Voxel-based simulation approach for molecular communications via diffusion

© . This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Molecular communications via diffusion (MCvD) systems are easily simulated for micro-scale topologies and applications. On the other hand, due to the high path loss, there is a need for the emission of a very large number of molecules to have a detectable signal for the macro-scale topologies. Therefore, the simulation of macro-scale MCvD systems or applications has its own challenges. In this work, a voxel-based simulator for MCvD is proposed and analyzed. The proposed simulator is able to consider a very large amount of molecules since it does not track every molecule, instead it simulates the aggregate behavior. We assess the correctness of such a simulation approach through comparative studies with a particle-based (i.e., per-molecule) simulation. We present the effect of voxel side-length on the modeling accuracy and devise a framework for selecting the optimal voxel side-length for high-accuracy simulations.Peer ReviewedPreprin

ISI-aware channel code design for molecular communication via diffusion

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.In molecular communication via diffusion, information molecules diffusing in the environment are subject to Brownian motion. Due to probabilistic propagation, the arrival of the molecules at the receiver is spread in time, leading to the reception of some molecules belonging to the previous symbol(s) during the upcoming symbol duration. Known as inter-symbol interference (ISI), this problem has been extensively studied in the literature by applying a large spectrum of techniques, mostly inspired by approaches in the wireless communication domain, including channel coding techniques. Unfortunately, many known channel codes do not perform well in the molecular communications domain since the diffusion channel features a significant memory component. In this paper, novel methods for channel coding by incorporating the effect of ISI in the design of the channel codes for the molecular diffusion channel are proposed. The results show that the proposed methods provide significant improvements in performance in terms of the codeword error rate.Postprint (author's final draft

Effect of receiver shape and volume on the Alzheimer disease for molecular communication via diffusion

The work of I. Isik and M. E. Tagluk was supported by the Inonu University Project of Scientific Research Unit (BAP) under the project number FBA-2018-1013. The authors thank HP Turkey section for providing a powerful computer for computational tasks in this study. The work of H.B. Yilmaz is supported by the Scientific and Technical Research Council of Turkey (TUBITAK) under grant no. 118C274. The work of I. Demirkol was supported by the Spanish Government, MINECO, through project RYC-2013-13029Peer ReviewedPostprint (published version

Transmitter localization in vessel-like diffusive channels using ring-shaped molecular receivers

© 2018 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Molecular communication via diffusion in vessellike environment targets critical applications such as detection of abnormal and unhealthy cells. In this work, we derive the analytical formulation of the channel model for diffusion dominated movement, considering ring-shaped (i.e., patch) observing receivers and Poiseuille flow with the aim of localization of the transmitter cell. Then, we derive formulations using this channel model for two different application scenarios. We assume that the emission start time is known in the first scenario, and unknown in the second one. We successfully localize the transmitter cell using a single receiver for the first scenario, whereas two receivers are used to localize the transmitter cell in the second scenario. Lastly, the devised analytical framework is validated with simulations.Postprint (author's final draft

Performance analysis of power adjustment methods in molecular communication via diffusion [Difuzyon ile moleküler iletisimdeki guç ayarlama metodlarinin performans analizi]

In this paper, performance of binary concentration shift keying (BCSK), BCSK with power adjustment (BCSK-PA), and BCSK with consecutive power adjustment (BCSK-CPA) are analyzed in terms of bit error rate (BER), energy, and memory within the context of molecular communication via diffusion. As the communication environment, vessel-like environment is realized. The results show that BCSK-PA outperforms BCSK and BCSK-CPA in BER and energy analysis. Yet, it is outperformed by BCSK and BCSK-CPA in memory requirements. BCSK-CPA performs between BCSK and BCSK-PA in all three analysis that shows BCSK-CPA is a nice option to have comparatively low BER and energy usage when the system has low memory requirement. © 2018 IEEE.Postprint (author's final draft

Performance analysis of power adjustment methods in molecular communication via diffusion [Difuzyon ile moleküler iletisimdeki guç ayarlama metodlarinin performans analizi]

In this paper, performance of binary concentration shift keying (BCSK), BCSK with power adjustment (BCSK-PA), and BCSK with consecutive power adjustment (BCSK-CPA) are analyzed in terms of bit error rate (BER), energy, and memory within the context of molecular communication via diffusion. As the communication environment, vessel-like environment is realized. The results show that BCSK-PA outperforms BCSK and BCSK-CPA in BER and energy analysis. Yet, it is outperformed by BCSK and BCSK-CPA in memory requirements. BCSK-CPA performs between BCSK and BCSK-PA in all three analysis that shows BCSK-CPA is a nice option to have comparatively low BER and energy usage when the system has low memory requirement. © 2018 IEEE

Two way molecular communications

For nano-scale communications, there must be cooperation and simultaneous communication between nano devices. To this end, we investigate two way (a.k.a. bi-directional) molecular communications between nano devises. By using a different type of molecules for the communication link, the proposed system eliminates the need to consider self-interference (SI). Using a different type of molecule for each communication link, however, is infeasible given the number of nano devices involved in such applications. Thus, we propose a two way molecular communication system using a single type of molecules. We analyze the proposed system's bit error rate (BER), throughput, channel models, and SI. Moreover, we propose analog- and digital- self-interference cancellation (SIC) techniques. Numerical and analytical results confirm the enhancement of linklevel performances.Postprint (published version

ISI-aware channel code design for molecular communication via diffusion

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.In molecular communication via diffusion, information molecules diffusing in the environment are subject to Brownian motion. Due to probabilistic propagation, the arrival of the molecules at the receiver is spread in time, leading to the reception of some molecules belonging to the previous symbol(s) during the upcoming symbol duration. Known as inter-symbol interference (ISI), this problem has been extensively studied in the literature by applying a large spectrum of techniques, mostly inspired by approaches in the wireless communication domain, including channel coding techniques. Unfortunately, many known channel codes do not perform well in the molecular communications domain since the diffusion channel features a significant memory component. In this paper, novel methods for channel coding by incorporating the effect of ISI in the design of the channel codes for the molecular diffusion channel are proposed. The results show that the proposed methods provide significant improvements in performance in terms of the codeword error rate

A survey on modulation techniques in molecular communication via diffusion

© 2021 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.This survey paper focuses on modulation aspects of molecular communication, an emerging field focused on building biologically-inspired systems that embed data within chemical signals. The primary challenges in designing these systems are how to encode and modulate information onto chemical signals, and how to design a receiver that can detect and decode the information from the corrupted chemical signal observed at the destination. In this article, we focus on modulation design for molecular communication via diffusion systems. In these systems, chemical signals are transported using diffusion, possibly assisted by flow, from the transmitter to the receiver. This tutorial presents recent advancements in modulation and demodulation schemes for molecular communication via diffusion. We compare five different modulation types: concentration-based, type-based, timing-based, spatial, and higher-order modulation techniques. The end-to-end system designs for each modulation scheme are presented. In addition, the key metrics used in the literature to evaluate the performance of these techniques are also presented. Finally, we provide a numerical bit error rate comparison of prominent modulation techniques using analytical models. We close the tutorial with a discussion of key open issues and future research directions for design of molecular communication via diffusion systems.This research is supported in part by the Scientific and Technical Research Council of Turkey (TUBITAK) under BIDEB-2232 program with the grant number 118C274, NSERC Discovery under Grant RGPIN-2020-04926, the NSF Center for Science of Information (CSoI) under grant CCF-0939370, and CFI John Evans Leaders Funds.Peer ReviewedPostprint (author's final draft

Channel model of molecular communication via diffusion in a vessel-like environment Considering a Partially Covering Receiver

By considering potential health problems that a fully covering receiver may cause in vessel-like environments, the implementation of a partially covering receiver is needed. To this end, distribution of hitting location of messenger molecules (MM) is analyzed within the context of molecular communication via diffusion with the aim of channel modeling. The distribution of these MMs for a fully covering receiver is analyzed in two parts: angular and radial dimensions. For the angular distribution analysis, the receiver is divided into 180 slices to analyze the mean, standard deviation, and coefficient of variation of these slices. For the axial distance distribution analysis, Kolmogorov-Smirnov test is applied for different significance levels. Also, two different implementations of the reflection from the vessel surface (i.e., rollback and elastic reflection) are compared and mathematical representation of elastic reflection is given. The results show that MMs have tendency to spread uniformly beyond a certain ratio of the distance to the vessel radius. By utilizing the uniformity, we propose a channel model for the partially covering receiver in vessel-like environments and validate the proposed model by simulations.Postprint (published version