arXiv subjects

Sanjin Marion

Publications and source records attributed to Sanjin Marion.

9 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

Latent space mapping of interpretable structural coordinates from stochastic single-molecule signals

Nanopores are versatile single-molecular sensors, but their utility is fundamentally constrained by stochastic translocation dynamics warping any encoded information. We resolve it by shifting from time-domain analysis to a learned latent-space mapping via a contrastive encoder trained exclusively on simulated signals from a physics-informed model. This encoder maps solid-state nanopore signals of engineered DNA barcodes into an interpretable molecular coordinate system. The learned representation is responsive to structural barcode parameters while remaining invariant to acquisition conditions and translocation conformation, allowing data pooling across devices. Molecule identification requires a single pass through the encoder, reducing computational cost by three orders of magnitude relative to alignment-based methods. We experimentally validate through mixture quantification, rare-variant detection, consensus barcode reconstruction, and real-time signal acquisition. This shift from temporal analysis to mapping structural coordinates into a latent space changes the paradigm behind analyzing stochastic sensor signals by linking classification to interpretable encoded molecular information.

physics.ins-det↗

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↗

arXiv2022

High-throughput nanopore fabrication and classification using FIB irradiation and automated pore edge analysis

Large-area nanopore drilling is a major bottleneck in state-of-the-art nanoporous 2D membrane fabrication protocols. In addition, high-quality structural and statistical descriptions of as-fabricated porous membranes are key to predicting the corresponding membrane-wide permeation properties. In this work, we investigate Xe-ion focused ion beam as a tool for scalable, large-area nanopore fabrication on atomically thin, free-standing molybdenum disulphide. The presented irradiation protocol enables designing ultrathin membranes with tunable porosity and pore dimension, along with spatial uniformity across large-area substrates. Fabricated nanoporous membranes were characterized using scanning transmission electron microscopy imaging and the observed nanopore geometries were analyzed through a pore-edge detection script. We further demonstrated that the obtained structural and statistical data can be readily passed on to computational and analytical tools to predict the permeation properties at both individual pore and membrane-wide scales. As an example, membranes featuring angstrom-scale pores were investigated in terms of their emerging water and ion flow properties through extensive all-atom molecular dynamics simulations. We believe that the combination of experimental and analytical approaches presented here should yield accurate physics-based property estimates and thus potentially enable a true function-by-design approach to fabrication for applications such as osmotic power generation, desalination/filtration, as well as their strain-tunable versions.

cond-mat.mtrl-sci↗

arXiv2020

Wetting of nanopores probed with pressure

Nanopores are both a tool to study single-molecule biophysics and nanoscale ion transport, but also a promising material for desalination or osmotic power generation. Understanding the physics underlying ion transport through nano-sized pores allows better design of porous membrane materials. Material surfaces can present hydrophobicity, a property which can make them prone to formation of surface nanobubbles. Nanobubbles can influence the electrical transport properties of such devices. We demonstrate an approach which uses hydraulic pressure to probe the electrical transport properties of solid state nanopores. We show how pressure can be used to wet pores, and how it allows control over bubbles in the nanometer scale range normally unachievable using only an electrical driving force. Molybdenum disulfide is then used as a typical example of a 2D material on which we demonstrate wetting and bubble induced nonlinear and linear conductance in the regimes typically used with these experiments. We show that by using pressure one can identify and evade wetting artifacts.

cond-mat.soft↗

arXiv2020

Pressure Induced Enlargement and Ionic Current Rectification in Symmetric Nanopores

Nanopores in solid state membranes are a tool able to probe nanofluidic phenomena or can act as a single molecular sensor. They also have diverse applications in filtration, desalination or osmotic power generation. Many of these applications involve chemical, or hydrostatic pressure differences, which act on both the supporting membrane and the ion transport through the pore. By using pressure differences between the sides of the membrane, and an alternating current approach to probe ion transport, we investigate two distinct physical phenomena: the elastic deformation of the membrane through the measurment of strain at the nanopore, and the growth of ionic current rectification with pressure due to pore entrance effects.

cond-mat.soft↗

arXiv2019

Nanocapillary Confinement of Imidazolium Based Ionic Liquids

Room temperature ionic liquids are salts which are molten at or around room temperature without any added solvent or solution. In bulk they exhibit glass like dependence of conductivity with temperature as well as coupling of structural and transport properties. Interfaces of ionic liquids have been found to induce structural changes with evidence of long range structural ordering on solid-liquid interfaces spanning length scales of $10-100$nm. Our aim is to characterize the influence of confinement on the structural properties of ionic liquids. We present first conductivity measurements on ionic liquids of the imidazolium type in single conical glass nanopores with confinements as low as tens of nanometers. We probe glassy dynamics of ionic liquids in a large range of temperatures ($-20$ to $70^\circ$C) and nanopore opening sizes ($20-600$nm) in silica glass nanocapillaries. Our results indicate no long range freezing effects due to confinement in nanopores with diameters as low as $20$nm. The studied ionic liquids are found to behave as glass like liquids across the whole accessible confinement size and temperature range.

physics.app-ph↗

arXiv2012

Role of microscopic phase separation in gelation of aqueous gelatin solutions

Using a unique home-made cell for four-contact impedance spectroscopy of conductive liquid samples, we establish the existence of two low frequency conductivity relaxations in aqueous solutions of gelatin, in both liquid and gel state. A comparison with diffusion measurements using pulsed field gradient NMR shows that the faster relaxation process is due to gelatin macromolecule self-diffusion. This single molecule diffusion is mostly insensitive to the macroscopic state of the sample, implying that the gelation of gelatin is not a percolative phenomenon, but is caused by aggregation of triple helices into a system-spanning fibre network.

cond-mat.soft↗

arXiv2011

Four-contact impedance spectroscopy of conductive liquid samples

We present an improved approach to the impedance spectroscopy of conductive liquid samples using four-electrode measurements. Our method enables impedance measurements of conductive liquids down to the sub-Hertz frequencies, avoiding the electrode polarization effects that usually cripple standard impedance analysers. We have successfully tested our apparatus with aqueous solutions of potassium chloride and gelatin. The first substance has shown flat spectra from $\sim$100 kHz down to sub-Hz range, while the results on gelatin clearly show the existence of two distinct low frequency conductive relaxations.

cond-mat.soft↗