Quantome: A Quantum Surrogate Model for Biophysical Landscapes

Malik, A. J.; Ascher, D.

doi:10.1101/2025.08.06.668871

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bioRxiv · 10.1101/2025.08.06.668871

Quantome: A Quantum Surrogate Model for Biophysical Landscapes

Malik, A. J.·Ascher, D.

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Abstract

Accurately modelling the potential energy landscapes that govern molecular interactions is a central challenge in computational biophysics. While quantum computers promise to solve such problems with high fidelity, a key bottleneck is the encoding of complex spatial information into low-qubit Hamiltonians suitable for near-term devices. Here, we introduce a generalisable framework for creating quantum surrogate models of 2D biophysical landscapes. Our method translates a discrete, classically-derived potential energy grid into a continuous quantum Hamiltonian by fitting it to a high-degree polynomial, where the polynomials coefficients directly define the potential energy operator. We demonstrate this pipeline on a custom-designed landscape featuring two asymmetric potential wells. By systematically varying a kinetic hopping term in the Hamiltonian, our variational quantum eigensolver simulations, averaged over 100 runs, successfully reproduce the physical transition from a localised ground state to a delocalised state governed by tunnelling. The entire framework is made accessible through the Quantome web application, a pedagogical platform that allows users to both design custom landscapes and explore pre-calculated results on EF-hand protein binding sites, which serve as a simplified real-world test bed for this framework. The web app is freely available at: https://biosig.lab.uq.edu.au/quantumlabs/quantome.

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Malik, A. J., Ascher, D.. 2025-08-08. Quantome: A Quantum Surrogate Model for Biophysical Landscapes. https://doi.org/10.1101/2025.08.06.668871

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