Channel Modelling of Blood Capillary-based Molecular Communication

Molecular communication (MC) is a new and promising interdisciplinary bio-inspired communication paradigm, which uses molecules as information carriers. Differing from traditional communication, MC is proposed as a feasible solution for nanoscale communication with the help of biological scenarios to overcome the communication limitations. Meanwhile, it is inspired by intracellular and intercellular communication, which involves exchange of information through the transmission, propagation, and reception of molecules. Blood capillaries, extensively distributed in the human body and mutually connected with tissues, are potentially applied to MC, which is the major motivation of this thesis. The focus of this PhD thesis is on the channel modelling of blood capillaries or blood vessels. The objectives of the research are to provide solutions to the modelling of blood capillary-based MC from a communication engineering and information theory perspective. The relationship of the biological scenario in blood capillaries to a communication system is studied. After demonstrating the mapping from biological phenomenon to emission, propagation and reception processes, system models are established. There are three models of blood capillaries behind different biological scenarios. Firstly, the thesis establishes a basic model of vesicle release, vesicle diffusion through blood capillary and ligand reception processes within the endocrine phenomenon. Moreover, differing from previous research in macroscopic Fick's diffusion, this work involves microscopic Langevin diffusion to describe the propagation process with a frequency domain method being proposed to calculate the information-theoretical performance channel capacity. Secondly, a much more realistic blood capillary model with blood flow drift which matches a laminar flow regime is presented, where a generalised Langevin equation is used to model the drift force exerted by blood flow. Finally, the thesis establishes a single input and multiple output MC model with hierarchical levels of Y-shaped bifurcation of blood capillaries, then BER, SNR, and channel capacity performance are analysed

Macro-Scale Molecular Communications

The use of electromagnetic (EM) waves to transmit information has allowed our society to collaborate and share information on a scale that was unimaginable just a few decades ago. But as with any technology, there are areas where EM-based communications do not function well. For example, underwater and underground communications where EM waves experience high attenuation. This limitation has generated interest in an alternative mode of information transmission, molecular communications. In this thesis, after giving a survey of micro- and macro-scale molecular communications, the two most important aspects of molecular communications are identified: macroscale molecular communications and the experimental analysis of molecular communications. Molecular communication has been dominated so far by interest in the nano-scale, where the application focus is on drug-delivery and DNA communications, etc. Studies in the macro-scale are relatively rare compared to nano- and micro-scale research. This thesis looks closely at macro-scale molecular communication and attempts to improve our understanding of this novel communication paradigm. To achieve this, a mathematical model was developed, based on the advective-diffusion equation (ADE). The model was compared with experimental results, and showed a strong correlation. In addition, a model was developed to simulate molecular communication in both 1D and 3D environments. To generate the modulated chemicals and transmit them in the environment, an inhouse- built odour generator was used, and to detect the chemicals in the environment a mass spectrometer (MS) with a quadrupole mass analyser (QMA) was employed. Mass spectrometers have the ability to distinguish multiple chemicals in the environment concurrently, making them ideal detectors for use in molecular communications. Based on the experimental setup, various aspects of the communication paradigm are investigated in the three main sections. The first section focuses on the fundamental parameters that govern the propagation of molecules in a flow. The second section delves into the communication properties of this new form of information transfer. The final section studies aspects of simultaneous multiple-chemical transmission. Based on this multiple-chemical transmission, modulation methods are developed that exploit this new approach for use in molecular communications

Modeling the Molecular Communication Nanonetworks

Nanotechnology is a cutting edge investigation area that has come out with new and unlimited applications. The recent explosion of research in this field, combined with important discoveries in molecular biology have created a new interest in bio-nanorobotic communication. This thesis provides a general theoretical understanding of nanonetworks and their multiple possibilities. It describes some basic concepts of architectures that compose nanotechnology topologies, as well as possible designs for the tiny nanonetwork components, the nanomachines. The thesis also reviews some promising methods proposed for communicating and coordinating in these nanonetworks. Molecular communication applied to nanonetworks presents indeed extremely appealing features in terms of energy consumption, reliability and robustness. Nevertheless, it remains to understand the impact of the extremely slow propagation of molecules and the highly variable environments. As a totally unexplored research area, it is important to establish thorough theoretical framework so that the applications and possible solutions can be validated. It is clear that many issues still need to be addressed in order to understand the limiting performance of information communications among nano-scale devices and design optimal and quasi-optimal encoding/decoding strategies. Such issues are believed to be of key relevance for allowing nanotechnologies display their full potential

A survey of molecular communication in cell biology : establishing a new hierarchy for interdisciplinary applications

Molecular communication (MC) engineering is inspired by the use of chemical signals as information carriers in cell biology. The biological nature of chemical signaling makes MC a promising methodology for interdisciplinary applications requiring communication between cells and other microscale devices. However, since the life sciences and communications engineering fields have distinct approaches to formulating and solving research problems, the mismatch between them can hinder the translation of research results and impede the development and implementation of interdisciplinary solutions. To bridge this gap, this survey proposes a novel communication hierarchy for MC signaling in cell biology and maps phenomena, contributions, and problems to the hierarchy. The hierarchy includes: 1) the physical propagation of cell signaling at the Physical Signal Propagation level; 2) the generation, reception, and biochemical pathways of molecular signals at the Physical and Chemical Signal Interaction level; 3) the quantification of physical signals, including macroscale observation and control methods, and conversion of signals to information at the Signal-Data Interface level; 4) the interpretation of information in cell signals and the realization of synthetic systems to store, process, and communicate molecular signals at the Local Data Abstraction level; and 5) applications relying on communication with MC signals at the Application level. To further demonstrate the proposed hierarchy, it is applied to case studies on quorum sensing, neuronal signaling, and communication via DNA. Finally, several open problems are identified for each level and the integration of multiple levels. The proposed hierarchy provides language for communication engineers to study and interface with biological systems, and also helps biologists to understand how communications engineering concepts can be exploited to interpret, control, and manipulate signaling in cell biology

Experimental and computational study of molecular communication in turbulent fluid environments

Molecular communication (MC) is a type of communication and networking in the electromagnetic (EM)-denied environments. MC is concerned with information transfer by preserving information in the structure of chemical flow through molecular diffusion, advection or reaction. Hence, the information transmission in MC is closely associated with the physics of fluid dynamics. The mechanism of MC, i.e., using chemical substances for information exchange, is prevalent in nature among organisms at various length scales, from intra-cell signaling and bacterial communication to airborne and waterborne pheromone signals. At nano-scale the physical conditions are such that the main mechanism of transport is mass diffusion. Therefore fluid turbulence, for which other transport mechanisms are relevant, have hitherto hardly been considered at all in the context of MC. Nevertheless, MC is obviously not restricted to nano-scales, as demonstrated by insect and crustacean pheromone signaling. Here turbulence does become a crucial issue affecting the reliability of the message transfer. The goal of this thesis is to draw on turbulence theory to assess implications of relevance to MC at macro scale. The results show that in turbulent channels, viscous shear stresses hinder a reliable transfer of the molecular information between the transmitter and the receiver which results in severe inter-symbol-interference (ISI). In order to mitigate the ISI in turbulent channels, vortex ring are proposed as coherent structures representing a means for modulating information symbols onto them. Each vortex ring can propagate approximately 100× the diameter of the transmission nozzle without losing its compact shape. It is shown that by maintaining a coherent signal structure, the signal-to-inference (SIR) ratio is higher over conventional puffs. Moreover, the results show that the received signals of the same transmitted symbols vary due to the presence of the underlying noise in turbulent channels. To understand the behaviour of the noise in turbulent channels, both of the additive and jitter noises distributions characterised statistically, and a new channel model is proposed. Thereafter, this channel model is used to quantify the mutual information in turbulent channels. Finally, the waterborne chemical plumes are investigated as a paradigm for a means of molecular communication at macro scales. Results from the Richardson’s energy cascade theory are applied and interpreted in the context of MC to characterise an information cascade and the information dissipation rate. The results show that the information dissipation rate decreases with increasing the Reynolds number and distance d from transmitter. This may appear counter intuitive because stronger turbulence levels at higher Reynolds numbers increases energy dissipation rates. However, increased turbulence leads to more efficient scalar mixing and, therewith, the power of the molecular signal quickly reduces to low levels. Accordingly the information dissipation rate necessarily reduces due to the remaining low information content available

Kolmogorov turbulence and information dissipation in molecular communication

Waterborne chemical plumes are studied as a paradigm for representing a means for molecular communication in a macro-scale system. Results from the theory of fluid turbulence are applied and interpreted in the context of molecular communication to characterize an information cascade, the information dissipation rate and the critical length scale below which information modulated onto the plume can no longer be decoded. The results show that the information dissipation decreases with increasing Reynolds number and that there exists a theoretical potential for encoding smaller information structures at higher Reynolds numbers

Coordination via Advection Dynamics in Nanonetworks with Molecular Communication

International audienceA key challenge in nanonetworking is to develop a means of coordinating a large number of nanoscale devices. Molecular communication has emerged as a promising technique to assist in the coordination problem. Devices in molecular communication systems—once information molecules are released— are typically viewed as passive, not reacting chemically with the information molecules. While this is an accurate model in diffusion-limited links, it is not the only scenario. In particular, the dynamics of molecular communication systems are more generally governed by reaction-diffusion, where the reaction dynamics can also dominate. This leads to the notion of reaction-limited molecular communication systems, where the concentration profiles of information molecules and other chemical species depends largely on reaction kinetics. In this regime, the system can be approximated by a chemical reaction network. In this paper, we exploit this observation to design new protocols for both point-to-point links with feedback and networks for event detection. In particular, using connections between consensus and advection theory and reaction networks lead to simple characterizations of equilibrium concentrations, which yield simple—but accurate— design rules even for networks with a large number of devices