Researcher:
Bavili, Nima

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PhD Student

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Nima

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Bavili

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Bavili, Nima

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2017 - 201942020 - 20236

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Researcher Of Publications: search.filters.isAuthorOfPublication.046edd8e-08a2-470a-a77a-9801837b54d2

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    Bypassing pro-survival and resistance mechanisms of autophagy in EGFR-positive lung cancer cells by targeted delivery of 5FU using theranostic Ag2S quantum dots
    (Royal Soc Chemistry, 2019) Akkoç, Yunus; Gözüaçık, Devrim; N/A; N/A; N/A; N/A; Department of Physics; Department of Chemistry; Demirci, Gözde; Duman, Fatma Demir; Bavili, Nima; Kiraz, Alper; Acar, Havva Funda Yağcı; PhD Student; Master Student; PhD Student; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; School of Medicine; College of Sciences; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; N/A; N/A; 22542; 178902
    Targeted drug delivery systems that combine imaging and therapeutic functions in a single structure have become very popular in nanomedicine. Near-infrared (NIR) emitting Ag2S quantum dots (QDs) are excellent candidates for this task. Here, we have developed PEGylated Ag2S QDs functionalized with Cetuximab (Cet) antibody and loaded with an anticancer drug, 5-fluorouracil (5FU). These theranostic QDs were used for targeted NIR imaging and treatment of lung cancer using low (H1299) and high (A549) Epidermal Growth Factor Receptor (EGFR) overexpressing cell lines. The Cet conjugated QDs effectively and selectively delivered 5FU to A549 cells and provided significantly enhanced cell death associated with apoptosis. Interestingly, while treatment of cells with free 5FU activated autophagy, a cellular mechanism conferring resistance to cell death, these EGFR targeting multimodal QDs significantly overcame drug resistance compared to 5FU treatment alone. The improved therapeutic outcome of 5FU delivered to A549 cells by Cet conjugated Ag2S QDs is suggested as the synergistic outcome of enhanced receptor mediated uptake of nanoparticles, and hence the drug, coupled with suppressed autophagy even in the absence of addition of an autophagy suppressor.
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    Use of an elastic buffer layer for improved performance of a polymer microcylinder ring resonator hydrogen sensor
    (Elsevier Science Sa, 2022) N/A; N/A; Department of Physics; Department of Mechanical Engineering; Department of Physics; Bavili, Nima; Ali, Basit; Morova, Berna; Alaca, Burhanettin Erdem; Kiraz, Alper; PhD Student; PhD Student; Researcher; Faculty Member; Faculty Member; Department of Mechanical Engineering; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Sciences; N/A; N/A; 152935; 115108; 22542
    The impact of substrate on Pd nanofilm expansion in a Pd-H-2 system is investigated using polymer microcylinder ring resonator (PMRR) platform. Being a highly sensitive platform for H-2 gas detection, PMRR comprises of an inner sensitive Pd nanofilm and an outer PDMS layer coated on a standard optical fiber. Optical whispering gallery modes (WGMs) are excited in the rim of the outermost PDMS layer through evanescent field of a tapered fiber. H-2 molecules penetrating the H-2-sensitive Pd nanofilm through the PDMS layer cause reversible expansion in the PMRR. This translates into shifts in spectral positions of the WGMs that are observed with tapered fiber transmission spectroscopy. Two types of PMRRs were fabricated. In the first type, Pd nanofilm was directly deposited on the silica surface of an optical fiber. In the other one, a PDMS buffer layer was precoated between Pd nanofilm and the silica surface, with different thicknesses. It is demonstrated that, the use of a PDMS buffer layer yields higher radial expansion of the nanofilm during the interaction with H-2 gas. A 180-nm-thick Pd nanofilm coated on similar to 2.5-mu m-thick PDMS buffer layer showed at least 18% higher radial expansion compared to the case without buffer layer. Identical thickness of Pd nanofilm on a similar to 3.5-mu m-thick PDMS buffer layer showed 30% higher radial expansion. Numerical and analytical calculations were also performed confirming the experimental results. Among mechanical properties of the PDMS buffer layer, Poisson's ratio was found to be the most significant parameter affecting the expansion of the nanofilm.
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    Optical sensors based on palladium and polymer-coated optical fiber resonators
    (Spie-Int Soc Optical Engineering, 2019) Eryürek, Mustafa; N/A; Department of Physics; Department of Chemistry; Department of Chemistry; Department of Physics; Bavili, Nima; Morova, Berna; Yılgör, İskender; Yılgör, Emel; Kiraz, Alper; PhD Student; Researcher; Faculty Member; Researcher; Faculty Member; Department of Chemistry; Department of Physics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; College of Science; College of Sciences; College of Sciences; College of Sciences; N/A; 152935; 24181; N/A; 22542
    In this work, we present robust and easy-to-fabricate optical gas and vapor sensors based on optical fiber resonators (OFR) coated with palladium (Pd) thin films, Pd micro-particles and polymer brushes (PB). Pd based sensors are used for hydrogen (H-2) gas detection in concentration range of 0% to 1% and polymer brush-coated OFR are used for detection of vapor in concentration range of 0 to 25%. Sensing mechanism of these sensors is based on spectral shift of resonance wavelength which are called whispering gallery modes (WGMs). This spectral shift is due to volume expansion of the sensing material. Tapered fiber is used in order to excite WGMs in coated OFRs. Good sensitivity and repeatability results are obtained for all three types of sensors.
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    Refractive index sensing by phase shift cavity ringdown spectroscopy
    (Springer Science and Business Media B.V., 2022) Cheema, M. Imran; N/A; N/A; N/A; N/A; Department of Physics; Ayaz, Rana Muhammed Armaghan; Uysallı, Yiğit; Bavili, Nima; Morova, Berna; Kiraz, Alper; PhD Student; PhD Student; Researcher; Researcher; Faculty Member; Department of Physics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; N/A; College of Sciences; N/A; N/A; N/A; N/A; 22542
    Cavity ring down spectroscopy is a sensitive optical detection technique but it makes use of expensive electronics and data fitting algorithm. Both of these factors put a limitation on its performance for sensing applications. In this study cost effective and easy to use phase shift cavity ring down spectroscopy (PS-CRDS) technique, has been demonstrated for refractive index sensing. A refractive index sensor consisting of a tapered single mode optical fiber and two fiber Bragg gratings (FBGs) is proposed. In this sensing methodology, an intensity modulated laser beam centered at 1550 nm from a DFB laser is scanned at a narrow wavelength range and cavity modes are excited. Later the phase shift corresponding to these cavity modes is measured using a lock-in amplifier. Sucrose solutions of various concentrations are used for performance analysis of the refractive index sensing device. The resultant limit of detection (LOD) came out to be ~6.4 × 10−6 refractive index units (RIUs), which can be improved further by using thinner fiber tapers or fiber Bragg gratings with higher reflectivity. © 2022, Springer Nature B.V.
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    Linear cavity tapered fiber sensor using mode-tracking phase-shift cavity ring-down spectroscopy
    (Optical Society of America (OSA), 2020) Ullah, Ubaid; Ghauri, M. Daniyal; Cheema, M. Imran; N/A; N/A; N/A; N/A; Department of Physics; Ayaz, Rana Muhammed Armaghan; Uysallı, Yiğit; Morova, Berna; Bavili, Nima; Kiraz, Alper; PhD Student; PhD Student; Researcher; PhD Student; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; N/A; 22542
    Phase-shift cavity ring-down spectroscopy (PS-CRDS) is an alternative CRDS approach that allows the detection of minute changes in cavity losses by measurement of the phase shift experienced by a modulated laser as it propagates through a high-quality factor cavity. Fiber loop resonators and microresonators have been employed in previous PS-CRDS demonstrations for liquid phase applications. Here we employ a tapered fiber-based linear fiber cavity for the demonstration of a highly sensitive sensor for sucrose concentration in water using PS-CRDS. Our linear fiber cavity has a small cavity length (similar to 1.25 m) that enables the observation and tracking of individual cavity modes in transmission and phase spectra recorded during laser sweeps. Hence, we eliminate the need for Pound-Drever-Hall locking of the laser source to the cavity resonance and thus provide a simpler experimental scheme. We analyze the recorded data sets to track the changes in phase shifts observed only when the laser wavelength is in resonance with the cavity modes. Such a mode-tracking PS-CRDS approach reveals limit of detection values less than around 400 mu M better than the performance of previously demonstrated PS-CRDS sucrose concentration sensors employing fiber loop resonators. The sensitivity of our sensor critically depends on the fiber taper diameter and can reach up to around 6 degrees/1 mM Suc. for 3.2 mu m taper diameter at 6 MHz modulation frequency using fiber Bragg gratings (FBGs) with reflectivities around 86%. This value can be further increased by employing FBGs with higher reflectivities or fiber tapers with smaller diameters provided that the cavity loss due to water absorption is compensated with an amplifier.
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    Metal-gas interaction studies using whispering gallery modes
    (Spie-Int Soc Optical Engineering, 2021) N/A; Department of Physics; Department of Physics; Bavili, Nima; Morova, Berna; Kiraz, Alper; PhD Student; Researcher; Faculty Member; Department of Physics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; 152935; 22542
    In this work, in addition to the sensor application of coated optical microresonator, we show the phase transition of Pd-H system using WGMs. WGMs are propagating on a cylindrical microresonator which is based on a single mode optical fiber coated with a desired metal thickness and desired morphology. Light coupling is achieved by tapered fiber connected to a tunable laser working in the infrared wavelength. WGMs are observed and tracked by transmitted laser light. The sensor consisting of the resonator and a tapered fiber is placed in a metal chamber that is connected to the gas tanks. Desired concentration of the gas is achieved by mixing the carrier gas (nitrogen) and hydrogen. By increasing or decreasing of the hydrogen concentration in the sensing chamber, palladium layer expands or contracts. The change in the radius of the resonator translates in to shifts in spectral positions of the WGMs. However, these expansion or contractions rates are different for different phases of the Pd - H system. For instance, solid solution of hydrogen in palladium, represented by alpha has the lowest expansion or contraction. In contrast beta phase has the highest rate. These phase transitions and intermediate phase are shown using the WGMs.
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    Cell cycle-dependent palmitoylation of protocadherin 7 by ZDHHC5 promotes successful cytokinesis
    (Company of Biologists Ltd, 2023) N/A; Department of Molecular Biology and Genetics; Department of Physics; N/A; N/A; Kiraz, Alper; Bavili, Nima; Kamacıoğlu, Altuğ; Küçük, Nazlı Ezgi Özkan; Qureshi, Mohammad Haroon; Yapıcı, Gamze Nur; Yiğit, Berfu Nur; Değirmenci, Beste Senem; Faculty Member; Faculty Member; PhD Student; Master Student; Researcher; PhD Student; PhD Student; PhD Student; PhD Student; Department of Molecular Biology and Genetics; Department of Physics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Sciences; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 105301; 22542; N/A; N/A; N/A; N/A; N/A; N/A; N/A
    Cell division requires dramatic reorganization of the cell cortex, which is primarily driven by the actomyosin network. We previously reported that protocadherin 7 (PCDH7) gets enriched at the cell surface during mitosis, which is required to build up the full mitotic rounding pressure. Here, we report that PCDH7 interacts with and is palmitoylated by the palmitoyltransferase, ZDHHC5. PCDH7 and ZDHHC5 colocalize at the mitotic cell surface and translocate to the cleavage furrow during cytokinesis. The localization of PCDH7 depends on the palmitoylation activity of ZDHHC5. Silencing PCDH7 increases the percentage of multinucleated cells and the duration of mitosis. Loss of PCDH7 expression correlates with reduced levels of active RhoA and phospho-myosin at the cleavage furrow. This work uncovers a palmitoylation-dependent translocation mechanism for PCDH7, which contributes to the reorganization of the cortical cytoskeleton during cell division.
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    Liquid refractometric sensors based on optical fiber resonators
    (Elsevier Science Sa, 2017) Jonas, Alexandr; Çiçek, Kenan; N/A; N/A; N/A; Department of Physics; Eryürek, Mustafa; Ghafoor, Moeen; Bavili, Nima; Kiraz, Alper; PhD Student; Researcher; PhD Student; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; N/A; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; 22542
    A robust, easy-to-fabricate, and sensitive liquid refractometric sensor utilizing optical fiber resonators (OFRs) obtained by simple stripping and cleaning of conventional optical fibers is presented. The sensing scheme is based on recording the spectral changes of the whispering gallery modes (WGMs) observed in the transmission spectrum of an OFR excited with a tunable laser coupled to the OFR through an independent tapered optical fiber. The demonstrated sensor device is tested and fully characterized with water solutions of ethanol and ethylene glycol (EG). Good agreements are obtained with theoretical predictions for both ethanol and EG cases when TE and TM polarized WGMs are considered. The limit of detection of the demonstrated sensor is determined to be between 2.7 and 4.7 x 10(-5) refractive index unit (RIU) comparable to the state-of-the-art when precise temperature control of the sample chamber is missing. (C) 2017 Elsevier B.V. All rights reserved.
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    PublicationOpen Access
    Highly sensitive optical sensor for hydrogen gas based on a polymer microcylinder ring resonator
    (Elsevier, 2020) Eryürek, Mustafa; Department of Physics; Department of Chemistry; Department of Electrical and Electronics Engineering; Bavili, Nima; Balkan, Timuçin; Morova, Berna; Uysallı, Yiğit; Kaya, Sarp; Kiraz, Alper; Researcher; Researcher; PhD Student; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Department of Electrical and Electronics Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; N/A; N/A; 116541; 22542
    A highly sensitive platform is demonstrated for hydrogen gas (H-2) sensing based on a polymer microcylinder ring resonator (PMRR) obtained by an optical fiber coated with an inner nanofilm of amorphous palladium (Pd) and an outer polymer layer of polydimethylsiloxane (PDMS) permeable to H-2. The sensing scheme is based on monitoring the spectral shifts of high-quality optical resonances called whispering gallery modes (WGMs) that propagate in the vicinity of the outer rim of the PDMS layer without being affected by the absorption and scattering losses caused by the Pd nanofilm. WGMs are excited by a single-mode tapered optical fiber evanescently coupled to the PMRR. The observed reversible spectral shifts of the WGMs are induced by changes in the diameter of the PDMS layer caused by expansion or contraction of the Pd nanofilm exposed to varying concentrations of H-2. Maximum spectral shift sensitivity of 140 pm/% H-2, a minimum response time of 95 s, and minimum limit of detection of similar to 60 ppm were measured for sensors prepared with different thicknesses of the amorphous Pd nanofilm and tested in the H-2 concentration range up to 1%, having nitrogen gas (N-2) as a carrier. Experiments were also conducted with Pd nanofilms annealed in air or N-2 atmosphere after the deposition. In both cases, smaller sensitivities were observed due to the formation of larger grains within the film, resulting in slower diffusion and reduced solubility of H in the Pd layer. The impacts of oxygen gas and humidity on sensor performance were also studied.
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    Fabrication and characterization of large numerical aperture, high-resolution optical fiber bundles based on high-contrast pairs of soft glasses for fluorescence imaging
    (Optical Society of America (OSA), 2019) Aydın, Musa; Doğan, Buket; Kasztelanic, Rafal; Pysz, Dariusz; Buczynski, Ryszard; Department of Physics; N/A; Department of Electrical and Electronics Engineering; Morova, Berna; Bavili, Nima; Yaman, Onur; Yiğit Alpdoğan, Buket; Zeybel, Müjdat; Kiraz, Alper; Researcher; Researcher; Doctor; Faculty Member; Faculty Member; Department of Physics; Department of Electrical and Electronics Engineering; College of Sciences; School of Medicine; College of Engineering; N/A; N/A; N/A; N/A; 214694; 22542
    Fabrication and characterization of flexible optical fiber bundles (FBs) with in-house synthesized high-index and low-index thermally matched glasses are presented. The FBs composed of around 15000 single-core fibers with pixel sizes between 1.1 and 10 mu m are fabricated using the stack-and-draw technique from sets of thermally matched zirconium-silicate ZR3, borosilicate SK222, sodium-silicate K209, and F2 glasses. With high refractive index contrast pair of glasses ZR3/SK222 and K209/F2, FBs with numerical apertures (NAs) of 0.53 and 0.59 are obtained, respectively. Among the studied glass materials, ZR3, SK222, and K209 are in-house synthesized, while F2 is commercially acquired. Seven different FBs with varying pixel sizes and bundle diameters are characterized. Brightfield imaging of a micro-ruler and a Convallaria majalis sample and fluorescence imaging of a dye-stained paper tissue and a cirrhotic mice liver tissue are demonstrated using these FBs. demonstrating their good potential for microendoscopic imaging. Brightfield and fluorescence imaging performance of the studied FBs are compared. For both sets of glass compositions, good imaging performance is observed for FBs, with core diameter and core-to-core distance values larger than 1.6 mu m and 2.3 mu m, respectively. FBs fabricated with K209/F2 glass pairs revealed better performance in fluorescence imaging due to their higher NA of 0.59.