arXiv subjects

Adam Noel

Publications and source records attributed to Adam Noel.

At least 37 records · Page 2Linked to original sources

arXiv2018

Channel Modeling for Diffusive Molecular Communication - A Tutorial Review

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 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 simulation-driven and experimentally-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.

cs.ET↗

arXiv2018

Symbol-by-Symbol Maximum Likelihood Detection for Cooperative Molecular Communication

In this paper, symbol-by-symbol maximum likelihood (ML) detection is proposed for a cooperative diffusion-based molecular communication (MC) system. In this system, the transmitter (TX) sends a common information symbol to multiple receivers (RXs) and a fusion center (FC) chooses the TX symbol that is more likely, given the likelihood of its observations from all RXs. The transmission of a sequence of binary symbols and the resultant intersymbol interference are considered in the cooperative MC system. Three ML detection variants are proposed according to different RX behaviors and different knowledge at the FC. The system error probabilities for two ML detector variants are derived, one of which is in closed form. The optimal molecule allocation among RXs to minimize the system error probability of one variant is determined by solving a joint optimization problem. Also for this variant, the equal distribution of molecules among two symmetric RXs is analytically shown to achieve the local minimal error probability. Numerical and simulation results show that the ML detection variants provide lower bounds on the error performance of simpler, non-ML cooperative variants and demonstrate that these simpler cooperative variants have error performance comparable to ML detectors.

cs.IT↗

arXiv2018

Diffusive Molecular Communication in a Biological Spherical Environment with Partially Absorbing Boundary

Diffusive molecular communication (DMC) is envisioned as a promising approach to help realize healthcare applications within bounded biological environments. In this paper, a DMC system within a biological spherical environment is considered, inspired by bounded biological sphere-like structures throughout the body. As a biological environment, it is assumed that the inner surface of the sphere's boundary is fully covered by biological receptors that may irreversibly react with hitting molecules. Moreover, information molecules diffusing in the sphere may undergo a degradation reaction and be transformed to another molecule type. Concentration Green's function (CGF) of diffusion inside this environment is analytically obtained in terms of a convergent infinite series. By employing the obtained CGF, the information channel between transmitter and transparent receiver of DMC in this environment is characterized. Interestingly, it is revealed that the information channel is reciprocal, i.e., interchanging the position of receiver and transmitter does not change the information channel. Our results indicate that the conventional simplifying assumption that the environment is unbounded may lead to an inaccurate characterization in such biological environments.

eess.SP↗

arXiv2018

Algorithm for Mesoscopic Advection-Diffusion

In this paper, an algorithm is presented to calculate the transition rates between adjacent mesoscopic subvolumes in the presence of flow and diffusion. These rates can be integrated in stochastic simulations of reaction-diffusion systems that follow a mesoscopic approach, i.e., that partition the environment into homogeneous subvolumes and apply the spatial stochastic simulation algorithm (spatial SSA). The rates are derived by integrating Fick's second law over a single subvolume in one dimension (1D), and are also shown to apply in three dimensions (3D). The proposed algorithm corrects the derived rates to ensure that they are physically meaningful and it is implemented in the AcCoRD simulator (Actor-based Communication via Reaction-Diffusion). Simulations using the proposed method are compared with a naive mesoscopic approach, microscopic simulations that track every molecule, and analytical results that are exact in 1D and an approximation in 3D. By choosing subvolumes that are sufficiently small, such that the Peclet number associated with a subvolume is sufficiently less than 2, the accuracy of the proposed method is comparable with the microscopic method, thus enabling the simulation of advection-reaction-diffusion systems with the spatial SSA.

physics.chem-ph↗

arXiv2018

Distortion Distribution of Neural Spike Train Sequence Matching with Optogenetics

This paper uses a simple optogenetic model to compare the timing distortion between a randomly-generated target spike sequence and an externally-stimulated neuron spike sequence. Optogenetics is an emerging field of neuroscience where neurons are genetically modified to express light-sensitive receptors that enable external control over when the neurons fire. Given the prominence of neuronal signaling within the brain and throughout the body, optogenetics has significant potential to improve the understanding of the nervous system and to develop treatments for neurological diseases. This paper primarily considers two different distortion measures. The first measure is the delay in externally-stimulated spikes. The second measure is the root mean square error between the filtered outputs of the target and stimulated spike sequences. The mean and the distribution of the distortion is derived in closed form when the target sequence generation rate is sufficiently low. All derived results are supported with simulations. This work is a step towards an analytical model to predict whether different spike trains were observed from the same stimulus, and the broader goal of understanding the quantity and reliability of information that can be carried by neurons.

q-bio.NC↗

arXiv2018

A New Simulation Algorithm for Absorbing Receiver in Molecular Communication

The simulation of diffusion-based molecular communication systems with absorbing receivers often requires a high computational complexity to produce accurate results. In this work, a new a priori Monte Carlo (APMC) algorithm is proposed to precisely simulate the molecules absorbed at a spherical receiver when the simulation time step length is relatively large. This algorithm addresses the limitations of the current refined Monte Carlo (RMC) algorithm, since the RMC algorithm provides accurate simulation only for a relatively small time step length. The APMC algorithm is demonstrated to achieve a higher simulation efficiency than the existing algorithms by finding that the APMC algorithm, for a relatively large time step length, absorbs the fraction of molecules expected by analysis, while other algorithms do not.

cs.ET↗

arXiv2018

Maximum Likelihood Detection for Cooperative Molecular Communication

In this paper, symbol-by-symbol maximum likelihood (ML) detection is proposed for a cooperative diffusion-based molecular communication (MC) system. In this system, a fusion center (FC) chooses the transmitter's symbol that is more likely, given the likelihood of the observations from multiple receivers (RXs). We propose three different ML detection variants according to different constraints on the information available to the FC, which enables us to demonstrate trade-offs in their performance versus the information available. The system error probability for one variant is derived in closed form. Numerical and simulation results show that the ML detection variants provide lower bounds on the error performance of the simpler cooperative variants and demonstrate that majority rule detection has performance comparable to ML detection when the reporting is noisy.

cs.IT↗

arXiv2018

Timing Control of Single Neuron Spikes with Optogenetic Stimulation

This paper predicts the ability to externally control the firing times of a cortical neuron whose behavior follows the Izhikevich neuron model. The Izhikevich neuron model provides an efficient and biologically plausible method to track a cortical neuron's membrane potential and its firing times. The external control is a simple optogenetic model represented by a constant current source that can be turned on or off. This paper considers a firing frequency that is sufficiently low for the membrane potential to return to its resting potential after it fires. The time required for the neuron to charge and for the neuron to recover to the resting potential are fitted to functions of the Izhikevich neuron model parameters. Results show that linear functions of the model parameters can be used to predict the charging times with some accuracy and are sufficient to estimate the highest firing frequency achievable without interspike interference.

q-bio.NC↗

arXiv2017

Modeling Duct Flow for Molecular Communication

Active transport such as fluid flow is sought in molecular communication to extend coverage, improve reliability, and mitigate interference. Flow models are often over-simplified, assuming one-dimensional diffusion with constant drift. However, diffusion and flow are usually encountered in three-dimensional bounded environments where the flow is highly non-uniform such as in blood vessels or microfluidic channels. For a qualitative understanding of the relevant physical effects inherent to these channels, based on the Peclet number and the transmitter-receiver distance, we study when simplified models of uniform flow and advection-only transport are applicable. For these two regimes, analytical expressions for the channel impulse response are derived and validated by particle-based simulation. Furthermore, as advection-only transport is typically overlooked and hence not analyzed in the molecular communication literature, we evaluate the symbol error rate for exemplary on-off keying as performance metric.

cs.ET↗

arXiv2017

Analyzing Large-Scale Multiuser Molecular Communication via 3D Stochastic Geometry

Information delivery using chemical molecules is an integral part of biology at multiple distance scales and has attracted recent interest in bioengineering and communication theory. Potential applications include cooperative networks with a large number of simple devices that could be randomly located (e.g., due to mobility). This paper presents the first tractable analytical model for the collective signal strength due to randomly-placed transmitters in a three-dimensional (3D) large-scale molecular communication system, either with or without degradation in the propagation environment. Transmitter locations in an unbounded and homogeneous fluid are modelled as a homogeneous Poisson point process. By applying stochastic geometry, analytical expressions are derived for the expected number of molecules absorbed by a fully-absorbing receiver or observed by a passive receiver. The bit error probability is derived under ON/OFF keying and either a constant or adaptive decision threshold. Results reveal that the combined signal strength increases proportionately with the transmitter density, and the minimum bit error probability can be improved by introducing molecule degradation. Furthermore, the analysis of the system can be generalized to other receiver designs and other performance characteristics in large-scale molecular communication systems.

cs.IT↗

arXiv2017

Simplified Cooperative Detection for Multi-Receiver Molecular Communication

Diffusion-based molecular communication (MC) systems experience significant reliability losses. To boost the reliability, an MC scheme where multiple receivers (RXs) work cooperatively to decide the signal of a transmitter (TX) by sending the same type of molecules to a fusion center (FC) is proposed in this paper. The FC observes the total number of molecules received and compares this number with a threshold to determine the TX's signal. The proposed scheme is more bio-realistic and requires relatively low computational complexity compared to existing cooperative schemes where the RXs send and the FC recognizes different types of molecules. Asymmetric and symmetric topologies are considered, and closed-form expressions are derived for the global error probability for both topologies. Results show that the trade-off for simplified computations leads to a slight reduction in error performance, compared to the existing cooperative schemes.

cs.IT↗

arXiv2017

Root Mean Square Error of Neural Spike Train Sequence Matching with Optogenetics

Optogenetics is an emerging field of neuroscience where neurons are genetically modified to express light-sensitive receptors that enable external control over when the neurons fire. Given the prominence of neuronal signaling within the brain and throughout the body, optogenetics has significant potential to improve the understanding of the nervous system and to develop treatments for neurological diseases. This paper uses a simple optogenetic model to compare the timing distortion between a randomly-generated target spike sequence and an externally-stimulated neuron spike sequence. The distortion is measured by filtering each sequence and finding the root mean square error between the two filter outputs. The expected distortion is derived in closed form when the target sequence generation rate is sufficiently low. Derivations are verified via simulations.

q-bio.NC↗

arXiv2017

Effect of Local Population Uncertainty on Cooperation in Bacteria

Bacteria populations rely on mechanisms such as quorum sensing to coordinate complex tasks that cannot be achieved by a single bacterium. Quorum sensing is used to measure the local bacteria population density, and it controls cooperation by ensuring that a bacterium only commits the resources for cooperation when it expects its neighbors to reciprocate. This paper proposes a simple model for sharing a resource in a bacterial environment, where knowledge of the population influences each bacterium's behavior. Game theory is used to model the behavioral dynamics, where the net payoff (i.e., utility) for each bacterium is a function of its current behavior and that of the other bacteria. The game is first evaluated with perfect knowledge of the population. Then, the unreliability of diffusion introduces uncertainty in the local population estimate and changes the perceived payoffs. The results demonstrate the sensitivity to the system parameters and how population uncertainty can overcome a lack of explicit coordination.

q-bio.CB↗

arXiv2017

Asynchronous Peak Detection for Demodulation in Molecular Communication

Molecular communication requires low-complexity symbol detection algorithms to deal with the many sources of uncertainty that are inherent in these channels. This paper proposes two variants of a high-performance asynchronous peak detection algorithm for a receiver that makes independent observations. The first variant has low complexity and measures the largest observation within a sampling interval. The second variant adds decision feedback to mitigate inter-symbol interference. Although the algorithm does not require synchronization between the transmitter and receiver, results demonstrate that the bit error performance of symbol-by-symbol detection using the first variant is better than using a single sample whose sampling time is chosen a priori. The second variant is shown to have performance comparable to that of an energy detector. Both variants of the algorithm demonstrate better resilience to timing offsets than that of existing detectors.

cs.IT↗

arXiv2017

Diffusive Mobile Molecular Communications Over Time-Variant Channels

This letter introduces a formalism for modeling time-variant channels for diffusive molecular communication systems. In particular, we consider a fluid environment where one transmitter nano-machine and one receiver nano-machine are subjected to Brownian motion in addition to the diffusive motion of the information molecules used for communication. Due to the stochastic movements of the transmitter and receiver nano-machines, the statistics of the channel impulse response change over time. We show that the time-variant behaviour of the channel can be accurately captured by appropriately modifying the diffusion coefficient of the information molecules. Furthermore, we derive an analytical expression for evaluation of the expected error probability of a simple detector for the considered system. The accuracy of the proposed analytical expression is verified via particle-based simulation of the Brownian motion.

cs.IT↗

arXiv2017

Simulating with AcCoRD: Actor-Based Communication via Reaction-Diffusion

This paper introduces AcCoRD (Actor-based Communication via Reaction-Diffusion) version 1.0. AcCoRD is a sandbox reaction-diffusion solver designed for the study of molecular communication systems. It uses a hybrid of microscopic and mesoscopic simulation models that enables scalability via user control of local accuracy. AcCoRD is developed in C as an open source command line tool and includes utilities to process simulation output in MATLAB. The latest code and links to user documentation can be found at https://github.com/adamjgnoel/AcCoRD/. This paper provides an overview of AcCoRD's design, including the motivation for developing a specialized reaction-diffusion solver. The corresponding algorithms are presented in detail, including the computational complexity of the microscopic and mesoscopic models. Other novel derivations include the transition rates between adjacent mesoscopic subvolumes of different sizes. Simulation results demonstrate the use of AcCoRD as both an accurate reaction-diffusion solver and one that is catered to the analysis of molecular communication systems. A link is included to videos that demonstrate many of the simulated scenarios. Additional insights from the simulation results include the selection of suitable hybrid model parameters, the impact of reactive surfaces that are in the proximity of a hybrid interface, and the size of a bounded environment that is necessary to assume that it is unbounded. The development of AcCoRD is ongoing, so its future direction is also discussed in order to highlight improvements that will expand its potential areas of application. New features that are being planned at the time of writing include a fluid flow model and more complex actor behavior.

physics.chem-ph↗

arXiv2016

Convex Optimization of Distributed Cooperative Detection in Multi-Receiver Molecular Communication

In this paper, the error performance achieved by cooperative detection among K distributed receivers in a diffusion-based molecular communication (MC) system is analyzed and optimized. In this system, the receivers first make local hard decisions on the transmitted symbol and then report these decisions to a fusion center (FC). The FC combines the local hard decisions to make a global decision using an N-out-of-K fusion rule. Two reporting scenarios, namely, perfect reporting and noisy reporting, are considered. Closed-form expressions are derived for the expected global error probability of the system for both reporting scenarios. New approximated expressions are also derived for the expected error probability. Convex constraints are then found to make the approximated expressions jointly convex with respect to the decision thresholds at the receivers and the FC. Based on such constraints, suboptimal convex optimization problems are formulated and solved to determine the optimal decision thresholds which minimize the expected error probability of the system. Numerical and simulation results reveal that the system error performance is greatly improved by combining the detection information of distributed receivers. They also reveal that the solutions to the formulated suboptimal convex optimization problems achieve near-optimal global error performance.

cs.IT↗

arXiv2016

Channel Impulse Responses in Diffusive Molecular Communication with Spherical Transmitters

Molecular communication is an emerging paradigm for systems that rely on the release of molecules as information carriers. Communication via molecular diffusion is a popular strategy that is ubiquitous in nature and very fast over distances on the order of a micron or less. Existing closed-form analysis of the diffusion channel impulse response generally assumes that the transmitter is a point source. In this paper, channel impulse responses are derived for spherical transmitters with either a passive or absorbing receiver. The derived channel impulse responses are in closed-form for a one-dimensional environment and can be found via numerical integration for a three-dimensional environment. The point transmitter assumption (PTA) is formally defined so that its accuracy can be measured in comparison to the derived spherical transmitter impulse responses. The spherical transmitter model is much more accurate than the PTA when the distance between a transmitter and its receiver is small relative to the size of the transmitter. The derived results are verified via microscopic particle-based simulations using the molecular communication simulation platform AcCoRD (Actor-based Communication via Reaction-Diffusion). A spherical transmitter variation where molecules are released from the surface of a solid sphere is also considered via simulation.

cs.ET↗