Biology subjects

Linke, H.

Publications and source records attributed to Linke, H..

2 recordsLinked to original sources

bioRxiv2025

Practically Error-Free Junctions Enable Solving Large Instances of Exact Cover Problems Using Network-Based Biocomputation

Network-based biocomputing (NBC) presents an energy-efficient, parallel computing approach for solving nondeterministic polynomial time (NP) complete problems by leveraging motor-driven cytoskeletal filaments that explore all possible solutions through nanofabricated networks in a massively parallel fashion. However, guiding errors at pass junctions, where filaments deviate from their intended path, currently limit the scalability of NBC systems. In this study, we addressed this critical challenge by fabricating sub-200 nm channel geometries using modified electron-beam-lithography and reactive-ion-etching protocols to physically constrain the trajectories of kinesin-driven microtubules and enhance path fidelity. Investigating junction designs with varying channel widths, we demonstrate that reducing channel width significantly lowers junction error rates. Practically error-free junction performance was achieved by scaling down the entire network geometry by a factor of two. These optimized junctions were incorporated into NBC networks that successfully solved 24- and 25-set instances of the Exact Cover problem, representing solution spaces of approximately 16 million and 33 million, respectively. This work establishes a new benchmark in NBC performance and represents a computational scale far beyond what has been achieved in prior demonstrations.

bioengineering↗

bioRxiv2025

Nanowire-based biosensor for short DNA using fluorescent silver nanoclusters

Sensitive detection of short nucleic acids is used to identify viral and bacterial diseases, detect biomarkers of cancer, as well as in gene expression studies. Currently available techniques such as PCR, electrochemical detection and SPR are typically costly and often require amplification of the DNA. Additionally, the PCR methods that involve enzymatic elongation of primers are often not optimal for short nucleic acids as a short target limits the size and specificity of the primers. Here, we demonstrate a sensing system for picomolar detection of short single-stranded DNA by fluorescence without any need for amplification, thermal cycling and expensive reagents. The platform harnesses the capability of waveguiding semiconductor nanowires to substantially enhance the signal of surface-bound fluorescent molecules. Employing molecular beacons based on DNA-templated silver nanoclusters that exhibit a larger signal in the presence of the target DNA, we improve the limit of detection by five orders of magnitude compared to flat substrates and demonstrate detection of HIV-1 DNA. The signal indicates single-molecule sensitivity of detection. Our sensor is easily adaptable for other short DNA and potentially can be mass-produced. The method requires only a small volume of analyte sample and a microscope for the detection of fluorescence on nanowires.

biophysics↗