1,721,218 research outputs found
Optimization of a plasmonic-based microfluidic biosensor for future application in handheld devices
No full textSCGCGR-53 1089; EPFL STI IBI-STI BIOS. Consultable sur demande à la Bibliothèque de l'EPFL / Offered in consultation at the EPFL library
Design and Application of Functional Mid-IR Metasurfaces for Enhanced Light-Matter Interaction and Sensing
No full textMetasurfaces, planar arrays of subwavelength resonators, have emerged as powerful tools for versatile light manipulation in compact formats across different spectral ranges. Among these, the mid-infrared (mid-IR) is uniquely characterized by its interaction with vibrational modes, making it especially valuable for biological and material sciences. Yet, the full potential and adoption of mid-IR metasurfaces remains untapped due to persistent material and design challenges. This thesis advances metasurface capabilities in the mid-IR through innovations in design, fabrication, and actuation, developing platforms tailored for enhanced lightâ matter interactions, label-free sensing, nonlinear optics, and chiral control.
We first introduce resonance-gradient metasurfaces, which combine broadband spectral coverage with high quality-factor (high-Q) resonances. By continuously varying the size of dielectric nanoresonators along the metasurface, we achieve a gapless spectrum of local high-Q resonances. This enables label-free molecular detection via surface-enhanced infrared absorption, resolving complex polymer mixtures, probing biomolecular interactions in multistep assays, and exploring vibrational strong coupling.
We then extend this concept to nonlinear optics. Using Germanium-based metasurfaces with bone-like resonator geometries, we demonstrate enhanced and tunable third- and fifth-harmonic generation. By engineering the local resonances to match pump wavelengths, we enable spatially selective and spectrally wide nonlinear responses, illustrating how structural design can be leveraged for broadband high-harmonic tuning.
Second, a symmetry-guided framework is developed for mid-IR chiral metasurfaces, overcoming the limitations of trial-and-error and black-box AI design. Group-theoretical analysis of meta-atom rotation and lattice symmetry led to metasurfaces with tunable circular dichroism across all planar Bravais lattices with predictable zero-chirality anchor points. Applications include dual-channel image encoding in both transmission and chiral response, offering routes to anti-counterfeiting and advanced polarization control.
Finally, the thesis addresses practical challenges in experimentally realizing ultra-high-Q resonances. By employing suspended crystalline silicon membranes, we eliminate losses in substrate and high refractive index resonator material, achieving Q-factors exceeding 2500 with modulation over 50% - an order-of-magnitude improvement over prior results. This advance enables the detection and control of increasingly subtle optical effects and is exemplified through voltage-controlled electro-thermal modulation of the resonances up to 15 kHz. These actively tunable metasurfaces approach the linewidths of gas-phase molecular absorption features, making them particularly promising for trace gas detection. Here, active tuning could facilitate spectral alignment with target absorption lines beyond fabrication limitations, offering a robust platform for reconfigurable mid-IR photonic devices.
Together, these contributions establish a versatile toolbox for designing, fabricating, and applying mid-IR metasurfaces in molecular spectroscopy, nonlinear optics, and chiral light control - advancing the field toward practical, scalable, and active photonic devices.BIO
Nanoparticle-enhanced Imaging Based Plasmonic Biosensor
No full textEfficient medical care fundamentally relies on the ability to provide a timely and accurate diagnosis. Thanks to advances in biomedical research, specific molecules called diagnostic molecular biomarkers have been discovered in the human body that help indicate diseases in highly specific ways. The small size and low concentration of many of these molecules pose a serious challenge to detecting them from the rich content of human blood and other liquid biopsies. Medical laboratories use large and complex tools to enable sensitive and robust quantification of such biomarkers. However, these approaches are time-consuming, require expensive equipment and delay the doctors' decision-making. Therefore, compact, cost-effective and rapid technologies that enable testing of biological fluids to identify low-abundance biomarkers directly at the patientâ s bedside are critically needed to assist the modern healthcare.
This doctoral thesis presents a novel biosensor that enables highly sensitive, accurate and rapid detection of disease biomarkers in a low-cost and portable device directly from patient blood serum. The first major and original contribution is on the introduction of an innovative sensing principle that uses sub-wavelength gold nanoparticles and large area periodic gold nanohole arrays. The nanohole arrays consist of millions of nano-perforations in a thin gold metal film on a glass substrate and enable a plasmonic phenomenon called extraordinary optical transmission. The interactions between nanoparticles and nanoholes are imaged in a spectrometer-free set-up and enable the detection of individual molecule binding in complex samples. Unlike conventional plasmonic sensing approaches that rely on spectral shifts of plasmonic resonances, our method exploits intensity modulations caused by individual nanoparticles on nanohole arrays. Therefore, the technology overcomes classical plasmonic detection limits imposed by refractive index sensitivity. The work shows that the biosensor achieves highly sensitive detection, meeting clinically relevant concentrations, and can provide a powerful platform for biomarkers testing.
The second major and original contribution includes the integration of the novel plasmonic sensor technology into a portable point-of-care (POC) device. It is deployed in a hospital and validated with a wide range of patient samples with inflammatory conditions. The device enables ultra-sensitive detection of two sepsis-related biomarkers, procalcitonin, and C-reactive protein. The tests with biobank patient samples revealed that the novel POC device provides diagnostic performance equivalent to gold standard laboratory immunoassays. Moreover, identification of biomarker levels can be performed in under 15 minutes on-site, providing critical advantage compared to laboratory testing.
The results of this thesis build upon a broad interdisciplinary knowledge ranging from engineering (including plasmonics, imaging, nanofabrication, and device integration) to chemistry, biology, and medical diagnostics. The plasmonic sensing principle introduced in this work offers a promising strategy for the development of many new biosensing applications, while the developed point-of-care biosensor has the potential to provide a rapid and accurate tool to assist the diagnosis and management of diseases in various settings, improving the quality of medical care for more people.BIO
Infrared nanoplasmonic metasurfaces augmented by artificial intelligence for universal biosensing
No full textNanoplasmonic metasurfaces have shown outstanding light-matter interaction enhancement capabilities, leading to their emergence as powerful platforms for highly sensitive biospectroscopy. Metasurface-enhanced biospectroscopy offers unprecedented opportunities for biological studies, and its full potential remains to be unleashed. Mid-IR metasurfaces, in particular, are very promising because they can act as amplifiers of fingerprint-like molecule vibrations, which are plentiful in this rich spectral range. In this thesis, we develop novel nanoplasmonic designs coupled with custom microfluidics and artificial intelligence-based data analysis models to demonstrate real-time, label-free, chemically-specific, and non-destructive monitoring of biomolecules and their interactions in aqueous media. Our first nanoplasmonic design combines optimized grating order-coupled nanoantenna arrays with protein-accessible nanogaps to enable the high sensitivity monitoring of proteins and their three-dimensional structures in aqueous media. The engineered nanoantennas reach electric field intensity enhancements of up to five orders of magnitude and provide chemically specific detection of proteins and their secondary structures down to picograms and nanograms per milliliter, respectively.
In the next part of the thesis, we develop multiresonant metasurfaces to monitor interactions between biomolecules with vibrational fingerprints in different parts of the mid-IR range. Our first effort focuses on developing a nanoplasmonic design for simultaneous monitoring of both proteins and lipid molecules. Lipids are another important class of biomolecules as they are the building blocks of biological membranes, and lipid-protein interactions are at the core of many cellular processes. New analytical tools for their study in water and at the monolayer level are of fundamental importance. Therefore, we introduce a dual-resonant nanoplasmonic design coupled to machine learning-based data analysis to overcome current sensor challenges. We apply our technology to a dynamic system involving synaptic vesicle mimics and demonstrate that we can resolve complex mass-preserving biological interactions in real-time. This is a remarkable feat that traditional non-chemically specific analytical measurement tools such as surface plasmon resonance or quartz crystal microbalance spectroscopy could not achieve. In the final part of the thesis, we develop yet another multiresonant design for broadband coverage of the whole mid-IR range. We couple our sensor to a deep learning model to resolve a dynamic biological system including all major classes of biomolecules simultaneously. Specifically, we resolve the toxic peptide-induced release of carbohydrates and nucleotides from exosome-like bionanoparticles.BIO
Mid-Infrared plasmonic nanoantennas for ultrasensitive detection of proteins and their secondary structure
No full textEngineered plasmonic nanostructures have emerged as powerful sensing platforms and are promoting novel applications in various fields. By providing extreme field confinement down to molecular dimensions and enhancing light-matter interaction at the nanoscale, nanoplasmonics demonstrate outstanding potential for biomolecular analysis. In addition to their extensive applications at visible and near-infrared range, such nanoplasmonic structures deliver unique possibilities for biomolecular studies with surface enhanced infrared absorption spectroscopy based on the distinct molecular vibrations in mid-infrared (mid-IR) spectral range. The mid-IR chemical fingerprints of proteins incorporate comprehensive insight into their secondary structures and thus can provide conformational information. The main goal of this thesis is to extend the applications of mid-IR nanoplasmonics in ultrasensitive detection and analysis of proteins towards enabling their in vitro characterization with innovative approaches.
First, we present suspended mid-IR polarization-insensitive nanoantennas on nanopedestals for ultrasensitive vibrational spectroscopy. This system provides fully accessible near-field intensity enhancements that are realized with a new isotropic etching nanofabrication process. Our experimental results demonstrate improved sensitivity compared to the conventional antennas on substrates based on the optimized field overlap with analytes as predicted in numerical simulations. Such a mid-IR plasmonic sensor can be effectively employed in chip-based ultrasensitive detection.
Next, we demonstrate for the first time the secondary structure identification of nanometer thin layers of proteins as small as 14 kDa using mid-IR plasmonic nanorods on IR transparent substrates for implementation of challenging in-solution measurements. We sensitively resolved the spectral content of plasmonically enhanced amide I fingerprint. Through its second derivative analysis, we successfully extracted major protein secondary conformations, random coil and cross β-sheet, related to aggregation of α-synuclein protein involved in Parkinsonâ s disease. Using an additional model protein with a native β-sheet structure, we demonstrate the sensitivity of our approach in extracting minute conformational differences. The tolerance of this new method for extracting the secondary structure signatures of thin protein layers to the resonance matching to amide I range due to any minor nanofabrication variations is an important finding for demonstrating its robustness and reproducibility.
Finally, we present our biosensor integrated with a fluidic device for dynamic in situ secondary structure analysis of a protein monolayer upon external stimuli. We monitored reversible conformational changes from random coil to β-sheet in immobilized α-synuclein in real-time. Additionally, we establish the correlation between the obtained vibrational components using nanoplasmonics and that of IR transmission with polymer thin films and therefore demonstrate the reliability of our approach for mid-IR protein conformational investigations.
Our platform can facilitate highly sensitive protein analysis at various conditions or in interactions with biomolecules such as lipids. These results are of great interest for multidisciplinary engineering and applied aspects of photonics and can open up a broad application area for mid-IR nanoplasmonics and devices.BIO
Label-free plasmonic biosensors for real-time live cell analysis
No full textFor decades, the understanding of life has been focused on its most fundamental building blocks: molecules. Deciphering the dynamic activities of protein molecules in human cells is of vital significance for fundamental and clinical studies. The minuscule scale of protein molecules poses a great challenge for precise quantification. Labeling the molecules of interest with fluorescent and enzymatic tags has thus become an effective strategy to indicate their existence. However, the addition of extrinsic fluorescent tags has shown a number of evident side effects interfering with protein functions and cell biology. The extra steps caused by molecular labeling also increase the complexity of the entire assay and decrease the temporal resolution of the measurement from hours to days. These drawbacks of traditional strategies inevitably hinder the real-time monitoring of cellular activities with minimum interval or external interference.
This doctoral thesis focuses on the engineering and demonstration of novel label-free biosensing platforms for real-time cell studies: (1) the secretion of protein molecules from live cells, and (2) the characterization of cellular interactions.
For the first topic, a biosensor using plasmonic nanohole arrays as the core sensing elements has been designed. These nanohole arrays consist of a thin gold film perforated with periodic nanoholes. They enable extraordinary optical transmission (EOT), an optical phenomenon that has shown promising capabilities for biochemical detection. This thesis demonstrates, for the first time the application of these structures for real-time monitoring of protein secretions from live cells. On the one hand, the secretion of VEGF (a type of growth factor) from live cancer cells has been monitored in real-time at the temporal resolution of seconds without any additional sample treatment. On the other hand, the integration with the advanced microfluidic system has enabled the biosensor to measure secretion events at the single-cell level by solving a number of technical issues (e.g., low analyte abundance, liquid evaporation). In particular, the real-time production of IL-2 (a cytokine) from single lymphoma cells were monitored for hours, which shows the exceptional versatility of this optofluidic nanobiosensor.
For the second topic, a multiparametric surface plasmon resonance (SPR) biosensor has been exploited to investigate interactions between T-cell receptors (TCR) and peptide-major histocompatibility complexes (pMHC). This type of interaction plays a central role in T cell-mediated immunity. Notably, intact human T cells - rather than purified recombinant TCR proteins - were directly used as analytes. A biomimicking lipid membrane was created on the sensor surface to present pMHC molecules, enabling the capture of T cells in vitro. Therefore, the affinity (e.g., binding kinetics) between different types of T cells and membrane-bound pMHC molecules can be readily measured in a label-free manner.
The results presented in this thesis rely on a wide range of engineering technologies (imaging, microfluidics, and micro-/nano-manufacturing) and knowledge of biology, chemistry, and optics. The proposed methods using label-free plasmonic biosensors represent a promising strategy to overcome the challenges related to current biochemical analyses. We anticipate that plasmonic biosensors will boost new biodetection methodologies for biomedical research.BIO
Dielectric metasurfaces and their applications for optical biosensing
No full textOver the past century, our understanding of life has been focused on its most fundamental building blocks: molecules. Biological molecules, such as proteins found in blood, other body fluids, or tissues, are excellent guides to identifying a normal or abnormal process, condition, or disease. Nonetheless, their minuscule scale presents challenges in accurately quantifying protein molecules. Photonic biosensors provide a convenient method for probing analytes using light. Nanophotonics, the study of light's interaction with nanoscale structures, has emerged as a promising platform to tightly confine the light and overcome the scale barrier between minuscule biomarkers and electromagnetic fields.
Metasurfaces have recently garnered considerable attention as an auspicious platform for biosensing applications. These two-dimensional engineered structures or artificial electromagnetic media are made of unit cells much smaller than their operating wavelength. High-index dielectric nanostructures are excellent candidates because of their ability to confine and scatter light strongly with relatively low absorption losses. Due to their unique optical characteristics, dielectric metasurfaces can realize sharp resonances that are highly sensitive to the minute changes of refractive index in the vicinity of the nanoresonators, making them favorable for label-free refractometric sensing and providing reliable quantitative information.
This doctoral thesis aims to demonstrate state-of-the-art metasurface technology for imaging-based refractometric biosensing in both end-point and real-time modalities and investigate dielectric metasurface resonance features and design parameters for optimal functionalities.
Novel applications of high-quality-factor (high-Q) dielectric metasurfaces supporting modes rooted in the physics of bound-states-in-the-continuum are exploited. The high-Q metasurface sensors coupled with an imaging-based optical setup and advanced data processing methods have enabled the construction of an end-point sensing platform with superior sensitivity. Our hyperspectral imaging setup provides spectral information from the sensing area with pixel resolution, which, combined with advanced data processing methods, allows for detecting highly diluted samples.
Additionally, a real-time imaging-based biosensor employing an optofluidic chip comprising high-Q dielectric metasurfaces and microfluidics has been demonstrated. The method implements an aided imaging approach based on novel data processing to extract spectral shift information from time-resolved single-wavelength intensity images for highly reliable performance. This approach is suitable for multiplexed detection of biomarkers in real-time for high-throughput monitoring. As a proof-of-concept, we performed real-time in-flow experiments using the optofluidic device to detect extracellular vesicles secreted from breast-cancer tumors with clinically relevant results.
The developed sensing devices rely on a wide range of engineering technologies. Innovative biosensing platforms have been presented by incorporating dielectric metasurfaces with imaging, microfluidics, micro- and nano-fabrication techniques, and novel data processing strategies. These methods hold great promise to overcome the challenges of biomedical diagnostics and pave the way for futuristic point-of-care devices enabling early diagnosis, treatment monitoring, personalized medicine, and democratized healthcare systems.BIO
Metasurfaces for label-free biosensing mid-infrared optics and active photonic devices
No full textNovel two-dimensional metamaterials, known as metasurfaces, have emerged as a breakthrough platform for controlling electromagnetic wave properties at the nanoscale. These metasurfaces consist of subwavelength nanoantennas or so-called meta-atoms, which can be engineered at will to obtain the desired optical functionalities. The doctoral thesis aims to advance the current state-of-the-art metasurface technology for mid-infrared (mid-IR) applications.
The first part of the thesis focuses on surface-enhanced infrared absorption spectroscopy with metasurfaces supporting high-quality (high-Q) resonances. Specifically, it introduces an imaging-based nanophotonic method for detecting mid-infrared molecular fingerprints and its' implementation in chemical identification and compositional analysis of surface-bound analytes. This technique features a two-dimensional pixelated dielectric metasurface with a range of spectrally selective resonances, each tuned to a discrete frequency. The method enables a molecular absorption signature read-out at multiple spectral points and the translation of resulting information into a barcode-like spatial absorption map. Furthermore, the thesis demonstrates high-Q angle-multiplexed metasurfaces, which deliver a large number of on-demand resonances in the mid-IR. This method combines chemically specific broadband IR detection with device-level simplicity and spectrometer-less operation of angle-scanning refractometry. Strikingly, these novel metasurface-based chemical detection methods are capable of resolving absorption fingerprints without the need for spectrometry, thereby paving the way toward sensitive and versatile miniaturized mid-IR spectroscopy devices.
Yet another major contribution of the thesis includes a universal method for large-scale nanofabrication of various mid-IR metasurfaces. The core of the approach is based on CMOS-compatible processes where the metasurfaces are fabricated on free-standing metal-oxide membranes. To demonstrate the versatility of our method, we realized metasurfaces for a diverse range of applications in the mid-IR, ranging from highly efficient optical wavefront and polarization control to plasmonic metasurfaces for label-free biochemical detection in aqueous solutions. The membrane-based metasurface concept overcomes the limitations of currently used materials in the mid-IR, therefore enabling mass-production of diverse photonic devices with applications in key areas such as biosensing, optical communications, thermal imaging and spectroscopy.
The last chapter of the doctoral thesis shows programmable all-dielectric Huygens' metasurfaces consisting of multi-layer Ge disk meta-units with strategically incorporated nonvolatile phase change material Ge3Sb2Te6. Switching the phase-change material between its' amorphous and crystalline structural states enables nearly full dynamic light phase control with high transmittance in the mid-IR. The versatility of the method is demonstrated by optically programming the spatial light phase distribution of the metasurface with single meta-unit precision and retrieving high-resolution phase-encoded images using hyperspectral measurements. The programmable metasurface concept overcomes the static limitations of previous dielectric metasurfaces and moves the metasurface-based technology one step closer to ultra-compact active optical elements encompassing tunable lenses, dynamic holograms, and solid-state spatial light modulators.BIO
Multimodal Imaging Platform for Spatiotemporal Interrogation of Dynamics in Single Cells and Spheroids
No full textCells function through a complex interplay of intracellular, membrane, and extracellular dynamics. Among these, extracellular dynamics involve interactions with the environment via biomolecule secretion, crucial for communication. Key factors influencing secretion-based communication include: (1) spatial and temporal regulation to ensure messages are delivered at the right time and place; (2) heterogeneous secretory behaviors for scenario-specific responses; and (3) varying culture conditions, such as 2D and 3D models. Understanding secretion-based signaling requires technologies that monitor secretions with temporal and spatial resolution, analyze single-cell variability, and operate across culture models.
Conventional methods, though informative, have limitations: they often assess populations, provide only end-point data, or compromise cell viability. Novel biosensors aim to overcome these drawbacks. Fluorescence-based methods allow high-throughput, multi-target analysis at the single-cell level but are limited to end-point measurements due to labeling and washing steps. To capture real-time kinetics non-invasively, label-free approaches have emerged. Various electrochemical and optical biosensors aim to retain conventional advantages while addressing their flaws, though many are still early in development.
In the first part of this thesis, we introduce a microwell array for spatiotemporal observation of extracellular secretions from hundreds of single cells. It integrates gold nanohole array biosensors leveraging extraordinary optical transmission, coupled with machine learning-enhanced image processing. This platform is demonstrated in three applications: monitoring secretion and motility of cell lines over time; tracking release kinetics during distinct cell death modalities; and visualizing antibody-secreting behaviors of human donor-derived cells.
The second part presents a multimodal imaging platform combining nanoplasmonic sensing with multichannel fluorescence imaging to analyze intra- and extracellular processes at single-cell resolution. The plasmonic module tracks secretion distribution in real time, while the fluorescence microscopy visualizes interconnected intracellular and membrane dynamics. This multiparametric approach is applied to studying secretion alongside organelles and metabolism, simultaneous protein expression and secretion, and correlating cell cycle phases with secretory profiles.
The third part extends the platform (introduced in previous chapter) to enable concurrent monitoring of dynamics within and around arrays of single spheroids at high spatiotemporal resolution. To support long-term, multiparametric analysis of multichannel data, we apply deep learning-enhanced image processing. Applied to tumor spheroids, the platform captures growth factor secretion patterns along with 2D/3D morphometric changes and viability, distinguishing between untreated and drug-treated groups.
In summary, the thesis demonstrates the potential of multimodal imaging for exploring interconnected cellular behaviors. Simultaneous analysis of processes like protein expression, metabolism, secretion, morphology, and viability yields holistic insights into cellular mechanisms, supporting advances in basic science, disease modeling, and therapeutic development.BIO
Label-free plasmonic microarray for multiplexed analysis of cells and tumor organoids
No full textInvestigating the dynamic activities of protein expression and signaling in living organisms is a crucial focus of intense research aimed at elucidating the processes that underlie disease progression and improving treatments and drug development. Resolving these activities from each individual provides particularly valuable information, as it helps decipher cell heterogeneity and enhances our understanding of numerous biological processes. However, quantifying protein secretion from single cells in real-time remains a challenging task due to the limitations of existing technologies. This is an area where nanophotonics offers promising opportunities, as it allows the detection of minute protein molecules in a label-free manner due to the strong light-matter interaction. Integration with microfluidic technology further enables high-throughput analysis, which is key to enabling potential screening applications.
This thesis reports on the development of a high-throughput spectroscopic imaging platform and advanced integrated optofluidic plasmonic biosensor arrays that enable the real-time monitoring of single-cell and single-organoid secretion in a label-free manner. The platform incorporates automated stage scanning and data collection of both spectroscopic and bright-field images, which allows the simultaneous measurement of a hundred individual cells/organoids at a time. The plasmon-mediated extraordinary optical transmission of the gold nanohole arrays enables the ultrasensitive detection of the secreted protein analytes. Additionally, a unique fabrication technique was developed for an open-top microwell membrane with polydimethylsiloxane (PDMS) to isolate single cells for on-chip measurements. For organoids, a special design of two-layer microwell structures was implemented to monitor the organoids while keeping the escaping cells and debris from entering the sensing area and disturbing the signal.
The novel platforms have been used to measure a large number of single cells and single organoids under various conditions, yielding a statistical distribution obtained from extracting the kinetic behavior of the signals of Interleukin-2 (IL-2) secretion from EL4 cells and vascular endothelial growth factor A (VEGFA) secretion from various colorectal tumor organoids. The optical images of the tumor organoids have been processed with machine-learning-based image analysis for an automated segmentation and size evaluation, revealing the organoid size reduction in the condition of drug treatment, consistent with previously reported studies. Furthermore, we leveraged the flexibility of PDMS to design microwell arrays with volumes down to ~65 pL to confine fluorescently labelled individual cancer cells and different types of immune cells. By coupling this chip with time lapse fluorescence microscopy and deep neural network algorithm, we studied quantitively cellular interactions in a high-throughput manner for elucidating the cytotoxity of CD4 and CD8 cells.
This research has addressed the challenges of quantifying protein secretion from single cells in real-time, offering a label-free approach with nanophotonics. These novel platforms make powerful tools to understand the biology of individual living organisms and paves the way for both fundamental biological studies and clinical translations. We anticipate that such interdisciplinary work will open new avenues in biomedical research.BIO
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