UC Santa Cruz

Low-abundance biosensing is constrained not only by the sensitivity of a transducer, but by the complete sequence of molecular transport, capture, recognition, translation, transduction, and statistical inference. This dissertation develops a unified framework connecting conventional surface-based electrochemical biosensors with single-molecule solid-state nanopore sensing. The framework addresses a central mismatch in miniaturized biosensors: nanoscale devices can respond strongly to an individual binding or translocation event while sampling so little area or volume that rare targets at femtomolar-to-attomolar concentrations are unlikely to reach the sensing region within a practical measurement time.To decouple molecular collection from transducer area, target capture is distributed throughout the sample volume using antibody-functionalized magnetic beads. Each captured recognition event is subsequently converted into an inert, approximately 200 nm dielectric surrogate through biomolecule-to-surrogate (B2S) translation. The same surrogate population is then measured through two independent physical readouts. In the digital branch, individual surrogates are counted as they translocate a giant solid-state nanopore. Applied to Zika virus NS1 in serum, this approach reaches an analytical limit of detection of 103 aM while preserving event-level current amplitude, dwell-time, and arrival-rate information. In the ensemble branch, translated surrogates are electrophoretically deposited onto an unfunctionalized screen-printed gold electrode, where they restrict redox-probe access and suppress square-wave-voltammetric current. Applied to SARS-CoV-2 nucleocapsid antigen, this portable electrochemical implementation achieves a 4.56 aM limit of detection, a 16.57 aM limit of quantification, and a 9.8-decade quantifiable range, and demonstrates feasibility with RT-PCR-characterized patient samples.A forward stochastic model links antigen abundance, magnetic-bead capture, transfer efficiency, surrogate generation, deposition, diffusional-shadow blocking, square-wave-voltammetric response, and measurement uncertainty without fitting the reported assay figures of merit. The measured performance falls within the model’s predicted distributions, and sensitivity analysis identifies nonspecific blank-surrogate count and its reproducibility as the dominant remaining constraints. Collectively, the results show that separating capture from transduction and translating rare molecular recognition events into robust physical surrogates provides a common route from ensemble electrochemical sensing to digital single-particle detection.