Research Project: Coordinating European Research on Molecular Communications
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Contributors
Funders
ID
EC.00081
Authors
Akan, Özgür Barış
Faculty Member
Publications
Anarchy versus cooperation on internet of molecular things
(IEEE-Inst Electrical Electronics Engineers Inc, 2017) Akan, Özgür Barış; Koca, Çağlar; N/A; Department of Electrical and Electronics Engineering; Next Generation and Wireless Communication Laboratory; Yes; College of Engineering; Laboratory
Using the advances in molecular communications (MCs), nanomachines as a group can undertake complex tasks. With the emergence of Internet of molecular things (IoMT), such nanomachine groups are now larger than ever. However, the minimal design of nanomachines makes cooperation difficult. In this paper, we investigate the performances of anarchic and cooperative transmitters in IoMT. We design an MC game in which nanomachines choose to cooperate or confront. We discuss the advantages and disadvantages of cooperation and state the possible transmitter personalities using game theoretic principles. Moreover, we focus on methods to ensure cooperation and we explore the optimal transmitter behavior if its partner rejects cooperation. Finally, we deduce that although ensuring cooperation may be done effectively with minimum hardware, anarchy is not necessarily a bad result. We also realize that in case a transmitter rejects cooperation, perpetual confrontation is not a good approach.
An information theoretical analysis of human insulin-glucose system toward the internet of bio-nano things
(Institute of Electrical and Electronics Engineers (IEEE), 2017) Abbasi, Naveed Ahmed; Akan, Özgür Barış; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Yes; College of Engineering; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
Molecular 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.
Controlled information transfer through an in vivo nervous system
(Nature Publishing Group (NPG), 2018) Abbasi, Naveed Ahmed; Akan, Özgür Barış; Lafçı, Dilan; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Yes; College of Engineering; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
The 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.
A fast algorithm for analysis of molecular communication in artificial synapse
(IEEE-Inst Electrical Electronics Engineers Inc, 2017) Akan, Özgür Barış; Bilgin, Bilgesu Arif; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Yes; College of Engineering; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
In this paper, we analyze molecular communications (MCs) in a proposed artificial synapse (AS), whose main difference from biological synapses (BSs) is that it is closed, i.e., transmitter molecules cannot diffuse out from AS. Such a setup has both advantages and disadvantages. Besides higher structural stability, being closed, AS never runs out of transmitters. Thus, MC in AS is disconnected from outer environment, which is very desirable for possible intra-body applications. On the other hand, clearance of transmitters from AS has to be achieved by transporter molecules on the presynaptic membrane of AS. Except from these differences, rest of AS content is taken to be similar to that of a glutamatergic BS. Furthermore, in place of commonly used Monte Carlo-based random walk experiments, we derive a deterministic algorithm that attacks for expected values of desired parameters such as evolution of receptor states. To assess validity of our algorithm, we compare its results with average results of an ensemble of Monte Carlo experiments, which shows near exact match. Moreover, our approach requires significantly less amount of computation compared with Monte Carlo approach, making it useful for parameter space exploration necessary for optimization in design of possible MC devices, including but not limited to AS. Results of our algorithm are presented in case of single quantal release only, and they support that MC in closed AS with elevated uptake has similar properties to that in BS. In particular, similar to glutamatergic BSs, the quantal size and the density of receptors are found to be main sources of synaptic plasticity. On the other hand, the proposed model of AS is found to have slower decaying transients of receptor states than BSs, especially desensitized ones, which is due to prolonged clearance of transmitters from AS.
Modeling convection-diffusion-reaction systems for microfluidic molecular communications with surface-based receivers in Internet of Bio-Nano Things
(Public Library of Science, 2018) Akan, Özgür Barış; Kuşcu, Murat; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Yes; College of Engineering; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
We consider a microfluidic molecular communication (MC) system, where the concentration-encoded molecular messages are transported via fluid flow-induced convection and diffusion, and detected by a surface-based MC receiver with ligand receptors placed at the bottom of the microfluidic channel. The overall system is a convection-diffusion-reaction system that can only be solved by numerical methods, e.g., finite element analysis (FEA). However, analytical models are key for the information and communication technology (ICT), as they enable an optimisation framework to develop advanced communication techniques, such as optimum detection methods and reliable transmission schemes. In this direction, we develop an analytical model to approximate the expected time course of bound receptor concentration, i.e., the received signal used to decode the transmitted messages. The model obviates the need for computationally expensive numerical methods by capturing the nonlinearities caused by laminar flow resulting in parabolic velocity profile, and finite number of ligand receptors leading to receiver saturation. The model also captures the effects of reactive surface depletion layer resulting from the mass transport limitations and moving reaction boundary originated from the passage of finite-duration molecular concentration pulse over the receiver surface. Based on the proposed model, we derive closed form analytical expressions that approximate the received pulse width, pulse delay and pulse amplitude, which can be used to optimize the system from an ICT perspective. We evaluate the accuracy of the proposed model by comparing model-based analytical results to the numerical results obtained by solving the exact system model with COMSOL Multiphysics.
