arXiv subjects

Jonathon L. Yuly

Publications and source records attributed to Jonathon L. Yuly.

4 recordsLinked to original sources

arXiv2026

Designing semiconductor-electrochemical junctions for bioinspired energy transduction

Long ago, life discovered how to efficiently push electrons thermodynamically uphill to lower potential by harnessing energy released by an equal number of electrons moving downhill. Known as electron bifurcation, this form of energy transduction has never been observed in the absence of natural enzymes. To successfully bifurcate electrons, a system must block short-circuit electron transfers that allow all electrons to flow downhill, while maintaining productive reactions. It is difficult to design systems that catalyze these highly-selective electron flows while minimizing free energy dissipation. Using theories of electron transfer and charge transport, I introduce semiconductor-electrolyte junctions that spontaneously bifurcate electrons analogously to natural enzymes (bifurcating junctions). I simulate a simple but illustrative bifurcating junction with typical material properties, and discuss how more complicated designs could achieve higher performance.

cond-mat.mes-hall↗

arXiv2024

Seeking a quantum advantage with trapped-ion quantum simulations of condensed-phase chemical dynamics

Simulating the quantum dynamics of molecules in the condensed phase represents a longstanding challenge in chemistry. Trapped-ion quantum systems may serve as a platform for the analog-quantum simulation of chemical dynamics that is beyond the reach of current classical-digital simulation. To identify a 'quantum advantage' for these simulations, performance analysis of both analog-quantum simulation on noisy hardware and classical-digital algorithms is needed. In this Review, we make a comparison between a noisy analog trapped-ion simulator and a few choice classical-digital methods on simulating the dynamics of a model molecular Hamiltonian with linear vibronic coupling. We describe several simple Hamiltonians that are commonly used to model molecular systems, which can be simulated with existing or emerging trapped-ion hardware. These Hamiltonians may serve as stepping stones toward the use of trapped-ion simulators for systems beyond the reach of classical-digital methods. Finally, we identify dynamical regimes where classical-digital simulations seem to have the weakest performance compared to analog-quantum simulations. These regimes may provide the lowest hanging fruit to exploit potential quantum advantages.

quant-ph↗

arXiv2022

Biological free energy transduction is an Achilles heel of mean-field transport theory

Studies of nanoscale biological transport often use a mean-field approximation that is exact only when the system is at equilibrium and there are no interactions between particles on different sites in the network. We explore the limitations of this approximation to describe many-particle transport in the context of enzyme function and biological transport networks. Our focus is on three bioenergetic networks: a linear electron transfer chain (as found in bacterial nanowires), a redox-coupled proton pump (as in complex IV of respiration), and a near reversible electron bifurcation network (as in complex III of respiration and other recently discovered structures). Away from equilibrium and with typical site-site interactions, we find that the mean-field approximation adequately describes linear transport chains. However, the mean-field approximation fails catastrophically to describe energy-transducing systems, as in the redox coupled proton pump and reversible electron bifurcation reactions. The mean-field approximation fails to capture the essential correlations that are needed to prevent slippage events and to produce efficient energy transduction.

physics.bio-ph↗

arXiv2020

Universal Free Energy Landscape Produces Efficient and Reversible Electron Bifurcation

For decades, it was unknown how electron bifurcating systems in Nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron bifurcating molecular machines could not be designed and built. The underpinning free energy landscapes for electron bifurcation were also enigmatic. We predict that a simple and universal free energy landscape enables electron bifurcation, and we show that it enables high-efficiency bifurcation with limited short-circuiting (the EB-scheme). The landscape relies on steep free energy slopes in the two redox branches to insulate against short-circuiting without relying on nuanced changes in the microscopic rate constants for the short-circuiting reactions. The EB-scheme thus provides a blueprint for future campaigns to establish synthetic electron bifurcating machines.

physics.bio-ph↗