Work

Continuous-Time Quantum-Walk Centrality for Protein Residue Interaction Networks

Year: 2026

Type: article

Abstract: We present a quantum-dynamical framework for identifying structurally and functionally important residues in proteins based on continuous-time quantum walks (CTQWs) on weighted residue-interaction networks constructed from experimentally resolved structures. By mapping the weighted adjacency matrix to a Hamiltonian, residue importance emerges from the long-time averaged occupation probability, confirmed analytically through its spectral decomposition. Across a data set of 150 proteins spanning diverse structural and functional classes, CTQW centrality exhibits consistently strong agreement with classical eigenvector centrality in identifying central residues, while extending beyond it through incorporating signatures of quantum interference. Analyzing the time-averaged quantum transition matrix reveals consistently larger spectral gaps than the classical random-walk operator. Furthermore, biological relevance is confirmed through recovery of experimentally established functional residues in proteins kinase A and oxytocin. CTQW-derived centrality rankings are accessible on near-term intermediate-scale quantum hardware, as we demonstrate through a proof-of-principle implementation on IBM superconducting quantum hardware. These results establish continuous-time quantum walks as a computationally tractable framework for protein network analysis, that connects network theoretical treatments of protein structural biology to continuous-time quantum walk dynamics.

Source: Journal of the American Chemical Society

DOI: 10.1021/jacs.6c08053

Authors: Shah Ishmam Mohtashim, Manas Sajjan, Sabre Kais

Institution: North Carolina State University

Language: English

Topic: Graph theory and applications

Subfield: Geometry and Topology

Field: Mathematics

Domain: Physical Sciences

Open Access status: green

Funder: Basic Energy Sciences

Award: G3582405953