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

Uncertainty Quantification in Molecular Signals using Polynomial Chaos Expansion

Molecular signals are abundant in engineering and biological contexts, and undergo stochastic propagation in fluid dynamic channels. The received signal is sensitive to a variety of input and channel parameter variations. Currently we do not understand how uncertainty or noise in a variety of parameters affect the received signal concentration, and nor do we have an analytical framework to tackle this challenge. In this paper, we utilize Polynomial Chaos Expansion (PCE) to show to uncertainty in parameters propagates to uncertainty in the received signal. In demonstrating its applicability, we consider a Turbulent Diffusion Molecular Communication (TDMC) channel and highlight which parameters affect the received signals. This can pave the way for future information theoretic insights, as well as guide experimental design

Study and Development of New Passive Micromixers Based on Split and Recombination Principle

Micromixers have been a major topic of research in the past decade and progress on recent development of micromixers has been reviewed by many researchers. Developing devices for microfluidic technology has been a major concern for industry and microfluidic devices offer many advantages over conventional techniques. Compared to conventional macroscopic methods, microfluidic devices have the advantages of reduced solvent, reagent and cell consumption, shorter reaction times, portability, low cost and low power consumption. Also, micromixers are key elements in microfluidic technology and have been addressed by a large body of research. Interestingly, the historical development of microfluidics and its preoccupation with micromixing are the main fields of microtechnology. Micromixers have a wide variety of potential applications in industry. In modern technology, micromixers are applied in microtechnologies such as biological systems, as microreactors for chemical reactions, and as MEMS and lab-on-a-chip devices. This means that the community of engineers and scientist now engaged in microfluidic devices and also mixing process in micro scales. Indeed, they have entered the field from a variety of different backgrounds and they would have been confronted by the problems of mixing processing and mass transport at the micro scales. According to the survey carried out in my research, the main driving forces for this investigation are applications in incompressible mixing processing at low Reynolds number range, 0.08<Re<4.16. As far as we know, the technology and science of microfluidics cover a wide spectrum ranging from fundamental studies to real applications in laboratories and industries. This research focuses on an important subject of microfluidics, namely mixing processing at the microscale. The science of such mixing has carried out on newly fabricated micro scale devices on an extensive collection of established knowledge. Due to its applied nature, my research discuss practical outcome in the design and characterization of micromixers. In this thesis, first and foremost, I describe the method that I've used for analyzing the experimental data. The laminar flow regime (0.08<Re<4.16) was considered during tests and image-based techniques are used to evaluate mixing efficiency. This study propose a novel generation of 3D splitting and recombination passive micromixers. Mixing characteristics of two species are elucidated via experimental and numerical studies associated with microchannels with various inlet flow rates (velocities) and results compared with the previous well-known micromixers. It was found that mixing performance is significantly affected by the split and recombination (SAR) flows and depends on Reynolds number (inlet velocities). As well as the efficiencies of my proposed mixer are almost quite the same with the well-known basic mixers at each desired region, the required pressure drop is approximately two times less than previous mixers. This is a good particular result that with higher efficiency the required pressure drop decreases. Hence, this new geometries satisfies both of targets in micromixer design which are higher mixing efficiency and lower pressure drop in comparison with previous well-known mixers. These results open the new operating windows for rapid mixing in the microchannel to overcome the fluid mixing which strongly limited to laminar regime with lower required pressure dro

Shock tube determination of the drag coefficient of small spherical particles

Shock tube determination of drag coefficient of small spherical particles accelerating in laminar, non-reacting, incompressible continuum flo

A non-contact laser ablation cell for mass spectrometry

A common analytical problem in applying LA sampling concerns dealing with large planar samples, e.g. gel plates, Si wafers, tissue sections or geological samples. As the current state of the art stands, there are two solutions to this problem: either sub-sample the substrate or build a custom cell. Both have their inherent drawbacks. With sub-sampling, the main issue is to ensure that a representative is sample taken to correctly determine the analytes of interest. Constructing custom cells can be time consuming, even for research groups that are experienced or skilled, as they have to be validated before data can be published. There are various published designs and ideas that attempt to deal with the issue of large samples, all of which ultimately enclose the sample in a box. The work presented in this thesis shows a viable alternative to enclosed sampling chambers. The non-contact cell is an open cell that uses novel gas dynamics to remove the necessity for an enclosed box and, therefore, enables samples of any arbitrary size to be sampled. The upper size limit of a sample is set by the travel of the XY stages on the laser ablation system, not the dimensions of the ablation cell

Channel modeling for diffusive molecular communication - a tutorial review

Molecular communication (MC) is a new communication engineering paradigm where molecules are employed as information carriers. MC systems are expected to enable new revolutionary applications such as sensing of target substances in biotechnology, smart drug delivery in medicine, and monitoring of oil pipelines or chemical reactors in industrial settings. As for any other kind of communication, simple yet sufficiently accurate channel models are needed for the design, analysis, and efficient operation of MC systems. In this paper, we provide a tutorial review on mathematical channel modeling for diffusive MC systems. The considered end-to-end MC channel models incorporate the effects of the release mechanism, the MC environment, and the reception mechanism on the observed information molecules. Thereby, the various existing models for the different components of an MC system are presented under a common framework and the underlying biological, chemical, and physical phenomena are discussed. Deterministic models characterizing the expected number of molecules observed at the receiver and statistical models characterizing the actual number of observed molecules are developed. In addition, we provide channel models for timevarying MC systems with moving transmitters and receivers, which are relevant for advanced applications such as smart drug delivery with mobile nanomachines. For complex scenarios, where simple MC channel models cannot be obtained from first principles, we investigate simulation-driven and experiment-driven channel models. Finally, we provide a detailed discussion of potential challenges, open research problems, and future directions in channel modeling for diffusive MC systems

Molecular Communication: From Theory to Practice

Always-on, always-available digital communication has changed the world – allowing us to collaborate and share information in ways unimaginable not long ago. Yet many of the physical principles used in everyday digital communication break down as the size of the devices approach micro- or nano-scale dimensions. As a result, tiny devices, with dimensions of microns or less, need to do something different in order to communicate. Moreover, at meter scales there are areas where use of radio signals is not possible or desirable. An emerging biomimetic technique called molecular communication, which relies on chemical signaling is a promising solution to these problems. Although biologists have studied molecular communication extensively, it is very poorly understood from a telecommunication engineering perspective. Engineering molecular communication systems is important since micro- and nano-scale systems are the key to unlocking a realm of futuristic possibilities such as: self-repairing machines, micro- and nano-scale robotics, synthetic biological devices, nanomedicine, and artificial immune systems that detect and kill cancer cells and pathogens. All these transformative applications have one feature in common: they involve not just single devices working independently, but swarms of devices working in concert. Besides solving the communication problem at small scales, use of molecular communication in areas such as robotics, and infrastructure monitoring can unlock new applications in smart cities and disaster search and rescue. In this dissertation, after providing a comprehensive survey of the field, two areas of study with high potential impact are identified: on-chip molecular communication, and experimental platforms for molecular communication. First, on-chip molecular communication is investigated towards the goal of networking components within lab-on-chip devices and point-of-care diagnostic devices. This has numerous applications in medicine, environmental monitoring systems, and the food industry. Then in the second part of the dissertation, a tabletop demonstrator for molecular communication is designed and built that could be used for research and experimentation. In particular, no macroscale or microscale molecular communication platform capable of reliably transporting sequential data had existed in the past, and this platform is used to send the world's first text message ("O Canada") using chemical signals

Mechanisms of Odor-Tracking: Multiple Sensors for Enhanced Perception and Behavior

Early in evolution, the ability to sense and respond to changing environments must have provided a critical survival advantage to living organisms. From bacteria and worms to flies and vertebrates, sophisticated mechanisms have evolved to enhance odor detection and localization. Here, we review several modes of chemotaxis. We further consider the relevance of a striking and recurrent motif in the organization of invertebrate and vertebrate sensory systems, namely the existence of two symmetrical olfactory sensors. By combining our current knowledge about the olfactory circuits of larval and adult Drosophila, we examine the molecular and neural mechanisms underlying robust olfactory perception and extend these analyses to recent behavioral studies addressing the relevance and function of bilateral olfactory input for gradient detection. Finally, using a comparative theoretical approach based on Braitenberg's vehicles, we speculate about the relationships between anatomy, circuit architecture and stereotypical orientation behaviors