Researcher:
Malak, Derya

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PhD Student

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Derya

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Malak

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Malak, Derya

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2012 - 201610

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    Molecular communication nanonetworks inside human body
    (Elsevier, 2012) N/A; N/A; Department of Electrical and Electronics Engineering; Malak, Derya; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647
    To realize molecular nanonetworks, the foundations of molecular information theory should be established through identification of the existing molecular communication mechanisms, and architectures and networking techniques for nanomachines should be developed, which demand novel engineering efforts. Luckily, these engineering skills and technology have been prepared for us by the natural evolution in the last several billions of years. Indeed, the human body is a massive nanoscale molecular communications network as it is composed of billions of interacting nanomachines, i.e., cells. Intra-body biological systems are closely linked to each other and communicate primarily through molecular transactions. Thus, vital activities inside the human body are regulated by everlasting communication performance and operations of intra-body molecular nanonetworks. However, natural intra-body molecular nanonetworks are yet to be explored with the elegant tools of information and communication theories. In this paper, first, the elementary models for significant intra-body molecular communication channels, i.e., nanoscale neuro-spike communication channel, action potential-based cardiomyocyte molecular communication channel, and hormonal molecular communication channel, are introduced. Next, molecular nanonetworks belonging to multi-terminal extensions of channel models, i.e., nervous, cardiovascular molecular, and endocrine nanonetworks are discussed. Furthermore, heterogeneous communication network of intra-body molecular nanonetworks together with five senses, i.e., nanosensory networks, is explored from the perspectives of communication and network theories. Moreover, open research challenges, such as extension of molecular channel models to multi-terminal cases, and developing a communication theory perspective to understand the physiology and to capture potential communication failures of intra-body biological systems, are provided. Our objectives are to learn from the elegant molecular communication mechanisms inside us for engineering practical communication techniques for emerging nanonetworks, as well as to pave the way for the advancement of revolutionary diagnosis and treatment techniques inspired from information and communication technologies, which is promising for future nanomedicine and bio-inspired molecular communication applications.
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    Rate-delay tradeoff with network coding in molecular nanonetworks
    (IEEE-Inst Electrical Electronics Engineers Inc, 2013) N/A; N/A; Department of Electrical and Electronics Engineering; Ünlütürk, Bige Deniz; Malak, Derya; Akan, Özgür Barış; Master 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; 6647
    Molecular communication is a novel nanoscale communication paradigm, in which information is encoded in messenger molecules for transmission and reception. However, molecular communication is unreliable and has highly varying long propagation delays mainly due to the stochastic behavior of the freely diffusing molecules. Thus, it is essential to analyze its delay characteristics, as well as the tradeoff between the rate and delay, in order to reveal the capabilities and limitations of molecular information transmission in nanonetworks. In this paper, first, a new messenger-based molecular communication model, which includes a nanotransmitter sending information to a nanoreceiver, is introduced. The information is encoded on a polyethylene molecule, CH3(CHX)(n)CH2F, where X stands for H and F atoms representing 0 and 1 bits, respectively. The emission of the molecules is modeled by puffing process which is inspired by the alarm pheromone release by animals in dangerous situations. In this work, the rate-delay characteristics of this messenger-based molecular communication model are explored. Then, a Nano-Relay is inserted in the model, which XOR's the incoming messages from two different nanomachines. Performance evaluation shows that indeed, a simple network coding mechanism significantly improves the rate given delay of the system, and vice versa.
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    Synaptic interference channel
    (Institute of Electrical and Electronics Engineers (IEEE), 2013) N/A; N/A; Department of Electrical and Electronics Engineering; Malak, Derya; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647
    Synaptic channels automatically adapt their weights to compensate for the variations resulted from the input and output characteristics, i.e., spike frequency, time correlation among inputs, time difference between presynaptic and postsynaptic action potentials. Modification of the synaptic conductances, i.e., channel weights, is the main mechanism that enables learning in neurons. In this paper, we approach this learning mechanism from a different perspective. First, we analyze the single-input single-output (SISO) and multi-input single-output (MISO) synaptic interference channels, and achievable communication rates. Furthermore, we provide the natural adaptive weight update algorithm for neurons based on experimental findings. Our results demonstrate that neurons are capable of mitigating the interference, and achieve rates close to the capacity.
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    An information theoretical analysis of broadcast networks and channel routing for FRET-based nanoscale communications
    (Ieee, 2012) N/A; N/A; N/A; Department of Electrical and Electronics Engineering; Kuşcu, Murat; Malak, Derya; Akan, Özgür Barış; Master 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; 316349; N/A; 6647
    Nanoscale communication based on Forster Resonance Energy Transfer (FRET) enables nanomachines to communicate with each other using the excited state of the fluorescent molecules as the information conveyer. In this study, FRET-based nanoscale communication is further extended to realize FRET-based nanoscale broadcast communication with one transmitter and many receiver nanomachines, and the performance of the broadcast channel is analyzed information theoretically. Furthermore, an electrically controllable routing mechanism is proposed exploiting the Quantum Confined Stark Effect (QCSE) observed in quantum dots. It is shown that by appropriately selecting the employed molecules on the communicating nanomachines, it is possible to control the route of the information flow by externally applying electric field in FRET-based nanonetworks.
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    On the node density limits and rate-delay-energy tradeoffs in ad Hoc nanonetworks with minimum energy coding
    (IEEE, 2012) N/A; N/A; N/A; Kocaoğlu, Murat; Malak, Derya; PhD Student; PhD Student; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; N/A
    Ad-hoc nanonetworks are collections of nanonodes without central controller units, and are the most promising network architectures in nano communications. Derivation of maximum nanonode density can pave the way for determining the capacity of ad-hoc nanonetworks. We consider ad-hoc nanonetworks with minimum energy coding (MEC). Maximum nanonode density for reliable communication in an ad-hoc nanonetwork without any medium access control is derived, and density dependent reliability analysis is conducted. Rate-delay-energy tradeoffs are also investigated with achievable rates, with constant codebook size and constant Hamming distance, separately.
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    A communication theoretical analysis of synaptic multiple-access channel in hippocampal-cortical neurons
    (IEEE-Inst Electrical Electronics Engineers Inc, 2013) N/A; N/A; Department of Electrical and Electronics Engineering; Malak, Derya; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647
    Communication between neurons occurs via transmission of neural spike trains through junctional structures, either electrical or chemical synapses, providing connections among nerve terminals. Since neural communication is achieved at synapses, the process of neurotransmission is called synaptic communication. Learning and memory processes are based on the changes in strength and connectivity of neural networks which usually contain multiple synaptic connections. In this paper, we investigate multiple-access neuro-spike communication channel, in which the neural signal, i.e., the action potential, is transmitted through multiple synaptic paths directed to a common postsynaptic neuron terminal. Synaptic transmission is initiated with random vesicle release process from presynaptic neurons to synaptic paths. Each synaptic channel is characterized by its impulse response and the number of available postsynaptic receptors. Here, we model the multiple-access synaptic communication channel, and investigate the information rate per spike at the postsynaptic neuron, and how postsynaptic rate is enhanced compared to single terminal synaptic communication channel. Furthermore, we analyze the synaptic transmission performance by incorporating the role of correlation among presynaptic terminals, and point out the postsynaptic rate improvement.
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    Communication theoretic analysis of the synaptic channel for cortical neurons
    (Elsevier, 2013) N/A; N/A; N/A; Department of Electrical and Electronics Engineering; Malak, Derya; Kocaoğlu, Murat; 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; 6647
    In this paper, we develop a realistic model of the synaptic multiple-input single-output (MISO) communication channel for cortical neurons. The synaptic channel weights change adaptively according to the rules of spike timing-dependent plasticity (STDP) to enable learning and memory within neuronal connections. We calculate the ergodic capacity of the synaptic multiple-input multiple-output (MIMO) communication channel, and investigate its performance using the statistical properties of neuro-spike communication. Moreover, we analyze the communication performance of synaptic channels in terms of decoding error probability, and define a lower bound on the synaptic multiple-input single-output (MISO) communication channel.
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    PublicationOpen Access
    An information theoretical analysis of broadcast networks and channel routing for FRET-based nanoscale communications
    (Institute of Electrical and Electronics Engineers (IEEE), 2012) Kuşcu, Murat; Malak, Derya; Akan, Özgür Barış; Faculty Member; College of Engineering
    Nanoscale communication based on Forster Resonance Energy Transfer (FRET) enables nanomachines to communicate with each other using the excited state of the fluorescent molecules as the information conveyer. In this study, FRET-based nanoscale communication is further extended to realize FRET-based nanoscale broadcast communication with one transmitter and many receiver nanomachines, and the performance of the broadcast channel is analyzed information theoretically. Furthermore, an electrically controllable routing mechanism is proposed exploiting the Quantum Confined Stark Effect (QCSE) observed in quantum dots. It is shown that by appropriately selecting the employed molecules on the communicating nanomachines, it is possible to control the route of the information flow by externally applying electric field in FRET-based nanonetworks.
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    PublicationOpen Access
    Diversity in diffusion-based molecular communication channel with drift
    (Institute of Electrical and Electronics Engineers (IEEE), 2016) Department of Electrical and Electronics Engineering; Malak, Derya; Ramezani, Hamideh; Kocaoğlu, Murat; Akan, Özgür Barış; PhD Student; Department of Electrical and Electronics Engineering; College of Engineering
    We utilize the well known Additive Inverse Gaussian Noise (AIGN) communication channel to investigate the effect of diversity in diffusion-based molecular communication with drift, where the transmitter releases different types of molecules to the fluid medium by encoding the information onto the release time and type of molecules. The fluid channel imposes extra delay on the communication, and the receiver decodes the encoded information by solely utilizing the molecular arrival times. In this paper, simple receiver models based on maximum likelihood estimation (MLE) are investigated. Furthermore, upper and lower bounds on the capacity of AIGN communication channel with molecular diversity are derived.
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    PublicationOpen Access
    Fundamentals of green communications and computing: modeling and simulation
    (Institute of Electrical and Electronics Engineers (IEEE), 2012) Department of Electrical and Electronics Engineering; Akan, Özgür Barış; Malak, Derya; Kocaoğlu, Murat; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering
    A layered architecture incorporates the concept of minimum energy consumption for communication links and computer networks with multiple terminals, where emission-reduction approaches based on information theory are impractical.