Introducing purely hydrodynamic networking mechanisms in microfluidic systems

Microfluidic is a multidisciplinary field with prac- tical applications to the design of systems, called Lab-on-a- Chip (LoC), where tiny volumes of fluids are circulated through channels with millimeter size and driven into structures where precise chemical/physical processes take place. One subcategory of microfluidic is droplet-based microfluidic, which disperse discrete volumes of fluids into a continuous stream of another immiscible fluid, which act as droplet carrier. Droplets can then be moved, merged, split, or processed in many other ways by suitably managing the hydrodynamic parameters of the LoC. A very interesting research challenge consists in developing basic microfluidic structures able to interconnect specialized LoCs by means of a flexible and modular microfluidic network. The aim of this paper is to exploit the properties of droplet- based microfluidics to realize purely hydrodynamic microfluidic elements that provide basic networking functionalities, such as addressing and switching. We define some simple mathematical models that capture the macroscopic behavior of droplets in microfluidic networks and use such models to design and analyze a simple microfluidic network system with bus topology

Novel Network Paradigms: Microfluidic and M2M Communications

The present thesis focuses on two appealing paradigms that are expected to characterize the next generation of communication systems: microfluidic networking and Machine to Machine (M2M) Communications. Concerning the former topic, we show how it is possible to introduce switching and routing mechanism in microfluidic systems. We define some simple mathematical models that capture the macroscopic behavior of droplets in microfluidic networks. Then, we use them to implement a simulator that is able to reproduce the motion and predict the path of droplets in a generic microfluidic system. We validate the simulator and apply it to design a network with bus topology. Finally, we prove the feasibility of attaining molecular communication in this domain by describing a simple protocol that exploits droplets length/interdistance modulation to send information. The research activity on M2M, instead, is aimed at the investigation of two critical issues that are expected to affect Machine-Type Communication (MTC), i.e. energy efficiency and massive access. Regarding energy efficiency, we address the problem of delivering a fixed data payload over a Rayleigh fading wireless channel with the purpose of minimizing the average total energy cost, given by the sum of the transmit energy and an overhead circuit energy, to complete it. This scenario is well suited for uplink cellular MTC in future 5G Internet of Things (IoT) use cases, where the focus is more on device energy efficiency than on throughput. We describe the optimal transmission policies to be used under various coordinated access scenarios with different levels of channel state information and transmitter/receiver capabilities, and show the corresponding theoretical bounds. In the last part of the work, we study the asymptotic performance of uncoordinated access schemes with Multi Packet Reception (MPR) and Successive Interference Cancellation (SIC) techniques for contention resolution at the receiver. The corresponding results in terms of throughput in a massive access M2M scenario are finally evaluated and discussed

A comprehensive survey of recent advancements in molecular communication

With much advancement in the field of nanotechnology, bioengineering and synthetic biology over the past decade, microscales and nanoscales devices are becoming a reality. Yet the problem of engineering a reliable communication system between tiny devices is still an open problem. At the same time, despite the prevalence of radio communication, there are still areas where traditional electromagnetic waves find it difficult or expensive to reach. Points of interest in industry, cities, and medical applications often lie in embedded and entrenched areas, accessible only by ventricles at scales too small for conventional radio waves and microwaves, or they are located in such a way that directional high frequency systems are ineffective. Inspired by nature, one solution to these problems is molecular communication (MC), where chemical signals are used to transfer information. Although biologists have studied MC for decades, it has only been researched for roughly 10 year from a communication engineering lens. Significant number of papers have been published to date, but owing to the need for interdisciplinary work, much of the results are preliminary. In this paper, the recent advancements in the field of MC engineering are highlighted. First, the biological, chemical, and physical processes used by an MC system are discussed. This includes different components of the MC transmitter and receiver, as well as the propagation and transport mechanisms. Then, a comprehensive survey of some of the recent works on MC through a communication engineering lens is provided. The paper ends with a technology readiness analysis of MC and future research directions

Microfluidic Communications Protocol Design and Transmission Performance Analysis

The new field of nanocommunications aims to develop communication systems at the nanoscale. It has developed into two main communication directions: molecular communications andelectromagnetic communications. Microfluidic communications is a subtype of molecular communications. Existing liquid based microfluidics applications are the main target for the integration of a communication feature. Currently, there are still no standards for microfluidics communications protocol. The protocols should consider particular phenomena such as noise, transmission access priorities, and probability of coalescence between microdroplets. Those phenomena bring challenges in protocol development of microfluidics communications. In this thesis, the protocol stack for microfluidics communications is developed. Starting from the physical layer, feasible modulation schemes for data transmission suitable for microfluidics communications is examined. Later, medium access control layer protocols is discussed in order to optimize transmission medium access for the network entities. This is done to avoid droplet coalescence. Specification of the addressing and routing methods is defined to ensure data submission to the destination point. Finally, the performance of the proposed schemes and numerical comparison to viable alternatives are analyzed. The results of the evaluation are reached through MATLAB software simulations. This work concentrates on Communication through Silence (CtS) where the payload is represented as distance between two droplets. Two schemes of CtS (decimal and hexadeximal) are investigated. Both CtS schemes with particular optimum amount binary payload outperforms OOK in throughput performance. The fairness of the transmission system can be achieved for a decentralized system by combining slotted (TDMA) scheme and a probability-based algorithm

Engineering single-molecule, nanoscale, and microscale bio-functional materials via click chemistry

To expand the design envelope and supplement the materials library available to biomaterials scientists, the copper(I)-catalyzed azide-alkyne cycloaddition (CuCAAC) was explored as a route to design, synthesize and characterize bio-functional small-molecules, nanoparticles, and microfibers. In each engineered system, the use of click chemistry provided facile, bio-orthogonal control for materials synthesis; moreover, the results provided a methodology and more complete, fundamental understanding of the use of click chemistry as a tool for the synergy of biotechnology, polymer and materials science. Fluorophores with well-defined photophysical characteristics (ranging from UV to NIR fluorescence) were used as building blocks for small-molecule, fluorescent biosensors. Fluorophores were paired to exhibit fluorescence resonant energy transfer (FRET) and used to probe the metabolic activity of carbazole 1,9a-dioxygenase (CARDO). The FRET pair exhibited a signicant variation in PL response with exposure to the lysate of Pseudomonas resinovorans CA10, an organism which can degrade variants of both the donor and acceptor fluorophores. Nanoparticle systems were modified via CuCAAC chemistry to carry affinity tags for CARDO and were subsequently utilized for affinity based bioseparation of CARDO from crude cell lysate. The enzymes were baited with an azide-modified carbazolyl-moiety attached to a poly(propargyl acrylate) nanoparticle. Magnetic nanocluster systems were also modified via CuCAAC chemistry to carry fluorescent imaging tags. The iron-oxide nanoclusters were coated with poly(acrylic acid-co-propargyl acrylate) to provide a clickable surface. Ultimately, alternate Cu-free click chemistries were utilized to produce biohybrid microfibers. The biohybrid microfibers were synthesized under benign photopolymerization conditions inside a microchannel, allowing the encapsulation of viable bacteria. By adjusting pre-polymer solutions and laminar flow rates within the microchannel, the morphology, hydration, and thermal properties of the fibers were easily tuned. The methodology produced hydrogel fibers that sustained viable cells as demonstrated by the encapsulation and subsequent proliferation of Bacillus cereus and Escherichia coli communities

High-Performance Computing of Flow, Diffusion, and Hydrodynamic Dispersion in Random Sphere Packings

This thesis is dedicated to the study of mass transport processes (flow, diffusion, and hydrodynamic dispersion) in computer-generated random sphere packings. Periodic and confined packings of hard impermeable spheres were generated using Jodrey–Tory and Monte Carlo procedure-based algorithms, mass transport in the packing void space was simulated using the lattice Boltzmann and random walk particle tracking methods. Simulation codes written in C programming language using MPI library allowed an efficient use of the high-performance computing systems (supercomputers). The first part of this thesis investigates the influence of the cross-sectional geometry of the confined random sphere packings on the hydrodynamic dispersion. Packings with different values of porosity (interstitial void space fraction) generated in containers of circular, quadratic, rectangular, trapezoidal, and irregular (reconstructed) geometries were studied, and resulting pre-asymptotic and close-to-asymptotic hydrodynamic dispersion coefficients were analyzed. It was demonstrated i) a significant impact of the cross-sectional geometry and porosity on the hydrodynamic dispersion coefficients, and ii) reduction of the symmetry of the cross section results in longer times to reach close-to-asymptotic values and larger absolute values of the hydrodynamic dispersion coefficients. In case of reconstructed geometry, good agreement with experimental data was found. In the second part of this thesis i) length scales of heterogeneity persistent in unconfined and confined sphere packings were analyzed and correlated with a time behavior of the hydrodynamic dispersion coefficients; close-to-asymptotic values of the dispersion coefficients (expressed in terms of plate height) were successfully fitted to the generalized Giddings equation; ii) influence of the packing microstructural disorder on the effective diffusion and hydrodynamic dispersion coefficients was investigated and clear qualitative corellation with geometrical descriptors (which are based on Delaunay and Voronoi spatial tessellations) was demonstrated

THE ROLE OF FLOW IN THE SELF-ASSEMBLY OF DRAGLINE SPIDER SILK PROTEINS

Silk fibers are outstandingly tough biomaterials, a result of the controlled self-assembly of their protein building blocks, spidroins. The combination of extensibility and high tensile strength relies on the microscopic composition within the fiber: small and strong beta-sheet crystals formed mainly by poly-alanine repeats enclosed into a flexible amorphous matrix of glycine-rich repeats. The internal molecular structure of silk proteins makes them sensitive to an elongational flow, which is a crucial factor for spider silk fiber spinning. However, the mechanism of flow-induced silk self-assembly, as well as the relevant dynamics of single silk proteins under flow remain largely unknown. In the present work, a bottom-up approach was used to study the dynamics and self-assembly of spider silk proteins under uniform flow conditions. We used non-equilibrium molecular dynamics (MD) simulations to study these processes at two scales, an atomistic model with explicit water, and a coarse-grained model with hydrodynamics incorporated by multi-particle collision dynamics. To be able to analyze the role of the flow on spider silk molecules atomistically, a prior implementation and systematic study of uniform flow MD simulations were carried out based on the GROMACS MD software. Subjecting a tethered single silk peptide to uniform flow leads to a coiled-to-stretch transition involving a multitude of intermediates states, the process of which depends on the mean flow velocity. The flow-induced structural changes of single spidroins exhibit a prominent tendency of alanine residues to be in beta-sheet conformation. All-atom simulations of the assembly process at low flow regimes revealed that the interchain contacts happen primarily in the poly-alanine repeats, which is a suitable condition for crystal formation and fibrillation. We also found beta-sheets formation at low flow regimes, confirming that flow promotes crystal formation. We complemented these findings to the more coarse-grained hydrodynamic simulations at aminoacid resolution, treating the silk proteins as semi-flexible block copolymers. We observed that the spidroins aggregate faster when they are less extended by monitoring oligomer formation in time. At medium peptide extensions (around 60-70%), the spidroin alignment increases, while their assembly slows down because of the reduced fluctuations orthogonal to the flow direction. The microscopic understanding of the spidroin dynamics provided in this work is likely relevant for other flow-dependent proteins