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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Coverage and throughput analysis for FRET-based mobile molecular sensor/actor nanonetworks(Elsevier, 2014) Kuşcu, Murat; Akan, Özgür Barış; Faculty Member; College of EngineeringNanonetworks are envisaged to expand the capabilities of single nanomachines by enabling collaboration through communication between them. Forster Resonance Energy Transfer (FRET) observed among fluorescent molecules is a promising means of high-rate and reliable information transfer between single fluorophore-based nanoscale molecular machines. Recent theoretical studies have underlined its practicality for mobile ad hoc nanonetworks consisting of functionalized fluorescent molecules. In this study, we focus on the spatial characteristics of FRET-Based Mobile Molecular Sensor/Actor Nanonetworks (FRET-MSAN) by investigating the network performance in terms of communication coverage, network throughput and information propagation rate through extensive Monte Carlo simulations. The effect of fundamental system parameters related to FRET and to the mobility of the network nodes on the network performance is revealed. The results of the simulations indicate that the throughput and propagation rate as a function of distance from the information source are well-fitted by exponential curves. We also observe that the impact of FRET mechanism suppresses the effect of Brownian motion of network nodes on the exciton mobility.Publication Open Access Nanoscale communication with molecular arrays in nanonetworks(Institute of Electrical and Electronics Engineers (IEEE), 2012) Galmes, Sebastia; Atakan, Barış; Akan, Özgür Barış; PhD Student; Faculty Member; College of EngineeringMolecular communication is a promising nanoscale communication paradigm that enables nanomachines to exchange information by using molecules as communication carrier. Up to now, the molecular communication channel between a transmitter nanomachine (TN) and a receiver nanomachine (RN) has been modeled as either concentration channel or timing channel. However, these channel models necessitate exact time synchronization of the nanomachines and provide a relatively low communication bandwidth. In this paper, the Molecular ARray-based COmmunication (MARCO) scheme is proposed, in which the transmission order of different molecules is used to convey molecular information without any need for time synchronization. The MARCO channel model is first theoretically derived, and the intersymbol interference and error probabilities are obtained. Based on the error probability, achievable communication rates are analytically obtained. Numerical results and performance comparisons reveal that MARCO provides significantly higher communication rate, i.e., on the scale of 100 Kbps, than the previously proposed molecular communication models without any need for synchronization. More specifically, MARCO can provide more than 250 Kbps of molecular communication rate if intersymbol time and internode distance are set to 2 mu s and 2 nm, respectively.Publication Open Access Temperature control in dissipative cavities by entangled dimers(American Chemical Society (ACS), 2019) Dağ, Ceren B.; Niedenzu, Wolfgang; Özaydın, Fatih; Kurizki, Gershon; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674We show that the temperature of a cavity field can be drastically varied by its interaction with suitably entangled atom pairs (dimers) traversing the cavity under realistic atomic decoherence. To this end we resort to the hitherto untapped resource of naturally entangled dimers whose state can be simply controlled via molecular dissociation, collisions forming the dimer, or unstable dimers such as positronium. Depending on the chosen state of the dimer, the cavity-field mode can be driven to a steady-state temperature that is either much lower or much higher than the ambient temperature, despite adverse effects of cavity loss and atomic decoherence. Entangled dimers enable much broader range of cavity temperature control than single "phaseonium" atoms with coherently superposed levels. Such dimers are shown to constitute highly caloric fuel that can ensure high efficiency or power in photonic thermal engines. Alternatively, they can serve as controllable thermal baths for quantum simulation of energy exchange in photosynthesis or quantum annealing.Publication Open Access Luminescent PbS and PbS/CdS quantum dots with hybrid coatings as nanotags for authentication of petroleum products(American Chemical Society (ACS), 2019) Durmuşoğlu, Emek Göksu; Türker, Yurdanur; Acar, Havva Funda Yağcı; Faculty Member; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; N/A; 178902There is an urgent need to tag some valuable liquid products, such as petroleum products, for authentication. However, it is a challenging task because of the strong autofluorescence of liquid petroleum products in the visible range and the chemically active and harsh medium. Therefore, strongly luminescent, near-infrared (NIR) fluorophores with long-term stability are needed. The use of NIR quantum dots (QDs), such as lead chalcogenides, seems to be the best approach; however, most widely used coatings do not provide enough stability, and QDs are quenched in a short time in liquid petroleum products. Here, we report for the first time the synthesis of highly luminescent, ultrasmall, NIR-emitting PbS and PbS/CdS QDs with a hybrid coating consisting of oleylamine (OLA), 1-dodecanethiol (DT), and poly(methacrylic acid) (PMAA), adopting a simple, greener synthetic method. The photoluminescence (PL) emission wavelengths of these QDs were tuned between 700 and 1100 nm for detection with low-cost, widely used silicon detectors, which allows easy translation of such QDs as luminescent nanotags to serve as a means for the authentication of goods, such as petroleum. In the nanoparticle design, a thin layer of a CdS shell deposited by a cation-exchange process was adopted to enhance the emission intensity and stability of PbS QDs. The influence of postsynthetic ligand exchange of OLA with DT on the stability is also shown. PMAA in the coating provided a significant blue shift in the peak maxima, enhanced the luminescence intensity, and, most importantly, improved the long-term stability of QDs, especially in liquid petroleum products (oil, gasoline, and diesel). Such stability and size tunability was utilized to create binary barcodes. Hence, these QDs are shown as promising luminescent nanotags for liquid petroleum products. The development of such stable QD-based nanotags offers an invaluable use of nanotechnology for optical barcode generation.Publication Open Access Lead halide perovskite quantum dots for photovoltaics and photocatalysis: a review(American Chemical Society (ACS), 2022) Department of Chemistry; Peighambardoust, Naeimeh Sadat; Sadeghi, Ebrahim; Aydemir, Umut; Researcher; PhD Student; Faculty Member; Department of Chemistry; Koç University AKKİM Boron-Based Materials _ High-technology Chemicals Research _ Application Center (KABAM) / Koç Üniversitesi AKKİM Bor Tabanlı Malzemeler ve İleri Teknoloji Kimyasallar Uygulama ve Araştırma Merkezi (KABAM); College of Sciences; Graduate School of Sciences and Engineering; N/A; N/A; 58403Lead halide-based perovskite quantum dots (PQDs) have recently emerged as an important class of nanocrystal (NC) materials for optoelectronic and photoelec-trochemical applications. Thanks to their intriguing features including tunable band gap, narrow emission, high charge carrier mobility, remarkable light-absorbing factors, and long charge diffusion length, there has been a surge in research on lead halide-based PQDs and their applications. In this review, we showcase the fundamentals of PQDs and two principal applications including PQD solar cells (PQDSCs) and photocatalytic conversion. First, a thorough discussion on PQDSCs, their structure, surface treat-ment, and interface engineering along with their recent progress are presented. It is highlighted that the improvement of the efficiency of PQDSCs from below 10% to beyond 16% in a matter of a few years has turned them into promising candidates for future SC applications. Subsequently, the application of PQDs in photocatalytic reactions such as hydrogen production, CO2 reduction, and organic compounds' degradation is summarized. Not to mention that, despite the remarkable properties of PQDs in SCs and photocatalysis, the inferior stability of PV devices based thereon under operation as well as their poor tolerance under air, water, light, and heat impede their widespread application. For this, the practical efforts and possible solutions are extensively addressed. Finally, an outlook is provided, addressing further merits, and demerits of each application as well as prospective opportunities.Publication Open Access Effect of native oxide on stress in silicon nanowires: implications for nanoelectromechanical systems(American Chemical Society (ACS), 2022) Esfahani, Mohammad Nasr; Li, Taotao; Li, XueFei; Tasdemir, Zuhal; Wollschlaeger, Nicole; Leblebici, Yusuf; Department of Mechanical Engineering; Alaca, Burhanettin Erdem; Zarepakzad, Sina; Faculty Member; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; Graduate School of Sciences and Engineering; 115108; N/AUnderstanding the origins of intrinsic stress in Si nanowires (NWs) is crucial for their successful utilization as transducer building blocks in next-generation, miniaturized sensors based on nanoelectromechanical systems (NEMS). With their small size leading to ultrahigh-resonance frequencies and extreme surface-to-volume ratios, silicon NWs raise new opportunities regarding sensitivity, precision, and speed in both physical and biochemical sensing. With silicon optoelectromechanical properties strongly dependent on the level of NW intrinsic stress, various studies have been devoted to the measurement of such stresses generated, for example, as a result of harsh fabrication processes. However, due to enormous NW surface area, even the native oxide that is conventionally considered as a benign surface condition can cause significant stresses. To address this issue, a combination of nanomechanical characterization and atomistic simulation approaches is developed. Relying only on low-temperature processes, the fabrication approach yields monolithic NWs with optimum boundary conditions, where NWs and support architecture are etched within the same silicon crystal. Resulting NWs are characterized by transmission electron microscopy and micro-Raman spectroscopy. The interpretation of results is carried out through molecular dynamics simulations with ReaxFF potential facilitating the incorporation of humidity and temperature, thereby providing a close replica of the actual oxidation environment-in contrast to previous dry oxidation or self-limiting thermal oxidation studies. As a result, consensus on significant intrinsic tensile stresses on the order of 100 MPa to 1 GPa was achieved as a function of NW critical dimension and aspect ratio. The understanding developed herein regarding the role of native oxide played in the generation of NW intrinsic stresses is important for the design and development of silicon-based NEMS.Publication Open Access Statistical characterization and analysis of low-THz communication channel for 5G Internet of Things(Elsevier, 2019) Department of Electrical and Electronics Engineering; Akan, Özgür Barış; Abbasi, Naveed Ahmed; Khalid, Nabil; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 6647; N/A; N/AThis paper presents measurements and statistical characterization to compare three potential bands of the low-THz channel, namely, the 300 to 319 GHz, 340 to 359 GHz and 380 to 399 GHz bands. From the large set of measurements performed in line-of-sight (LoS) and non-LoS (NLoS) environments, parameters for path loss model with shadowing are evaluated. Our results show that the path loss exponents for the band around 310 GHz, 350 GHz, and 390 GHz is 2.07, 1.90 and 1.96, respectively. The impacts of different materials acting as surfaces in LoS channels and reflectors in NLoS environments are also examined. Additionally, the statistical analysis due to temporal, spatial and multipath propagation is performed to determine the best fit distributions. Finally, we look at some networking scenarios in THz Band communication to derive the expressions for the number of connections a user can make based on antenna characteristics, data rate requirements and antenna mobility as well as network density. Our results suggest fundamental parameters that can be used in future THz Band analysis with applications in both macro and micro scale Internet of Things (IoT).Publication Open Access Theranostic potential of self-luminescent branched polyethyleneimine-coated superparamagnetic iron oxide nanoparticles(Beilstein-Institut, 2022) N/A; Khodadust, Rouhollah; Acar, Havva Funda Yağcı; Ünal, Özlem; PhD Student; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; N/A; 178902; N/APolyethylenimine (PEI), which is frequently used for polyplex formation and effective gene transfection, is rarely recognized as a luminescent polymer. Therefore, it is usually tagged with an organic fluorophore to be optically tracked. Recently, we developed branched PEI (bPEI) superparamagnetic iron oxide nanoparticles (SPION@bPEI) with blue luminescence 1200 times stronger than that of bPEI without a traditional fluorophore, due to partial PEI oxidation during the synthesis. Here, we demonstrate in vitro dye free optical imaging and successful gene transfection with luminescent SPION@bPEI, which was further modified for receptor mediated delivery of the cargo selectively to cancer cell lines overexpressing the epidermal growth factor receptor (EGFR). Proapoptotic polyinosinic-polycytidylic acid sodium (PIC) was delivered to HeLa cells with SPION@bPEI and caused a dramatic reduction in the cell viability at otherwise non-toxic nanoparticle concentrations, proving that bPEI coating is still an effective component for the delivery of an anionic cargo. Besides, a strong intracellular optical signal supports the optically traceable nature of these nanoparticles. SPION@bPEI nanoparticles were further conjugated with Erbitux (Erb), which is an anti-EGFR antibody for targeting EGFR-overexpressing cancer cell lines. SPION@bPEI-Erb was used for the delivery of a GFP plasmid wherein the transfection was confirmed by the luminescence of the expressed gene within the transfected cells. Poor GFP expression in MCF7, a slightly better expression in HeLa, and a significant enhancement in the transfection of HCT116 cells proved a selective uptake and hence the targeting ability of Erb-tagged nanoparticles. Altogether, this study proves luminescent, cationic, and small SPION@bPEI nanoparticles as strong candidates for imaging and gene therapy.Publication Open Access Sum rate analysis of multiple-access neuro-spike communication channel with dynamic spiking threshold(Elsevier, 2019) Department of Electrical and Electronics Engineering; Akan, Özgür Barış; Khan, Tooba; Faculty Member; PhD Student; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 6647; N/AThe information from outside world is encoded into spikes by the sensory neurons. These spikes are further propagated to different brain regions through various neural pathways. In the cortical region, each neuron receives inputs from multiple neurons that change its membrane potential. If the accumulated change in the membrane potential is more than a threshold value, a spike is generated. According to various studies in neuroscience, this spiking threshold adapts with time depending on the previous spike. This causes short-term changes in the neural responses giving rise to short-term plasticity. Therefore, in this paper, we analyze a multiple-input single-output (MISO) neuro-spike communication channel and study the effects of dynamic spiking threshold on mutual information and maximum achievable sum rate of the channel. Since spike generation consumes a generous portion of the metabolic energy provided to the brain, we further put metabolic constraint in calculating the mutual information and find a trade-off between maximum achievable sum rate and metabolic energy consumed. Moreover, we analyze three types of neurons present in the cortical region, i.e., Regular spiking, Intrinsic bursting and Fast spiking neurons. We aim to characterize these neurons in terms of encoding/transmission rates and energy expenditure. It will provide a guideline for the practical implementation of bio-inspired nanonetworks as well as for the development of ICT-based diagnosis and treatment techniques for neural diseases.Publication Open Access Glioma-on-a-chip models(Multidisciplinary Digital Publishing Institute (MDPI), 2021) İlçi, İrem Sultan; Department of Mechanical Engineering; N/A; N/A; Önder, Tuğba Bağcı; Taşoğlu, Savaş; Üstün, Merve; Dabbagh, Sajjad Rahmani; Faculty Member; Department of Mechanical Engineering; KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Social Sciences and Humanities; 184359; 291971; N/A; N/AGlioma, as an aggressive type of cancer, accounts for virtually 80% of malignant brain tumors. Despite advances in therapeutic approaches, the long-term survival of glioma patients is poor (it is usually fatal within 12-14 months). Glioma-on-chip platforms, with continuous perfusion, mimic in vivo metabolic functions of cancer cells for analytical purposes. This offers an unprecedented opportunity for understanding the underlying reasons that arise glioma, determining the most effective radiotherapy approach, testing different drug combinations, and screening conceivable side effects of drugs on other organs. Glioma-on-chip technologies can ultimately enhance the efficacy of treatments, promote the survival rate of patients, and pave a path for personalized medicine. In this perspective paper, we briefly review the latest developments of glioma-on-chip technologies, such as therapy applications, drug screening, and cell behavior studies, and discuss the current challenges as well as future research directions in this field.