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From DNA Detection to Organs-on-Chip Monitoring: Fabrication Solutions for Integrated Biosensing
KTH, School of Electrical Engineering and Computer Science (EECS), Micro and Nanosystems.ORCID iD: 0000-0003-0960-9931
2026 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Bringing a biosensor from laboratory demonstration to practical use depends as much on fabrication as on the sensing principle itself. This thesis develops fabrication strategies that overcome specific technological barriers across biosensing domains: from single-molecule electrochemical detection to real-time optical monitoring in organ-on-chip platforms.

In the electrochemical domain, the thesis identifies the conditions under which metal-assisted chemical etching enters the self-limiting regime in ultrathin silicon-on-insulator membranes, where catalyst size decouples from pore size, yielding ~5 nm pores with 1 nm variability (Papers I, II). A complementary approach translates micrometer-scale lithographic features into sub-10 nm pores through controlled fracture of pre-stressed membranes, validated for both electrical and optical single-molecule DNA detection down to 30 bases (Paper III). A two-tier fabrication architecture for organic electrochemical transistors decouples electrode routing from polymer channel definition via direct femtosecond laser writing, achieving single-micrometer resolution outside the cleanroom; channel outlining confines the ion-transport volume and improves switching speed by three orders of magnitude (Paper V). Colloidal self-assembly of polystyrene beads in silk fibroin produces biocompatible photonic crystals in which the defect-layer bead diameter programs the passband wavelength, establishing a design principle for spectral control in biocompatible optical structures (Paper IV). This fabrication logic, using particle size to define a functional feature in a host material, extends from the silicon nanopore work and enables the design of biocompatible photonic crystals.

In the optical integration domain, laser-machined PMMA modules with commodity optoelectronics replace benchtop instruments for continuous pH and dissolved oxygen monitoring in microfluidic systems (Paper VI). The modular architecture integrates with the bioreactor design without modification and operates autonomously from single-bioreactor cell culture through five-day multi-organ drug testing, enabling detection of liver-mediated drug conversion that is unobservable in single-organ systems (Paper VII).

Across those domains, understanding the sensing principle, material properties, and available fabrication tools guides the development of processes that achieve application-relevant precision while reducing costs and infrastructure requirements.

Abstract [sv]

Att ta en biosensor från laboratoriedemonstration till praktisk användning beror lika mycket på tillverkning som på sensorprincipen i sig. Denna avhandling utvecklar tillverkningsstrategier som övervinner specifika tekniska hinder inom biosensordomäner: från elektrokemisk detektering av enskilda molekyler till optisk realtidsövervakning i organ-på-chip-plattformar.

Inom den elektrokemiska domänen identifierar avhandlingen de förhållanden under vilka metallassisterad kemisk etsning övergår till ett självbegränsande regime i ultratunna kisel-på-isolator-membran, där katalysatorstorleken frikopplas från porstorleken och ger ~5 nm porer med 1 nm variabilitet (Artikel I, II). En kompletterande metod översätter litografiska strukturer på mikrometerskala till porer under 10 nm genom kontrollerad fraktur av förspända membran, validerad för både elektrisk och optisk detektion av enskilda DNA-molekyler ned till 30 baser (Artikel III). En tvånivå-tillverkningsarkitektur för organiska elektrokemiska transistorer frikopplar elektrodledningar från polymerkanalsdefinition via direkt femtosekundslaserskrivning och uppnår upplösning på enstaka mikrometer utanför renrummet; kanalkonturering begränser jontransportvolymen och förbättrar switchhastigheten med tre storleksordningar (Artikel V). Kolloidal självorganisering av polystyrenkulor i silkesfibroin ger biokompatibla fotoniska kristaller där kuldiametern i defektlagret programmerar passbandsvåglängden och etablerar en designprincip för spektral styrning i biokompatibla optiska strukturer (Artikel IV). Denna tillverkningslogik, att använda partikelstorleken för att definiera en funktionell egenskap i ett värdmaterial, utgår från arbetet med kiselnanoporer och möjliggör design av biokompatibla fotoniska kristaller.

Inom den optiska integrationsdomänen ersätter laserskurna PMMA-moduler med standardkomponenter inom optoelektronik bänkinstrument för kontinuerlig pH- och syreövervakning i mikrofluidiska system (Artikel VI). Den modulära arkitekturen integreras i bioreaktordesignen utan modifikationer och arbetar autonomt från cellodling i enskilda bioreaktorer till femdagars läkemedelstestning i flerorgansystem, vilket möjliggör detektering av leverförmedlad läkemedelsomvandling som inte är observerbar i enkelorgansystem (Artikel VII).

Inom dessa domäner vägleder förståelsen av sensorprincipen, materialegenskaperna och de tillgängliga tillverkningsverktygen utvecklingen av processer som uppnår applikationsrelevant precision med minskade kostnader och infrastrukturkrav.

Abstract [it]

Il passaggio di un biosensore dalla fase di dimostrazione in laboratorio all'uso pratico dipende tanto dal processo di fabbricazione quanto dal principio stesso di rilevamento. Questa tesi sviluppa strategie di fabbricazione volte a superare specifiche barriere tecnologiche in quattro ambiti: dal rilevamento elettrochimico di una singola molecola al monitoraggio ottico in tempo reale nelle piattaforme «organ-on-chip» (organi-su-chip).

La prima parte riguarda i nanopori: minuscoli fori in una membrana di silicio, talmente piccoli che una singola molecola di DNA li occupa quasi interamente. Facendo passare la molecola attraverso il poro, è possibile identificarla. Produrre fori di questa dimensione, pochi miliardesimi di metro, è una sfida tecnologica che oggi richiede strumenti costosi e operatori specializzati. Questa tesi mostra come, sfruttando un fenomeno chimico autolimitante finora non riportato in letteratura, sia possibile fabbricare questi fori in parallelo su larga scala.

La seconda parte è dedicata ai cristalli fotonici biocompatibili, strutture capaci di manipolare la luce e realizzate con materiali compatibili con l'organismo umano, come la seta. La tesi mostra un metodo per introdurre nanostrutture all’interno della seta che permettono di scegliere la lunghezza d’onda della luce trasmessa, aprendo la strada a sensori ottici impiantabili.

La terza parte è dedicata ai transistor elettrochimici organici, dispositivi che permettono di misurare molecole come il glucosio o componenti del sudore, e che potrebbero contribuire alla prossima generazione di sensori indossabili a basso costo. Per definire le geometrie di questi sensori, è solitamente necessario ricorrere all’uso di una camera bianca. Questa tesi presenta una tecnica basata sulla scrittura laser che raggiunge la stessa precisione, ma al di fuori della camera bianca.

L'ultima parte è dedicata agli organi-su-chip, piattaforme miniaturizzate dove cellule umane vengono coltivate per ricreare il funzionamento di tessuti ed organi. Queste piattaforme potrebbero ridurre il ricorso alla sperimentazione animale per testare nuovi farmaci. La tesi sviluppa un sensore ottico a basso costo, in grado di monitorare in tempo reale le funzioni vitali delle cellule, tramite parametri come il pH e l'ossigeno.

Il filo conduttore di tutto il lavoro è uno: comprendere a fondo il principio fisico del sensore, le proprietà dei materiali, e le possibilità degli strumenti a disposizione. Questa comprensione permette di sviluppare processi di fabbricazione più semplici, più economici, e più pronti a uscire dal laboratorio rispetto agli approcci tradizionali.

Place, publisher, year, edition, pages
KTH Royal Institute of Technology, 2026. , p. 87
Series
TRITA-EECS-AVL ; 2026:35
National Category
Nanotechnology Nanotechnology for/in Life Science and Medicine
Identifiers
URN: urn:nbn:se:kth:diva-381000ISBN: 978-91-8106-585-5 (print)OAI: oai:DiVA.org:kth-381000DiVA, id: diva2:2058396
Public defence
2026-06-09, https://kth-se.zoom.us/j/63919672218, F3, Lindstedtsvägen 26, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

QC 20260507

Available from: 2026-05-08 Created: 2026-05-07 Last updated: 2026-05-12Bibliographically approved
List of papers
1. Scalable Fabrication of 4 nm Silicon Nanopores by Self-Limiting Metal-Assisted Chemical Etching Combined with Optical Process Control
Open this publication in new window or tab >>Scalable Fabrication of 4 nm Silicon Nanopores by Self-Limiting Metal-Assisted Chemical Etching Combined with Optical Process Control
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Solid-state nanopores in ultrathin (<20 nm) membranes enable label-free single-molecule sensing, but their adoption as sensors is limited by the lack of scalable manufacturing methods that deliver nanopores with single-nanometer reproducibility. Self-limiting metal-assisted chemical etching (MACE) in silicon-on-insulator (SOI) membranes offers a parallel wet-chemical route for nanopore fabrication, yet prior demonstrations lacked a predictive design rule and required electron microscopy or electrical tests for confirming presence and number of pores. Here, we convert self-limiting MACE into a manufacturing-oriented workflow with optical process control to obtain and verify the formation of 4 nm nanopores in a scalable fashion. We decouple the deposition of 200 ± 10 nm gold (Au) nanoparticles from etching, enabling independent optimization of the two steps. The nanoparticle size allows for particle-per-membrane counting by dark-field optical microscopy, so that deposition can be repeated when counts are below target. We then map etching behavior across Au nanoparticle diameter d (10–200 nm) and silicon (Si) device-layer thickness t (5–18 nm), finding that d/t ≥ 0.8 ratio predicts self-limiting MACE behavior, where pore diameter becomes independent of particle size. In this regime, 200 ± 10 nm catalysts yield 4 ± 1 nm pores, corresponding to a reduction of ~50× in pore diameter and ~10× in pore-diameter variability compared to the catalyst diameter and related variability. Successful through-membrane pore formation produces undercuts in the buried oxide (typically ~200–300 nm diameter) beneath each pore, which can be characterized for each membrane by bright-field microscopy and used as proxy for the otherwise optically invisible 4 nm pores. Together, the predictive d/t framework and two-stage optical verification establish a scalable wet-chemical route to fabricate nanopores for biomolecular sensing and related nanofluidic devices.

Keywords
nanopore sensors, ultrathin membranes, silicon-on-insulator, MACE, self-limiting etching, parallel fabrication, process monitoring
National Category
Nanotechnology for/in Life Science and Medicine Nanotechnology Nanotechnology for Material Science
Identifiers
urn:nbn:se:kth:diva-380997 (URN)
Note

QC 20260508

Available from: 2026-05-07 Created: 2026-05-07 Last updated: 2026-06-08Bibliographically approved
2. Sub-5 nm Silicon Nanopore Sensors: Scalable Fabrication via Self-Limiting Metal-Assisted Chemical Etching
Open this publication in new window or tab >>Sub-5 nm Silicon Nanopore Sensors: Scalable Fabrication via Self-Limiting Metal-Assisted Chemical Etching
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2025 (English)In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 17, no 6, p. 9047-9058Article in journal (Refereed) Published
Abstract [en]

Solid-state nanopores offer unique possibilities for biomolecule sensing; however, scalable production of sub-5 nm pores with precise diameter control remains a manufacturing challenge. In this work, we developed a scalable method to fabricate sub-5 nm nanopores in silicon (Si) nanomembranes through metal-assisted chemical etching (MACE) using gold nanoparticles. Notably, we present a previously unreported self-limiting effect that enables sub-5 nm nanopore formation from both 10 and 40 nm nanoparticles in the 12 nm thick monocrystalline device layer of a silicon-on-insulator substrate. This effect reveals distinctive etching dynamics in ultrathin Si nanomembranes, enabling precise control over nanopore dimensions. The resulting nanopore sensor, suspended over self-aligned spheroidal oxide undercuts with diameters of just a few hundred nanometers, exhibited low electrical noise and high stability due to encapsulation within dielectric layers. In DNA translocation experiments, our nanopore platform could distinguish folded and unfolded DNA conformations and maintained stable baseline conductance for up to 6 h, demonstrating both sensitivity and robustness. Our scalable nanopore fabrication method is compatible with wafer-level and batch processing and holds promise for advancing biomolecular sensing and analysis.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2025
Keywords
nanopores sensing nanofluidic devices MACE DNA translocation
National Category
Nano Technology
Identifiers
urn:nbn:se:kth:diva-359677 (URN)10.1021/acsami.4c19750 (DOI)001409913500001 ()39882662 (PubMedID)2-s2.0-85216612370 (Scopus ID)
Funder
Swedish Research Council, 2018-06169Swedish Research Council, 2021-00171Knut and Alice Wallenberg Foundation, KAW 2003.0198
Note

QC 20250214

Available from: 2025-02-07 Created: 2025-02-07 Last updated: 2026-05-12Bibliographically approved
3. Stress-induced ripping enables ultrathin nanopores with sub-lithographic resolution
Open this publication in new window or tab >>Stress-induced ripping enables ultrathin nanopores with sub-lithographic resolution
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Nanopores in ultrathin membranes are central to single-molecule sensing, filtration, and energy conversion, yet fabrication of solid-state nanopores remains limited by fundamental trade-off between resolution, throughput, and tool complexity. Here, we report a scalable process that exploits stress-induced mechanical ripping in ultrathin membranes to detach a nanoscale membrane patch, enabling the deterministic formation of sub-lithographic nanopores scaling down to the sub-10 nm regime. Using this approach, we demonstrate wafer scale fabrication of nanopores at densities exceeding 10⁵ pores per cm² in dielectric (HfO₂), semiconducting (SiGe), and metallic (Cr) membranes, including suspended HfO₂ membranes as thin as 2 nm. We demonstrate the utility of the fabricated nanopores for high-performance surface enhanced Raman readouts of single molecule translocations. Beyond nanopore fabrication, this fracture-based approach points to broader opportunities for nanometer- and atomic-scale structuring of ultrathin materials.

National Category
Nanotechnology
Identifiers
urn:nbn:se:kth:diva-380998 (URN)
Note

QC 20260512

Available from: 2026-05-07 Created: 2026-05-07 Last updated: 2026-06-08Bibliographically approved
4. Engineering optical defects in biopolymer photonic lattices
Open this publication in new window or tab >>Engineering optical defects in biopolymer photonic lattices
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2018 (English)In: Journal of Materials Chemistry C, ISSN 2050-7526, E-ISSN 2050-7534, Vol. 6, no 5, p. 966-971Article in journal (Refereed) Published
National Category
Nano Technology
Identifiers
urn:nbn:se:kth:diva-290815 (URN)
Note

QC 20210224

Available from: 2021-02-24 Created: 2021-02-24 Last updated: 2026-05-07Bibliographically approved
5. Cleanroom‐Free Direct Laser Micropatterning of Polymers for Organic Electrochemical Transistors in Logic Circuits and Glucose Biosensors
Open this publication in new window or tab >>Cleanroom‐Free Direct Laser Micropatterning of Polymers for Organic Electrochemical Transistors in Logic Circuits and Glucose Biosensors
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2024 (English)In: Advanced Science, E-ISSN 2198-3844, Vol. 11, no 27Article in journal (Refereed) Published
Abstract [en]

Organic electrochemical transistors (OECTs) are promising devices for bioelectronics, such as biosensors. However, current cleanroom-based microfabrication of OECTs hinders fast prototyping and widespread adoption of this technology for low-volume, low-cost applications. To address this limitation, a versatile and scalable approach for ultrafast laser microfabrication of OECTs is herein reported, where a femtosecond laser to pattern insulating polymers (such as parylene C or polyimide) is first used, exposing the underlying metal electrodes serving as transistor terminals (source, drain, or gate). After the first patterning step, conducting polymers, such as poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS), or semiconducting polymers, are spin-coated on the device surface. Another femtosecond laser patterning step subsequently defines the active polymer area contributing to the OECT performance by disconnecting the channel and gate from the surrounding spin-coated film. The effective OECT width can be defined with high resolution (down to 2 µm) in less than a second of exposure. Micropatterning the OECT channel area significantly improved the transistor switching performance in the case of PEDOT:PSS-based transistors, speeding up the devices by two orders of magnitude. The utility of this OECT manufacturing approach is demonstrated by fabricating complementary logic (inverters) and glucose biosensors, thereby showing its potential to accelerate OECT research.

Place, publisher, year, edition, pages
Wiley, 2024
Keywords
conjugated polymer, direct writing, organic electrochemical transistor, poly(3, 4-ethylenedioxythiophene) polystyrene sulfonate, ultrashort pulsed lasers
National Category
Organic Chemistry Other Electrical Engineering, Electronic Engineering, Information Engineering Other Materials Engineering
Identifiers
urn:nbn:se:kth:diva-342521 (URN)10.1002/advs.202307042 (DOI)001142422700001 ()38225700 (PubMedID)2-s2.0-85182492139 (Scopus ID)
Funder
Swedish Research Council, 2018‐03483Swedish Research Council, 2022‐04060Swedish Research Council, 2022‐02855Knut and Alice Wallenberg Foundation, 2015.0178Knut and Alice Wallenberg Foundation, 2020.0206Knut and Alice Wallenberg Foundation, 2021.0312Swedish Research Council, 2022-00374
Note

QC 20240123

Available from: 2024-01-23 Created: 2024-01-23 Last updated: 2026-05-07Bibliographically approved
6. A microfluidic optical platform for real-time monitoring of pH and oxygen in microfluidic bioreactors and organ-on-chip devices
Open this publication in new window or tab >>A microfluidic optical platform for real-time monitoring of pH and oxygen in microfluidic bioreactors and organ-on-chip devices
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2016 (English)In: Biomicrofluidics, E-ISSN 1932-1058, Vol. 10, no 4Article in journal (Refereed) Published
Abstract [en]

There is a growing interest to develop microfluidic bioreactors and organ-on-chipplatforms with integrated sensors to monitor their physicochemical properties and tomaintain a well-controlled microenvironment for cultured organoids. Conventionalsensing devices cannot be easily integrated with microfluidic organ-on-chip systemswith low-volume bioreactors for continual monitoring. This paper reports on thedevelopment of a multi-analyte optical sensing module for dynamic measurementsof pH and dissolved oxygen levels in the culture medium. The sensing system wasconstructed using low-cost electro-optics including light-emitting diodes and siliconphotodiodes. The sensing module includes an optically transparent window formeasuring light intensity, and the module could be connected directly to a perfusionbioreactor without any specific modifications to the microfluidic device design. Acompact, user-friendly, and low-cost electronic interface was developed to controlthe optical transducer and signal acquisition from photodiodes. The platformenabled convenient integration of the optical sensing module with a microfluidicbioreactor. Human dermal fibroblasts were cultivated in the bioreactor, and thevalues of pH and dissolved oxygen levels in the flowing culture medium were measuredcontinuously for up to 3 days. Our integrated microfluidic system providesa new analytical platform with ease of fabrication and operation, which can beadapted for applications in various microfluidic cell culture and organ-on-chipdevices.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2016
National Category
Medical Biotechnology
Identifiers
urn:nbn:se:kth:diva-290818 (URN)10.1063/1.4955155 (DOI)000383911400024 ()27648113 (PubMedID)2-s2.0-84984829648 (Scopus ID)
Note

QC 20210225

Available from: 2021-02-24 Created: 2021-02-24 Last updated: 2026-05-07Bibliographically approved
7. Multisensor-integrated organs-on-chips platform for automated and continual in situ monitoring of organoid behaviors
Open this publication in new window or tab >>Multisensor-integrated organs-on-chips platform for automated and continual in situ monitoring of organoid behaviors
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2017 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 12, p. E2293-E2302Article in journal (Refereed) Published
Abstract [en]

Organ-on-a-chip systems areminiaturizedmicrofluidic 3D human tissue and organ models designed to recapitulate the important biological and physiological parameters of their in vivo counterparts. They have recently emerged as a viable platform for personalized medicine and drug screening. These in vitro models, featuring biomimetic compositions, architectures, and functions, are expected to replace the conventional planar, static cell cultures and bridge the gap between the currently used preclinical animal models and the human body. Multiple organoid models may be further connected together through the microfluidics in a similar manner in which they are arranged in vivo, providing the capability to analyze multiorgan interactions. Although a wide variety of human organ-on-a-chip models have been created, there are limited efforts on the integration of multisensor systems. However, in situ continual measuring is critical in precise assessment of the microenvironment parameters and the dynamic responses of the organs to pharmaceutical compounds over extended periods of time. In addition, automated and noninvasive capability is strongly desired for long-term monitoring. Here, we report a fully integrated modular physical, biochemical, and optical sensing platform through a fluidics-routing breadboard, which operates organ-on-a-chip units in a continual, dynamic, and automated manner.We believe that this platform technology has paved a potential avenue to promote the performance of current organ-on-a-chip models in drug screening by integrating a multitude of real-time sensors to achieve automated in situ monitoring of biophysical and biochemical parameters.

Place, publisher, year, edition, pages
National Academy of Sciences, 2017
National Category
Medical Biotechnology
Identifiers
urn:nbn:se:kth:diva-290816 (URN)10.1073/pnas.1612906114 (DOI)000396893600007 ()28265064 (PubMedID)2-s2.0-85016119264 (Scopus ID)
Note

QC 20210226

Available from: 2021-02-24 Created: 2021-02-24 Last updated: 2026-05-07Bibliographically approved

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