Modeling of Ligand-Receptor Protein Interaction in Biodegradable Spherical Bounded Biological Micro-Environments

Al-Zu'bi, Muneer M.; Mohan, A.S.

doi:10.1109/access.2018.2829658

Cited by 32 publications

(36 citation statements)

References 40 publications

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“…In this pursuit, molecular communication via diffusion (MCvD) channels has been explored extensively in the literature [2,3]. Although analytical results are derived for some simple diffusion channels, such as a point transmitter and a spherical absorbing receiver in an unbounded environment [4] and in bounded environments [5,6], a deeper analysis including more complicated structures requires fast and reliable simulations of sophisticated diffusion channels. To meet this demand, many different simulation frameworks have been proposed in the literature, such as N3Sim [7], NanoNS [8], BiNS2 [9] and AcCoRD [10].…”

Section: Introductionmentioning

confidence: 99%

The effective geometry Monte Carlo algorithm: Applications to molecular communication

2019

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In this work, we address the systematic biases and random errors stemming from finite step sizes encountered in diffusion simulations. We introduce the Effective Geometry Monte Carlo (EG-MC) simulation algorithm which modifies the geometry of the receiver. We motivate our approach in a 1D toy model and then apply our findings to a spherical absorbing receiver in a 3D unbounded environment. We show that with minimal computational cost the impulse response of this receiver can be precisely simulated using EG-MC. Afterwards, we demonstrate the accuracy of our simulations and give tight constraints on the single free parameter in EG-MC. Finally, we comment on the range of applicability of our results. While we present the EG-MC algorithm for the specific case of molecular diffusion, we believe that analogous methods with effective geometry manipulations can be utilized to approach a variety of problems in other branches of physics such as condensed matter physics and cosmological large scale structure simulations. * The first two authors contributed equally to this work.

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Section: Introductionmentioning

confidence: 99%

The effective geometry Monte Carlo algorithm: Applications to molecular communication

2019

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“…. as a sequence of roots of (21), is equivalent to the system √ rJ v+0.5 (λ vk r) with λ vk , k = 0, 1, . .…”

Section: Appendixmentioning

confidence: 99%

“…Another useful and relevant geometry is the bounded spherical environment, as considered in [21], [22] which is inspired by some sphere-like entities in the body, e.g., stomach, lung, kidney, cells, nucleus, etc. In [21], [22], the outer boundaries are idealized as fully absorbing and fully reflective boundaries, respectively, and the receiver is assumed to be located at the center of the bounded sphere. In [21], the authors consider a DMC system in a bounded sphere whose boundary is fully absorbing and a spherical receiver is assumed to be located at the center of the sphere and its surface is covered by ligand receptors.…”

Section: Introductionmentioning

confidence: 99%

“…In [21], [22], the outer boundaries are idealized as fully absorbing and fully reflective boundaries, respectively, and the receiver is assumed to be located at the center of the bounded sphere. In [21], the authors consider a DMC system in a bounded sphere whose boundary is fully absorbing and a spherical receiver is assumed to be located at the center of the sphere and its surface is covered by ligand receptors. Therefore, the analysis proposed by these works cannot account for the diffusion asymmetry in the elevation and azimuth coordinates, which may be unavoidable depending on the locations of the transmitter and receiver.…”

Section: Introductionmentioning

confidence: 99%

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

Arjmandi

Zoofaghari

Noel

2019

IEEE Trans. Commun.

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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 (BSE) 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. Results indicate that the conventional simplifying assumption that the environment is unbounded may lead to an inaccurate characterization in such biological environments. Index TermsDiffusive molecular communication (DMC), bounded biological environment, Green's function, Error probability.

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“…Diffusion in bounded spherical environment has also been considered in some works. The authors in [17] consider a DMC system in bounded spherical environment where the transmitter is a point source, the receiver is located at the center of the sphere and covered by ligand receptors, and the sphere boundary is pure absorbing. In [18], a spherical environment with reflective boundary is considered for DMC with a spherical absorbing receiver and a point source transmitter.…”

Section: Introductionmentioning

confidence: 99%

Diffusive Molecular Communication in Biological Cylindrical Environment

Zoofaghari

Arjmandi

2019

IEEE Trans.on Nanobioscience

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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, 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.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 corresponding error probability. Index TermsDiffusive molecular communication (DMC), biological environment, partial differential equation, Green's function.

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Modeling of Ligand-Receptor Protein Interaction in Biodegradable Spherical Bounded Biological Micro-Environments

Cited by 32 publications

References 40 publications

The effective geometry Monte Carlo algorithm: Applications to molecular communication

The effective geometry Monte Carlo algorithm: Applications to molecular communication

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

Diffusive Molecular Communication in Biological Cylindrical Environment

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