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Publication Open Access A new type of microphotoreactor with integrated optofluidic waveguide based on solid-air nanoporous aerogels(Royal Society of Chemistry (RSC), 2018) Jonas, Alexandr; Department of Chemistry; Department of Electrical and Electronics Engineering; Department of Physics; Department of Chemistry; Department of Electrical and Electronics Engineering; Department of Physics; Özbakır, Yaprak; Erkey, Can; Kiraz, Alper; PhD Student; Faculty Member; Faculty Member; College of Engineering; College of Sciences; N/A; 29633; 22542In this study, we developed a new type of microphotoreactor based on an optofluidic waveguide with aqueous liquid core fabricated inside a nanoporous aerogel. To this end, we synthesized a hydrophobic silica aerogel monolith with a density of 0.22 g cm(-3) and a low refractive index of 1.06 that-from the optical point of view-effectively behaves like solid air. Subsequently, we drilled an L-shaped channel within the monolith that confined both the aqueous core liquid and the guided light, the latter property arising due to total internal reflection of light from the liquid-aerogel interface. We characterized the efficiency of light guiding in liquid-filled channel and-using the light delivered by waveguiding-we carried out photochemical reactions in the channel filled with aqueous solutions of methylene blue dye. We demonstrated that methylene blue could be efficiently degraded in the optofluidic photoreactor, with conversion increasing with increasing power of the incident light. The presented optofluidic microphotoreactor represents a versatile platform employing light guiding concept of conventional optical fibres for performing photochemical reactions.Publication Open Access A queueing-theoretical delay analysis for intra-body nervous nanonetwork(Elsevier, 2015) Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Abbasi, Naveed Ahmed; Akan, Özgür Barış; Faculty Member; College of EngineeringNanonetworks is an emerging field of study where nanomachines communicate to work beyond their individual limited processing capabilities and perform complicated tasks. The human body is an example of a very large nanoscale communication network, where individual constituents communicate by means of molecular nanonetworks. Amongst the various intra-body networks, the nervous system forms the largest and the most complex network. In this paper, we introduce a queueing theory based delay analysis model for neuro-spike communication between two neurons. Using standard queueing model blocks such as servers, queues and fork-join networks, impulse reception and processing through the nervous system is modeled as arrival and service processes in queues. Simulations show that the response time characteristics of the model are comparable to those of the biological neurons.Publication Open Access All optical control of magnetization in quantum confined ultrathin magnetic metals(Nature Publishing Group (NPG), 2021) Department of Physics; Department of Electrical and Electronics Engineering; N/A; Department of Physics; Department of Electrical and Electronics Engineering; Müstecaplıoğlu, Özgür Esat; Onbaşlı, Mehmet Cengiz; Naseem, Muhammad Tahir; Zanjani, Saeedeh Mokarian; Faculty Member; Faculty Member; College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; 1674; 258783; N/A; N/AAll-optical control dynamics of magnetization in sub-10 nm metallic thin films are investigated, as these films with quantum confinement undergo unique interactions with femtosecond laser pulses. Our theoretical analysis based on the free electron model shows that the density of states at Fermi level (DOSF) and electron-phonon coupling coefficients (G(ep)) in ultrathin metals have very high sensitivity to film thickness within a few angstroms. We show that completely different magnetization dynamics characteristics emerge if DOSF and G(ep) depend on thickness compared with bulk metals. Our model suggests highly efficient energy transfer from femtosecond laser photons to spin waves due to minimal energy absorption by phonons. This sensitivity to the thickness and efficient energy transfer offers an opportunity to obtain ultrafast on-chip magnetization dynamics.Publication Open Access An information theoretical analysis of human insulin-glucose system toward the internet of bio-nano things(Institute of Electrical and Electronics Engineers (IEEE), 2017) Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Abbasi, Naveed Ahmed; Akan, Özgür Barış; Faculty Member; Graduate School of Sciences and EngineeringMolecular communication is an important tool to understand biological communications with many promising applications in Internet of Bio-Nano Things (IoBNT). The insulin-glucose system is of key significance among the major intra-body nanonetworks, since it fulfills metabolic requirements of the body. The study of biological networks from information and communication theoretical (ICT) perspective is necessary for their introduction in the IoBNT framework. Therefore, the objective of this paper is to provide and analyze for the first time in the literature, a simple molecular communication model of the human insulin-glucose system from ICT perspective. The data rate, channel capacity, and the group propagation delay are analyzed for a two-cell network between a pancreatic beta cell and a muscle cell that are connected through a capillary. The results point out a correlation between an increase in insulin resistance and a decrease in the data rate and channel capacity, an increase in the insulin transmission rate, and an increase in the propagation delay. We also propose applications for the introduction of the system in the IoBNT framework. Multi-cell insulin glucose system models may be based on this simple model to help in the investigation, diagnosis, and treatment of insulin resistance by means of novel IoBNT applications.Publication Open Access An LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction(Public Library of Science, 2022) Aydın, Musa; Doğan, Buket; Department of Physics; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Physics; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Kiraz, Alper; Karalar, Elif Nur Fırat; Morova, Berna; Uysallı, Yiğit; Özgönül, Ekin; Faculty Member; Researcher; PhD Student; PhD Student; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; 22542; 206349; N/A; N/A; N/AWhen combined with computational approaches, fluorescence imaging becomes one of the most powerful tools in biomedical research. It is possible to achieve resolution figures beyond the diffraction limit, and improve the performance and flexibility of high-resolution imaging systems with techniques such as structured illumination microscopy (SIM) reconstruction. In this study, the hardware and software implementation of an LED-based superresolution imaging system using SIM employing GPU accelerated parallel image reconstruction is presented. The sample is illuminated with two-dimensional sinusoidal patterns with various orientations and lateral phase shifts generated using a digital micromirror device (DMD). SIM reconstruction is carried out in frequency space using parallel CUDA kernel functions. Furthermore, a general purpose toolbox for the parallel image reconstruction algorithm and an infrastructure that allows all users to perform parallel operations on images without developing any CUDA kernel code is presented. The developed image reconstruction algorithm was run separately on a CPU and a GPU. Two different SIM reconstruction algorithms have been developed for the CPU as mono-thread CPU algorithm and multi-thread OpenMP CPU algorithm. SIM reconstruction of 1024 × 1024 px images was achieved in 1.49 s using GPU computation, indicating an enhancement by*28 and*20 in computation time when compared with mono-thread CPU computation and multi-thread OpenMP CPU computation, respectively.Publication Open Access Bio-inspired robotic collectives(Nature Publishing Group (NPG), 2019) Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Sitti, Metin; Faculty Member; School of Medicine; College of EngineeringA robotic system has been demonstrated in which the random motion of individual components leads to deterministic behaviour, much as occurs in living systems. Environmental and medical applications could follow.Publication Open Access Bioabsorbable polymer optical waveguides for deep-tissue photomedicine(Nature Publishing Group (NPG), 2016) Gather, Malte C.; Humar, Matjaz; Choi, Myunghwan; Kim, Seonghoon; Kim, Ki Su; Hahn, Sei Kwang; Scarcelli, Giuliano; Randolph, Mark; Redmond, Robert W.; Yun, Seok Hyun.; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Nizamoğlu, Sedat; Faculty Member; College of Engineering; 130295Advances in photonics have stimulated significant progress in medicine, with many techniques now in routine clinical use. However, the finite depth of light penetration in tissue is a serious constraint to clinical utility. Here we show implantable light-delivery devices made of bio-derived or biocompatible, and biodegradable polymers. In contrast to conventional optical fibres, which must be removed from the body soon after use, the biodegradable and biocompatible waveguides may be used for long-term light delivery and need not be removed as they are gradually resorbed by the tissue. As proof of concept, we demonstrate this paradigm-shifting approach for photochemical tissue bonding (PTB). Using comb-shaped planar waveguides, we achieve a full thickness ( 410 mm) wound closure of porcine skin, which represents similar to 10-fold extension of the tissue area achieved with conventional PTB. The results point to a new direction in photomedicine for using light in deep tissues.Publication Open Access Biocompatible quantum funnels for neural photostimulation(American Chemical Society (ACS), 2019) N/A; Department of Chemical and Biological Engineering; N/A; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; N/A; Department of Chemical and Biological Engineering; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Jalali, Houman Bahmani; Doğru-Yüksel, Itır Bakış; Eren, Güncem Özgün; Nizamoğlu, Sedat; Karatüm, Onuralp; Melikov, Rustamzhon; Dikbaş, Uğur Meriç; Kavaklı, İbrahim Halil; Sadeghi, Sadra; Yıldız, Erdost; Ergün, Çağla; Şahin, Afsun; PhD Student; Faculty Member; PhD Student; Master Student; Faculty Member; PhD Student; PhD Student; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; School of Medicine; N/A; N/A; N/A; 130295; N/A; N/A; N/A; 40319; N/A; N/A; N/A; 171267Neural photostimulation has high potential to understand the working principles of complex neural networks and develop novel therapeutic methods for neurological disorders. A key issue in the light-induced cell stimulation is the efficient conversion of light to bioelectrical stimuli. In photosynthetic systems developed in millions of years by nature, the absorbed energy by the photoabsorbers is transported via nonradiative energy transfer to the reaction centers. Inspired by these systems, neural interfaces based on biocompatible quantum funnels are developed that direct the photogenerated charge carriers toward the bionanojunction for effective photostimulation. Funnels are constructed with indium-based rainbow quantum dots that are assembled in a graded energy profile. Implementation of a quantum funnel enhances the generated photoelectrochemical current 215% per unit absorbance in comparison with ungraded energy profile in a wireless and free-standing mode and facilitates optical neuromodulation of a single cell. This study indicates that the control of charge transport at nanoscale can lead to unconventional and effective neural interfaces.Publication Open Access Control and local measurement of the spin chemical potential in a magnetic insulator(The American Association for the Advancement of Science (AAAS), 2017) Du, Chunhui; Van der Sar, Toeno; Zhou, Tony X.; Upadhyaya, Pramey; Casola, Francesco; Zhang, Huiliang; Ross, Caroline A.; Walsworth, Ronald L.; Tserkovnyak, Yaroslav; Yacoby, Amir; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Onbaşlı, Mehmet Cengiz; Faculty Member; College of Engineering; 258783The spin chemical potential characterizes the tendency of spins to diffuse. Probing this quantity could provide insight into materials such as magnetic insulators and spin liquids and aid optimization of spintronic devices. Here we introduce single-spin magnetometry as a generic platform for nonperturbative, nanoscale characterization of spin chemical potentials. We experimentally realize this platform using diamond nitrogen-vacancy centers and use it to investigate magnons in a magnetic insulator, finding that the magnon chemical potential can be controlled by driving the system's ferromagnetic resonance. We introduce a symmetry-based two-fluid theory describing the underlying magnon processes, measure the local thermomagnonic torque, and illustrate the detection sensitivity using electrically controlled spin injection. Our results pave the way for nanoscale control and imaging of spin transport in mesoscopic systems.Publication Open Access Controlled information transfer through an in vivo nervous system(Nature Publishing Group (NPG), 2018) Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Abbasi, Naveed Ahmed; Lafçı, Dilan; Akan, Özgür Barış; Faculty Member; Graduate School of Sciences and EngineeringThe nervous system holds a central position among the major in-body networks. It comprises of cells known as neurons that are responsible to carry messages between different parts of the body and make decisions based on those messages. In this work, further to the extensive theoretical studies, we demonstrate the first controlled information transfer through an in vivo nervous system by modulating digital data from macro-scale devices onto the nervous system of common earthworms and conducting successful transmissions. The results and analysis of our experiments provide a method to model networks of neurons, calculate the channel propagation delay, create their simulation models, indicate optimum parameters such as frequency, amplitude and modulation schemes for such networks, and identify average nerve spikes per input pulse as the nervous information coding scheme. Future studies on neuron characterization and artificial neurons may benefit from the results of our work.