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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Objective-free ultrasensitive biosensing on large-area metamaterial surfaces in the near-IR(AMER CHEMICAL SOC, 2024) Department of Physics; Ramazanoğlu, Serap Aksu; Öktem, Evren; Department of Physics; College of Sciences; Graduate School of Sciences and EngineeringPlasmonic metamaterials have opened new avenues in medical diagnostics. However, the transfer of the technology to the markets has been delayed due to multiple challenges. The need of bulky optics for signal reading from nanostructures patterned on submillimeter area limits the miniaturization of the devices. The use of objective-free optics can solve this problem, which necessitates large area patterning of the nanostructures. In this work, we utilize laser interference lithography (LIL) to pattern nanodisc-shaped metamaterial absorber nanoantennas over a large area (4 cm(2)) within minutes. The introduction of a sacrificial layer during the fabrication process enables an inverted hole profile and a well-controlled liftoff, which ensures perfectly defined uniform nanopatterning almost with no defects. Furthermore, we use a macroscopic reflection probe for optical characterization in the near-IR, including the detection of the binding kinematics of immunologically relevant proteins. We show that the photonic quality of the plasmonic nanoantennas commensurates with electron-beam-lithography-fabricated ones over the whole area. The refractive index sensitivity of the LIL-fabricated metasurface is determined as 685 nm per refractive index unit, which demonstrates ultrasensitive detection. Moreover, the fabricated surfaces can be used multiple times for biosensing without losing their optical quality. The combination of rapid and large area nanofabrication with a simple optical reading not only simplifies the detection process but also makes the biosensors more environmentally friendly and cost-effective. Therefore, the improvements provided in this work will empower researchers and industries for accurate and real-time analysis of biological systems.Publication Metadata only Phase behaviour and dynamics of three-dimensional active dumbbell systems(Royal Society of Chemistry, 2024) Caporusso, C.B.; Negro, G.; Suma, A.; Digregorio, P.; Gonnella G; Cugliandolo, L.F.; Department of Physics; Carenza, Livio Nicola; Department of Physics; College of SciencesWe present a comprehensive numerical study of the phase behavior and dynamics of a three-dimensional active dumbbell system with attractive interactions. We demonstrate that attraction is essential for the system to exhibit nontrivial phases. We construct a detailed phase diagram by exploring the effects of the system's activity, density, and attraction strength. We identify several distinct phases, including a disordered, a gel, and a completely phase-separated phase. Additionally, we discover a novel dynamical phase, that we name percolating network, which is characterized by the presence of a spanning network of connected dumbbells. In the phase-separated phase we characterize numerically and describe analytically the helical motion of the dense cluster.Publication Metadata only Localized thermal emission from topological interfaces(American Association for the Advancement of Science, 2024) Ergöktaş, M. Said; Keçebaş, Ali; Despotelis, Konstantinos; Soleymani, Sina; Bakan, Gökhan; Principi, Alessandro; Rotter, Stefan; Özdemir, Şahin K.; Kocabaş, Coşkun; Department of Physics; Kocabaş, Aşkın; Department of Physics; College of SciencesThe control of thermal radiation by shaping its spatial and spectral emission characteristics plays a key role in many areas of science and engineering. Conventional approaches to tailoring thermal emission using metamaterials are hampered both by the limited spatial resolution of the required subwavelength material structures and by the materials' strong absorption in the infrared. In this work, we demonstrate an approach based on the concept of topology. By changing a single parameter of a multilayer coating, we were able to control the reflection topology of a surface, with the critical point of zero reflection being topologically protected. The boundaries between subcritical and supercritical spatial domains host topological interface states with near-unity thermal emissivity. These topological concepts enable unconventional manipulation of thermal light for applications in thermal management and thermal camouflage.Publication Metadata only Identifying connectivity for two sympatric carnivores in human-dominated landscapes in central Iran (vol 17, e0269179, 2022)(Public Library Science, 2023) Rezaei, Sahar; Mohammadi, Alireza; Bencini, Roberta; Rooney, Thomas; Department of Physics; Department of Physics; ; College of Sciences;The affiliation for the last author is incorrect. The correct affiliation for Morteza Naderi is Arak University. An additional affiliation is missing for the last author. Morteza Naderi is also affiliated with the Department of Molecular Biology and Genetics, Faculty of Sciences, Koc University, Istanbul, Turkey. © 2023 Rezaei et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Publication Metadata only Er3+:YLiF4 channeled waveguide laser near 2.7-2.8 μm fabricated by femtosecond laser inscription(Optica Publishing Group, 2024) Tonelli, Mauro; Department of Physics; Ayevi, Berke; Morova, Yağız; Sennaroğlu, Alphan; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Sciences;We report, for the first time to our knowledge, a demonstration of robust waveguide lasing near 2.7-2.8 mu m in an erbium -doped fluoride host. Femtosecond laser inscription was employed to fabricate 50- and 70-mu m diameter channeled waveguides inside an Er3+:YLiF4 crystal. The best power performance was obtained with the 70-mu m diameter waveguide and 16% transmitting output coupler. The propagation loss and refractive index contrast were measured as 0.23 dB/cm and 7.1 x 10-4, respectively, for the 70-mu m diameter waveguide. Both self-Q-switched (SQS) and continuous-wave (CW) operations could be obtained. During the SQS operation, as short as 240-ns pulses with average power of 51 mW, repetition rate of 368 kHz, and power slope efficiency of 15.2% were generated at the wavelength of 2717 nm with 465 mW of the pump power. During the CW operation, as high as 66 mW of output power was achieved at 2808 nm by using 460 mW of pump power at 798 nm, with a power slope efficiency of 19.6%. (c) 2024 Optica Publishing GroupPublication Metadata only Reorganization of brain connectivity across the spectrum of clinical cognitive decline(SPRINGER-VERLAG ITALIA SRL, 2024) Dal, Demet Yüksel; Yıldırım, Zerrin; Gurvit, Hakan; Acar, Burak; Department of Physics; Kabakçıoğlu, Alkan; Department of Physics; ; College of Sciences;Clinical cognitive decline, leading to Alzheimer's Disease Dementia (ADD), has long been interpreted as a disconnection syndrome, hindering the information flow capacity of the brain, hence leading to the well-known symptoms of ADD. The structural and functional brain connectome analyses play a central role in studies of brain from this perspective. However, most current research implicitly assumes that the changes accompanying the progression of cognitive decline are monotonous in time, whether measured across the entire brain or in fixed cortical regions. We investigate the structural and functional connectivity-wise reorganization of the brain without such assumptions across the entire spectrum. We utilize nodal assortativity as a local topological measure of connectivity and follow a data-centric approach to identify and verify relevant local regions, as well as to understand the nature of underlying reorganization. The analysis of our preliminary experimental data points to statistically significant, hyper and hypo-assortativity regions that depend on the disease's stage, and differ for structural and functional connectomes. Our results suggest a new perspective into the dynamic, potentially a mix of degenerative and compensatory, topological alterations that occur in the brain as cognitive decline progresses.Publication Metadata only Effects of transcranial direct current stimulation on clinical outcomes, calcitonin gene-related peptide, and pituitary adenylate cyclase-activating polypeptide-38 levels in menstrual migraine(International Neuromodulation Society, 2024) Hasırcı Bayır, Buse Rahime; Aksu, Serkan; Gezegen, Haşim; Karaaslan, Zerrin; Yüceer, Hande; Cerrahoğlu Şirin, Tuba; Küçükali, Cem İsmail; Yılmaz, Vuslat; Baykan, Betül; Department of Physics; Kurt, Adnan; Karamürsel, Sacit; Department of Physics; ; School of Medicine; College of Sciences;Objectives: Transcranial direct current stimulation (tDCS) has been suggested as an alternative treatment option for migraine. The present study aimed to evaluate the efficacy of tDCS on clinical outcomes in addition to calcitonin gene-related peptide (CGRP) and pituitary adenylate cyclase-activating peptide 38 (PACAP-38) levels in individuals with menstrual-related migraine (MRM) for the first time. Materials and Methods: In this parallel study, 58 female patients between the ages of 18 and 45 years, including 36 with MRM and 22 with nonmenstrual migraines (nMM), were recruited. Sessions of 2-mA 20-minute anodal tDCS were administered over the left dorsolateral prefrontal cortex within three consecutive days (1:1 active and sham stimulation). Migraine attack frequency, severity, analgesic usage, CGRP, and PACAP-38 levels of the patients were evaluated before and one month after tDCS. Results: After tDCS, in the active group compared with the sham group, the frequency (p = 0.031), the severity of attacks (p = 0.003), the number of days with headache (p = 0.004), and the analgesic usage (p = 0.024) were all decreased. In both MRM and nMM groups, the frequency and severity of attacks and analgesic usage were decreased in those receiving active stimulation (p < 0.001 for each). CGRP and PACAP-38 levels were no different in the active group and the sham group after tDCS. Conclusions: tDCS was shown to be efficacious in migraine prophylaxis and a valuable option for migraine and MRM treatment. The absence of changes in serum CGRP and PACAP-38 levels suggests that tDCS efficacy may stem from distinct cerebral electrophysiological mechanisms. © 2024 International Neuromodulation SocietyPublication Metadata only Enhancing resolution and contrast in fibre bundle-based fluorescence microscopy using generative adversarial network(Wiley, 2024) Morova, Berna; Aydin, Musa; Eren, Furkan; Pysz, Dariusz; Buczynski, Ryszard; Department of Physics; Ketabchi, Amir Mohammad; Uysallı, Yiğit; Bavili, Nima; Kiraz, Alper; Department of Physics; Graduate School of Sciences and Engineering; College of SciencesFibre bundle (FB)-based endoscopes are indispensable in biology and medical science due to their minimally invasive nature. However, resolution and contrast for fluorescence imaging are limited due to characteristic features of the FBs, such as low numerical aperture (NA) and individual fibre core sizes. In this study, we improved the resolution and contrast of sample fluorescence images acquired using in-house fabricated high-NA FBs by utilising generative adversarial networks (GANs). In order to train our deep learning model, we built an FB-based multifocal structured illumination microscope (MSIM) based on a digital micromirror device (DMD) which improves the resolution and the contrast substantially compared to basic FB-based fluorescence microscopes. After network training, the GAN model, employing image-to-image translation techniques, effectively transformed wide-field images into high-resolution MSIM images without the need for any additional optical hardware. The results demonstrated that GAN-generated outputs significantly enhanced both contrast and resolution compared to the original wide-field images. These findings highlight the potential of GAN-based models trained using MSIM data to enhance resolution and contrast in wide-field imaging for fibre bundle-based fluorescence microscopy. Lay Description: Fibre bundle (FB) endoscopes are essential in biology and medicine but suffer from limited resolution and contrast for fluorescence imaging. Here we improved these limitations using high-NA FBs and generative adversarial networks (GANs). We trained a GAN model with data from an FB-based multifocal structured illumination microscope (MSIM) to enhance resolution and contrast without additional optical hardware. Results showed significant enhancement in contrast and resolution, showcasing the potential of GAN-based models for fibre bundle-based fluorescence microscopy.Publication Metadata only Siamese graph convolutional network quantifies increasing structure-function discrepancy over the cognitive decline continuum(ELSEVIER IRELAND LTD, 2024) Gamgam, Gurur; Yildirim, Zerrin; Gurvit, Hakan; Demiralp, Tamer; Acar, Burak; Department of Physics; Kabakçıoğlu, Alkan; Department of Physics; College of SciencesBackground and Objective: Alzheimer's disease dementia (ADD) is well known to induce alterations in both structural and functional brain connectivity. However, reported changes in connectivity are mostly limited to global/local network features, which have poor specificity for diagnostic purposes. Following recent advances in machine learning, deep neural networks, particularly Graph Neural Network (GNN) based approaches, have found applications in brain research as well. The majority of existing applications of GNNs employ a single network (uni-modal or structure/function unified), despite the widely accepted view that there is a nontrivial interdependence between the brain's structural connectivity and the neural activity patterns, which is hypothesized to be disrupted in ADD. This disruption is quantified as a discrepancy score by the proposed "structure-function discrepancy learning network"(sfDLN) and its distribution is studied over the spectrum of clinical cognitive decline. The measured discrepancy score is utilized as a diagnostic biomarker and is compared with state-of-the-art diagnostic classifiers. Methods: sfDLN is a GNN with a siamese architecture built on the hypothesis that the mismatch between structural and functional connectivity patterns increases over the cognitive decline spectrum, starting from subjective cognitive impairment (SCI), passing through a mid-stage mild cognitive impairment (MCI), and ending up with ADD. The structural brain connectome (sNET) built using diffusion MRI-based tractography and the novel, sparse (lean) functional brain connectome (lNET) built using fMRI are input to sfDLN. The siamese sfDLN is trained to extract connectome representations and a discrepancy (dissimilarity) score that complies with the proposed hypothesis and is blindly tested on an MCI group. Results: The sfDLN generated structure-function discrepancy scores show high disparity between ADD and SCI subjects. Leave-one-out experiments of SCI-ADD classification over a cohort of 42 subjects reach 88% accuracy, surpassing state-of-the-art GNN-based classifiers in the literature. Furthermore, a blind assessment over a cohort of 46 MCI subjects confirmed that it captures the intermediary character of the MCI group. GNNExplainer module employed to investigate the anatomical determinants of the observed discrepancy confirms that sfDLN attends to cortical regions neurologically relevant to ADD. Conclusion: In support of our hypothesis, the harmony between the structural and functional organization of the brain degrades with increasing cognitive decline. This discrepancy, shown to be rooted in brain regions neurologically relevant to ADD, can be quantified by sfDLN and outperforms state-of-the-art GNN-based ADD classification methods when used as a biomarker.Publication Metadata only What is quantum in probabilistic explanations of the sure-thing principle violation?(Elsevier Ireland Ltd, 2024) Department of Physics; Mahalli, Nematollah Farhadi; Pusuluk, Orhan; Department of Physics; College of SciencesThe Prisoner's Dilemma game (PDG) is one of the simple test-beds for the probabilistic nature of the human decision-making process. Behavioral experiments have been conducted on this game for decades and show a violation of the so-called sure-thing principle, a key principle in the rational theory of decision. Quantum probabilistic models can explain this violation as a second-order interference effect, which cannot be accounted for by classical probability theory. Here, we adopt the framework of generalized probabilistic theories and approach this explanation from the viewpoint of quantum information theory to identify the source of the interference. In particular, we reformulate one of the existing quantum probabilistic models using density matrix formalism and consider different amounts of classical and quantum uncertainties for one player's prediction about another player's action in PDG. This enables us to demonstrate that what makes possible the explanation of the violation is the presence of quantum coherence in the player's initial prediction and its conversion to probabilities during the dynamics. Moreover, we discuss the role of other quantum information-theoretical quantities, such as quantum entanglement, in the decision-making process. Finally, we propose a three-choice extension of the PDG to compare the predictive powers of quantum probability theory and a more general probabilistic theory that includes it as a particular case and exhibits third-order interference. © 2024 Elsevier B.V.