Research Project: engineering ligand-REceptor INteractions FOR Molecular communicATIONs
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Contributors
Funders
ID
EC.00152
Authors
Kuşcu, Murat
Faculty Member
Publications
Capacity analysis of molecular communications with ratio shift keying modulation
(Association for Computing Machinery (ACM), 2022) Araz, Mustafa Okan; Emirdağı, Ahmet Rasim; Kopuzlu, Mahmut Serkan; Kuşcu, Murat; Department of Electrical and Electronics Engineering; Yes; College of Engineering
Molecular Communications (MC) is a bio-inspired communication technique that uses molecules to encode and transfer information. Many efforts have been focused on developing new modulation techniques for MC by exploiting distinguishable properties of molecules. In this paper, we investigate a particular modulation scheme where the information is encoded into the concentration ratio of two different types of molecules. To evaluate the performance of this so-called Ratio Shift Keying (RSK) modulation, we carry out an information theoretical analysis and derive the capacity of the end-to-end MC channel where the receiver performs ratio estimation based on ligand-receptor binding statistics in an optimal or suboptimal manner. The numerical results, obtained for varying similarity between the ligand types employed for ratio-encoding, and number of receptors, indicate that the RSK can outperform the concentration shift keying (CSK) modulation, the most common technique considered in literature, when the transmitter is power-limited. The results also indicate the potential advantages of RSK over other modulation methods under time-varying channel conditions, when the effects of the dynamic conditions are invariant to the type of the molecules.
Microfluidic pulse shaping methods for molecular communications
(Elsevier, 2023) Bolhassan, Iman Mokari; Kahvazi Zadeh, Maryam; Kuşcu, Murat; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Yes; College of Engineering; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
Molecular Communication (MC) is a bio-inspired communication modality that utilizes chemical signals in the form of molecules to exchange information between spatially separated entities. Pulse shaping is an important process in all communication systems, as it modifies the waveform of transmitted signals to match the characteristics of the communication channel for reliable and high-speed information transfer. In MC systems, the unconventional architectures of components, such as transmitters and receivers, and the complex, nonlinear, and time-varying nature of MC channels make pulse shaping even more important. While several pulse shaping methods have been theoretically proposed for MC, their practicality and performance are still uncertain. Moreover, the majority of recently proposed experimental MC testbeds that rely on microfluidics technology lack the incorporation of programmable pulse shaping methods, which hinders the accurate evaluation of MC techniques in practical settings. To address the challenges associated with pulse shaping in microfluidic MC systems, we provide a comprehensive overview of practical microfluidic chemical waveform generation techniques that have been experimentally validated and whose architectures can inform the design of pulse shaping methods for microfluidic MC systems and testbeds. These techniques include those based on hydrodynamic and acoustofluidic force fields, as well as electrochemical reactions. We also discuss the fundamental working mechanisms and system architectures of these techniques, and compare their performances in terms of spatiotemporal resolution, selectivity, system complexity, and other performance metrics relevant to MC applications, as well as their feasibility for practical MC applications.
Frequency-domain detection for molecular communication with cross-reactive receptors
(IEEE-Inst Electrical Electronics Engineers Inc, 2024) Akan, Özgür Barış; Civaş, Meltem; Kuşcu, Murat; ; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Yes; College of Engineering; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
Molecular Communications (MC) is a bio-inspired communication paradigm using molecules as information carriers, necessitating novel transceivers and modulation/detection techniques. In realizing practical MC receivers (MC-Rxs), biosensor field-effect transistor (bioFET)-based architectures are promising, having surface receptors that undergo reversible reactions with ligands. These interactions are converted into electrical signals via field effect, enabling the decoding of transmitted information. A significant challenge in these receivers is the limited specificity of receptors to target ligands, which leads to molecular cross-talk from similar interfering ligands co-existing in the MC channel. Decoding transmitted symbols under such interference is challenging in the time domain, especially when MC-Rx lacks prior knowledge of interferer statistics or operates near saturation. To address this, we introduce a frequency-domain detection (FDD) technique for bioFET-based MC-Rxs, which exploits the distinct binding reaction rates of different ligand types, reflected in the power spectrum of binding noise. Compared to conventional time-domain detection (TDD) technique, this method offers improved detection performance under stochastic molecular interference. We analyze the bit error probability (BEP) of FDD, confirming its superior performance in various interference scenarios. Moreover, the theoretical performance limits of FDD are validated through a particle-based spatial stochastic simulator, simulating binding reactions on MC-Rx within microfluidic channels. © 1972-2012 IEEE.
Graphene and related materials for the Internet of Bio-Nano Things
(AIP Publishing, 2023) Civaş, Meltem; Kuşcu, Murat; Akan, Özgür Barış; Çetinkaya, Oktay; Ortlek, Beyza Ezgi; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Yes; College of Engineering; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
The Internet of Bio-Nano Things (IoBNT) is a transformative communication framework characterized by heterogeneous networks comprising both biological entities and artificial micro/nano-scale devices, so-called Bio-Nano Things (BNTs), interfaced with conventional communication networks for enabling innovative biomedical and environmental applications. Realizing the potential of IoBNT requires the development of new and unconventional communication technologies, such as molecular communications, as well as the corresponding transceivers, bio-cyber interfacing technologies connecting the biochemical domain of IoBNT to the electromagnetic domain of conventional networks, and miniaturized energy harvesting and storage components for the continuous power supply to BNTs. Graphene and related materials (GRMs) exhibit exceptional electrical, optical, biochemical, and mechanical properties, rendering them ideal candidates for addressing the challenges posed by IoBNT. This perspective article highlights recent advancements in GRM-based device technologies that are promising for implementing the core components of IoBNT. By identifying the unique opportunities afforded by GRMs and aligning them with the practical challenges associated with IoBNT, particularly in the materials domain, our aim is to accelerate the transition of envisaged IoBNT applications from theoretical concepts to practical implementations while also uncovering new application areas for GRMs.
Internet of Everything (IoE) - from molecules to the universe
(Institute of Electrical and Electronics Engineers Inc., 2023) Kuşcu, Murat; Akan, Özgür Barış; Çetinkaya, Oktay; Dinc, Ergin; Bilgin, Bilgesu A.; Department of Electrical and Electronics Engineering; Yes; College of Engineering
As the Internet of Things (IoT) technologies continue to advance, they are becoming increasingly specialized and compartmentalized into non-interacting application domains, which we call IoXs with X referring to the particular application areas, e.g., Internet of Energy (IoEn), Internet of Vehicles (IoV). This trend has also led to the emergence of unconventional IoXs, such as the Internet of Nano Things (IoNT), further increasing the heterogeneity of the future IoT landscape, in terms of not only the underlying technologies but also the spatiotemporal scale and medium of applications, as well as the material nature of things and the type and semantics of data produced and exchanged. This article explores the potential synergies and opportunities that may arise from such diversity through the interactions between heterogeneous IoXs, enabling unprecedented applications beyond the current confines of IoT. Inspired by the ubiquitous connectivity and seamless interoperability of the universe, which is a vast network of heterogeneous entities interconnected through various forms of interactions (e.g., chemical, electromagnetic, acoustic, and gravitational), we propose the Internet of Everything (IoE) framework. The IoE framework aims to facilitate cooperation of both existing and future IoXs on a diverse scale ranging from molecules to the universe. We discuss potential IoE applications that can be enabled by such synergies and identify the unique challenges for bringing this holistic IoE picture into reality. To address some of these challenges, we propose a layered network architecture for IoE, which includes an IoE middleware that provides a semantic interface among IoXs based on the introduced concept of 'IoX-as-a-Service.' Lastly, we recommend future research directions for enabling the IoE applications.
