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H. Aydogmus

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14 records found

Low-temperature (≤ 350 °C) aluminum-induced layer exchange enables the integration of large-grained polycrystalline silicon–germanium layers into silicon-based optical, electronic, and electromechanical sensors, either in post-processing or at the back-end-of-line of a CMOS flow. We systematically investigate how annealing conditions, metal composition, diffusion control layer, and Al/a-Ge thicknesses influence the crystallization process and the resulting silicon–germanium layer. Our results reveal tunable correlations between process parameters and layer properties, demonstrating that both the crystallinity and the composition of the final layer can be precisely controlled. This work provides practical guidelines for tailoring aluminum-induced layer exchange for silicon–germanium integration across diverse device applications. ...
The mechanisms governing the onset and eventual progression of several neurodegenerative disorders remain poorly understood or even undiscovered. This lack of pathophysiological insight can be partly attributed to reliance on inaccurate in vitro models. Notwithstanding research efforts towards recapitulating brain functions on flat devices, mimicking the brain's three-dimensional (3D) architecture in vitro remains a prime target, as 3D models more closely resemble the functional behavior and dynamic responses of in vivo organs. In this work, we present a novel, wafer-scale approach for microfabrication of soft and transparent 3D microelectrode arrays (MEAs) for in vitro electrical recording and optical inspection of electrogenic cell cultures. The proposed 3D MEAs entail 90μ m -high polydimethylsiloxane-based micro-pyramids featuring multiple, electrically-distinct and vertically-stacked titanium nitride electrodes on their slanted facets. Our innovative 3D MEAs will facilitate the development of physiologically-accurate brain-on-a-chip models capable of monitoring 3D electrical communication in neuronal networks while allowing their simultaneous optical characterization. ...
Conference paper (2025) - Pratik V. Tawade, Hande Aydogmus, Lovro Ivancevic, Jia Jun Yeh, Vasiliki Gkouzioti, Jean Philippe Frimat, Jaap Den Toonder, Massimo Mastrangeli
We present a novel silicon-based organ-on-chip (OoC) device featuring integrated microelectrodes to assess barrier function in biological tissue co-cultures. The microfluidic device consists of two vertically-stacked microchannels separated by a submicron-thin, microporous silicon nitride membrane, enabling in vivo-like proximity for co-cultured tissues. The integrated four-probe electrode geometry on slanted microchannel sidewalls ensures unobstructed optical access to the membrane and consistent measurement repeatability. Experimental validation through electrical impedance spectroscopy supported the device's sensitivity to sodium chloride concentration. Fabricated through a scalable, wafer-scale batch process, the device additionally demonstrated biocompatibility and optical transparency, representing a significant advancement for in situ tissue barrier assessments. ...

Scalable lightsails with enhanced acceleration via neural topology optimization

Journal article (2025) - Lucas Norder, Shunyu Yin, Matthijs H.J. de Jong, Francesco Stallone, Hande Aydogmus, Paolo M. Sberna, Miguel A. Bessa, Richard A. Norte
The Starshot Breakthrough Initiative aims to send gram-scale microchip probes to Alpha Centauri within 20 years, propelled by laser-driven lightsails at a fifth of light speed. This mission demands innovative lightsail materials with meter-scale dimensions, nanoscale thickness, and billions of nanoscale holes for enhanced reflectivity and reduced mass. Unlike the microchip payload, lightsail fabrication requires breakthroughs in optics, materials science, and structural engineering. Our study uses neural topology optimization, revealing a novel pentagonal lattice-based photonic crystal (PhC) reflector. The optimized designs significantly lower the acceleration times and, thereby, launch cost. Crucially, they also enabled orders-of-magnitude fabrication cost reduction. We fabricated a 60 × 60 mm2, 200 nm thick reflector with over a billion nanoscale features, achieving a 9000-fold cost reduction per m2. This represents the highest aspect ratio nanophotonic element to date. While stringent requirements remain for lightsails, scalable, cost-effective nanophotonics present promising solutions for next-generation space exploration. ...
Conference paper (2025) - Jia Jun Yeh, Pratik Tawade, Hande Aydogmus, Aniruddha Paul, Germaine Aalderink, Hans Bouwmeester, Mathieu Odijk, Jaap M.J. Den Toonder, Massimo Mastrangeli
We present the fluidic and electrical packaging of a novel silicon-based trans-epithelial electrical resistance (TEER) sensor chip designed for a modular and standardized organ-on-chip (OoC) platform. The package comprises three key components: the housing of the TEER chip, microfluidic routing for seamless integration with the platform, and electrical connections to a platform-integrated potentiostat. This modular solution enables continuous impedance measurements while maintaining unobstructed optical access to the tissue culture region. Experiments confirmed leak-free fluid flow across the stacked microfluidic channels and stable sensitivity of TiN electrodes to PBS. The TEER module retains optical transparency, bi-ocompatibility, and industrial scalability, supporting advanced in situ tissue barrier assessments in standardized OoC systems. ...
Doctoral thesis (2024) - H. Aydogmus, P.M. Sarro, M. Mastrangeli
Organs-on-Chip (OoC) has been an advancing biotechnological field for the last two decades. By combining engineering and biology, OoC technology makes it possible to mimic the in-vivo behavior of human organs to investigate personalized medicine and disease modeling in-vitro.
Integrating sensors into cell cultures is crucial since the well-being of the culture needs to be monitored in real-time and without compromising cell viability. Monitoring the pH level of the micro-environment is particularly important since it is an indicator of homeostasis for the cell well-being and products of cell metabolism can cause changes in pH, reflecting certain disease phenotypes.
In this work, the integration of electrochemical sensors into OoC devices was shown. The sensors are based on a floating-gate field-effect transistor (FG-FET), a variation of a common active electronic component, and are sensitive to local electric charge. The active component provides inherent amplification, which translates to higher sensitivity and resolution for smaller changes from segregated analytes. The FG-FET was capacitively coupled to two control-gates to determine the working point of the transistor. The sensing area (FG extension) was separated fromthe active FET area to ease the handling of analytes. When there is a net charge in close proximity to the extension of the FG, it induces a change in the formation of the channel of the transistor. This change can be monitored by the drain current.... ...
Review (2024) - Renée Moerkens, Dennis M. Nahon, H. Aydogmus, Bas Lendemeijer, M. Dostanic, P.A. Motreuil-Ragot, Massimo Mastrangeli, Andries D. van der Meer, Christine Mummery, More Authors...
Microphysiological systems (MPSs) are cellular models that replicate aspects of organ and tissue functions in vitro. In contrast with conventional cell cultures, MPSs often provide physiological mechanical cues to cells, include fluid flow and can be interlinked (hence, they are often referred to as microfluidic tissue chips or organs-on-chips). Here, by means of examples of MPSs of the vascular system, intestine, brain and heart, we advocate for the development of standards that allow for comparisons of quantitative physiological features in MPSs and humans. Such standards should ensure that the in vivo relevance and predictive value of MPSs can be properly assessed as fit-for-purpose in specific applications, such as the assessment of drug toxicity, the identification of therapeutics or the understanding of human physiology or disease. Specifically, we distinguish designed features, which can be controlled via the design of the MPS, from emergent features, which describe cellular function, and propose methods for improving MPSs with readouts and sensors for the quantitative monitoring of complex physiology towards enabling wider end-user adoption and regulatory acceptance. ...
Journal article (2023) - Hande Aydogmus, Michel Hu, Lovro Ivancevic, Jean Philippe Frimat, Arn M.J.M. van den Maagdenberg, Pasqualina M. Sarro, Massimo Mastrangeli
Continuous monitoring of tissue microphysiology is a key enabling feature of the organ-on-chip (OoC) approach for in vitro drug screening and disease modeling. Integrated sensing units are particularly convenient for microenvironmental monitoring. However, sensitive in vitro and real-time measurements are challenging due to the inherently small size of OoC devices, the characteristics of commonly used materials, and external hardware setups required to support the sensing units. Here we propose a silicon-polymer hybrid OoC device that encompasses transparency and biocompatibility of polymers at the sensing area, and has the inherently superior electrical characteristics and ability to house active electronics of silicon. This multi-modal device includes two sensing units. The first unit consists of a floating-gate field-effect transistor (FG-FET), which is used to monitor changes in pH in the sensing area. The threshold voltage of the FG-FET is regulated by a capacitively-coupled gate and by the changes in charge concentration in close proximity to the extension of the floating gate, which functions as the sensing electrode. The second unit uses the extension of the FG as microelectrode, in order to monitor the action potential of electrically active cells. The layout of the chip and its packaging are compatible with multi-electrode array measurement setups, which are commonly used in electrophysiology labs. The multi-functional sensing is demonstrated by monitoring the growth of induced pluripotent stem cell-derived cortical neurons. Our multi-modal sensor is a milestone in combined monitoring of different, physiologically-relevant parameters on the same device for future OoC platforms. ...
Conference paper (2021) - Hande Aydogmus, H. Joost van Ginkel, Anna-Danai Galiti, Michel Hu, Jean-Philippe Frimat, Arn van den Maagdenberg, GuoQi Zhang, Massimo Mastrangeli, Pasqualina M. Sarro
Continuous monitoring of tissue microphysiology is a key enabling feature of the organ-on-chip (OoC) approach for drug screening and disease modeling. Sensing charged species in OoC tissue microenvironments is thereby essential. However, the inherently small (i.e., cm) size of OoC devices poses the challenging requirement to integrate miniaturized and highly sensitive in situ charge sensing components to maximize signal extraction from small volumes (nL to L, range) of media used in these devices. Here we meet this need by presenting a novel dual-gate field-effect transistor-based charge sensor integrated within an optically transparent microelectromechanical (MEM) OoC device. Post-process mask-less decoration of Ti sensing electrodes by spark-ablated Au nanoparticle films significantly increases the effective electrode surface area and thus sensor sensitivity while retaining the CMOS-compatibility of the wafer-level fabrication process. We validate the biocompatibility of the sensor and its selective response to poly-D-lsine and KC1, and provide a perspective on monitoring cultures and differentiation of hiPSC-derived cortical neurons on our OoC device. ...
Stemming from the convergence of tissue engineering and microfluidics, organ-on-chip (OoC) technology can reproduce in vivo-like dynamic microphysiological environments for tissues in vitro. The possibility afforded by OoC devices of realistic recapitulation of tissue and organ (patho)physiology may hold the key to bridge the current translational gap in drug development, and possibly foster personalized medicine. Here we underline the biotechnological convergence at the root of OoC technology, and outline research tracks under development in our group at TU Delft along two main directions: fabrication of innovative microelectromechanical OoC devices, integrating stimulation and sensing of tissue activity, and their embedding within advanced platforms for pre-clinical research. We conclude with remarks on the role of open technology platforms for the broader establishment of OoC technology in pre-clinical research and drug development. ...
Conference paper (2020) - H. Aydogmus, M. Dostanic, M. Jahangiri, Rajarshi Sinha, W.F. Quiros Solano, M. Mastrangeli, P.M. Sarro
We present an extremely compact field effect transistor (FET)-based electrochemical sensor for in situ real-time and label-free measurement of ion concentrations in the cell culture area of organs-on-chip (OoCs) devices. This sensor replaces the functionality of an external reference electrode, crucial in standard electrochemical sensing, by controlling the FET threshold voltage via a capacitive control gate. The silicon- and polymer-based charge sensor can be integrated in OoC platforms by means of a wafer-scale and CMOS-compatible microfabrication process. This fabrication approach inherently allows a superior level of accuracy, repeatability and scalability compared to common OoC manufacturing methods. The sensor combines in a single device the complementary benefits of silicon-based electronics and of flexible polymer membranes with integrated microelectrodes – congenial substrates to sustain dynamic stimuli and mimic physiological tissue microenvironments. The integration of the polymer membrane in the sensing region makes this miniature sensor a preferable option for high sensitivity biochemical measurements in OoC applications, including monitoring the pH of cell culture media and of tissue culturing microenvironments, quantification of ion displacement in cells, and complementary research on disease modeling. ...
Monitoring cell conditions and microenvironment in real time is crucial for Organ-on-Chip (OoC) functionality. In particular, biological cues such as ions, including metals and metabolites, play a critical role in physiology and homeostasis in the human body. • Real-time monitoring of ions without optical systems is an unmet need for OOCs [1]. • Electrochemical sensors, such as organic electrochemical [2] and thin-film transistors [3], may address this need. Most of these sensors however rely on reference electrodes. ...