  Imaging individual conformational instances of generic, inhomogeneous,
transient or intrinsically disordered protein systems at the single molecule
level in situ is one of the notable challenges in structural biology. Present
techniques access averaged structural information by measuring over large
ensembles of proteins in nearly uniform conformational states in synthetic
environments. This poses significant implications for diagnostics and drug
design which require a detailed understanding of subtle conformational changes,
small molecule interactions and ligand dynamics. Here we tackle the problem by
designing a single molecule imaging platform technology embracing the
advantages silicon-based spin qubits offer in terms of quantum coherence and
established fabrication pathways. We demonstrate through detailed simulation,
that this platform enables scalable atomic-level structure-determination of
individual molecular systems in native environments. The approach is
particularly well suited to the high-value lipid-membrane context, and as such
its experimental implementation could have far-reaching consequences for the
understanding of membrane biology and drug development.
