Closed-Loop Long-Term Experimental Molecular Communication System

TL;DR

This work tackles the challenge of conducting long-duration, closed-loop molecular communication experiments. It introduces a self-contained testbed that uses media modulation with reversible GFPD signaling, enabling reuse of signaling molecules and outside-the-tube TX/EX/RX components to mitigate channel soling. The study identifies four ISI forms unique to closed-loop operation, develops a synchronization- and detection-centric communication scheme (including wake-up, data-based and blind receive filters, and adaptive thresholds), and demonstrates both a 5370-bit error-free transmission at 36 bit/min and a long-term, error-free 90k-bit run over 125 hours. The work also provides comprehensive performance analyses (BER, AMED, eye diagrams) and shares data/code openly to promote reproducibility and further research, highlighting the potential of closed-loop MC for long-term health monitoring and IoBNT interfaces.

Abstract

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.

Figures (8)

• Figure 1: (a) Schematic representation of the testbed consisting of the propagation channel, pump, test tube, two LED-arrays serving as TX and EX, respectively, a flow cell, and a spectrometer acting as RX. The switching processes of GFPD are depicted next to the components in which they occur. (b) Photo of the experimental setup during operation. (c) LED array of the TX module (the LED module of the EX looks similar). Individual LED of the array are highlighted by red circles.
• Figure 2: Data-based receive filters and blind receive filters in comparison for two different configurations: $T_{\mathrm{I}}=3s$, $T_{\mathrm{S}}=5s$ (on the left) and $T_{\mathrm{I}}=10s$, $T_{\mathrm{S}}=15s$ (on the right) for the CS (a) and the DCS scheme (b), respectively.
• Figure 3: $r(t_n)$ of single symbol transmissions with $i \in \{0, 1, 2, 3\}$ for different irradiation durations $T_{\mathrm{I}} = 10 \,s$ and $T_{\mathrm{I}} = 20 \,s$, and TX-RX distances $d_{\mathrm{TX},\mathrm{RX}} = 6 \,cm$ and $d_{\mathrm{TX},\mathrm{RX}} = 35 \,cm$. Three forms of ISI are visualized: channel ISI, inter-loop ISI, and offset ISI.
• Figure 4: Evaluation of a long-term binary transmission with $T_{\mathrm{S}} = 5\text{s}$, $N_{\mathrm{Bit}} = 90000.0$, $p_\mathrm{FA} = 10 \, \times \, 10^{-10}$, $\Delta t = 0.1\text{s}$, $\mathrm{N} = \lfloor \frac{T_{\mathrm{S}}}{\Delta t} \rfloor$, $N_\mathrm{T} = 50$, $r = 0.04$, $W = 50$, $F = 1$, $\chi = 80$, and $P = 130$ with (blue curves) and without (orange curves) EX. (a) Received signal over time. Shaded areas in the insets correspond to bit 1 transmissions. (b) Detection samples for different detection schemes using data-based receive filters and the corresponding adaptive thresholds, cf. Sections \ref{['sec:init_thresholds']} and \ref{['sec:adaption_algorithm']}, around $27h$ after the start of data transmission (left panel) and at the end of transmission (right panel). (c) AMED between bit 1 and bit 0 transmissions over time.
• Figure 5: (d) Moving average BER (computed over the most recent $2000.0$ bit) for the different detection schemes.