No file available
To read the file of this research,
you can request a copy directly from the authors.
Analysis of Receiver Covered by Heterogeneous Receptors in Molecular Communications
Preprints and early-stage research may not have been peer reviewed yet.
Abstract
This paper analyzes the channel impulse response of an absorbing receiver (RX) covered by multiple non-overlapping receptors with different sizes and arbitrary locations in a molecular communication system. In this system, a point transmitter (TX) is assumed to be uniformly located on a virtual sphere at a fixed distance from the RX. Considering molecule degradation during the propagation from the TX to the RX, the expected molecule hitting rate at the RX over varying locations of the TX is analyzed as a function of the size and location of each receptor. Notably, this analytical result is applicable for different numbers, sizes, and locations of receptors, and its accuracy is demonstrated via particle-based simulations. Numerical results show that (i) the expected number of absorbed molecules at the RX increases with an increasing number of receptors, when the total area of receptors on the RX surface is fixed, and (ii) evenly distributed receptors lead to the largest expected number of absorbed molecules.
ResearchGate has not been able to resolve any citations for this publication.
To communicate at the nanoscale, researchers have proposed molecular communication as an energy-efficient solution. The drawback to this solution is that the histogram of the molecules' hitting times, which constitute the molecular signal at the receiver, has a heavy tail. Reducing the effects of this heavy tail, inter-symbol interference (ISI), has been the focus of most prior research. In this paper, a novel way of decreasing the ISI by defining a counting region on the spherical receiver's surface facing towards the transmitter node is proposed. The beneficial effect comes from the fact that the molecules received from the back lobe of the receiver are more likely to be coming through longer paths that contribute to ISI. In order to justify this idea, the joint distribution of the arrival molecules with respect to angle and time is derived. Using this distribution, the channel model function is approximated for the proposed system, i.e., the partially counting absorbing spherical receiver. After validating the channel model function, the characteristics of the molecular signal are investigated and improved performance is presented. Moreover, the optimal counting region in terms of bit error rate is found analytically.
This paper focuses on trapping of diffusing particles by a sphere with an absorbing cap of arbitrary size on the otherwise reflecting surface. We approach the problem using boundary homogenization which is an approximate replacement of non-uniform boundary conditions on the surface of the sphere by an effective uniform boundary condition with appropriately chosen effective trapping rate. One of the main results of our analysis is an expression for the effective trapping rate as a function of the surface fraction occupied by the absorbing cap. As the cap surface fraction increases from zero to unity, the effective trapping rate increases from that for a small absorbing disk on the otherwise reflecting sphere to infinity which corresponds to a perfectly absorbing sphere. The obtained expression for the effective trapping rate is applied to find the rate constant describing trapping of diffusing particles by an absorbing cap on the surface of the sphere. Finally, we find the capacitance of a metal cap of arbitrary size on a dielectric sphere using the relation between the capacitance and the rate constant of the corresponding diffusion-limited reaction. The relative error of our approximate expressions for the rate constant and the capacitance is less than 5% over the entire range of the cap surface fraction from zero to unity.
The performance of molecular communication is significantly impacted by the
reception process of the messenger molecules. The receptors' size and density,
however, have yet to be investigated. In this letter, we analyze the effect of
receptor density and size on the signal reception of an absorbing receiver with
receptors. The results show that, when the total receptor area is the same,
better hitting probability is achieved by using a higher number of relatively
small receptors. In addition, deploying receptors, which cover a small
percentage of the receiver surface, is able to create an effective
communication channel that has a detectable signal level.
In the nanonetworking literature, many solutions have been suggested to
enable the nanomachine-to-nanomachine communication. Among these solutions, we
focus on what constitutes the basis for molecular communication paradigms
--molecular communication via diffusion (MCvD). In this paper, we start with an
analytical modeling of a spherical absorbing receiver under messenger molecule
degradation and show that our formulations are in agreement with the simulation
results of a similar topology. Next, we identify how such signal
characteristics as pulse peak time and pulse amplitude are affected by
degradation. Indeed, we show analytically how in MCvD, signal shaping is
achieved through degradation. We also compare communication under messenger
molecule degradation with the case of no-degradation and electromagnetic
communication in terms of channel characteristics. Lastly, we evaluate the
communication performance of the scenarios having various degradation rates.
Here, we assess the system performance according to traditional network metrics
such as the level of inter-symbol interference, detection performance, bit
error rate, and channel capacity. Our results indicate that introducing
degradation significantly improves the system performance when the rate of
degradation is appropriately selected. We make a thorough analysis of the
communication scenario by taking into account different detection thresholds,
symbol durations, and communication distances.
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 end with a technology readiness analysis of MC and future research directions.
Within the domain of molecular communications, researchers mimic the
techniques in nature to come up with alternative communication methods for
collaborating nanomachines. This work investigates the channel transfer
function for molecular communication via diffusion. In nature,
information-carrying molecules are generally absorbed by the target node via
receptors. Using the concentration function, without considering the absorption
process, as the channel transfer function implicitly assumes that the receiver
node does not affect the system. In this letter, we propose a solid analytical
formulation and analyze the signal metrics (attenuation and propagation delay)
for molecular communication via diffusion channel with an absorbing receiver in
a 3-D environment. The proposed model and the formulation match well with the
simulations without any normalization.
The area of a spherical region can be easily measured by considering which sampling points of a lattice are located inside or outside the region. This point-counting technique is frequently used for measuring the Earth coverage of satellite constellations, employing a latitude-longitude lattice. This paper analyzes the numerical errors of such measurements, and shows that they could be greatly reduced if the Fibonacci lattice were used instead. The latter is a mathematical idealization of natural patterns with optimal packing, where the area represented by each point is almost identical. Using the Fibonacci lattice would reduce the root mean squared error by at least 40%. If, as is commonly the case, around a million lattice points are used, the maximum error would be an order of magnitude smaller.
Synaptic communication is based on a biological Molecular Communication (MC) system which may serve as a blueprint for the design of synthetic MC systems. However, the physical modeling of synaptic MC is complicated by the possible saturation of the molecular receiver caused by the competition of neurotransmitters (NTs) for postsynaptic receptors. Receiver saturation renders the system behavior nonlinear in the number of released NTs and is commonly neglected in existing analytical models. Furthermore, due to the ligands’ competition for receptors (and vice versa), the individual binding events at the molecular receiver are in general not statistically independent and the commonly used binomial model for the statistics of the received signal does not apply. Hence, in this work, we propose a novel deterministic model for receptor saturation in terms of a state-space description based on an eigenfunction expansion of Fick’s diffusion equation. The presented solution is numerically stable and computationally efficient. Employing the proposed deterministic model, we show that saturation at the molecular receiver effectively reduces the peak-value of the expected received signal and accelerates the clearance of NTs as compared to the case when receptor occupancy is neglected. We further derive a statistical model for the received signal in terms of the hypergeometric distribution which accounts for the competition of NTs for receptors
and
the competition of receptors for NTs. The proposed statistical model reveals how the signal statistics are shaped by the number of released NTs, the number of receptors, and the binding kinetics of the receptors, respectively, in the presence of competition. In particular, we show that the impact of these parameters on the signal variance is qualitatively different depending on the relative numbers of NTs and receptors. Finally, the accuracy of the proposed deterministic and statistical models is verified by particle-based computer simulations.
This letter focuses on the diffusive molecular communication system with a reversible reactive receiver. By assuming the receiver is uniformly covered by finite receptors, a new boundary condition is proposed to model the reception reaction. In addition, an iterative approximation method is developed to model the expected received signal in this system. The simulation results verify the effectiveness of the approximation method.
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 the channel models for time-varying 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 the simulation- 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.
We study the first passage time problem for a diffusing molecule in an enclosed region to hit a small spherical target whose surface contains many small absorbing traps. This study is motivated by two examples of cellular transport. The first is the intracellular process through which proteins transit from the cytosol to the interior of the nucleus through nuclear pore complexes that are distributed on the nuclear surface. The second is the problem of chemoreception, in which cells sense their surroundings through diffusive contact with receptors distributed on the cell exterior. Using a matched asymptotic analysis in terms of small absorbing pore radius, we derive and numerically verify a high order expansion for the capacitance of the structured target which incorporates surface effects and gives explicit information on interpore interaction through a Coulomb-type discrete energy with additional logarithmic dependencies. In the large N dilute surface trap fraction limit, a single homogenized Robin boundary condition ℓnv+kv=0 is derived in which κ depends on the total absorbing fraction, the characteristic pore scale, and parameters relating to interpore interactions.
Receptor-ligand interactions (RLIs) are at the base of all biological events occurring in living cells. The understanding of interactions between complementary macromolecules in biological systems represents a high-priority research area in bionanotechnology to design the artificial systems mimicking natural processes. This review summarizes and analyzes RLIs in some cutting-edge biomedical fields, in particular, for the preparation of novel stationary phases to separate complex biological mixtures in medical diagnostics, for the design of ultrasensitive biosensors for identification of biomarkers of various diseases at early stages, as well as in the development of innovative biomaterials and approaches for regenerative medicine. All these biotechnological fields are closely related, because their success depends on a proper choice, combination and spatial disposition of the single components of ligand-receptor pairs on the surface of appropriately designed support.
This paper studies the problem of receiver modeling in molecular communication systems. We consider the diffusive molecular communication channel between a transmitter nano-machine and a receiver nano-machine in a fluid environment. The information molecules released by the transmitter nano-machine into the environment can degrade in the channel via a first-order degradation reaction and those that reach the receiver nano-machine can participate in a reversible bimolecular reaction with receiver receptor proteins. Thereby, we distinguish between two scenarios. In the first scenario, we assume that the entire surface of the receiver is covered by receptor molecules. We derive a closed-form analytical expression for the expected received signal at the receiver, i.e., the expected number of activated receptors on the surface of the receiver. Then, in the second scenario, we consider the case where the number of receptor molecules is finite and the uniformly distributed receptor molecules cover the receiver surface only partially. We show that the expected received signal for this scenario can be accurately approximated by the expected received signal for the first scenario after appropriately modifying the forward reaction rate constant. The accuracy of the derived analytical results is verified by Brownian motion particle-based simulations of the considered environment, where we also show the impact of the effect of receptor occupancy on the derived analytical results.
Development, regeneration, and even day-to-day physiology require plant and animal cells to make decisions based on their locations. The principles by which cells may do this are deceptively straightforward. But when reliability needs to be high--as often occurs during development--successful strategies tend to be anything but simple. Increasingly, the challenge facing biologists is to relate the diverse diffusible molecules, control circuits, and gene regulatory networks that help cells know where they are to the varied, sometimes stringent, constraints imposed by the need for real-world precision and accuracy.
Receptor clustering is a well-established feature of transmembrane signalling. In some cellular systems, clusters form dynamically in response to activation by an extracellular ligand; in others, extensive 2-dimensional arrays of receptors persist for long periods of time on the cell surface. Compelling evidence has accumulated that the interactions between receptors within a cluster play an important role in the signalling process. Here, we review statistical mechanical models that describe how clusters may be generated and maintained by the equilibrium thermodynamic interactions between receptors, the extracellular ligands that bind to their periplasmic domains, and cytosolic 'adaptor proteins' that bind to the cytoplasmic domains of the receptors. We discuss how adaptor proteins might permit cells to exert control over the propensity of cluster formation, and to target clusters to specific locations on the cell surface. We further outline how differential interactions between active and inactive receptors can enhance the sensitivity of the cellular response through the mechanism of 'conformational spread'.
Statistical fluctuations limit the precision with which a microorganism can, in a given time T, determine the concentration of a chemoattractant in the surrounding medium. The best a cell can do is to monitor continually the state of occupation of receptors distributed over its surface. For nearly optimum performance only a small fraction of the surface need be specifically adsorbing. The probability that a molecule that has collided with the cell will find a receptor is Ns/(Ns + pi a), if N receptors, each with a binding site of radius s, are evenly distributed over a cell of radius a. There is ample room for many indenpendent systems of specific receptors. The adsorption rate for molecules of moderate size cannot be significantly enhanced by motion of the cell or by stirring of the medium by the cell. The least fractional error attainable in the determination of a concentration c is approximately (TcaD) - 1/2, where D is diffusion constant of the attractant. The number of specific receptors needed to attain such precision is about a/s. Data on bacteriophage absorption, bacterial chemotaxis, and chemotaxis in a cellular slime mold are evaluated. The chemotactic sensitivity of Escherichia coli approaches that of the cell of optimum design.
Physical Chemistry for the Biosciences
- R Chang
R. Chang, Physical Chemistry for the Biosciences. Sausalito, CA, USA:
Univ. Science Books, 2005.
- K Schulten
- I Kosztin
K. Schulten and I. Kosztin, Lectures in Theoretical Biophysics. Urbana,
IL, USA: Univ. of Illinois Press, 2000, vol. 117.