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Publication Metadata only A communication theoretical modeling of axonal propagation in hippocampal pyramidal neurons(IEEE-Inst Electrical Electronics Engineers Inc, 2017) 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; 6647Understandingthe fundamentals of communication among neurons, known as neuro-spike communication, leads to reach bio-inspired nanoscale communication paradigms. In this paper, we focus on a part of neuro-spike communication, known as axonal transmission, and propose a realistic model for it. The shape of the spike during axonal transmission varies according to previously applied stimulations to the neuron, and these variations affect the amount of information communicated between neurons. Hence, to reach an accurate model for neuro-spike communication, the memory of axon and its effect on the axonal transmission should be considered, which are not studied in the existing literature. In this paper, we extract the important factors on the memory of axon and define memory states based on these factors. We also describe the transition among these states and the properties of axonal transmission in each of them. Finally, we demonstrate that the proposed model can follow changes in the axonal functionality properly by simulating the proposed model and reporting the root mean square error between simulation results and experimental data.Publication Metadata only Asymmetrical relaying in molecular communications(IEEE-Inst Electrical Electronics Engineers Inc, 2022) Pusane, Ali E.; Yılmaz, H. Birkan; Tuğcu, Tuna; N/A; Department of Electrical and Electronics Engineering; Angjo, Joana; Başar, Ertuğrul; Master Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 149116Molecular communication via diffusion (MCvD) is a novel communication technique that uses the diffusive characteristics of molecules for enabling the communication between nanomachines. Since the molecules propagate following a random motion, MCvD schemes are usually limited to a short communication range. Most of the molecular relaying schemes in the literature consider symmetric setups where transmitters and receivers are placed at the same distance from the relay, which is difficult to provide in practical scenarios and a possible cause of failure. In this study, asymmetric molecular links of a relay system are investigated. In order to achieve a satisfactory overall performance in spite of the asymmetries, two parameter optimization methods are proposed for the uplink of a relaying system, based on emitting different types of molecules with different diffusion coefficient values from the transmitters. Due to the channel symmetry, the solutions presented in this study are expected to hold for the downlink as well. The resulting bit error rate (BER) performances are presented and discussed.Publication Open Access Classification of drug molecules considering their IC(50) values using mixed-integer linear programming based hyper-boxes method(BioMed Central, 2008) Department of Industrial Engineering; Department of Chemical and Biological Engineering; Armutlu, Pelin; Özdemir, Muhittin Emre; Yüksektepe, Fadime Üney; Kavaklı, İbrahim Halil; Türkay, Metin; Faculty Member; Department of Industrial Engineering; Department of Chemical and Biological Engineering; The Center for Computational Biology and Bioinformatics (CCBB); College of Engineering; N/A; N/A; N/A; 40319; 24956Background: A priori analysis of the activity of drugs on the target protein by computational approaches can be useful in narrowing down drug candidates for further experimental tests. Currently, there are a large number of computational methods that predict the activity of drugs on proteins. In this study, we approach the activity prediction problem as a classification problem and, we aim to improve the classification accuracy by introducing an algorithm that combines partial least squares regression with mixed-integer programming based hyper-boxes classification method, where drug molecules are classified as low active or high active regarding their binding activity (IC(50) values) on target proteins. We also aim to determine the most significant molecular descriptors for the drug molecules. Results: We first apply our approach by analyzing the activities of widely known inhibitor datasets including Acetylcholinesterase (ACHE), Benzodiazepine Receptor (BZR), Dihydrofolate Reductase (DHFR), Cyclooxygenase-2 (COX-2) with known IC(50) values. The results at this stage proved that our approach consistently gives better classification accuracies compared to 63 other reported classification methods such as SVM, Naive Bayes, where we were able to predict the experimentally determined IC50 values with a worst case accuracy of 96%. To further test applicability of this approach we first created dataset for Cytochrome P450 C17 inhibitors and then predicted their activities with 100% accuracy. Conclusion: Our results indicate that this approach can be utilized to predict the inhibitory effects of inhibitors based on their molecular descriptors. This approach will not only enhance drug discovery process, but also save time and resources committed.Publication Open Access Detection of biological switches using the method of Groebner bases(BioMed Central, 2019) Department of Chemical and Biological Engineering; Arkun, Yaman; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 108526Background: bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellular information to the nucleus where important biological functions are executed. Results in this work we show how the method of Groebner bases can be used to detect bistability and output switchability. The method of Groebner bases can be seen as a multivariate, non-linear generalization of the Gaussian elimination for linear systems which conveniently seperates the variables and drastically simplifies the simultaneous solution of polynomial equations. A necessary condition for fixed-point state bistability is for the Grobner basis to have three distinct solutions for the state. A sufficient condition is provided by the eigenvalues of the local Jacobians. We also introduce the concept of output switchability which is defined as the ability of an output of a bistable system to switch between two different stable steady-state values. It is shown that bistability does not necessarily guarantee switchability of every state variable of the system. We further show that, for a bistable system, the necessary conditions for output switchability can be derived using the Groebner basis. The theoretical results are incorporated into an analysis procedure and applied to several systems including the AKT (Protein kinase B), RAS (Rat Sarcoma) and MAPK (Mitogen-activated protein kinase) signal transduction pathways. Results demonstrate that the Groebner bases can be conveniently used to analyze biological switches by simultaneously detecting bistability and output switchability. Conclusion: the Groebner bases provides a novel methodology to analyze bistability. Results clarify the distinction between bistability and output switchability which is lacking in the literature. We have shown that theoretically, it is possible to have an output subspace of an n-dimensional bistable system where certain variables cannot switch. It is possible to construct such systems as we have done with two reaction networks.Publication Metadata only Rate of information flow across layered neuro-spike network in the spinal cord(IEEE-Inst Electrical Electronics Engineers Inc, 2020) N/A; Department of Electrical and Electronics Engineering; Civaş, Meltem; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647Spinal Cord Injury (SCI) is a severe condition that can result in loss of motor and sensory functions by disrupting communication among neurons, i.e., neuro-spike communication. Future information and communication technology (ICT) based treatment techniques for SCI are expected to rely on nano networks, deployed inside the body. In this respect, modeling neuro-spike communication channels in the spinal cord and revealing the relationship between channel metrics and SCI are required to realize these treatment techniques and diagnosis tools such as replacement neural implants, high-performance diagnosis tools, which are based on ICT metrics instead of large medical data. Therefore, in this study, we focus on a spinal cord network, namely the descending spinal cord pathway, which is responsible for the transmission of brain motor signals to the spinal cord. We aim to analyze the rate of motor information flow to the corresponding muscle. To this end, we model the spinal cord motor network as a layered network consisting of a cascade of two independent neuro-spike channels, which are brain-spinal cord network and spinal cord interneuron-spinal cord motoneuron network. We derive upper and lower bounds for the total rate across the brain-spinal cord network and interneuron-spinal cord network. Our evaluations demonstrate that the total rate in the case of upper motor neuron syndrome (UMNS), which manifests itself with muscle weakness, approaches zero, where the brain-spinal cord network becomes a bottleneck. In lower motor neuron syndrome (LMNS), which results in muscle atrophy, the total rate again approaches zero with the loss of spinal cord motoneurons (MN).Publication Metadata only Sum rate of MISO neuro-spike communication channel with constant spiking threshold(IEEE-Inst Electrical Electronics Engineers Inc, 2018) N/A; N/A; N/A; Department of Electrical and Electronics Engineering; Ramezani, Hamideh; Khan, Tooba; Akan, Özgür Barış; PhD Student; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 6647Communication among neurons, known as neuro-spike communication, is the most promising technique for realization of a bio-inspired nanoscale communication paradigm to achieve biocompatible nanonetworks. In neuro-spike communication, the information, encoded into spike trains, is communicated to various brain regions through neuronal network. An output neuron needs to receive signal from multiple input neurons to generate a spike. Hence, in this paper, we aim to quantify the information transmitted through the multiple-input single-output (MISO) neuro-spike communication channel by considering models for axonal propagation, synaptic transmission, and spike generation. Moreover, the spike generation and propagation in each neuron requires opening and closing of numerous ionic channels on the cell membrane, which consumes considerable amount of ATP molecules called metabolic energy. Thus, we evaluate how applying a constraint on available metabolic energy affects the maximum achievable mutual information of this system. To this aim, we derive a closed form equation for the sum rate of the MISO neuro-spike communication channel and analyze it under the metabolic cost constraints. Finally, we discuss the impacts of changes in number of pre-synaptic neurons on the achievable rate and quantify the tradeoff between maximum achievable sum rate and the consumed metabolic energy.Publication Metadata only Theoretical limits on multiuser molecular communication in internet of nano-bio things(IEEE-Inst Electrical Electronics Engineers Inc, 2017) N/A; Department of Electrical and Electronics Engineering; Dinç, Ergin; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647In nano-bio networks, multiple transmitterreceiver pairs will operate in the same medium. Both inter-symbol interference and multi-user interference can cause saturation at the receiver side, and this effectmay cause an outage. Thus, we propose a tractable framework to calculate the theoretical operating points for fully absorbing receiver.