On-chip molecular communication: analysis and design

Analyzing of Alzheimer’s Disease Based on Biomedical and Socio-Economic Approach Using Molecular Communication, Artificial Neural Network, and Random Forest Models

Alzheimer’s disease will affect more people with increases in the elderly population, as the elderly population of countries everywhere generally rises significantly. However, other factors such as regional climates, environmental conditions and even eating and drinking habits may trigger Alzheimer’s disease or affect the life quality of individuals already suffering from this disease. Today, the subject of biomedical engineering is being studied intensively by many researchers considering that it has the potential to produce solutions to various diseases such as Alzheimer’s caused by problems in molecule or cell communication. In this study, firstly, a molecular communication model with the potential to be used in the treatment and/or diagnosis of Alzheimer’s disease was proposed, and its results were analyzed with an artificial neural network model. Secondly, the ratio of people suffering from Alzheimer’s disease to the total population, along with data of educational status, income inequality, poverty threshold, and the number of the poor in Turkey were subjected to detailed distribution analysis by using the random forest model statistically. As a result of the study, it was determined that a higher income level was causally associated with a lower risk of Alzheimer’s disease.

Carbon Quantum Dots from Lemon Waste Enable Communication among Biodevices

A bioinspired method of communication among biodevices based on fluorescent nanoparticles is herein presented. This approach does not use electromagnetic waves but rather the exchange of chemical systems—a method known as molecular communication. The example outlined was based on the fluorescence properties of carbon dots and follows a circular economy approach as the method involves preparation from the juice of lemon waste. The synthesis is herein presented, and the fluorescence properties and diffusion coefficient are evaluated. The application of carbon dots to molecular communication was studied from a theoretical point of view by numerically solving the differential equation that governs the phenomenon. The theoretical results were used to develop a prototype molecular communication platform that enables the communication of simple messages via aqueous fluids to a fluorescence-detecting biodevice receiver.

Molecular Communication for Equilibrium State Estimation in Biochemical Processes on a Lab-on-a-Chip

A basic problem in molecular biology is to estimate equilibrium states of biochemical processes. To this end, advanced spectroscopy methods have been developed in order to estimate chemical concentrations in situ or in vivo. However, such spectroscopy methods can require special conditions that do not allow direct observation of the biochemical process. A natural means of resolving this problem is to transmit chemical signals to another location within a lab-on-a-chip device; that is, employing molecular communication in order to perform spectroscopy in a different location. In this paper, we develop such a signaling strategy and estimation algorithms for equilibrium states of a biochemical process. In two biologically-inspired models, we then study via simulation the tradeoff between the rate of obtaining spectroscopy measurements and the estimation error, providing insights into requirements of spectroscopy devices for high-throughput biological assays.

On Mathematical Analysis of Active Drug Transport Coupled With Flow-Induced Diffusion in Blood Vessels

Blood vessels are flow-induced diffusive molecular channels equipped with transport mechanisms across their walls for conveying substances between the organs in the body. Mathematical modeling of the blood vessel as a molecular transport channel can be used for the characterization of the underlying processes and higher-level functions in the circulatory system. Besides, the mathematical model can be utilized for designing and realizing nano-scale molecular communication systems for healthcare applications including drug delivery systems. In this paper, a continuous-time Markov chain framework is proposed to simply model active transport mechanisms e.g. transcytosis, across the single-layered endothelial cells building the inner vessel wall. Correspondingly, a general homogeneous boundary condition over the vessel wall is introduced. Coupled with the derived boundary condition, the flow-induced diffusion problem in an ideal vessel structure with a cylindrical shape is accurately formulated which takes into account variation in all three dimensions. The corresponding concentration Green's function is analytically derived in terms of a convergent infinite series. Particle-based simulation results confirm the proposed analysis. Also, the effects of system parameters on the concentration Green's function are examined.

Redox Is a Global Biodevice Information Processing Modality

Biology is well-known for its ability to communicate through (i) molecularly-specific signaling modalities and (ii) a globally-acting electrical modality associated with ion flow across biological membranes. Emerging research suggests that biology uses a third type of communication modality associated with a flow of electrons through reduction/oxidation (redox) reactions. This redox signaling modality appears to act globally and has features of both molecular and electrical modalities: since free electrons do not exist in aqueous solution, the electrons must flow through molecular intermediates that can be switched between two states - with electrons (reduced) or without electrons (oxidized). Importantly, this global redox modality is easily accessible through its electrical features using convenient electrochemical instrumentation. In this review, we explain this redox modality, describe our electrochemical measurements, and provide four examples demonstrating that redox enables communication between biology and electronics. The first two examples illustrate how redox probing can acquire biologically relevant information. The last two examples illustrate how redox inputs can transduce biologically-relevant transitions for patterning and the induction of a synbio transceiver for two-hop molecular communication. In summary, we believe redox provides a unique ability to bridge bio-device communication because simple electrochemical methods enable global access to biologically meaningful information. Further, we envision that redox may facilitate the application of information theory to the biological sciences.

Influence of Tissue Anisotropy on Molecular Communication

Many biological tissues inside the human body exhibit highly anisotropic diffusion properties; for example, tissues of the nervous system and white matter in the brain. Here, we present an improved stochastic molecular communication framework to model interaction between bionanomachines in three-dimensional (3D) anisotropic brain micro-environment. The results obtained using stochastic particle-based simulation model are validated with analytical expressions. We also derive expressions for peak amplitude and peak time for the received molecular signal. The results demonstrate that the channel impulse response in anisotropic biological media depends significantly on the diffusion tensor as well as on the locations of the nanomachines.

Diffusive Molecular Communication in Biological Cylindrical Environment

Diffusive molecular communication (DMC) is one of the most promising approaches for realizing nano-scale communications in biological environments for healthcare applications. In this paper, a DMC system in biological cylindrical environment is considered, inspired by blood vessel structures in the body. The internal surface of the cylinder boundary is assumed to be covered by the biological receptors which may irreversibly react with hitting molecules. Also, the information molecules diffusing in the fluid medium are subject to a degradation reaction and flow. The concentration Green's function of diffusion in this environment is analytically derived which takes into account asymmetry in all radial, axial, and azimuthal coordinates. Employing obtained Green's function, information channel between transmitter and transparent receiver of DMC is characterized. To evaluate the DMC system in the biological cylinder, a simple on-off keying modulation scheme is adopted and corresponding error probability is derived. The particle-based simulation results confirm the proposed analysis. Also, the effect of different system parameters on the concentration Green's function are examined. Our results reveal that the degradation reaction and the boundary covered by biological receptors may be utilized to mitigate intersymbol interference and outperform the corresponding error probability.

Biofabricating Functional Soft Matter Using Protein Engineering to Enable Enzymatic Assembly

Biology often provides the inspiration for functional soft matter, but biology can do more: it can provide the raw materials and mechanisms for hierarchical assembly. Biology uses polymers to perform various functions, and biologically derived polymers can serve as sustainable, self-assembling, and high-performance materials platforms for life-science applications. Biology employs enzymes for site-specific reactions that are used to both disassemble and assemble biopolymers both to and from component parts. By exploiting protein engineering methodologies, proteins can be modified to make them more susceptible to biology's native enzymatic activities. They can be engineered with fusion tags that provide (short sequences of amino acids at the C- and/or N- termini) that provide the accessible residues for the assembling enzymes to recognize and react with. This "biobased" fabrication not only allows biology's nanoscale components (i.e., proteins) to be engineered, but also provides the means to organize these components into the hierarchical structures that are prevalent in life.

Touchable Computing: Computing-Inspired Bio-Detection

We propose a new computing-inspired bio-detection framework called touchable computing (TouchComp). Under the rubric of TouchComp, the best solution is the cancer to be detected, the parameter space is the tissue region at high risk of malignancy, and the agents are the nanorobots loaded with contrast medium molecules for tracking purpose. Subsequently, the cancer detection procedure (CDP) can be interpreted from the computational optimization perspective: a population of externally steerable agents (i.e., nanorobots) locate the optimal solution (i.e., cancer) by moving through the parameter space (i.e., tissue under screening), whose landscape (i.e., a prescribed feature of tissue environment) may be altered by these agents but the location of the best solution remains unchanged. One can then infer the landscape by observing the movement of agents by applying the "seeing-is-sensing" principle. The term "touchable" emphasizes the framework's similarity to controlling by touching the screen with a finger, where the external field for controlling and tracking acts as the finger. Given this analogy, we aim to answer the following profound question: can we look to the fertile field of computational optimization algorithms for solutions to achieve effective cancer detection that are fast, accurate, and robust? Along this line of thought, we consider the classical particle swarm optimization (PSO) as an example and propose the PSO-inspired CDP, which differs from the standard PSO by taking into account realistic in vivo propagation and controlling of nanorobots. Finally, we present comprehensive numerical examples to demonstrate the effectiveness of the PSO-inspired CDP for different blood flow velocity profiles caused by tumor-induced angiogenesis. The proposed TouchComp bio-detection framework may be regarded as one form of natural computing that employs natural materials to compute.

Connecting Biology to Electronics: Molecular Communication via Redox Modality

Biology and electronics are both expert at for accessing, analyzing, and responding to information. Biology uses ions, small molecules, and macromolecules to receive, analyze, store, and transmit information, whereas electronic devices receive input in the form of electromagnetic radiation, process the information using electrons, and then transmit output as electromagnetic waves. Generating the capabilities to connect biology-electronic modalities offers exciting opportunities to shape the future of biosensors, point-of-care medicine, and wearable/implantable devices. Redox reactions offer unique opportunities for bio-device communication that spans the molecular modalities of biology and electrical modality of devices. Here, an approach to search for redox information through an interactive electrochemical probing that is analogous to sonar is adopted. The capabilities of this approach to access global chemical information as well as information of specific redox-active chemical entities are illustrated using recent examples. An example of the use of synthetic biology to recognize external molecular information, process this information through intracellular signal transduction pathways, and generate output responses that can be detected by electrical modalities is also provided. Finally, exciting results in the use of redox reactions to actuate biology are provided to illustrate that synthetic biology offers the potential to guide biological response through electrical cues.

Molecular Communication over Gas Stream Channels using Portable Mass Spectrometry

The synthetic generation/coding and transmission of olfactory information over a gas stream or an odor network is a new and unexplored field. Application areas vary from the entertainment or advertisement industry to security and telemedicine. However, current technological limitations frustrate the accurate reproduction of decoded and transmitted olfactory data. This study describes the development, testing, and characterization of a novel odor emitter (OE) that is used to investigate the generation-encoding of gaseous standards with odorous characteristics with a regulatable way, for scent transmission purposes. The calibration and the responses of a developed OE were examined using a portable quadrupole mass spectrometer (MS). Experiments were undertaken for a range of volatile organic compounds (VOCs) at different temperatures and flow rates. Individual compounds and mixtures were tested to investigate periodic and dynamic transmission characteristics within two different size tubular containers for distances up to 3 m. Olfactory information transmission is demonstrated using MS as the main molecular sensor for odor detection and monitoring and for the first time spatial encryption of olfactory information is shown. Graphical Abstract ᅟ.

Using a Redox Modality to Connect Synthetic Biology to Electronics: Hydrogel-Based Chemo-Electro Signal Transduction for Molecular Communication

A hydrogel-based dual film coating is electrofabricated for transducing bio-relevant chemical information into electronical output. The outer film has a synthetic biology construct that recognizes an external molecular signal and transduces this input into the expression of an enzyme that converts redox-inactive substrate into a redox-active intermediate, which is detected through an amplification mechanism of the inner redox-capacitor film.

Dielectrophoretic Relay Assisted Molecular Communication for In-Sequence Molecule Delivery

With current research focus to interconnect the molecular communication environment with external environment, it is imperative to design external devices working on molecular communication schemes to be interfaced with in-vivo molecular network. Recently, efforts have been made to integrate molecular communication with Lab-on-chip (LOC); one of the techniques used in LOC for manipulation and transportation of molecules is Dielctrophoresis (DEP). We propose the use of DEP in molecular communication to maintain in-sequence delivery of molecules. DEP planar electrodes are modeled as relays used in telecommunications. We describe the theoretical system model and analyze the effect of introducing DEP relays in diffusive channel in terms of probability of in-sequence delivery of molecules. Information rate of DEP-based channel is analytically obtained for in-sequence delivery. The numerical results obtained show that the information rate for in-sequence delivery of molecules through diffusive channel increases by 26% if DEP relays are used in the channel. Though the system is sensitive to noise variance, incorporation of DEP relay results in a substantial improvement in the capacity of the channel.

Characterizing Nanoscale Transient Communication

We consider the novel paradigm of nanoscale transient communication (NTC), where certain components of the small-scale communication link are physically transient. As such, the transmitter and the receiver may change their properties over a prescribed lifespan due to their time-varying structures. The NTC systems may find important applications in the biomedical, environmental, and military fields, where system degradability allows for benign integration into life and environment. In this paper, we analyze the NTC systems from the channel-modeling and capacity-analysis perspectives and focus on the stochastically meaningful slow transience scenario, where the coherence time of degeneration Td is much longer than the coding delay Tc. We first develop novel and parsimonious models to characterize the NTC channels, where three types of physical layers are considered: electromagnetism-based terahertz (THz) communication, diffusion-based molecular communication (DMC), and nanobots-assisted touchable communication (TouchCom). We then revisit the classical performance measure of ϵ-outage channel capacity and take a fresh look at its formulations in the NTC context. Next, we present the notion of capacity degeneration profile (CDP), which describes the reduction of channel capacity with respect to the degeneration time. Finally, we provide numerical examples to demonstrate the features of CDP. To the best of our knowledge, the current work represents a first attempt to systematically evaluate the quality of nanoscale communication systems deteriorating with time.

Simulating an Actomyosin in Vitro Motility Assay: Toward the Rational Design of Actomyosin-Based Microtransporters

We present a simulation study of an actomyosin in vitro motility assay. In vitro motility assays have served as an essential element facilitating the application of actomyosin in nanotechnology; such applications include biosensors and biocomputation. Although actomyosin in vitro motility assays have been extensively investigated, some ambiguities remain, as a result of the limited spatio-temporal resolution and unavoidable uncertainties associated with the experimental process. These ambiguities hamper the rational design of nanodevices for practical applications. Here, with the aim of moving toward a rational design process, we developed a 3D computer simulation method of an actomyosin in vitro motility assay, based on a Brownian dynamics simulation. The simulation explicitly included the ATP hydrolysis cycle of myosin. The simulation was validated by the reproduction of previous experimental results. More importantly, the simulation provided new insights that are difficult to obtain experimentally, including data on the number of myosin motors actually binding to actin filaments, the mechanism responsible for the guiding of actin filaments by chemical edges, and the effect of the processivity of motor proteins on the guiding probabilities. The simulations presented here will be useful in interpreting experimental results, and also in designing future nanodevices integrated with myosin motors.

Functionalizing Soft Matter for Molecular Communication

The information age was enabled by advances in microfabrication and communication theory that allowed information to be processed by electrons and transmitted by electromagnetic radiation. Despite immense capabilities, microelectronics has limited abilities to access and participate in the molecular-based communication that characterizes our biological world. Here, we use biological materials and methods to create components and fabricate devices to perform simple molecular communication functions based on bacterial quorum sensing (QS). Components were created by protein engineering to generate a multidomain fusion protein capable of sending a molecular QS signal, and by synthetic biology to engineer E. coli to receive and report this QS signal. The device matrix was formed using stimuli-responsive hydrogel-forming biopolymers (alginate and gelatin). Assembly of the components within the device matrix was achieved by physically entrapping the cell-based components, and covalently conjugating the protein-based components using the enzyme microbial transglutaminase. We demonstrate simple devices that can send or receive a molecular QS signal to/from the surrounding medium, and a two-component device in which one component generates the signal (i.e., issues a command) that is acted upon by the second component. These studies illustrate the broad potential of biofabrication to generate molecular communication devices.

Understanding the guiding of kinesin/microtubule-based microtransporters in microfabricated tracks

Microtransporters using cargo-laden microtubules propelled by kinesin motors are attractive for numerous applications in nanotechnology. To improve the efficiency of transport, the movement of microtubules must be guided by microfabricated tracks. However, the mechanisms of the guiding methods used are not fully understood. Here, using computer simulation, we systematically studied the guiding of such microtransporters by three different types of guiding methods: a chemical boundary, a physical barrier, and their combination. The simulation reproduced the probabilities of guiding previously observed experimentally for the three methods. Moreover, the simulation provided further insight into the mechanisms of guiding, which overturn previous assumptions and models.

Symbol interval optimization for molecular communication with drift

In this paper, we propose a symbol interval optimization algorithm in molecular communication with drift. Proper symbol intervals are important in practical communication systems since information needs to be sent as fast as possible with low error rates. There is a trade-off, however, between symbol intervals and inter-symbol interference (ISI) from Brownian motion. Thus, we find proper symbol interval values considering the ISI inside two kinds of blood vessels, and also suggest no ISI system for strong drift models. Finally, an isomer-based molecule shift keying (IMoSK) is applied to calculate achievable data transmission rates (achievable rates, hereafter). Normalized achievable rates are also obtained and compared in one-symbol ISI and no ISI systems.

Tabletop molecular communication: text messages through chemical signals

In this work, we describe the first modular, and programmable platform capable of transmitting a text message using chemical signalling – a method also known as molecular communication. This form of communication is attractive for applications where conventional wireless systems perform poorly, from nanotechnology to urban health monitoring. Using examples, we demonstrate the use of our platform as a testbed for molecular communication, and illustrate the features of these communication systems using experiments. By providing a simple and inexpensive means of performing experiments, our system fills an important gap in the molecular communication literature, where much current work is done in simulation with simplified system models. A key finding in this paper is that these systems are often nonlinear in practice, whereas current simulations and analysis often assume that the system is linear. However, as we show in this work, despite the nonlinearity, reliable communication is still possible. Furthermore, this work motivates future studies on more realistic modelling, analysis, and design of theoretical models and algorithms for these systems.