Molecular Communication Channel Research Articles

Performance Analysis of Convolutional Coding Techniques in Diffusion-Based Concentration-Encoded PAM Molecular Communication Systems

In this paper, we investigate the performance of convolutional coding techniques in an ideal diffusion-based concentration-encoded molecular communication (CEMC) channel with pulse amplitude modulation (PAM) transmission scheme. Convolutional codes have shown to provide a significant amount of gain in the signal-to-interference strength (energy) ratio between a pair of communicating nanomachines and thus help increase the communication range and improve the end-to-end system performance. We have also determined the impact of convolutional codes for several key performance factors, e.g. transmission data rate, communication range, and the constraint length of the convolutional code in the context of diffusion-based CEMC. In addition, we have compared the PAM system with the impulse modulation system in CEMC. We have found that the use of a multilevel (M-ary) signalling scheme in the CEMC system provides a degraded bit error rate performance even in short communication ranges. Therefore, a convolutional coded scheme with larger alphabet size should not be recommended for a CEMC system because of the stronger intersymbol interference produced within symbols. As an alternative, a convolutional coded scheme with binary alphabet and higher symbol rate was evaluated and found to provide a gain in the signal-to-interference energy ratio of the system and is therefore recommended for short- to medium-range CEMC. For long communication ranges, an uncoded system can rather be preferred to convolutional coded schemes.

Establishing A Molecular Communication Channel for Nano Networks

Establishing A Molecular Communication Channel for Nano Networks

Channel Model and Capacity Analysis of Molecular Communication with Brownian Motion

In this paper, we analyze the capacity of a molecular communication channel in a one dimensional environment where information is represented with molecules that are released by a transmitter nanomachine, propagate via Brownian motion, degrade over time, and stochastically reach the receiver nanomachine. The channel is modeled as a time slotted binary channel, and two modulation schemes are proposed: a naive modulation scheme and an extended modulation scheme with a redundant number of molecules. Our analysis demonstrates that the channel capacity is largely affected by the life expectancy of molecules. Our analysis also indicates that the extended modulation scheme can achieve nearly one bit per slot at the expense of extra molecules under optimal conditions.

Nanoscale Communication With Molecular Arrays in Nanonetworks

Molecular communication is a promising nanoscale communication paradigm that enables nanomachines to exchange information by using molecules as communication carrier. Up to now, the molecular communication channel between a transmitter nanomachine (TN) and a receiver nanomachine (RN) has been modeled as either concentration channel or timing channel. However, these channel models necessitate exact time synchronization of the nanomachines and provide a relatively low communication bandwidth. In this paper, the Molecular ARray-based COmmunication (MARCO) scheme is proposed, in which the transmission order of different molecules is used to convey molecular information without any need for time synchronization. The MARCO channel model is first theoretically derived, and the intersymbol interference and error probabilities are obtained. Based on the error probability, achievable communication rates are analytically obtained. Numerical results and performance comparisons reveal that MARCO provides significantly higher communication rate, i.e., on the scale of 100 Kbps, than the previously proposed molecular communication models without any need for synchronization. More specifically, MARCO can provide more than 250 Kbps of molecular communication rate if intersymbol time and internode distance are set to 2 μs and 2 nm, respectively.

A Physical Channel Model and Analysis for Nanoscale Molecular Communications With Förster Resonance Energy Transfer (FRET)

In this study, a novel and physically realizable nanoscale communication paradigm is introduced based on a well-known phenomenon, Förster resonance energy transfer (FRET), for the first time in the literature. FRET is a nonradiative energy transfer process between fluorescent molecules based on the dipole-dipole interactions of molecules. Energy is transferred rapidly from a donor to an acceptor molecule in a close proximity such as 0 to 10 nm without radiation of a photon. Low dependence on the environmental factors, controllability of its parameters, and relatively wide transfer range make FRET a promising candidate to be used for a high-rate nanoscale communication channel. In this paper, the simplest form of the FRET-based molecular communication channel comprising a single transmitter-receiver nanomachine pair and an extended version of this channel with a relay nanomachine for long-range applications are modeled considering nanomachines as nanoscale electromechanical devices with some sensing, computing, and actuating capabilities. Furthermore, using the information theoretical approach, the capacities of these communication channels are investigated and the dependence of the capacity on some environmental and intrinsic parameters is analyzed. It is shown that the capacity can be increased by appropriately selecting the donor-acceptor pair, the medium, the intermolecular distance, and the orientation of the molecules.

Molecular communication nanonetworks inside human body

To realize molecular nanonetworks, the foundations of molecular information theory should be established through identification of the existing molecular communication mechanisms, and architectures and networking techniques for nanomachines should be developed, which demand novel engineering efforts. Luckily, these engineering skills and technology have been prepared for us by the natural evolution in the last several billions of years. Indeed, the human body is a massive nanoscale molecular communications network as it is composed of billions of interacting nanomachines, i.e., cells. Intra-body biological systems are closely linked to each other and communicate primarily through molecular transactions. Thus, vital activities inside the human body are regulated by everlasting communication performance and operations of intra-body molecular nanonetworks. However, natural intra-body molecular nanonetworks are yet to be explored with the elegant tools of information and communication theories. In this paper, first, the elementary models for significant intra-body molecular communication channels, i.e., nanoscale neuro-spike communication channel, action potential-based cardiomyocyte molecular communication channel, and hormonal molecular communication channel, are introduced. Next, molecular nanonetworks belonging to multi-terminal extensions of channel models, i.e., nervous, cardiovascular molecular, and endocrine nanonetworks are discussed. Furthermore, heterogeneous communication network of intra-body molecular nanonetworks together with five senses, i.e., nanosensory networks, is explored from the perspectives of communication and network theories. Moreover, open research challenges, such as extension of molecular channel models to multi-terminal cases, and developing a communication theory perspective to understand the physiology and to capture potential communication failures of intra-body biological systems, are provided. Our objectives are to learn from the elegant molecular communication mechanisms inside us for engineering practical communication techniques for emerging nanonetworks, as well as to pave the way for the advancement of revolutionary diagnosis and treatment techniques inspired from information and communication technologies, which is promising for future nanomedicine and bio-inspired molecular communication applications.

Quick system design of vesicle-based active transport molecular communication by using a simple transport model

This paper will provide a guidepost to design an optimal molecular communication setup and protocol. A barrier to the design of vesicle-based molecular communication nanonetworks is the computational complexity of simulating them. In this paper, a computationally efficient transport model is presented, which could be employed to design active transport molecular communication systems, particularly to optimize the shape of the transmission zone. Furthermore, a vesicular encapsulation model is presented as an addition to the transport model, and it is shown that there exists an optimal vesicle size for each molecular communication channel. As an application, our transport model is used to estimate the channel capacity of a molecular communication nanonetwork in a computationally efficient manner compared to traditional Monte Carlo techniques. Moreover, it is shown that the derived optimal vesicle size maximizes channel capacity.

Toward in vivo nanoscale communication networks: utilizing an active network architecture

A safe and reliable in vivo nanoscale communication network will be of great benefit for medical diagnosis and monitoring as well as medical implant communication. This review article provides a brief introduction to nanoscale and molecular networking in general and provides opinions on the role of active networking for in vivo nanoscale information transport. While there are many in vivo communication mechanisms that can be leveraged, for example, forms of cell signaling, gap junctions, calcium and ion signaling, and circulatory borne communication, this review examines two in particular: molecular motor transport and neuronal information communication. Molecular motors transport molecules representing information and neural coding operates by means of the action potential; these mechanisms are reviewed within the theoretical framework of an active network. This review suggests that an active networking paradigm is necessary at the nanoscale along with a new communication constraint, namely, minimizing the communication impact upon the living environment. The goal is to assemble efficient nanoscale and molecular communication channels while minimizing disruption to the host organism.

On the implicit bond-dependency origins of bridge interactions

The indirect (through-bridge) components of chemical interactions between atomic orbitals (AO) are shown to originate from the indirect dependencies between AO due to the orbital intermediaries in the bond system of the molecule. They are expressed in terms of the bridge-coupling elements of the density matrix via the chain rule transformation of the implicit derivatives between the indirectly bonded AO in the molecular bond system. The elements of the charge-and-bond-order (CBO) matrix are interpreted as the canonical derivatives between the AO-projections onto the bond subspace combining the occupied Molecular Orbitals (MO). The chain-rule manipulations are then used to express the scattering amplitudes via AO intermediaries in terms of the relevant elements of the CBO matrix. The squares of such amplitudes are related to the Wiberg-type indirect bond components, which complement the familiar direct Wiberg bond-order contributions. The interference implications of the probability scatterings via the multiple cascades involving all basis functions are examined. These probability propagations are shown to preserve the stationary conditional probabilities of the underlying molecular communication channel in AO resolution.

Capacity analysis of a diffusion-based short-range molecular nano-communication channel

Simulation-based and information theoretic models for a diffusion-based short-range molecular communication channel between a nano-transmitter and a nano-receiver are constructed to analyze information rates between channel inputs and outputs when the inputs are independent and identically distributed (i.i.d.). The total number of molecules available for information transfer is assumed to be limited. It is also assumed that there is a maximum tolerable delay bound for the overall information transfer. Information rates are computed via simulation-based methods for different time slot lengths and transmitter–receiver distances. The rates obtained from simulations are then compared to those computed using information theoretic channel models which provide upper bounds for information rates. The results indicate that a 4-input–2-output discrete channel model provides a very good approximation to the nano-communication channel, particularly when the time slot lengths are large and the distance between the transmitter and the receiver is small. It is shown through an extensive set of simulations that the information theoretic channel capacity with i.i.d. inputs can be achieved when an encoder adjusts the relative frequency of binary zeros to be higher (between 50% and 70% for the scenarios considered) than binary ones, where a ‘zero’ corresponds to not releasing and a ‘one’ corresponds to releasing a molecule from the transmitter.

NanoNS: A nanoscale network simulator framework for molecular communications

A number of nanomachines that cooperatively communicate and share molecular information in order to achieve specific tasks is envisioned as a nanonetwork. Due to the size and capabilities of nanomachines, the traditional communication paradigms cannot be used for nanonetworks in which network nodes may be composed of just several atoms or molecules and scale on the orders of few nanometers. Instead, molecular communication is a promising solution approach for the nanoscale communication paradigm. However, molecular communication must be thoroughly investigated to realize nanoscale communication and nanonetworks for many envisioned applications such as nanoscale body area networks, and nanoscale molecular computers. In this paper, a simulation framework (NanoNS) for molecular nanonetworks is presented. The objective of the framework is to provide a simulation tool in order to create a better understanding of nanonetworks and facilitate the development of new communication techniques and the validation of theoretical results. The NanoNS framework is built on top of core components of a widely used network simulator (ns-2). It incorporates the simulation modules for various nanoscale communication paradigms based on a diffusive molecular communication channel. The details of NanoNS are discussed and some functional scenarios are defined to validate NanoNS. In addition to this, the numerical analyses of these functional scenarios and their experimental results are presented. The validation of NanoNS is shown via comparative evaluation of these experimental and numerical results.

Deterministic capacity of information flow in molecular nanonetworks

Molecular communication enables nanomachines to exchange information with each other by emitting molecules to their surrounding environment. Molecular nanonetworks are envisioned as a number of nanomachines that are deployed in an environment to share specific molecular information such as odor, flavor, or any chemical state. In this paper, using the stochastic model of molecular reactions in biochemical systems, a realistic channel model is first introduced for molecular communication. Then, based on the realistic channel model, we introduce a deterministic capacity expression for point-to-point, broadcast, and multiple-access molecular channels. We also investigate information flow capacity in a molecular nanonetwork for the realization of efficient communication and networking techniques for frontier nanonetwork applications. The results reveal that molecular point-to-point, broadcast, and multiple-access channels are feasible with a satisfactorily high molecular communication rate, which allows molecular information flow in nanonetworks. Furthermore, the derived molecular channel model with input-dependent noise term also reveals that unlike a traditional Gaussian communication channel, achievable capacity is affected by both lower and upper bounds of the channel input in molecular communication channels.

Information origins of the chemical bond: Bond descriptors from molecular communication channels in orbital resolution

AbstractThe flow of information in the molecular communication networks in the (condensed) atomic orbital (AO) resolution is investigated and the plane‐wave (momentum‐space) interpretation of the average Fisher information in the molecular information system is given. It is argued using the quantum‐mechanical superposition principle that, in the LCAO MO theory the squares of corresponding elements of the Charge and Bond‐Order (CBO) matrix determine the conditional probabilities between AO, which generate the molecular communication system of the Orbital Communication Theory (OCT) of the chemical bond. The conditional‐entropy (“noise,” information‐theoretic “covalency”) and the mutual‐information (information flow, information‐theoretic “ionicity”) descriptors of these molecular channels are related to Wiberg's covalency indices of chemical bonds. The illustrative application of OCT to the three‐orbital model of the chemical bond X—Y, which is capable of describing the forward‐ and back‐donations as well as the atom promotion accompanying the bond formation, is reported. It is demonstrated that the entropy/information characteristics of these separate bond‐effects can be extracted by an appropriate reduction of the output of the molecular information channel, carried out by combining several exits into a single (condensed) one. The molecular channels in both the AO and hybrid orbital representations are examined for both the molecular and representative promolecular input probabilities. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

Communication-theory perspective on valence-bond theory

The information-theoretic (IT) approach to the electronic structure of molecules, called the Communication Theory of the chemical bond, is used to explore the entropy/information “bond-orders” of the system Valence-Bond (VB) structures, and their covalent/ionic composition. The molecular communication channel in atomic resolution is interpreted as the ensemble-average of the elementary information networks corresponding to the system elementary VB structures, with the probability-weights generated by the coefficients of the familiar VB expansion of the system wave-function. The elementary probability-scattering networks corresponding to a single ionic and covalent bonds of the system constituent diatomic fragments, to be used to construct the communication systems of any VB structure, are identified and their entropy/information descriptors are summarized. The overall bond multiplicities of VB structures are generated using the relevant grouping rules for the entropy/information quantities and the molecular IT bond-order and its covalent/ionic components are obtained as the ensemble averages of the corresponding descriptors of individual VB structures. Illustrative applications to the hydrogen molecule and π-bonds in allyl, butadiene and benzene are reported and discussed. Equating the VB-ensemble average quantities for these π-electron systems with those resulting from the Huckel Molecular Orbital (MO) theory then allows one to extract the VB relative covalency and ionicity measures for all chemical bonds in the molecule. The simple MO and VB descriptions of the hydrogen molecule are compared and the role of a strong overlap between the VB structures is investigated in a more detail. Finally, the entropy/information descriptors of the information distribution in the resultant promolecule → Atoms-in-H2 channel resulting from the sequential information cascade consisting of the promolecular and VB probability propagation stages is examined to determine the dependence of the flow of information on the adopted reference system.

Chemical bonds through probability scattering: Information channels for intermediate-orbital stages

The information-theoretic (IT) approach to chemical bonds, based upon the molecular probability-scattering channels in orbital resolution, is developed to cover both the overall promotion of atomic orbitals (AO) and the partial communication systems due to typical intermediate stages of reconstructing the system electronic structure, due to the orbital hybridization, orthogonalization, mixing into the molecular orbitals (MO), etc. The geometric and physical orbital promotion channels are distinguished, with the former taking into account solely the elementary channels due to the orbital-mixing, and the latter additionally including the MO-occupation term, which effectively projects-out the orbital promotion via the occupied MO only. This IT development generates the complementary descriptors of the molecular communication channel, viz., its conditional entropy (IT-covalency) and mutual-information (IT-ionicity), which add up to the total IT bond-order. These components provide a transparent description of the covalent/ionic competition for the valence electrons of constituent atoms. Their orbital-promotion contributions, from the elementary sub-channels reflecting the familiar intermediate stages of the bond-formation process, offer a novel information-scattering perspective on the relative roles played by these partial transformations of orbitals in shaping the resultant entropy/information descriptors of the system chemical bonds. The combination (grouping) rules for the consecutive and parallel arrangements of the elementary sub-channels are summarized and the stage-additivity of the IT bond- descriptors in the molecular sequential cascade of the elementary sub-channels for the intermediate sets of orbitals is examined in a more detail. A distinction between the molecular information channels describing the separated atoms and the free-atoms in the system atomic promolecule, respectively, is stressed and their entropy/information descriptors are briefly summarized. The associated difference descriptors of the overall IT bond-orders with respect to the promolecular reference are introduced and similar displacement measures are designed for the molecular promotion of intermediate orbitals. The illustrative results for the simplest model of a single chemical bond originating from an interaction between two overlapping atomic orbitals are presented. In particular, the bond-increments due to the orthogonalization and de-orthogonalization sub-channels of the overall AO-promotion cascade will be investigated.

Entropic bond indices from molecular information channels in orbital resolution: ground-state systems

The molecular communication channels of Information Theory (IT) are constructed within the orbital description of molecular electronic structure using the superposition principle of quantum mechanics. Two types of such information systems are introduced, called the “geometric” and “physical” channels. The communication network of the former is determined by all molecular orbitals (MO), occupied and virtual, which result from the specified set of atomic orbitals (AO). The geometric channel thus reflects the relative “rotation” of MO relative to AO in the molecular Hilbert space, and the associated “promotion” of AO in the molecule due to the probability scattering via the communication network generated by the complete set of MO. They are devoid of the physical content embodied in the MO-occupations, which distinguish one electron configuration of the molecule from another. The latter information is included in the physical AO-promotion channels, which involve the probability scattering via the occupied MO alone. The probability conditioning is shown to be related to the appropriate projection in the orbital Hilbert space. The geometric and the physical (ground-state) bond indices of the conditional-entropy (IT-covalency) and mutual-information (IT-ionicity) are generated for the 2-AO model and selected π-electron systems (ethylene, allyl, butadiene, and benzene) in the Huckel approximation. They are shown to compare favorably with the previously reported IT bond-orders obtained from the two-electron molecular information channels in atomic resolution.

Molecular communication channels of model excited electron configurations†

In the Communication Theory of the chemical bond, molecular systems are interpreted in atomic resolution as the information channels, in which ‘signals' of the electron allocations to constituent atoms are propagated from the molecular/promolecular input (‘source'), to the molecular output (‘receiver'). The electron delocalization throughout the system is responsible for the effective ‘noise' affecting the transmission of such atom-assignment signals. The conditional entropy and mutual-information descriptors of such molecular communication channels, measuring the average noise and the amount of information flowing through the molecular channel, respectively, provide measures of the covalent and ionic bond components, respectively. This work examines the influence of the relative phases of the atomic orbitals (AO) in the occupied molecular orbitals (MO) on these entropy/information indices of the chemical bond in the 2-AO, two-electron model. First, the singly- and doubly-excited-state configurations of the model are examined to investigate the influence of the occupied bonding and anti-bonding molecular orbitals on the previously proposed (phase-insensitive) entropy/information descriptors of the ground-state configuration. They in principle correctly identify the non-bonding character of the singly-excited configuration, but fail to recognize the anti-bonding character of the doubly-excited state. This is because the relative phases of AO in MO and those of the elementary valence-bond structures in the configuration wave-function are lost in the corresponding electron probabilities, which determine the molecular channel. A resolution of this difficulty is proposed through partition of the overall input probabilities of the molecular channel into the partial (phase-dependent) ‘forward' and ‘backward' inputs, which determine the entropy/information flows associated with the ‘positive' and ‘negative' phases of the wave-function components in the AO representation. †Dedicated to Professor A. Sadlej on the occasion of his 65th birthday.

Comparison between valence bond and communication theories of the chemical bond in H2

In the communication theory of the chemical bond the molecular systems in atomic resolution are interpreted as information channels, in which ‘signals' of the electron allocations to constituent atoms are propagated from the molecular/promolecular input (source), determined by either the free atoms of the promolecule or the bonded atoms in the molecule, to the molecular output (receiver) of atoms in molecules. The transmission network of the system chemical bonds is determined by the molecular conditional two-electron probabilities in atomic resolution. The electron delocalization throughout the system is responsible for the effective ‘noise' affecting the transmission of such atom-assignment signals, which inhibits the amount of information passing through the molecular communication system. The conditional entropy and mutual information descriptors of such molecular communication channels, measuring the average noise and the amount of information flowing through the molecular channel, accordingly, provide the overall measures of the covalent and ionic bond components, respectively. The communication theory approach to the chemical bond in H2 is compared with the familiar valence bond (VB) description of Heitler and London. In the information-theoretic (IT) approach the non-bonding, purely covalent, and purely ionic combinations of the elementary VB structures are defined and their information channels are discussed. It is demonstrated, that the VB covalent and VB ionic components of the molecular ground state wavefunction are in fact both IT ionic. The purely IT covalent components of the molecular ground state are established and their communication channels are examined. The communication origins of the information ionicity and entropy covalency are identified and a distinction between the electron-sharing (covalent) and pair-sharing (coordination) bonds is briefly explored.

Communication Theory Approach to the Chemical Bond

Recently proposed communication theory treatment of the chemical bond is outlined. The molecular systems in atomic resolution are interpreted as “communication” systems in which “signals” of the electron allocations to constituent atoms are propagated from the molecular input (source), e.g., the atomic promolecule reference, to the molecular output (receiver) via a network defined by the conditional two-electron probabilities. The electron delocalization accompanying the bond formation is responsible for the noise affecting the flow of information throughout the system. The conditional entropy and mutual information descriptors of such molecular communication channels are identified as overall measures of the covalent and ionic components of the system chemical bonds, and a distinction between the electron-sharing and coordination (donor–acceptor) bonds is investigated. These entropy/information descriptors of the chemical bond are illustrated in the two-electron, two-orbital model. This analysis covers the orbital and spin channels for the singlet (bonding) and triplet (nonbonding) states. The overall bond-order conservation in the model and the competition between the bond ionicity and covalency is stressed. The model polyatomic systems discussed include the π bonds in butadiene and benzene in the Huckel theory approximation. The predictions from the communication theory approach compare favorably with the chemical intuitive values and bond orders from other orbital approaches, e.g., the quadratic index of Wiberg and the two-electron multiplicities of the difference approach. The Hirshfeld partition of molecular electron density is briefly summarized and the average entropies of the local stockholder communication channel it generates are proposed as alternative information descriptors of the chemical bonds in molecules.