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Publication Open Access A communication theoretical analysis of FRET-based mobile ad hoc molecular nanonetworks(Institute of Electrical and Electronics Engineers (IEEE), 2014) Kuşcu, Murat; Akan, Özgür Barış; Faculty Member; College of EngineeringNanonetworks refer to a group of nano-sized machines with very basic operational capabilities communicating to each other in order to accomplish more complex tasks such as in-body drug delivery, or chemical defense. Realizing reliable and high-rate communication between these nanomachines is a fundamental problem for the practicality of these nanonetworks. Recently, we have proposed a molecular communication method based on Forster Resonance Energy Transfer (FRET) which is a nonradiative excited state energy transfer phenomenon observed among fluorescent molecules, i.e., fluorophores. We have modeled the FRET-based communication channel considering the fluorophores as single-molecular immobile nanomachines, and shown its reliability at high rates, and practicality at the current stage of nanotechnology. In this study, for the first time in the literature, we investigate the network of mobile nanomachines communicating through FRET. We introduce two novel mobile molecular nanonetworks: FRET-based mobile molecular sensor/actor nanonetwork (FRET-MSAN) which is a distributed system of mobile fluorophores acting as sensor or actor node; and FRET-based mobile ad hoc molecular nanonetwork (FRETMAMNET) which consists of fluorophore-based nanotransmitter, nanoreceivers and nanorelays. We model the single message propagation based on birth death processes with continuous time Markov chains. We evaluate the performance of FRETMSAN and FRET-MAMNET in terms of successful transmission probability and mean extinction time of the messages, system throughput, channel capacity and achievable communication rates.Publication Open Access Efficient photocapacitors via ternary hybrid photovoltaic optimization for photostimulation of neurons(Optical Society of America (OSA), 2020) Department of Electrical and Electronics Engineering; Srivastava, Shashi Bhushan; Melikov, Rustamzhon; Yıldız, Erdost; Han, Mertcan; Şahin, Afsun; Nizamoğlu, Sedat; Researcher; PhD Student; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Graduate School of Health Sciences; School of Medicine; College of Engineering; N/A; N/A; N/A; N/A; 171267; 130295Optoelectronic photoelectrodes based on capacitive charge-transfer offer an attractive route to develop safe and effective neuromodulators. Here, we demonstrate efficient optoelectronic photoelectrodes that are based on the incorporation of quantum dots (QDs) into poly(3-hexylthiophene-2,5-diyl) (P3HT) and [6,6]-Phenyl-C61-butyric acid methyl ester (PCBM) bulk heterojunction. We control the performance of the photoelectrode by the blend ratio, thickness, and nanomorphology of the ternary bulk heterojunction. The optimization led to a photocapacitor that has a photovoltage of 450 mV under a light intensity level of 20 mW.cm(-2) and a responsivity of 99 mA/W corresponding to the most light-sensitive organic photoelectrode reported to date. The photocapacitor can facilitate action potential generation by hippocampal neurons via burst waveforms at an intensity level of 20 mW.cm(-2). Therefore, the results point to an alternative direction in the engineering of safe and ultra-light-sensitive neural interfaces.
Publication Metadata only Impact of long term plasticity on information transmission over neuronal networks(Institute of Electrical and Electronics Engineers (IEEE), 2020) Ramezani, Hamideh; Abbasi, Naveed A.; N/A; Department of Electrical and Electronics Engineering; Khan, Tooba; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647The realization of bio-compatible nanomachines would pave the way for developing novel diagnosis and treatment techniques for the dysfunctions of intra-body nanonetworks and revolutionize the traditional healthcare methodologies making them less invasive and more efficient. The network of these nanomachines is aimed to be used for treating neuronal diseases such as developing an implant that bridges over the injured spinal cord to regain its normal functionality. Thus, nanoscale communication paradigms are needed to be investigated to facilitate communication between nanomachines. Communication among neurons is one of the most promising nanoscale communication paradigm, which necessitates the thorough communication theoretical analysis of information transmission among neurons. The information flow in neuro-spike communication channel is regulated by the ability of neurons to change synaptic strengths over time, i.e. synaptic plasticity. Thus, the performance evaluation of the nervous nanonetwork is incomplete without considering the influence of synaptic plasticity. In this paper, we focus on information transmission among hippocampal pyramidal neurons and provide a comprehensive channel model for MISO neuro-spike communication, which includes axonal transmission, vesicle release process, synaptic communication and spike generation. In this channel, the spike timing dependent plasticity (STDP) model is used to cover both synaptic depressiofan and potentiation depending on the temporal correlation between spikes generated by input and output neurons. Since synaptic strength changes depending on different physiological factors such as spiking rate of presynaptic neurons, number of correlated presynaptic neurons and the correlation factor among them, we simulate this model with correlated inputs and analyze the evolution of synaptic weights over time. Moreover, we calculate average mutual information between input and output of the channel and find the impact of plasticity and correlation among inputs on the information transmission. The simulation results reveal the impact of different physiological factors related to either presynaptic or postsynaptic neurons on the performance of MISO neuro-spike communication. Moreover, they provide guidelines for selecting the system parameters in a bio-inspired neuronal network according to the requirements of different applications.Publication Metadata only Impacts of spike shape variations on synaptic communication(Institute of Electrical and Electronics Engineers (IEEE), 2018) N/A; N/A; Department of Electrical and Electronics Engineering; Ramezani, Hamideh; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647Understanding the communication theoretical capabilities of information transmission among neurons, known as neuro-spike communication, is a significant step in developing bio-inspired solutions for nanonetworking. In this paper, we focus on a part of this communication known as synaptic transmission for pyramidal neurons in the Cornu Ammonis area of the hippocampus location in the brain and propose a communication-based model for it that includes effects of spike shape variation on neural calcium signaling and the vesicle release process downstream of it. For this aim, we find impacts of spike shape variation on opening of voltage-dependent calcium channels, which control the release of vesicles from the pre-synaptic neuron by changing the influx of calcium ions. Moreover, we derive the structure of the optimum receiver based on the Neyman-Pearson detection method to find the effects of spike shape variations on the functionality of neuro-spike communication. Numerical results depict that changes in both spike width and amplitude affect the error detection probability. Moreover, these two factors do not control the performance of the system independently. Hence, a proper model for neuro-spike communication should contain effects of spike shape variations during axonal transmission on both synaptic propagation and spike generation mechanisms to enable us to accurately explain the performance of this communication paradigm.Publication Metadata only Increasing the packing density of assays in paper-based microfluidic devices(Aip Publishing, 2021) Becher, Elaina; Ghaderinezhad, Fariba; Özkan, Mehmed; Yetişen, Ali Kemal; N/A; Department of Mechanical Engineering; N/A; Department of Media and Visual Arts; Dabbagh, Sajjad Rahmani; Taşoğlu, Savaş; Havlucu, Hayati; Özcan, Oğuzhan; N/A; Faculty Member; PhD Student; Faculty Member; Department of Mechanical Engineering; Department of Media and Visual Arts; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Social Sciences and Humanities; College of Social Sciences and Humanities; N/A; 291971; N/A; 12532Paper-based devices have a wide range of applications in point-of-care diagnostics, environmental analysis, and food monitoring. Paper-based devices can be deployed to resource-limited countries and remote settings in developed countries. Paper-based point-of-care devices can provide access to diagnostic assays without significant user training to perform the tests accurately and timely. The market penetration of paper-based assays requires decreased device fabrication costs, including larger packing density of assays (i.e., closely packed features) and minimization of assay reagents. In this review, we discuss fabrication methods that allow for increasing packing density and generating closely packed features in paper-based devices. To ensure that the paper-based device is low-cost, advanced fabrication methods have been developed for the mass production of closely packed assays. These emerging methods will enable minimizing the volume of required samples (e.g., liquid biopsies) and reagents in paper-based microfluidic devices.Publication Metadata only Label-free differentiation of functional zones in mature mouse placenta using micro-Raman imaging(Optica Publishing Group, 2024) İnanç, Arda; Bektaş, Nayce İlayda; Kecoğlu, İbrahim; Parlatan, Uğur; Unlu, Mehmet Burçin; Durkut, Begüm; Uçak, Melike; Özenci, Çiler Çelik; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; School of MedicineIn histopathology, it is highly crucial to have chemical and structural information about tissues. Additionally, the segmentation of zones within a tissue plays a vital role in investigating the functions of these regions for better diagnosis and treatment. The placenta plays a vital role in embryonic and fetal development and in diagnosing some diseases associated with its dysfunction. This study provides a label -free approach to obtain the images of mature mouse placenta together with the chemical differences between the tissue compartments using Raman spectroscopy. To generate the Raman images, spectra of placental tissue were collected using a custom-built optical setup. The pre-processed spectra were analyzed using statistical and machine learning methods to acquire the Raman maps. We found that the placental regions called decidua and the labyrinth zone are biochemically distinct from the junctional zone. A histologist performed a comparison and evaluation of the Raman map with histological images of the placental tissue, and they were found to agree. The results of this study show that Raman spectroscopy offers the possibility of label -free monitoring of the placental tissue from mature mice while simultaneously revealing crucial structural information about the zones.Publication Open Access Machine learning-enabled multiplexed microfluidic sensors(American Institute of Physics (AIP) Publishing, 2020) Yetişen, Ali Kemal; N/A; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; Dabbagh, Sajjad Rahmani; Rabbi, Fazle; Doğan, Zafer; Taşoğlu, Savaş; Faculty Member; Faculty Member; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Graduate School of Social Sciences and Humanities; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 280658; 291971High-throughput, cost-effective, and portable devices can enhance the performance of point-of-care tests. Such devices are able to acquire images from samples at a high rate in combination with microfluidic chips in point-of-care applications. However, interpreting and analyzing the large amount of acquired data is not only a labor-intensive and time-consuming process, but also prone to the bias of the user and low accuracy. Integrating machine learning (ML) with the image acquisition capability of smartphones as well as increasing computing power could address the need for high-throughput, accurate, and automatized detection, data processing, and quantification of results. Here, ML-supported diagnostic technologies are presented. These technologies include quantification of colorimetric tests, classification of biological samples (cells and sperms), soft sensors, assay type detection, and recognition of the fluid properties. Challenges regarding the implementation of ML methods, including the required number of data points, image acquisition prerequisites, and execution of data-limited experiments are also discussed.Publication Metadata only Molecular beamforming for actuation in molecular communication networks(IEEE-Inst Electrical Electronics Engineers Inc, 2024) Pusane, Ali E.; Yılmaz, H. Birkan; Tuğcu, Tuna; Department of Electrical and Electronics Engineering; Angjo, Joana; Başar, Ertuğrul; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of EngineeringThe actuation accuracy of sensing tasks performed by molecular communication (MC) schemes is a very important metric. Reducing the effect of sensors fallibility can be achieved by improvements and advancements in the sensor and communication networks design. Inspired by the technique of beamforming used extensively in radio frequency communication systems, a novel molecular beamforming design is proposed in this paper. This design can find application in tasks related to actuation of nano machines in MC networks. The main idea behind the proposed scheme is that the utilization of more sensing nano machines in a network can increase the overall accuracy of that network. In other words, the probability of an actuation error reduces as the number of sensors that collectively take the actuation decision increases. In order to achieve this, several design procedures are proposed. Three different scenarios for the observation of the actuation error are investigated. For each case, the analytical background is provided and compared with the results obtained by computer simulations. The improvement in the actuation accuracy by means of molecular beamforming is verified for a uniform linear array as well as for a random topology.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 Metadata only Rapid diagnosis of spinal muscular atrophy using tetra-primer ARMS PCR assay: Simultaneous detection of SMN1 and SMN2 deletion(Elsevier, 2010) Etlik, Ozdal; Koksal, Vedat; Arican-Baris, S. Tugba; Department of Molecular Biology and Genetics; Barış, İbrahim; Teaching Faculty; Department of Molecular Biology and Genetics; College of Sciences; 111629Spinal muscular atrophy (SMA), the leading genetic cause of death in childhood, is an autosomal recessive neuromuscular disorder characterized by progressive muscle weakness, associated with deletions of the survival motor neuron 1 (SMN1) gene. Approximately 94% of SMA patients carry homologous deletions of SMN1 exon(s) 7 (and 8). Because of the high incidence and severity of the disease, precise detection and quantification of SMN1 and SMN2 gene copy numbers is essential for diagnosis and genetic counseling. We have developed a reliable single-tube tetra-primer PCR assay to simultaneously detect both the SMN1 and SMN2 exon 7 deletion using the advantage of C/T difference at nucleotide position of 840 in exon 7. The assay has been optimized and tested in 48 healthy controls, 20 known patients with SMA, 12 carriers (one SMN1 copy), and 8 amniotic fluids suspected of having SMA for whom we had determined the SMN1/SMN2 deletion by an additional PCR-RFLP method. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for simultaneous detection of both SMN1 and SMN2 deletion, which could be used even in "low-tech" laboratories.