Birkan YILMAZ | Bogazici University (original) (raw)

Papers by Birkan YILMAZ

arXiv (Cornell University), Nov 25, 2020

This survey paper focuses on modulation aspects of molecular communication, an emerging field foc... more This survey paper focuses on modulation aspects of molecular communication, an emerging field focused on building biologically-inspired systems that embed data within chemical signals. The primary challenges in designing these systems are how to encode and modulate information onto chemical signals, and how to design a receiver that can detect and decode the information from the corrupted chemical signal observed at the destination. In this paper, we focus on modulation design for molecular communication via diffusion systems. In these systems, chemical signals are transported using diffusion, possibly assisted by flow, from the transmitter to the receiver. This tutorial presents recent advancements in modulation and demodulation schemes for molecular communication via diffusion. We compare five different modulation types: concentration-based, type-based, timing-based, spatial, and higher-order modulation techniques. The end-to-end system designs for each modulation scheme are presented. In addition, the key metrics used in the literature to evaluate the performance of these techniques are also presented. Finally, we provide a numerical bit error rate comparison of prominent modulation techniques using analytical models. We close the tutorial with a discussion of key open issues and future research directions for design of molecular communication via diffusion systems.

arXiv (Cornell University), Nov 18, 2016

A molecular communication channel is determined by the received signal. Received signal models fo... more A molecular communication channel is determined by the received signal. Received signal models form the basis for studies focused on modulation, receiver design, capacity, and coding depend on the received signal models. Therefore, it is crucial to model the number of received molecules until time t analytically. Modeling the diffusion-based molecular communication channel with the first-hitting process is an open issue for a spherical transmitter. In this paper, we utilize the artificial neural networks technique to model the received signal for a spherical transmitter and a perfectly absorbing receiver (i.e., first hitting process). The proposed technique may be utilized in other studies that assume a spherical transmitter instead of a point transmitter.

arXiv (Cornell University), Jan 14, 2014

Communication via diffusion (CvD) is an effective and energy efficient method for transmitting in... more Communication via diffusion (CvD) is an effective and energy efficient method for transmitting information in nanonetworks. In this work, we focus on a diffusion-based communication system where the reception process is an absorption via receptors. Whenever a molecule hits to the receiver it is removed from the environment. This kind of reception process is called first passage process and it is more complicated compared to diffusion process only. In 3-D environments, obtaining analytical solution for hitting time distribution for realistic cases is complicated, hence we develop an end-to-end simulator for he diffusion-based communication system that sends consecutive symbols. In CvD, each symbol is modulated and demodulated in a time slot called symbol duration, however the long tail distribution of hitting time is the main challenge that affects the symbol detection error. The molecules arriving in the following slots become an interference source when detection takes place. Endto-end simulator enables us to analyze the effect of inter symbol interference (ISI) without making any assumptions on the ISI. We propose an ISI cancellation technique that utilizes decision feedback for compensating the effect of previously demodulated symbol. Three different modulation types are considered with pulse, square, and cosine carrier waves. In case of constraints on transmitter or receiver node it may not be possible to use pulse as a carrier, and peak-to-average messenger molecule metric is defined for this purpose. Results show that, the proposed ISI mitigation technique improves the symbol detection performance and the amplitude-based modulations are improved more than frequency-based modulations.

2017 International Artificial Intelligence and Data Processing Symposium (IDAP), Sep 1, 2017

Molecular Communication (MC) is a new multidisciplinary subject concerning medicine, biology, and... more Molecular Communication (MC) is a new multidisciplinary subject concerning medicine, biology, and communication engineering. MC concept is introduced for modeling of communication of nano/micro scale devices. In MC systems, chemical signals carrying information in gaseous or liquid media are used. Similar to other communication systems, in MC sending information from transmitter to receiver with minimum error is one of the most important goals. In MC systems due to physical characteristics of medium, higher rates of inter symbol interference (ISI) and noise increase error probability. Figures of receiver mechanisms and signal detection techniques are therefore the main factors to be tuned for decreasing error probability. In this view, so far, many receiver models such as reversible adsorption and desorption (A&D), protrusion method, ligand receptor, and linear catalytic or CAT receiver models have been introduced. In this study, these models and the results obtained through their implementation are investigated and briefly reviewed.

In this paper, we consider the block synchronization issue in molecular communications via diffus... more In this paper, we consider the block synchronization issue in molecular communications via diffusion (MCvD). To maintain an internal clock with a fixed clock offset in both transmitter and receiver requires additional energy in nanosensors that have limited power and chemical budget. Therefore, synchronization becomes a challenging issue to handle complex tasks in the nanonetworks. In MCvD systems, most of the transmitted molecules hit the receiver surface at the start of the symbol interval. Therefore, while detecting the start of the symbol duration, a small synchronization error results in a high symbol detection error. To address the issue, we suggest several synchronization frameworks for the MCvD systems that can be categorized into two main classes: per-symbol and per-block synchronization. Moreover, we investigate the impact of synchronization error on the symbol-error-rate (SER) performance.

arXiv (Cornell University), Oct 17, 2015

In active transport molecular communication (ATMC), information particles are actively transporte... more In active transport molecular communication (ATMC), information particles are actively transported from a transmitter to a receiver using special proteins. Prior work has demonstrated that ATMC can be an attractive and viable solution for on-chip applications. The energy consumption of an ATMC system plays a central role in its design and engineering. In this work, an energy model is presented for ATMC and the model is used to provide guidelines for designing energy efficient systems. The channel capacity per unit energy is analyzed and maximized. It is shown that based on the size of the symbol set and the symbol duration, there is a vesicle size that maximizes rate per unit energy. It is also demonstrated that maximizing rate per unit energy yields very different system parameters compared to maximizing the rate only.

arXiv (Cornell University), Jul 26, 2015

This article examines recent research in molecular communications from a telecommunications syste... more This article examines recent research in molecular communications from a telecommunications system design perspective. In particular, it focuses on channel models and stateof-the-art physical layer techniques. The goal is to provide a foundation for higher layer research and motivation for research and development of functional prototypes. In the first part of the article, we focus on the channel and noise model, comparing molecular and radio-wave pathloss formulae. In the second part, the article examines, equipped with the appropriate channel knowledge, the design of appropriate modulation and error correction coding schemes. The third reviews transmitter and receiver side signal processing methods that suppress intersymbol-interference. Taken together, the three parts present a series of physical layer techniques that are necessary to producing reliable and practical molecular communications.

IEEE Access, 2019

Synchronization is a critical issue in molecular communications (MC). Additionally, the lack of a... more Synchronization is a critical issue in molecular communications (MC). Additionally, the lack of an appropriate time-slotted framework for MC systems hinders the in-depth analysis of desynchronization. Therefore, this paper addresses both issues. First, taking inspiration from oscillators found in nature, we propose a time-slotted framework suitable for MC systems where the time instances of the oscillations demarcate the time-slot boundaries. The use of biological oscillators readily satisfies biocompatibility requirements. We name such system as a time-slotted molecular communication-based (TS-MOC) system. A TS-MOC system will be beneficial to many MC applications, such as when multiple nanomachines have to transmit data simultaneously to a control/sink node or share the channel in a time-division multiplexing manner. Second, oscillation perturbations induce desynchronization-the misalignment of time-slots. Desynchronization combined with large propagation delay results in a time difference between the arrival of a signal and the beginning of a time-slot. This phenomenon is called time-slot error, and it can degrade a system's performance. Therefore, the immediate goal is to mitigate time-slot errors. Depending on the initiation type, we propose two synchronization schemes: sender-initiated time-slot alignment and receiver-initiated time-slot alignment. An analytical model for time-slot error is also derived. Our analysis demonstrates that the proposed schemes are robust and energy-efficient-they achieve relatively low errors indicating robustness and relatively less synthesizing energy costs indicating energy efficiency. Our analysis also highlights the good agreement between the simulations and the analytical model. Finally, in conclusion, we provide brief insights into key open research challenges.

IEEE Transactions on Communications, Jun 1, 2020

For nano-scale communications, there must be cooperation and simultaneous communication between n... more For nano-scale communications, there must be cooperation and simultaneous communication between nano devices. To this end, in this paper, we investigate two-way (a.k.a. bidirectional) molecular communications between nano devices. If different types of molecules are used for the communication links, the two-way system eliminates the need to consider selfinterference. However, in many systems, it is not feasible to use a different type of molecule for each communication link. Thus, we propose a two-way molecular communication system that uses a single type of molecule. We derive a channel model for this system and use it to analyze the proposed system's bit error rate, throughput, and self-interference. Moreover, we propose analog-and digital-self-interference cancellation techniques. The enhancement of link-level performance using these techniques is confirmed with both particle-based simulations and analytical results.

IEEE Access, 2018

In this paper, spatial transmission techniques in the area of multiple-input multipleoutput (MIMO... more In this paper, spatial transmission techniques in the area of multiple-input multipleoutput (MIMO) diffusion-based molecular communications (DBMC) are investigated. For transmitter-side spatial coding, Alamouti-type coding and repetition MIMO coding are analyzed. At the receiver-side, selection diversity and equal-gain combining are studied as combining strategies. Throughout the numerical analysis, a symmetrical 2 × 2 MIMO-DBMC system is assumed. Furthermore, a trained artificial neural network is utilized to acquire the channel impulse responses. The numerical analysis demonstrates that there is no spatial diversity gain in the DBMC system under investigation, but that it is possible to achieve an array gain instead. In addition, it is shown that for MIMO-DBMC systems repetition MIMO coding is superior to Alamouti-type coding. INDEX TERMS Array gain, artificial neural network, channel modeling, molecular communication via diffusion, multiple-input multiple-output, spatial diversity.

bioRxiv (Cold Spring Harbor Laboratory), Apr 18, 2023

Developments in bioengineering and nanotechnology have ignited the research on biological and mol... more Developments in bioengineering and nanotechnology have ignited the research on biological and molecular communication systems. Despite potential benefits, engineering communication systems to carry data signals using biological messenger molecules is challenging. Diffusing molecules may fall behind their schedule to arrive at a receiver, interfering with symbols of subsequent time slots and distorting the signal. Theoretical molecular communication models often focus solely on the characteristics of the communication channel and fail to provide an end-to-end system response, since they assume a simple thresholding process for a receiver cell and overlook how the receiver can detect the incoming distorted molecular signal. There is a need to develop viable end-to-end communication models. In this paper, we present a model-based framework for designing diffusion-based molecular communication systems coupled with synthetic 1. CC-BY-NC-ND 4.

arXiv (Cornell University), Sep 2, 2016

In a diffusion-based molecular communication system, molecules are employed to convey information... more In a diffusion-based molecular communication system, molecules are employed to convey information. When propagation and reception processes are considered in a framework of first passage processes, we need to focus on absorbing receivers. For this kind of molecular communication system, the characteristics of the channel is also affected by the shape of the transmitter. In the literature, most studies focus on systems with a point transmitter due to circular symmetry. In this letter, we address propagation and reception pattern for chemical signals emitted from a spherical transmitter. We also investigate the directivity gain achieved by the reflecting spherical transmitter. We quantify the power gain by measuring the received power at different angles on a circular region. Moreover, we define three metrics, i.e., the half-power pattern-width, the directivity gain, and the peak time of the signal, for analyzing the received signal pattern. Index Terms-Molecular communication, spherical transmitter, propagation pattern, chemical signal, absorbing receiver. I. INTRODUCTION T HE developments in nanotechnology research have resulted in implementation of simple nano and micro nodes capable of carrying out simple tasks. Designing and enabling communication between these nodes emerged as a new need for achieving complex tasks at small scales [1]-[4]. Various molecular communication systems were proposed in the literature, such as molecular communication via diffusion (MCvD), ion signaling, active transport, and bacterium-based communication. Among these systems, a particularly effective and energy-efficient method of exchanging information is MCvD, a short-to-medium range molecular communication technique in which the molecules diffuse in the propagation medium to transfer the intended information. MCvD consists of three main processes: emission, propagation, and absorption. In MCvD, analyzing the received molecule distribution with respect to time is crucial for characterizing the channel [5]. Channel characteristics for molecular communication with an absorbing receiver in a 3-dimensional (3D) environment are analyzed in [5]. In [6], the authors formulated the hitting rate of the molecules to the receptors of an absorbing receiver in a 3D medium while varying the density and the size of receptors. Inspired by smart antennas in conventional wireless communications, the authors in [7] designed a specialized receiver to achieve directivity gain.

Turkish Journal of Electrical Engineering and Computer Sciences, 2023

In this paper, we propose a distributed algorithm that determines effective Overlapping Basic Ser... more In this paper, we propose a distributed algorithm that determines effective Overlapping Basic Service Set/Preamble Detection (OBSS/PD) threshold levels in each WiFi6 device to maximize the total throughput by increasing the spectral efficiency. Within WiFi6 standard, OBSS/PD mechanism is introduced to increase the overall efficiency of WiFi networks by tuning the receiver sensitivity as well as the transmission power. In a nutshell, the proposed algorithm, RACEBOT, tunes the hearing (i.e. reception) and speaking (i.e. transmission) parameters of each WiFi device individually for the betterment of the WiFi experience of all WiFi networks in a neighborhood. WiFi experience is not only affected by the spectral efficiency but also by the so-called rate selection algorithms that aims to select the ideal modulation and coding levels according to the ever-changing channel conditions. For higher flexibility, the proposed algorithm works agnostically to the selected rate selection mechanism. Moreover, RACEBOT is a distributed algorithm working independently in all WiFi devices in a given environment. We have conducted extensive simulations in NS3 to evaluate the performance of our proposed algorithm and compare its results with other prominent carrier sensitivity threshold algorithms, both pre-WiFi6 and post-WiFi6. Our results show that RACEBOT outperforms its competitors the RTOT and DSC algorithms in terms of aggregate throughput by 10%-20% in dense networks and 5%-10% in sparse networks considering modern rate selection algorithms such as Thompson.

IEEE Journal on Selected Areas in Communications, Mar 1, 2016

In diffusion-based molecular communication, information transport is governed by diffusion throug... more In diffusion-based molecular communication, information transport is governed by diffusion through a fluid medium. The achievable data rates for these channels are very low compared to the radio-based communication system, since diffusion can be a slow process. To improve the data rate, a novel multiple-input multiple-output (MIMO) design for molecular communication is proposed that utilizes multiple molecular emitters at the transmitter and multiple molecular detectors at the receiver (in RF communication these all correspond to antennas). Using particle-based simulators, the channel's impulse response is obtained and mathematically modeled. These models are then used to determine inter-link interference (ILI) and intersymbol interference (ISI). It is assumed that when the receiver has incomplete information regarding the system and the channel state, low complexity symbol detection methods are preferred since the receiver is small and simple. Thus four detection algorithms are proposed-adaptive thresholding, practical zero forcing with channel models excluding/including the ILI and ISI, and Genie-aided zero forcing. The proposed algorithms are evaluated extensively using numerical and analytical evaluations.

arXiv (Cornell University), Apr 18, 2016

In molecular communication via diffusion (MCvD), the inter-symbol interference (ISI) is a well kn... more In molecular communication via diffusion (MCvD), the inter-symbol interference (ISI) is a well known severe problem that deteriorates both data rates and link reliability. ISI mainly occurs due to the slow and highly random propagation of the messenger molecules, which causes the emitted molecules from the previous symbols to interfere with molecules from the current symbol. An effective way to mitigate the ISI is using enzymes to degrade undesired molecules. Prior work on ISI mitigation by enzymes has assumed an infinite amount of enzymes randomly distributed around the molecular channel. Taking a different approach, this paper assumes an MCvD channel with a limited amount of enzymes. The main question this paper addresses is how to deploy these enzymes in an effective structure so that ISI mitigation is maximized. To find an effective MCvD channel environment, this study considers optimization of the shape of the transmitter node, the deployment location and structure, the size of the enzyme deployed area, and the half-lives of the enzymes. It also analyzes the dependence of the optimum size of the enzyme area on the distance and half-life.

arXiv (Cornell University), May 30, 2016

The performance of communication systems is fundamentally limited by the loss of energy through p... more The performance of communication systems is fundamentally limited by the loss of energy through propagation and circuit inefficiencies. In this article, we show that it is possible to achieve ultra low energy communications at the nanoscale, if diffusive molecules are used for carrying data. While the energy of electromagnetic waves will inevitably decays as a function of transmission distance and time, the energy in individual molecules does not. Over time, the receiver has an opportunity to recover some, if not all of the molecular energy transmitted. The article demonstrates the potential of ultra-low energy simultaneous molecular information and energy transfer (SMIET) through the design of two different nano-relay systems. It also discusses how molecular communications can benefit more from crowd energy harvesting than traditional wave-based systems.

Iet Nanobiotechnology, Sep 1, 2020

Nano-devices are featured to communicate via molecular interaction, the so-called molecular commu... more Nano-devices are featured to communicate via molecular interaction, the so-called molecular communication (MC). In MC systems, the information is carried by molecules where the amount of molecules constitutes the level of the signal. In this study, an MC-based system was analysed with different receiver topology and related parameters, such as size, shape, and orientation of receptors on the receiver. Also in the concept of nano-medicine, the effect of amyloid-beta ([inline-formula removed]), which is believed as the main cause of Alzheimer disease, on the successful reception ratio of molecules with the proposed receiver models was investigated. It was demonstrated that the cubic receiver model is superior to sphere one in terms of the correct reception ratio of the molecular signal. A cubic model where its edge (not rotated around the centre) is placed across the transmitter demonstrated a better performance in reducing the effect of [inline-formula removed] as compared to the sphere model while a cubic model where its corner (rotated around the centre) is placed across the transmitter demonstrated a worse performance than the spherical model. From this expression, it may be concluded that with the adjustment of topological system parameters the probability of successful reception ratio in MC may be possible.

IEEE Transactions on Antennas and Propagation, Jul 1, 2022

Matching media are used in various applications to increase the power transmitted into the human ... more Matching media are used in various applications to increase the power transmitted into the human body. The selection of the optimum matching medium permittivity is not a straightforward task, as the optimum value maximizing the transmitted power depends on the thickness of the matching medium and the electromagnetic properties of the target tissue. In this paper, a computationally heavy empirical approach and a machine learning-based approach are utilized for the selection of the matching medium. The empirical approach demonstrates that the matching medium can increase the |S 21 | values up to 8 dB, which is validated with measurements. Next, a machine learning-based tool is proposed to predict the optimum matching medium permittivity for any target tissue and any matching medium thickness. A one-dimensional convolutional neural network followed by a multi-layer perceptron is trained with the simulated average Poynting vector magnitudes for muscle and fat as target tissues. The average Poynting vector magnitude and the dipole length for given system parameters are predicted by the trained artificial neural network. The accuracy is calculated by comparison with the results of the empirical analysis and found to be 1% and 12.3% mean absolute percentage error for dipole length and average Poynting vector magnitude, respectively. The proposed tool decreases the time required to milliseconds.

2021 29th Signal Processing and Communications Applications Conference (SIU)

Molecular communication is applied to advance the capabilities of healthcare and medical systems.... more Molecular communication is applied to advance the capabilities of healthcare and medical systems. These systems may be utilized for cancer cell localization, in-body synchronization, and anomaly detection applications. In this paper, a mock circulatory network testbed for molecular communication is introduced. A realistic mock circulary network is important to understand the human circulatory hemodynamics from molecular communication's perspective. The mock circulatory network testbed basically consists of a pulsatile pump (for mimicking heart), 3D printed left and right pulmonary artery, silicone mock vessel network, non-invasive pressure sensors, valves, information molecules, chemical sensors, and data acquisition center.

Nano Communication Networks, 2018

Recent breakthroughs in bio-nano technology have motivated molecular communication as a biologica... more Recent breakthroughs in bio-nano technology have motivated molecular communication as a biologically-inspired technique for nano communication networks. Understanding and realizing molecular communication between and among nanomachines and living organisms in point-to-point, multiple-access, broadcast, and relay channels will enable their cooperation and coordination to perform complex tasks in medical and environmental applications, such as targeted drug delivery, tumor cell detection, and monitoring of pollutants. Even with growing academic research and interest in the field of molecular and nano communication networks, challenges still exist to convert theory to practical implementation. Most of these challenges come from the need to develop: 1) sufficiently detailed mathematical models of molecular communication systems with realistic biotransceivers in practical environments; 2) theory for designing molecular communication systems that are sufficiently reliable and efficient; and 3) knowledge and experience of how to design, build, and control nanomachines with basic functionality. This Special Issue is a collection of original technical articles on molecular communication networks that aims to address some of these challenges, with a particular emphasis on robust molecular communication system design. Five papers were selected for inclusion in this Special Issue after two rigorous rounds of peer review. Each accepted paper represents a timely contribution that pushes the state-of-the-art in this growing field. In the following, we briefly summarize each of these contributions. The paper ''Simulation Framework for Touchable Communication on NS3Sim'' by Yu Zhou, Yifan Chen, Ross Murch, Rui Wang, and Qingfeng Zhang presents a nanoscale simulation package that is being developed for Network Simulation 3 (NS-3). The package implements the touchable communication scheme (TouchCom), which is designed to control and track message carriers for applications including targeted drug delivery by nanobots. The paper maps the TouchCom architecture to the fundamental nanoscale components defined in the newly-developed IEEE 1906.1 framework (Recommended Practice for Nanoscale and Molecular Communication Framework). The comprehensive NS-3 example module, which is available on Github, captures the propagation delay and path loss of molecules traveling through a fractal-based structure representing a vascular network. The paper ''Molecule-as-a-Frame: A Frame Based Communication Approach for Nanonetworks'' by Mustafa Can Gursoy, Ali Emre Pusane, and Tuna Tugcu proposes the concept of Moleculeas-a-Frame (MaaF), which encodes a complete data frame in the