Capacity of Diffusion-based Molecular Communication with Ligand Receptors

A diffusion-based molecular communication system has two major components: the diffusion in the medium, and the ligand-reception. Information bits, encoded in the time variations of the concentration of molecules, are conveyed to the receiver front through the molecular diffusion in the medium. The receiver, in turn, measures the concentration of the molecules in its vicinity in order to retrieve the information. This is done via ligand-reception process. In this paper, we develop models to study the constraints imposed by the concentration sensing at the receiver side and derive the maximum rate by which a ligand-receiver can receive information. Therefore, the overall capacity of the diffusion channel with the ligand receptors can be obtained by combining the results presented in this paper with our previous work on the achievable information rate of molecular communication over the diffusion channel.Comment: Published in Information Theory Workshop 2011 (ITW '2011

On the Capacity of Diffusion-Based Molecular Communications with SiNW FET-Based Receiver

Molecular communication (MC) is a bio-inspired communication method based on the exchange of molecules for information transfer among nanoscale devices. Although MC has been extensively studied from various aspects, limitations imposed by the physical design of transceiving units have been largely neglected in the literature. Recently, we have proposed a nanobioelectronic MC receiver architecture based on the nanoscale field effect transistor-based biosensor (bioFET) technology, providing noninvasive and sensitive molecular detection at nanoscale while producing electrical signals at the output. In this paper, we derive analytical closed-form expressions for the capacity and capacity-achieving input distribution for a memoryless MC channel with a silicon nanowire (SiNW) FET-based MC receiver. The resulting expressions could be used to optimize the information flow in MC systems equipped with nanobioelectronic receivers.Comment: To be presented at IEEE EMBC 2016, Orlando, FL, US

On the Capacity of Level and Type Modulation in Molecular Communication with Ligand Receptors

In this paper, we consider the bacterial point-to-point communication problem with one transmitter and one receiver by considering the ligand receptor binding process. The most commonly investigated signalling model, referred to as the Level Scenario (LS), uses one type of a molecule with different concentration levels for signaling. An alternative approach is to employ multiple types of molecules with a single concentration level, referred to as the Type Scenario (TS). We investigate the trade-offs between the two scenarios for the ligand receptor from the capacity point of view. For this purpose, we evaluate the capacity using numerical algorithms. Moreover, we derive an upper bound on the capacity of the ligand receptor using a Binomial Channel (BIC) model using symmetrized Kullback-Leibler (KL) divergence. A lower bound is also derived when the environment noise is negligible. Finally, we analyse the effect of blocking of a receptor by a molecule of a different type, by proposing a new Markov model in the multiple-type signalling.Comment: 18 pages, Accepted at ISIT conferenc

On the Capacity of Point-to-Point and Multiple-Access Molecular Communications with Ligand-Receptors

In this paper, we consider the bacterial point-to-point and multiple-access molecular communications with ligand-receptors. For the point-to-point communication, we investigate common signaling methods, namely the Level Scenario (LS), which uses one type of a molecule with different concentration levels, and the Type Scenario (TS), which employs multiple types of molecules with a single concentration level. We investigate the trade-offs between the two scenarios from the capacity point of view. We derive an upper bound on the capacity using a Binomial Channel (BIC) model and the symmetrized Kullback-Leibler (KL) divergence. A lower bound is also derived when the environment noise is negligible. For the TS, we also consider the effect of blocking of a receptor by a different molecule type. Then, we consider multiple-access communications, for which we investigate three scenarios based on molecule and receptor types, i.e., same types of molecules with Different Labeling and Same types of Receptors (DLSR), Different types of Molecules and Receptors (DMDR), and Same types of Molecules and Receptors (SMSR). We investigate the trade-offs among the three scenarios from the total capacity point of view. We derive some inner bounds on the capacity region of these scenarios when the environment noise is negligible

A molecular communications model for drug delivery

This paper considers the scenario of a targeted drug delivery system, which consists of deploying a number of biological nanomachines close to a biological target (e.g. a tumor), able to deliver drug molecules in the diseased area. Suitably located transmitters are designed to release a continuous flow of drug molecules in the surrounding environment, where they diffuse and reach the target. These molecules are received when they chemically react with compliant receptors deployed on the receiver surface. In these conditions, if the release rate is relatively high and the drug absorption time is significant, congestion may happen, essentially at the receiver site. This phenomenon limits the drug absorption rate and makes the signal transmission ineffective, with an undesired diffusion of drug molecules elsewhere in the body. The original contribution of this paper consists of a theoretical analysis of the causes of congestion in diffusion-based molecular communications. For this purpose, it is proposed a reception model consisting of a set of pure loss queuing systems. The proposed model exhibits an excellent agreement with the results of a simulation campaign made by using the Biological and Nano-Scale communication simulator version 2 (BiNS2), a well-known simulator for molecular communications, whose reliability has been assessed through in-vitro experiments. The obtained results can be used in rate control algorithms to optimally determine the optimal release rate of molecules in drug delivery applications

On the Physical Design of Molecular Communication Receiver Based on Nanoscale Biosensors

Molecular communications (MC), where molecules are used to encode, transmit, and receive information, is a promising means of enabling the coordination of nanoscale devices. The paradigm has been extensively studied from various aspects, including channel modeling and noise analysis. Comparatively little attention has been given to the physical design of molecular receiver and transmitter, envisioning biological synthetic cells with intrinsic molecular reception and transmission capabilities as the future nanomachines. However, this assumption leads to a discrepancy between the envisaged applications requiring complex communication interfaces and protocols, and the very limited computational capacities of the envisioned biological nanomachines. In this paper, we examine the feasibility of designing a molecular receiver, in a physical domain other than synthetic biology, meeting the basic requirements of nanonetwork applications. We first review the state-of-the-art biosensing approaches to determine whether they can inspire a receiver design. We reveal that nanoscale field effect transistor based electrical biosensor technology (bioFET) is a particularly useful starting point for designing a molecular receiver. Focusing on bioFET-based molecular receivers with a conceptual approach, we provide a guideline elaborating on their operation principles, performance metrics and design parameters. We then provide a simple model for signal flow in silicon nanowire (SiNW) FET-based molecular receiver. Lastly, we discuss the practical challenges of implementing the receiver and present the future research avenues from a communication theoretical perspective

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.Comment: Accepted for publication in IEEE Communications Surveys & Tutorial

Diffusion Based Molecular Communication: Principle, Key Technologies, and Challenges

Molecular communication (MC) is a kind of communication technology based on biochemical molecules for internet of bio-nano things, in which the biochemical molecule is used as the information carrier for the interconnection of nano-devices. In this paper, the basic principle of diffusion based MC and the corresponding key technologies are comprehensively surveyed. In particular, the state-of-the-art achievements relative to the diffusion based MC are discussed and compared, including the system model, the system performance analysis with key influencing factors, the information coding and modulation techniques. Meanwhile, the multi-hop nano-network based on the diffusion MC is presented as well. Additionally, given the extensiveness of the research area, open issues and challenges are presented to spur future investigations, in which the involvement of channel model, information theory, self-organizing nano-network, and biochemical applications are put forward

Using spatial partitioning to reduce the bit error rate of diffusion-based molecular communications

This work builds on our earlier work on designing demodulators for diffusion-based molecular communications using a Markovian approach. The demodulation filters take the form of an ordinary differential equation (ODE) which computes the log-posteriori probability of observing a transmission symbol given the continuous history of receptor activities. A limitation of our earlier work is that the receiver is assumed to be a small cubic volume called a voxel. In this work, we extend the maximum a-posteriori demodulation to the case where the receiver may consist of multiple voxels and derive the ODE for log-posteriori probability calculation. This extension allows us to study receiver behaviour of different volumes and shapes. In particular, it also allows us to consider spatially partitioned receivers where the chemicals in the receiver are not allowed to mix. The key result of this paper is that spatial partitioning can be used to reduce bit-error rate in diffusion-based molecular communications.Comment: 39 pages, 20 figures, submitted for possible publication in IEE

The Channel Capacity of Channelrhodopsin and Other Intensity-Driven Signal Transduction Receptors

Biological systems transduce signals from their surroundings through a myriad of pathways. In this paper, we describe signal transduction as a communication system: the signal transduction receptor acts as the receiver in this system, and can be modeled as a finite-state Markov chain with transition rates governed by the input signal. Using this general model, we give the mutual information under IID inputs in discrete time, and obtain the mutual information in the continuous-time limit. We show that the mutual information has a concise closed-form expression with clear physical significance. We also give a sufficient condition under which the Shannon capacity is achieved with IID inputs. We illustrate our results with three examples: the light-gated Channelrhodopsin-2 (ChR2) receptor; the ligand-gated nicotinic acetylcholine (ACh) receptor; and the ligand-gated Calmodulin (CaM) receptor. In particular, we show that the IID capacity of the ChR2 receptor is equal to its Shannon capacity. We finally discuss how the results change if only certain properties of each state can be observed, such as whether an ion channel is open or closed.Comment: Accepted for publication in IEEE Transactions on Molecular, Biological, and Multi-Scale Communication