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Publication Metadata only An ultra-compact and wireless tag for battery-free sweat glucose monitoring(Elsevier Advanced Technology, 2022) N/A; Department of Mechanical Engineering; N/A; N/A; Department of Mechanical Engineering; N/A; N/A; N/A; N/A; Department of Mechanical Engineering; Mirzajani, Hadi; Abbasiasl, Taher; Mirlou, Fariborz; İstif, Emin; Bathaei, Mohammad Javad; Dağ, Çağdaş; Deyneli, Oğuzhan; Dereli, Dilek Yazıcı; Beker, Levent; Researcher; PhD Student; PhD Student; Other; PhD Student; Faculty Member; Faculty Member; Faculty Member; Faculty Member; Department of Mechanical Engineering; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); n2STAR-Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced Research; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; N/A; School of Medicine; School of Medicine; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 171914; 179659; 308798Glucose monitoring before, during, and after exercise is essential for people with diabetes as exercise increases the risk of activity-induced hyper- and hypo-glycemic events. The situation is even more challenging for athletes with diabetes as they have impaired metabolic control compared to sedentary individuals. In this regard, a compact and noninvasive wearable glucose monitoring device that can be easily worn is critical to enabling glucose monitoring. This report presents an ultra-compact glucose tag with a footprint and weight of 1.2 cm(2) and 0.13 g, respectively, for sweat analysis. The device comprises a near field communication (NFC) chip, antenna, electrochemical sensor, and microfluidic channels implemented in different material layers. The device has a flexible and conformal structure and can be easily attached to different body parts. The battery-less operation of the device was enabled by NFC-based wireless power transmission and the compact antenna. Femtosecond laser ablation was employed to fabricate a highly compact and flexible NFC antenna. The proposed device demonstrated excellent operating characteristics with a limit of detection (LOD), limit of quantification (LOQ), and sensitivity of 24 mu M, 74 mu M, and 1.27 mu A cm(-2) mM(-1), respectively. The response of the proposed sensor in sweat glucose detection and quantification was validated by nuclear magnetic resonance spectroscopy (NMR). Also, the device's capability in attachment to the body, sweat collection, and glucose measurement was demonstrated through in vitro and in vivo experiments, and satisfactory results were obtained.Publication Metadata only Deep insight into PEGylation of bioadhesive chitosan nanoparticles: sensitivity study for the key parameters through artificial neural network model(Amer Chemical Soc, 2018) N/A; N/A; Department of Chemical and Biological Engineering; Bozüyük, Uğur; Doğan, Nihal Olcay; Kızılel, Seda; PhD Student; Master Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 28376lonically cross-linked chitosan nanoparticles have great potential in nanomedicine due to their tunable properties and cationic nature. However, low solubility of chitosan severely limits their potential clinical translation. PEGylation is a well-known method to increase solubility of chitosan and chitosan nanoparticles in neutral media; however, effect of PEG chain length and chitosan/PEG ratio on particle size and zeta potential of nanoparticles are not known. This study presents a systematic analysis of the effect of PEG chain length and chitosan/PEG ratio on size and zeta potential of nanoparticles. We prepared PEGylated chitosan chains prior to the nanoparticle synthesis with different PEG chain lengths and chitosan/PEG ratios. To precisely estimate the influence of critical parameters on size and zeta potential of nanoparticles, we both developed an artificial neural network (ANN) model and performed experimental characterization using the three independent input variables: (i) PEG chain length, (ii) chitosan/PEG ratio, and (iii) pH of solution. We studied the influence of PEG chain lengths of 2, 5, and 10 kDa and three different chitosan/PEG ratios (25 mg chitosan to 4, 12, and 20 mu moles of PEG) for the synthesis of chitosan nanoparticles within the pH range of 6.0-7.4. Artificial neural networks is a modeling tool used in nanomedicine to optimize and estimate inherent properties of the system. Inherent properties of a nanoparticle system such as size and zeta potential can be estimated based on previous experiment results, thus, nanoparticles with desired properties can be obtained using an ANN. With the ANN model, we were able to predict the size and zeta potential of nanoparticles under different experimental conditions and further confirmed the cell-nanoparticle adhesion behavior through experiments. Nanoparticle groups that had higher zeta potentials promoted adhesion of HEK293-T cells to nanoparticle-coated surfaces in cell culture medium, which was predicted through ANN model prior to experiments. Overall, this study comprehensively presents the PEGylation of chitosan, synthesis of PEGylated chitosan nanoparticles, utilizes ANN model as a tool to predict important properties such as size and zeta potential, and further captures the adhesion behavior of cells on surfaces prepared with these engineered nanoparticles.Publication Metadata only Diffusion-based model for synaptic molecular communication channel(IEEE-Inst Electrical Electronics Engineers Inc, 2017) N/A; N/A; N/A; Department of Electrical and Electronics Engineering; Khan, Tooba; Bilgin, Bilgesu Arif; Akan, Özgür Barış; PhD Student; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 6647Computational methods have been extensively used to understand the underlying dynamics of molecular communication methods employed by nature. One very effective and popular approach is to utilize a Monte Carlo simulation. Although it is very reliable, this method can have a very high computational cost, which in some cases renders the simulation impractical. Therefore, in this paper, for the special case of an excitatory synaptic molecular communication channel, we present a novel mathematical model for the diffusion and binding of neurotransmitters that takes into account the effects of synaptic geometry in 3-D space and re-absorption of neurotransmitters by the transmitting neuron. Based on this model we develop a fast deterministic algorithm, which calculates expected value of the output of this channel, namely, the amplitude of excitatory postsynaptic potential (EPSP), for given synaptic parameters. We validate our algorithm by a Monte Carlo simulation, which shows total agreement between the results of the two methods. Finally, we utilize our model to quantify the effects of variation in synaptic parameters, such as position of release site, receptor density, size of postsynaptic density, diffusion coefficient, uptake probability, and number of neurotransmitters in a vesicle, on maximum number of bound receptors that directly affect the peak amplitude of EPSP.Publication Metadata only Ecofriendly and efficient luminescent solar concentrators based on fluorescent proteins(amer Chemical Soc, 2019) N/A; N/A; N/A; N/A; Department of Electrical and Electronics Engineering; N/A; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Sadeghi, Sadra; Melikov, Rustamzhon; Jalali, Houman Bahmani; Karatüm, Onuralp; Srivastava, Shashi Bhushan; Çonkar, Deniz; Karalar, Elif Nur Fırat; Nizamoğlu, Sedat; PhD Student; PhD Student; PhD Student; PhD Student; Researcher; PhD Student; Faculty Member, Faculty Member; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 206349; 130295In recent years, luminescent solar concentrators (LSCs) have received renewed attention as a versatile platform for large-area, high-efficiency, and low-cost solar energy harvesting. So far, artificial or engineered optical materials, such as rare-earth ions, organic dyes, and colloidal quantum dots (QDs) have been incorporated into LSCs. Incorporation of nontoxic materials into efficient device architectures is critical for environmental sustainability and clean energy production. Here, we demonstrated LSCs based on fluorescent proteins, which are biologically produced, ecofriendly, and edible luminescent biomaterials along with exceptional optical properties. We synthesized mScarlet fluorescent proteins in Escherichia coli expression system, which is the brightest protein with a quantum yield of 61% in red spectral region that matches well with the spectral response of silicon solar cells. Moreover, we integrated fluorescent proteins in an aqueous medium into solar concentrators, which preserved their quantum efficiency in LSCs and separated luminescence and wave-guiding regions due to refractive index contrast for efficient energy harvesting. Solar concentrators based on mScarlet fluorescent proteins achieved an external LSC efficiency of 2.58%, and the integration at high concentrations increased their efficiency approaching to 5%, which may facilitate their use as “luminescent solar curtains” for in-house applications. The liquid-state integration of proteins paves a way toward efficient and “green” solar energy harvesting.Publication Metadata only Liquid metal microdroplet-initiated ultra-fast polymerization of a stimuli-responsive hydrogel composite(Wiley-V C H Verlag Gmbh, 2023) Zhang, Jianhua; Liao, Jiahe; Liu, Zemin; Zhang, Rongjing; Department of Mechanical Engineering; Sitti, Metin; Department of Mechanical Engineering; College of Engineering; School of MedicineRecent advances in composite hydrogels achieve material enhancement or specialized stimuli-responsive functionalities by pairing with a functional filler. Liquid metals (LM) offer a unique combination of chemical, electrical, and mechanical properties that show great potential in hydrogel composites. Polymerization of hydrogels with LM microdroplets as initiators is a particularly interesting phenomenon that remains in its early stage of development. In this work, an LM-hydrogel composite is introduced, in which LM microdroplets dispersed inside the hydrogel matrix have dual functions as a polymerization initiator for a polyacrylic acid-poly vinyl alcohol (PAA/PVA) network and, once polymerized, as passive inclusion to influence its material and stimuli-responsive characteristics. It is demonstrated that LM microdroplets enable ultra-fast polymerization in approximate to 1 min, compared to several hours by conventional polymerization techniques. The results show several mechanical enhancements to the PAA/PVA hydrogels with LM-initiated polymerization. It is found that LM ratios strongly influence stimuli-responsive behaviors in the hydrogels, including swelling and ionic bending, where higher LM ratios are found to enhance ionic actuation performance. The dual roles of LM in this composite are analyzed using the experimental characterization results. These LM-hydrogel composites, which are biocompatible, open up new opportunities in future soft robotics and biomedical applications. A composite hydrogel embedded with liquid metal (LM) microdroplets is introduced, where the LM microdroplets have dual roles of initiating ultra-fast polymerization and passive inclusion. The physical effects of LM on polymerization and stimuli-responsive behaviors are analyzed, including swelling and ionic actuation due to osmotic pressure differences. Their benefits to the LM-hydrogel functionalities, such as robot locomotion, are demonstrated.Publication Metadata only Monolithic composites of silica aerogels by reactive supercritical deposition of hydroxy-terminated poly(dimethylsiloxane)(amer Chemical Soc, 2013) N/A; Department of Chemical and Biological Engineering; Şanlı, Deniz; Erkey, Can; Researcher; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 29633Monolithic composites of silica aerogels with hydroxyl-terminated poly(dimethylsiloxane) (PDMS(OH)) were developed with a novel reactive supercritical deposition technique. the method involves dissolution of PDMS(OH) in supercritical CO2 (scCO(2)) and then exposure of the aerogel samples to this single phase mixture of PDMS(OH)-CO2. the demixing pressures of the PDMS(OH)-CO2 binary mixtures determined in this study indicated that PDMS(OH) forms miscible mixtures with CO2 at a wide composition range at easily accessible pressures. Upon supercritical deposition, the polymer molecules were discovered to react with the hydroxyl groups on the silica aerogel surface and form a conformal coating on the surface. the chemical attachment of the polymer molecules on the aerogel surface were verified by prolonged extraction with pure scCO(2), simultaneous deposition with superhydrophobic and hydrophilic silica aerogel samples and aTR-FTIR analysis. all of the deposited silica aerogel samples were obtained as monoliths and retained their transparency up to around 30 wt % of mass uptake. PDMS(OH) molecules were found to penetrate all the way to the center of the monoliths and were distributed homogenously throughout the cylindrical aerogel samples. Polymer loadings as high as 75.4 wt % of the aerogel mass could be attained. It was shown that the polymer uptake increases with increasing exposure time, As well as the initial polymer concentration in the vessel.Publication Metadata only Novel nanostructured composites of silica aerogels with a metal organic framework(Elsevier, 2013) N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Ülker, Zeynep; Eruçar, İlknur; Keskin, Seda; Erkey, Can; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; 262388; 260094; 40548; 29633Novel nanostructured composites of silica aerogel with Cu-BTC were synthesized using a slightly modified version of the conventional sol-gel method used to synthesize silica aerogels. The composite materials had monolithic structures with blue color consisting of well dispersed microporous domains of Cu-BTC in the mesoporous inorganic silica aerogel network. The Cu-BTC content in the composites ranged from 5 to 30 weight percent and the total surface area of the composites ranged from 1025 to 1138 m(2)/g. The microporosity of the composites increased with the increasing amount of Cu-BTC indicating that the micropores of Cu-BTC were accessible and functional. XRD analysis indicated that Cu-BTC retained its crystal structure in the composite despite being immersed in a solution containing water, ethanol and tetraethylorthosilicate. Additionally, it was observed that increasing Cu-BTC content caused a decrease in the average desorption pore radius with a wider pore size distribution. Nitrogen adsorption isotherms for composites could be predicted using the experimentally obtained pure component isotherm for the silica aerogel, theoretically obtained isotherm for Cu-BTC and the weight fractions of the components within the composite material.Publication Open Access RGDS-functionalized polyethylene glycol hydrogel-coated magnetic iron oxide nanoparticles enhance specific intracellular uptake by HeLa cells(Dove Medical Press, 2012) N/A; Department of Chemical and Biological Engineering; Department of Chemistry; Nazlı, Caner; Ergenç, Tuğba İpek; Yar, Yasemin; Acar, Havva Funda Yağcı; Kızılel, Seda; PhD Student; Undergraduate Student; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; 178902; 28376The objective of this study was to develop thin, biocompatible, and biofunctional hydrogel-coated small-sized nanoparticles that exhibit favorable stability, viability, and specific cellular uptake. This article reports the coating of magnetic iron oxide nanoparticles (MIONPs) with covalently cross-linked biofunctional polyethylene glycol (PEG) hydrogel. Silanized MIONPs were derivatized with eosin Y, and the covalently cross-linked biofunctional PEG hydrogel coating was achieved via surface-initiated photopolymerization of PEG diacrylate in aqueous solution. The thickness of the PEG hydrogel coating, between 23 and 126 nm, was tuned with laser exposure time. PEG hydrogel-coated MIONPs were further functionalized with the fibronectin-derived arginine-glycine-aspartic acid-serine (RGDS) sequence, in order to achieve a biofunctional PEG hydrogel layer around the nanoparticles. RGDS-bound PEG hydrogel-coated MIONPs showed a 17-fold higher uptake by the human cervical cancer HeLa cell line than that of amine-coated MIONPs. This novel method allows for the coating of MIONPs with nano-thin biofunctional hydrogel layers that may prevent undesirable cell and protein adhesion and may allow for cellular uptake in target tissues in a specific manner. These findings indicate that the further biofunctional PEG hydrogel coating of MIONPs is a promising platform for enhanced specific cell targeting in biomedical imaging and cancer therapy.Publication Open Access Zr-MOFs for CF4/CH4, CH4/H-2, and CH4/N-2 separation: towards the goal of discovering stable and effective adsorbents(Royal Society of Chemistry (RSC), 2021) Department of Chemical and Biological Engineering; Demir, Hakan; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; N/A; 40548Zirconium metal-organic frameworks (MOFs) can be promising adsorbents for various applications as they are highly stable in different chemical environments. In this work, a collection of Zr-MOFs comprised of more than 100 materials is screened for CF4/CH4, CH4/H-2, and CH4/N-2 separations using atomistic-level simulations. The top three MOFs for the CF4/CH4 separation are identified as PCN-700-BPDC-TPDC, LIFM-90, and BUT-67 exhibiting CF4/CH4 adsorption selectivities of 4.8, 4.6, and 4.7, CF4 working capacities of 2.0, 2.0, and 2.1 mol kg(-1), and regenerabilities of 85.1, 84.2, and 75.7%, respectively. For the CH4/H-2 separation, MOF-812, BUT-67, and BUT-66 are determined to be the top performing MOFs demonstrating CH4/H-2 selectivities of 61.6, 36.7, and 46.2, CH4 working capacities of 3.0, 4.1, and 3.4 mol kg(-1), and CH4 regenerabilities of 70.7, 82.7, and 74.7%, respectively. Regarding the CH4/N-2 separation, BUT-67, Zr-AbBA, and PCN-702 achieving CH4/N-2 selectivities of 4.5, 3.4, and 3.8, CH4 working capacities of 3.6, 3.9, and 3.5 mol kg(-1), and CH4 regenerabilities of 81.1, 84.0, and 84.5%, in successive order, show the best overall separation performances. To further elucidate the adsorption in top performing adsorbents, the adsorption sites in these materials are analyzed using radial distribution functions and adsorbate density profiles. Finally, the water affinities of Zr-MOFs are explored to comment on their practical use in real gas separation applications. Our findings may inspire future studies probing the adsorption/separation mechanisms and performances of Zr-MOFs for different gases.