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Publication Open Access Biophotonic sensor applications based on photonic atoms - art. no. 60990Q(Society of Photo-optical Instrumentation Engineers (SPIE), 2006) Demir, Abdullah; Department of Physics; Serpengüzel, Ali; Faculty Member; Department of Physics; College of Sciences; 27855Microsphere resonators, i.e., photonic atoms, have found wide area of application in optical spectroscopy, quantum optics, cavity QED, switching, and sensing. Photonic atoms have unique optical properties such as high quality factor (Q-factor) morphology dependent resonances (MDR's), and relatively small volumes. High-Q MDR's are very sensitive to the refractive index change and microsphere uniformity. These tiny optical cavities, whose diameters vary from a few to several hundred micrometers, have resonances with reported Q-factors as large as 3x10(9). Due to their sensitivity, MDR's are also considered for biosensor applications. Binding of a protein or other biomolecules can be monitored by observing the wavelength shift of MDR's. A biosensor, based on this optical phenomenon, can even detect a single molecule, depending on the quality of the system. In this work, elastic scattering spectra from photonic atoms of different materials are experimentally obtained and MDR'S are observed. Preliminary results of unspecific binding of biomolecules are presented. Elastic light scattering spectra of MDR's for biosensor applications are calculated numerically for biomolecules such as Bovine Serum Albumin (BSA) and for Deoxyribo Nucleic Acid (DNA).
Publication Metadata only Chiropractic alters TMS induced motor neuronal excitability: preliminary findings(Springer International Publishing Ag, 2014) Haavik, Heidi; Niazi, Imran Khan; Duehr, Jens; Kinget, Mat; Ugincius, Paulius; Department of Physics; N/A; Sebik, Oğuz; Yılmaz, Gizem; Türker, Kemal Sıtkı; Researcher; PhD Student; Faculty Member; Department of Physics; College of Sciences; Graduate School of Health Sciences; School of Medicine; Koç University Hospital; N/A; N/A; 6741The objective of this study was to use the electromyography (EMG) via surface and intramuscular single motor unit recordings to further characterize the immediate sensorimotor effects of spinal manipulation and a control intervention using TMS. The results provide evidence that spinal manipulation of dysfunctional spinal segments increases low threshold motoneurone excitability.Publication Metadata only Design and instrumentation of an opto-digital confocal microscope(Institute of Electrical and Electronics Engineers (IEEE), 2018) Kurt, Adnan; Kiraz, Berna; N/A; Department of Physics; Zengin, Berk; Kiraz, Alper; Master Student; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; N/A; 22542Confocal microscopy has become a vital technique for life sciences due to higher lateral and axial resolution it provides compared to standard epifluorescence microscopy. On the contrary, accessibility to confocal microscopes did not escalate in proportion to its usage around the globe. Therefore, it was aimed to build an opto-digital confocal microscope, eventually leading to a product which will be affordable for research groups, institutes and hospitals. In this work, we present a home-built confocal microscopy setlp using commercially available equipment. The design of the setup was realized using a 488 nm laser, an inverted microscope and optical/optomechanical parts including mirrors, lenses, beam splitter, scan lens. In addition, X-Y galvo scanner was controlled by using a custom-built control electronics. Instrumentation was made using a National Instruments DAQ card and LabVIEW based software. For characterization purposes reference samples were successfully imaged, following imaging of biological specimen. Gained know-how during development and prototyping will contribute vastly to process of producing a robust, desktop, easy to use and affordable confocal microsocope for researchers and organizations at a diverse scale.Publication Metadata only Er : YAG laser ablation of cerebellar and cerebral tissue(Springer-Verlag London Ltd, 2001) Gulsoy, M; Celikel, T; Canbeyli, R; Cilesiz, I; Department of Physics; Kurt, Adnan; Teaching Faculty; Department of Physics; College of Sciences; 194455With the availability of suitable fibres, the Er:YAG laser has become an indispensable tool for invasive neurosurgical applications as a source of precise ablation. The aim of this study was to investigate the ablative effects of the Er:YAG laser on brain tissue. The response of neuronal. tissue to 2.94 mum Er:YAG laser irradiation was investigated on excised rat brain specimens. Ablation craters were created in cerebral and cerebellar tissues using 0.3, 0.5 and 1.0 J single pulses of 150 mus duration. The corresponding average irradiances were 37.7 J/cm(2), 62.9 J/cm(2) and 125.8 J/cm(2), respectively. Craters were checked qualitatively, crater dimensions were measured and compared, and volume of ablated tissue was estimated. Laser-induced crater dimensions were found to be significantly different at different energy levels applied. Moreover, dimensions of craters on cerebral and cerebellar tissues were significantly different in terms of dimensions. We observed that with the Er:YAG laser ablation craters were created with practically no thermal damage to adjacent tissues. The differences observed in the response of cerebral and cerebellar cortical tissues were dependent on the anatomical and chemical differences.Publication Metadata only Femtosecond laser ablated tracks on smart surfaces for droplet manipulation applications(Institute of Electrical and Electronics Engineers (IEEE), 2018) Coskun, Umut Can; Morova, Yaǧız; Bozkurt, Asuman Asikoglu; Erten, Ahmet Can; Jonas, Alexandr; Aktürk, Selcuk; N/A; Department of Physics; Department of Physics; Rashid, Muhammed Zeeshan; Morova, Berna; Kiraz, Alper; PhD Student; Researcher; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; N/A; 22542In droplet based microfluidics, ability of controlling the motion of the droplets insidechips have great importance for the applications such guiding, sorting, mixing and dividing of liquid droplets. In this study, we fabricated hydrophilic microchannels inside the chips by femtosecond laser ablation technique in order to control droplet motion. The laser beam focused on PDMS converts the irradiated regions to hydrophilic by ablating the coating entirely from the surface. Droplets follow the tracks because of the difference in wettability of ablated region and PDMS surfaces together with the topographical profile of the ablated tracks. Within this study, we investigated the manipulation of three kind of liquid droplets (water/surfactant mixture, pure water and pure etylene glycol) along microchannels with depths of 1μm, 1.5μm and 2μm. We verified the experimental results with simulations and analyzed the trajectories of the moving droplets with the different wettability along the tracks of different depths. Our results showed that, while topographical effects play role in droplet guiding for 1.5μm and 2μm tracks, for the case of 1μm depth of channel, surface energy modifications cause the guiding rather than the topographical step on the surface. These results will pioneer for sorting applicaitons of different microdroplets mixed in the same microfluidic chip. / Damla temelli mikroakışkan sistemlerinde, damlaların yonga içerisindeki hareketlerinin kontrolü, yönlendirme, ayrıştırma, birleştirme ve bölme gibi uygulamalarda oldukça önemlidir. Bu çalışmada, damlaların hareketinin kontrolünü sağlamak için mikroakışkan yonga içerisinde hidrofilik mikrokanalları femtosaniye lazer ablasyon tekniği ile ürettik. Polydimethylsiloxane (PDMS) üzerine odakladığımız fs lazer hüzmesi uyarılan bölgeyi tamamen aşındırarak hidrofilik hale getirmektedir. Damlalar, aşındırılan hidrofilik bölge ile PDMS yüzeyi arasındaki ıslanabilirlik ve topografik farklılık sebebiyle bu kanallara eşlenerek ilerlemektedir. Bu çalışma kapsamında, üç farklı polar akışkandan (su/yüzey aktif madde karışımı, saf su ve saf etilen glikol) yağ içerisinde ürettiğimiz damlaların, 1μm, 1.5μm ve 2μm derinliklerine sahip işlenmiş mikrokanallar aracılığıyla yönlendirilmesini araştırdık. Deneysel olarak gerçekleştiridiğimiz çalışmaların sonuçlarını simülasyon değerleri ile karşılaştırdık ve farklı yapıdaki akışkan damlaların farklı derinliklerdeki kanallara sahip yongalardaki hareket yörüngelerini inceledik. Elde ettiğimiz sonuçlarla 1.5μm ve 2μm derinliğindeki kanallarda damlaların yönlendirilmesi hususunda kanal topografisinin etkili olduğunu, 1μm derinliğindeki kanallar için ise kanalın yüzeyde sahip olduğu derinlik yerine yüzey enerjisindeki değişimin etkili olduğunu gösterdik. Elde ettiğimiz bu sonuçlar, aynı yonga içerisinde bulunan farklı ıslanabilirlik özeliklerine sahip akışkanların ayrıştırılması gibi uygulamalara imkan sağlayacaktır.Publication Metadata only Haptic manipulation of microspheres using optical tweezers under the guidance of artificial force fields(Ieee Computer Soc, 2006) N/A; Department of Physics; Department of Physics; Büküşoğlu, İbrahim; Kiraz, Alper; Kurt, Adnan; Master Student; Faculty Member; Teaching Faculty; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; 22542; 194455We report the manipulation of glass microspheres having a diameter of 3-10 mu m using optical tweezers and with haptic feedback. We detect the position of a microsphere manipulated in a fluid bed using a CCD camera and calculate the forces acting on it due to the optical trap and viscous drag. We calculate the optical forces between the laser beam and the manipulated particle using a mass-spring-damper model. For this put-pose, we calibrated the optical trap and used image processing and curve fitting techniques to evaluate the coefficients of the mass-spring-damper model. The drag force is calculated using the velocity of the sphere and the viscous damping coefficient of the fluid. We then use a potential field approach to generate a collision-free path for the manipulated microsphere among other spheres and display the optical trapping and drag forces and the forces due the artificial potential field to a user of the system via a haptic device for better manipulation and steering. We have observed performance improvements over manual control in our preliminary manipulation experiments.Publication Open Access Microsphere-based optical system for biosensor applications(Society of Photo-optical Instrumentation Engineers (SPIE), 2004) Department of Physics; Department of Electrical and Electronics Engineering; İşçi, Şenol; Bilici, Temel; Serpengüzel, Ali; Kurt, Adnan; Faculty Member; Teaching Faculty; Department of Physics; Department of Electrical and Electronics Engineering; College of Sciences; N/A; N/A; 27855; 194455Optical microsphere resonators have been recently utilized in quantum optics, laser science, spectroscopy, and optoelectronics and attracted increasing interest due to their unique optical properties. Microspheres possess high quality factor (Q-factor) optical morphology dependent resonances, and have relatively small volumes. High-Q morphology dependent resonances are very sensitive to the refractive index change and microsphere uniformity. These tiny optical cavities, whose diameters may vary from a few to several hundred micrometers, have resonances with reported Q-factors as large as 3 x 10(9). Due to their sensitivity, morphology dependent resonances of microspheres are also considered for biosensor applications. Binding of a protein or other biomolecules can be monitored by observing the wavelength shift of morphology dependent resonances. A biosensor, based on this optical phenomenon, can even detect a single molecule, depending on the quality of the system design. In this work, elastic scattering spectra from the microspheres of different materials are experimentally obtained and morphology dependent resonances are observed. Preliminary results of unspecific binding of biomolecules onto the microspheres are presented. Furthermore, the morphology dependent resonances of the microspheres for biosensor applications are analyzed theoretically both for proteins such as bovine serum albumin.Publication Metadata only Yağ mikrodamlacıklarının gliserol-su çözeltisinde hidrodinamik tuzaklanması(IEEE, 2014) Tanyeri, M.; N/A; Department of Physics; Department of Physics; Kayıllıoğlu, Oğuz; Erten, Ahmet Can; Kiraz, Alper; PhD Student; Teaching Faculty; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; 233923; 22542We demonstrate a novel method for trapping and manipulating microdroplets in liquid media using a hydrodynamic trap. This method enables confinement and long-term observation of biological objects such as cells and macromolecules. / Mikrodamlacıkların sıvı içerisinde tuzaklanmasına ve hareket ettirilmesine olanak sağlayan yeni bir tuzaklama yöntemi sunuyoruz. Geliştirdiğimiz metot hücre ve biyolojik makromoleküllerin sıvı içerisinde tuzaklanması ve uzun süre gözlemlenmesini mümkün kılmaktadır.