arXiv subjects

Andreas Burkovski

Publications and source records attributed to Andreas Burkovski.

10 recordsLinked to original sources

arXiv2025

Closed-Loop Long-Term Experimental Molecular Communication System

We present a fluid-based experimental molecular communication (MC) testbed which uses media modulation. Motivated by the natural human cardiovascular system, the testbed operates in a closed-loop tube system. The proposed system is designed to be biocompatible, resource-efficient, and controllable from outside the tube. As signaling molecule, the testbed employs the green fluorescent protein variant "Dreiklang" (GFPD). GFPDs can be reversibly switched via light of different wavelengths between a bright fluorescent state and a less fluorescent state. GFPDs in solution are filled into the testbed prior to the start of information transmission and remain there for an entire experiment. For information transmission, an optical transmitter (TX) and an optical eraser (EX), which are located outside the tube, are used to write and erase the information encoded in the state of the GFPDs, respectively. At the receiver (RX), the state of the GFPDs is read out by fluorescence detection. In our testbed, due to the closed-loop setup, we observe new forms of inter-symbol interferences (ISI), which do not occur in short experiments and open-loop systems. For the testbed, we developed a communication scheme, which includes blind transmission start detection, symbol-by-symbol synchronization, and adaptive threshold detection. We comprehensively analyze our MC experiments using different performance metrics. Moreover, we experimentally demonstrate the error-free transmission of 5370 bit at a data rate of 36 $\textrm{bit}\, \textrm{min}^{\boldsymbol{-1}}$ using 8-ary modulation and the error-free binary transmission of around 90000 bit at a data rate of 12 $\textrm{bit}\, \textrm{min}^{\boldsymbol{-1}}$. For the latter experiment, data was transmitted for a period of 125 hours. All signals recorded and parts of the evaluation code are publicly available on Zenodo and Github, respectively.

cs.ET↗

arXiv2023

Closed Loop Molecular Communication Testbed: Setup, Interference Analysis, and Experimental Results

In this paper, we present a fluid-based experimental molecular communication (MC) testbed that, similar to the human cardiovascular system, operates in a closed circuit tube system. The proposed system is designed to be biocompatible, resource-efficient, and controllable from outside the tube. As signaling molecule, the testbed employs the green fluorescent protein variant "Dreiklang" (GFPD). GFPDs can be reversibly switched via light of different wavelengths between a bright fluorescent state and a less fluorescent state. Hence, this property allows for writing and erasing information encoded in the state of the GFPDs already present in the fluid via radiation from outside the tube. The concept of modulating the GFPDs existing in the channel at the transmitter for information transmission, instead of releasing new molecules, is a form of media modulation. In our testbed, due to the closed loop setup and the long experiment durations of up to 250 min, we observe new forms of inter-symbol interferences (ISI), which do not occur in short experiments and open loop systems. In particular, up to four different forms of ISI, namely channel ISI, inter-loop ISI, offset ISI, and permanent ISI, occur in the considered system. To mitigate inter-loop ISI and offset ISI, we propose a light based eraser unit. We experimentally demonstrate reliable information transmission in our testbed achieving error-free transmission of 500 bit at a data rate of 6 bit/min based on a sub-optimal low-complexity detection scheme.

cs.ET↗

arXiv2023

Switchable Signaling Molecules for Media Modulation: Fundamentals, Applications, and Research Directions

Although visionary applications of molecular communication (MC), such as long-term continuous health monitoring by cooperative in-body nanomachines, have been proposed, MC is still in its infancy when it comes to practical implementation. In particular, long-term experiments and applications face issues such as depletion of signaling molecules (SMs) at the transmitter (TX) and inter-symbol interference (ISI) at the receiver (RX). To overcome these practical challenges, a new class of SMs with switchable states seems to be promising for future MC applications. In this work, we provide an overview of existing switchable SMs, and classify them according to their properties. Furthermore, we highlight how switchable SMs can be utilized as information carriers for media modulation. In addition, we present theoretical and experimental results for an end-to-end MC system employing the green fluorescent protein variant "Dreiklang" (GFPD) as switchable SM. Our experimental results show, for the first time, successful information transmission in a closed-loop pipe system using media modulation. Finally, we discuss media modulation specific challenges and opportunities.

cs.ET↗

arXiv2023

Media Modulation based Molecular Communication

In conventional molecular communication (MC) systems, the signaling molecules used for information transmission are stored, released, and then replenished by a transmitter (TX). However, the replenishment of signaling molecules at the TX is challenging in practice. Furthermore, in most envisioned MC applications, e.g., in the medical field, it is not desirable to insert the TX into the MC system, as this might impair natural biological processes. In this paper, we propose the concept of media modulation based MC where the TX is placed outside the channel and utilizes signaling molecules already present inside the system. The signaling molecules can assume different states which can be switched by external stimuli. Hence, in media modulation based MC, the TX modulates information into the state of the signaling molecules. In particular, we exploit the group of photochromic molecules, which undergo light-induced reversible state transitions, for media modulation. We study the usage of these molecules for information transmission in a three-dimensional duct system, which contains an eraser, a TX, and a receiver for erasing, writing, and reading of information via external light, respectively. We develop a statistical model for the received signal which accounts for the distribution of the signaling molecules in the system, the initial states of the signaling molecules, the reliability of the state control mechanism, the randomness of irrepressible, spontaneous state switching, and the randomness of molecule propagation. We adopt a maximum likelihood detector and a threshold based detector. Furthermore, we derive analytical expressions for the optimal threshold value and the resulting bit error rate (BER), respectively. Our results reveal that media modulation enables reliable information transmission, validating it as a promising alternative to MC based on molecule emitting TXs.

q-bio.BM↗

arXiv2020

A Survey of Biological Building Blocks for Synthetic Molecular Communication Systems

Synthetic molecular communication (MC) is a new communication engineering paradigm which is expected to enable revolutionary applications such as smart drug delivery and real-time health monitoring. The design and implementation of synthetic MC systems (MCSs) at nano- and microscale is very challenging. This is particularly true for synthetic MCSs employing biological components as transmitters and receivers or as interfaces with natural biological MCSs. Nevertheless, since such biological components have been optimized by nature over billions of years, using them in synthetic MCSs is highly promising. This paper provides a survey of biological components that can potentially serve as the main building blocks, i.e., transmitter, receiver, and signaling particles, for the design and implementation of synthetic MCSs. Nature uses a large variety of signaling particles of different sizes and with vastly different properties for communication among biological entities. Here, we focus on three important classes of signaling particles: cations (specifically protons and calcium ions), neurotransmitters (specifically acetylcholine, dopamine, and serotonin), and phosphopeptides. For each of these candidate signaling particles, we present several specific transmitter and receiver structures mainly built upon proteins that are capable of performing the distinct physiological functionalities required from the transmitters and receivers of MCSs. Moreover, we present options for both microscale implementation of MCSs as well as the micro-to-macroscale interfaces needed for experimental evaluation of MCSs. Furthermore, we outline new research directions for the implementation and the theoretical design and analysis of the proposed transmitter and receiver architectures.

cs.ET↗

arXiv2018

Biological Optical-to-Chemical Signal Conversion Interface: A Small-scale Modulator for Molecular Communications

Although many exciting applications of molecular communication (MC) systems are envisioned to be at microscale, the MC testbeds reported so far are mostly at macroscale. To link the macroworld to the microworld, we propose and demonstrate a biological signal conversion interface that can also be seen as a microscale modulator. In particular, the proposed interface transduces an optical signal, which is controlled using an LED, into a chemical signal by changing the pH of the environment. The modulator is realized using E. coli bacteria as microscale entity expressing the light-driven proton pump gloeorhodopsin from Gloeobacter violaceus. Upon inducing external light stimuli, these bacteria locally change their surrounding pH level by exporting protons into the environment. To verify the effectiveness of the proposed optical-to-chemical signal converter, we analyze the pH signal measured by a pH sensor, which serves as receiver. We develop an analytical parametric model for the induced chemical signal as a function of the applied optical signal. Using this model, we derive a training-based channel estimator which estimates the parameters of the proposed model to fit the measurement data. We further derive the optimal maximum likelihood detector and a suboptimal low-complexity detector to recover the transmitted data from the measured received signal. It is shown that the proposed parametric model is in good agreement with the measurement data. Moreover, for an example scenario, we show that the proposed setup is able to successfully convert an optical signal representing a sequence of binary symbols into a chemical signal with a bit rate of 1 bit/minute and recover the transmitted data from the chemical signal using the proposed estimation and detection~schemes. The proposed modulator may form the basis for future MC testbeds and applications at microscale.

cs.ET↗

arXiv2018

Biological Optical-to-Chemical Signal Conversion Interface: A Small-scale Modulator for Molecular Communications

Although many exciting applications of molecular communication (MC) systems are envisioned to be at microscale, the available MC testbeds reported in the literature so far are mostly at macroscale. This may partially be due to the fact that controlling an MC system at microscale is quite challenging. To link the macroworld to the microworld, we propose a biological signal conversion interface that can also be seen as a microscale modulator. This interface translates an optical signal, which can be easily controlled using a light-emitting diode (LED), into a chemical signal by changing the pH of the environment. The modulator is realized using \textit{Escherichia coli} bacteria that express the light-driven proton pump gloeorhodopsin from \textit{Gloeobacter violaceus}. Upon inducing external light stimuli, these bacteria can locally change their surrounding pH level by exporting protons into the environment. Based on measurement data from a testbed, we develop an analytical model for the induced chemical signal as a function of the applied optical signal. Finally, using a pH sensor as detector, we show for an example scenario that the proposed setup is able to successfully convert an optical signal representing a sequence of binary symbols into a chemical signal with a bit rate of $1$~bit/min.

cs.ET↗

arXiv2016

Comprehensive Reactive Receiver Modeling for Diffusive Molecular Communication Systems: Reversible Binding, Molecule Degradation, and Finite Number of Receptors

This paper studies the problem of receiver modeling in molecular communication systems. We consider the diffusive molecular communication channel between a transmitter nano-machine and a receiver nano-machine in a fluid environment. The information molecules released by the transmitter nano-machine into the environment can degrade in the channel via a first-order degradation reaction and those that reach the receiver nano-machine can participate in a reversible bimolecular reaction with receiver receptor proteins. Thereby, we distinguish between two scenarios. In the first scenario, we assume that the entire surface of the receiver is covered by receptor molecules. We derive a closed-form analytical expression for the expected received signal at the receiver, i.e., the expected number of activated receptors on the surface of the receiver. Then, in the second scenario, we consider the case where the number of receptor molecules is finite and the uniformly distributed receptor molecules cover the receiver surface only partially. We show that the expected received signal for this scenario can be accurately approximated by the expected received signal for the first scenario after appropriately modifying the forward reaction rate constant. The accuracy of the derived analytical results is verified by Brownian motion particle-based simulations of the considered environment, where we also show the impact of the effect of receptor occupancy on the derived analytical results.

cs.ET↗

arXiv2015

Reactive Receiver Modeling for Diffusive Molecular Communication Systems with Molecule Degradation

In this paper, we consider the diffusive molecular communication channel between a transmitter nano-machine and a receiver nano-machine in a fluid environment. The information molecules released by the transmitter nano-machine into the environment can degrade in the channel via a first-order degradation reaction and those that reach the receiver nano-machine can participate in a reversible bimolecular-reaction with receiver receptor proteins. We derive a closed-form analytical expression for the expected received signal at the receiver, i.e., the expected number of activated receptors on the surface of the receiver. The accuracy of the derived analytical result is verified with a Brownian motion particle-based simulation of the environment.

cs.ET↗

arXiv2015

Amplify-and-Forward Relaying in Two-Hop Diffusion-Based Molecular Communication Networks

This paper studies a three-node network in which an intermediate nano-transceiver, acting as a relay, is placed between a nano-transmitter and a nano-receiver to improve the range of diffusion-based molecular communication. Motivated by the relaying protocols used in traditional wireless communication systems, we study amplify-and-forward (AF) relaying with fixed and variable amplification factor for use in molecular communication systems. To this end, we derive a closed-form expression for the expected end-to-end error probability. Furthermore, we derive a closed-form expression for the optimal amplification factor at the relay node for minimization of an approximation of the expected error probability of the network. Our analytical and simulation results show the potential of AF relaying to improve the overall performance of nano-networks.

cs.IT↗