of electron transfer energetics over deep time. ProtReDox is designed to include user-contributed submissions with the intention of making it a valuable resource for researchers in this field.
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    Microwave Transitions and Synthetic Dimensions in Rydberg Atoms
    (2025-03-05) Lu, Yi; Killian, Thomas C
    The marriage between Rydberg physics and ultracold atomic systems have hatched so many fascinating achievements. The exaggerated properties of Rydberg states, combined with the pristine environments provided by the ultracold atoms, can lead to realizations of exotic physical systems. One particularly innovative direction that emerged recently is to use microwave-frequency transitions between Rydberg levels to simulate the dynamics of a particle hopping between lattice sites. Such approach, referred to as Rydberg synthetic dimensions, falls under the broad scheme of quantum simulations. Here we present description of the infrastructure used for Rydberg excitation and coherent microwave transitions, which are essential to the realization of Rydberg synthetic dimensions. We will also present experimental results on simulating the Su-Schireffer-Heeger Hamiltonian, a canonical model with paradigmatic importance in topological physics.