arXiv subjects

Wouter Botermans

Publications and source records attributed to Wouter Botermans.

2 recordsLinked to original sources

arXiv2026

Precise Positional Readout of Molecular Barcode Structures using Solid-State Nanopores

Fast and nonuniform translocation through solid-state nanopores limits both the detection of small molecular labels and their precise localization along molecular carriers. In this work we report the detection and localization performance of nucleotide-based molecular labels along double-stranded DNA scaffolds using solid-state nanopores in thin planar membranes. For small labels that are challenging to resolve individually, we introduce an anchoring strategy where readily detectable bulky labels serve as reference points to align multiple translocation events, enabling population-based detection and localization of smaller molecular features. The measured anchor positions constrain a probabilistic model of translocation velocity, identifying the most probable velocity profile for each event and enabling nonlinear trace "unwarping" for improved multi-event alignment. A complementary window-based evidence aggregation procedure accumulates weak but consistent label signatures across events, enabling detection of features that are individually masked by noise. These approaches enable robust recovery of single-dumbbell labels (DB1) on the order of 28 nucleotides and reduce mean localization errors to as low as 10 base pairs for DB3 labels and 40 base pairs for DB1 labels when averaging over multiple events. Stronger fractional DNA-associated current blockades, used as proxy for smaller pore geometries, are additionally associated with improved detection and lower localization error across membrane-based nanopore fabrication techniques. Overall, anchor-guided alignment provides a route to higher-density molecular information readout without compromising throughput via controlled translocation approaches.

q-bio.BM↗

arXiv2026

Data Sieving for Scalable Real-Time Multichannel Nanopore Sensing

High-throughput solid-state nanopore experiments generate continuous MHz-rate data streams in which only a small fraction of data contains informative molecular information. This creates storage and processing bottlenecks that limit experimental scalability. We introduce Data Sieving, a GPU-accelerated acquisition framework that integrates real-time event detection directly into the measurement pipeline and selectively stores and allows real-time analysis of snapshots around molecular translocations. The system employs a lightweight rolling-average and min-max trigger to identify event candidates in parallel across channels. This architecture reduces stored data volume by up to 98% while preserving complete molecular signatures across a wide temporal range, from microsecond-scale protein dynamics to second-scale nucleic acid nanoparticle events. Continuous baseline monitoring enables autonomous closed-loop actuation; in high-concentration DNA experiments, automatic declogging restored pore conductance, reducing the time spent in a non-productive clogged state to near-zero and without interrupting parallel measurements. Validated across DNA, protein, and nucleic acid nanoparticle measurements, Data Sieving links data storage directly to molecular information content rather than experiment duration, enabling scalable, real-time operation of parallel nanopore sensors. The approach provides a hardware-agnostic foundation for long-duration, high-bandwidth single-molecule experiments and other event-driven sensing platforms. By using algorithms intrinsically compatible with low-latency digital architectures, this framework provides a clear path toward high-bandwidth, highly multiplexed recording across hundreds of individual nanopore channels in both solid-state and biological pores.

physics.ins-det↗