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The notion of synthetic molecular communication (MC) refers to the transmission of information via molecules and is largely foreseen for use within the human body, where traditional electromagnetic wave (EM)-based communication is impractical. MC is anticipated to enable innovative medical applications, such as early-stage tumor detection, targeted drug delivery, and holistic approaches like the Internet of Bio-Nano Things (IoBNT). Many of these applications involve parts of the human cardiovascular system (CVS), here referred to as networks, posing challenges for MC due to their complex, highly branched vessel structures. To gain a better understanding of how the topology of such branched vessel networks affects the reception of a molecular signal at a target location, e.g., the network outlet, we present a generic analytical end-to-end model that characterizes molecule propagation and reception in linear branched vessel networks (LBVNs). We specialize this generic model to any MC system employing superparamagnetic iron-oxide nanoparticles (SPIONs) as signaling molecules and a planar coil as receiver (RX). By considering components that have been previously established in testbeds, we effectively isolate the impact of the network topology and validate our theoretical model with testbed data. Additionally, we propose two metrics, namely the molecule delay and the multi-path spread, that relate the LBVN topology to the molecule dispersion induced by the network, thereby linking the network structure to the signal-to-noise ratio (SNR) at the target location. This allows the characterization of the SNR at any point in the network solely based on the network topology. Consequently, our framework can, e.g., be exploited for optimal sensor placement in the CVS or identification of suitable testbed topologies for given SNR requirements., Comment: 6 pages, 4 figures

We prove that, unlike in the case of paths, the signature matrix of a membrane does not satisfy any algebraic relations. We derive novel closed-form expressions for the signatures of polynomial membranes and piecewise bilinear interpolations for arbitrary $2$-parameter data in $d$-dimensional space. We show that these two families of membranes admit the same set of signature matrices and scrutinize the corresponding affine variety., Comment: 24 pages, comments are welcome!

The modern road network topology comprises intricately designed structures that introduce complexity when automatically reconstructing road networks. While open resources like OpenStreetMap (OSM) offer road networks with well-defined topology, they may not always be up to date worldwide. In this paper, we propose a fully automated pipeline for extracting road networks from very-high-resolution (VHR) satellite imagery. Our approach directly generates road line-strings that are seamlessly connected and precisely positioned. The process involves three key modules: a CNN-based neural network for road segmentation, a graph optimization algorithm to convert road predictions into vector line-strings, and a machine learning model for classifying road materials. Compared to OSM data, our results demonstrate significant potential for providing the latest road layouts and precise positions of road segments.

Molecular Communications (MC) research is increasingly focused on applications within the human body, such as health monitoring and drug delivery. These applications require testing in realistic and living environments. Thus, advancing experimental MC research to the next level requires the development of in vivo experimental testbeds. In this paper, we introduce the Chorioallantoic Membrane ( CAM ) model as a versatile 3D in vivo MC testbed. The CAM is a highly vascularized membrane formed in fertilized chicken eggs and has gained significance in various research fields, including bioengineering, cancer research, and drug development. Its versatility, reproducibility, and realistic biological properties make the CAM model perfectly suited for next-generation MC testbeds, facilitating the transition from proof-of-concept systems to practical applications. We provide a comprehensive introduction to the CAM model, its properties, and its applications in practical research. Additionally, we present a characterization of the CAM model as an MC system. As a preliminary experimental study, we investigate the distribution of fluorescent molecules in the closed-loop vascular system of the CAM model. We also derive an approximate analytical model for the propagation of molecules in closed-loop systems, and show that the proposed model is able to approximate molecule propagation in the CAM model., Comment: 7 pages, 10 figures. This work has been submitted to the 11th ACM International Conference on Nanoscale Computing and Communication, Milan, Italy

This paper introduces a novel optically controllable molecular communication (MC) transmitter (TX) design, which is based on a vesicular nanodevice (ND) functionalized for the release of signaling molecules via transmembrane proteins. Due to its optical-to-chemical conversion capability, the ND can be used as an externally controllable TX for several MC applications such as bit transmission and targeted drug delivery. The proposed TX design comprises two cooperating modules, an energizing module and a release module, and depending on the specific choices for the modules allows for the release of different types of signaling molecules. After setting up a general system model for the proposed TX design, we conduct a detailed mathematical analysis of a specific realization. In particular, we derive an exact analytical and an approximate closed-form solution for the concentration of the released signaling molecules and validate our results by comparison with a numerical solution. Moreover, we consider the impact of a buffering medium, which is typically present in experimental and application environments, in both our analytical and numerical analyses to evaluate the feasibility of our proposed TX design for practical chemical implementation. The proposed analytical and closed-form models facilitate system parameter optimization, which can accelerate the experimental development cycle of the proposed ND architecture in the future., Comment: 7 pages double-column, 5 figures, 1 table. This work has been submitted to the 11th ACM International Conference on Nanoscale Computing and Communication, Milan, Italy

In the context of the Internet of Bio-Nano Things (IoBNT), nano-devices are envisioned to perform complex tasks collaboratively, i.e., by communicating with each other. One candidate for the implementation of such devices are engineered cells due to their inherent biocompatibility. However, because each engineered cell has only little computational capabilities, transmitter and receiver (RX) functionalities can afford only limited complexity. In this paper, we propose a simple, yet modular, architecture for a cellular RX that is capable of processing a stream of observed symbols using chemical reaction networks. Furthermore, we propose two specific detector implementations for the RX. The first detector is based on a machine learning model that is trained offline, i.e., before the cellular RX is deployed. The second detector utilizes pilot symbol-based training and is therefore able to continuously adapt to changing channel conditions online, i.e., after deployment. To coordinate the different chemical processing steps involved in symbol detection, the proposed cellular RX leverages an internal chemical timer. Furthermore, the RX is synchronized with the transmitter via external, i.e., extracellular, signals. Finally, the proposed architecture is validated using theoretical analysis and stochastic simulations. The presented results confirm the feasibility of both proposed implementations and reveal that the proposed online learning-based RX is able to perform reliable detection even in initially unknown or slowly changing channels. By its modular design and exclusively chemical implementation, the proposed RX contributes towards the realization of versatile and biocompatible nano-scale communication networks for IoBNT applications narrowing the existing implementation gap in cellular molecular communication (MC).

We scrutinise the notions of cohomologically smooth morphisms and smooth objects for the six functor formalism of \'etale $\mathbb F_p$-sheaves on schemes in characteristic $p$. We show that only cohomologically \'etale morphisms are cohomologically smooth in this setting. This is complemented by a characterisation of cohomologically \'etale morphisms in arbitrary characteristic. In fact, we prove that such a morphism is already \'etale up to universal homeomorphism., Comment: 36 pages, comments are welcome!

Future communication systems are envisioned to employ intelligent reflecting surfaces (IRSs) and the millimeter wave (mmWave) frequency band to provide reliable high-rate services. For mobile users, the time-varying channel state information (CSI) requires adequate adjustment of the reflection pattern of the IRS. We propose a novel codebook-based user tracking (UT) algorithm for IRS-assisted mmWave communication, allowing suitable reconfiguration of the IRS unit cell phase shifts, resulting in a high reflection gain. The presented algorithm acquires the direction information of the user based on a peak likelihood-based direction estimation. Using the direction information, the user's trajectory is extrapolated to proactively update the adopted codeword and adjust the IRS phase shift configuration accordingly. Furthermore, we conduct a theoretical analysis of the direction estimation error and utilize the obtained insights to design a codebook specifically optimized for direction estimation. Our numerical results reveal a lower direction estimation error of the proposed UT algorithm when employing our designed codebook compared to codebooks from the literature. Furthermore, the average achieved signal-to-noise ratio (SNR) as well as the average effective rate of the proposed UT algorithm are analyzed. The proposed UT algorithm requires only a low overhead for direction and channel estimation and avoids outdated IRS phase shifts. Furthermore, it is shown to outperform two benchmark schemes based on direct phase shift optimization and hierarchical codebook search, respectively, via computer simulations.

The recently emerged molecular communication (MC) paradigm intends to leverage communication engineering tools for the design of synthetic chemical communication systems. These systems are envisioned to operate at nanoscale and in biological environments, such as the human body, and catalyze the emergence of revolutionary applications in the context of early disease monitoring and drug targeting. Despite the abundance of theoretical (and recently also experimental) MC system designs proposed over the past years, some fundamental questions remain unresolved, hindering the breakthrough of MC in real-world applications. One of these questions is: What can be a useful measure of information in the context of MC applications? While most existing works on MC build upon the concept of syntactic information as introduced by Shannon, in this paper, we explore the framework of semantic information as introduced by Kolchinsky and Wolpert for the information-theoretic analysis of a natural MC system, namely bacterial chemotaxis. Exploiting computational agent-based modeling (ABM), we are able to quantify, for the first time, the amount of information that the considered chemotactic bacterium (CB) utilizes to adapt to and survive in a dynamic environment. In other words, we show how the flow of information between the environment and the CB is related to the effectiveness of communication. Effectiveness here refers to the adaptation of the CB to the dynamic environment in order to ensure survival. Our analysis reveals that it highly depends on the environmental conditions how much information the CB can effectively utilize for improving their survival chances. Encouraged by our results, we envision that the proposed semantic information framework can open new avenues for the development of theoretical and experimental MC system designs for future nanoscale applications., Comment: 7 pages, 5 figures, This work has been submitted in part for possible publication to the IEEE Global Communications Conference (GLOBECOM) 2024

Explainability is a longstanding challenge in deep learning, especially in high-stakes domains like healthcare. Common explainability methods highlight image regions that drive an AI model's decision. Humans, however, heavily rely on language to convey explanations of not only "where" but "what". Additionally, most explainability approaches focus on explaining individual AI predictions, rather than describing the features used by an AI model in general. The latter would be especially useful for model and dataset auditing, and potentially even knowledge generation as AI is increasingly being used in novel tasks. Here, we present an explainability strategy that uses a vision-language model to identify language-based descriptors of a visual classification task. By leveraging a pre-trained joint embedding space between images and text, our approach estimates a new classification task as a linear combination of words, resulting in a weight for each word that indicates its alignment with the vision-based classifier. We assess our approach using two medical imaging classification tasks, where we find that the resulting descriptors largely align with clinical knowledge despite a lack of domain-specific language training. However, our approach also identifies the potential for 'shortcut connections' in the public datasets used. Towards a functional measure of explainability, we perform a pilot reader study where we find that the AI-identified words can enable non-expert humans to perform a specialized medical task at a non-trivial level. Altogether, our results emphasize the potential of using multimodal foundational models to deliver intuitive, language-based explanations of visual tasks., Comment: To be published in the Proceedings of the 3rd Machine Learning for Health symposium, Proceedings of Machine Learning Research (PMLR)

Integrating different functionalities, conventionally implemented as dedicated systems, into a single platform allows utilising the available resources more efficiently. We consider an integrated sensing and power transfer (ISAPT) system and propose the joint optimisation of the rectangular pulse-shaped transmit signal and the beamforming vector to combine sensing and wireless power transfer (WPT) functionalities efficiently. In contrast to prior works, we adopt an accurate non-linear circuit-based energy harvesting (EH) model. We formulate and solve a non-convex optimisation problem for a general number of EH receivers to maximise a weighted sum of the average harvested powers at the EH receivers while ensuring the received echo signal reflected by a sensing target (ST) has sufficient power for estimating the range to the ST with a prescribed accuracy within the considered coverage region. The average harvested power is shown to monotonically increase with the pulse duration when the average transmit power budget is sufficiently large. We discuss the trade-off between sensing performance and power transfer for the considered ISAPT system. The proposed approach significantly outperforms a heuristic baseline scheme based on a linear EH model, which linearly combines energy beamforming with the beamsteering vector in the direction to the ST as its transmit strategy., Comment: 7 pages, 2 figures, six page version of this paper has been submitted to IEEE ICC 2024

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., Comment: 7 pages, 5 figures, 1 table. This work has been submitted for possible publication to the IEEE International Conference on Communications (ICC) 2024

In order to fully exploit the potential of molecular communication (MC) for intra-body communication, practically implementable cellular receivers are an important long-term goal. A variety of receiver architectures based on chemical reaction networks (CRNs) and gene-regulatory networks (GRNs) has been introduced in the literature, because cells use these concepts to perform computations in nature. However, practical feasibility is still limited by stochastic fluctuations of chemical reactions and long computation times in GRNs. Therefore, in this paper, we propose two receiver designs based on stochastic CRNs, i.e., CRNs that perform computations by exploiting the intrinsic fluctuations of chemical reactions with very low molecule counts. The first CRN builds on a recent result from chemistry that showed how Boltzmann machines (BMs), a commonly used machine learning model, can be implemented with CRNs. We show that BMs with optimal parameter values and their CRN implementations can act as maximum-a-posteriori (MAP) detectors. Furthermore, we show that BMs can be efficiently trained from simulation data to achieve close-to-MAP performance. While this approach yields a fixed CRN once deployed, our second approach based on a manually designed CRN can be trained with pilot symbols even within the cell and thus adapt to changing channel conditions. We extend the literature by showing that practical robust detectors can achieve close-to-MAP performance even without explicit channel knowledge., Comment: 7 pages, 4 figures. This paper has been submitted to the 10th ACM International Conference on Nanoscale Computing and Communication, Coventry, UK

Controlled drug delivery (CDD), the controlled release and delivery of therapeutic drugs inside the human body, is a promising approach to increase the efficacy of drug administration and reduce harmful side effects to the body. CDD has been a major research focus in the field of molecular communications (MC) with the goal to aid the design and optimization of CDD systems with communication theoretical analysis. However, the existing studies of CDD under the MC framework are purely theoretical, and the potential of MC for the development of practical CDD applications remains yet to be shown. This paper presents a step towards filling this research gap. Specifically, we present a novel MC-based model for a specific CDD system in which drugs are embedded into microparticles and released gradually towards the target site. It is demonstrated that the proposed model is able to faithfully reproduce experimental data. Furthermore, statistical analysis is conducted to explore the impact of the microparticle size on the drug release. The presented results reveal the sensitivity of the drug release to changes in the microparticle size. In this way, the proposed model can be used for the design of future microparticle-based CDD systems., Comment: 9 pages, 3 figures, 2 tables. This paper has been submitted in part to the 2023 IEEE Global Communications Conference (Globecom)

Understanding pedestrian dynamics and the interaction of pedestrians with their environment is crucial to the safe and comfortable design of pedestrian facilities. Experiments offer the opportunity to explore the influence of individual factors. In the context of the project CroMa (Crowd Management in transport infrastructures), experiments were conducted with about 1000 participants to test various physical and social psychological hypotheses focusing on people's behaviour at railway stations and crowd management measures. The following experiments were performed: i) Train Platform Experiment, ii) Crowd Management Experiment, iii) Single-File Experiment, iv) Personal Space Experiment, v) Boarding and Alighting Experiment, vi) Bottleneck Experiment and vii) Tiny Box Experiment. This paper describes the basic planning and implementation steps, outlines all experiments with parameters, geometries, applied sensor technologies and pre- and post-processing steps. All data can be found in the pedestrian dynamics data archive., Comment: 58 pages, 19 figures, under review Collective Dynamics

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., Comment: 7 pages, 6 figures. This work has been accepted for publication in IEEE Communications Magazine

In this second part of our survey on experimental research in Synthetic Molecular Communication (SMC), we review works on long-range SMC systems, i.e., systems with communication ranges of more than a few millimeters. Despite the importance of experimental research for the evolution of SMC towards a mature communication paradigm that will eventually support revolutionary applications beyond the reach of today's prevalent communication paradigms, the existing body of literature is still comparatively sparse. Long-range SMC systems have been proposed in the literature for information transmission in two types of fluid media, liquid and air. While both types of SMC systems, liquid-based and air-based systems, rely on encoding and transmitting information using molecules, they differ substantially in terms of the physical system designs and in the type of applications they are intended for. In this paper, we present a systematic characterization of experimental works on long-range SMC that reveals the major drivers of these works in terms of the respective target applications. Furthermore, the physical designs for long-range SMC proposed in the literature are comprehensively reviewed. In this way, our survey will contribute to making experimental research in this field more accessible and identifying novel directions for future research., Comment: 10 pages, 2 tables, 4 figures. Accepted for publication in the IEEE Nanotechnology Magazine

Since its emergence from the communication engineering community around one and a half decades ago, the field of Synthetic Molecular Communication (SMC) has experienced continued growth, both in the number of technical contributions from a vibrant community and in terms of research funding. Throughout this process, the vision of SMC as a novel, revolutionary communication paradigm has constantly evolved, driven by feedback from theoretical and experimental studies, respectively. It is believed that especially the latter ones will be crucial for the transition of SMC towards a higher technology readiness level in the near future. In this spirit, we present here a comprehensive survey of experimental research in SMC. In particular, this survey focuses on highlighting the major drivers behind different lines of experimental research in terms of the respective envisioned applications. This approach allows us to categorize existing works and identify current research gaps that still hinder the development of practical SMC-based applications. Our survey consists of two parts; this paper and a companion paper. While the companion paper focuses on SMC with relatively long communication ranges, this paper covers SMC over short distances of typically not more than a few millimeters., Comment: 10 pages, 1 table, 5 figures. Accepted for publication in the IEEE Nanotechnology Magazine