Modeling, Methodologies and Tools for Molecular and Nano-scale Communications: Modeling, Methodologies and Tools PDF
Preview Modeling, Methodologies and Tools for Molecular and Nano-scale Communications: Modeling, Methodologies and Tools
Modeling and Optimization in Science and Technologies Junichi Suzuki Tadashi Nakano Michael John Moore Editors Modeling, Methodologies and Tools for Molecular and Nano-scale Communications Modeling, Methodologies and Tools Modeling and Optimization in Science and Technologies Volume 9 Series editors Srikanta Patnaik, SOA University, Bhubaneswar, India e-mail: [email protected] Ishwar K. Sethi, Oakland University, Rochester, USA e-mail: [email protected] Xiaolong Li, Indiana State University, Terre Haute, USA e-mail: [email protected] Editorial Board Li Cheng, The Hong Kong Polytechnic University, Hong Kong Jeng-Haur Horng, National Formosa University, Yulin, Taiwan Pedro U. Lima, Institute for Systems and Robotics, Lisbon, Portugal Mun-Kew Leong, Institute of Systems Science, National University of Singapore Muhammad Nur, Diponegoro University, Semarang, Indonesia Luca Oneto, University of Genoa, Italy Kay Chen Tan, National University of Singapore, Singapore Sarma Yadavalli, University of Pretoria, South Africa Yeon-Mo Yang, Kumoh National Institute of Technology, Gumi, South Korea Liangchi Zhang, The University of New South Wales, Australia Baojiang Zhong, Soochow University, Suzhou, China Ahmed Zobaa, Brunel University, Uxbridge, Middlesex, UK About this Series The book series Modeling and Optimization in Science and Technologies (MOST) publishesbasicprinciplesaswellasnoveltheoriesandmethodsinthefast-evolving fieldofmodelingandoptimization.Topicsofinterestinclude,butarenotlimitedto: methods for analysis, design and control of complex systems, networks and machines; methods for analysis, visualization and management of large data sets; use of supercomputers for modeling complex systems; digital signal processing; molecular modeling; and tools and software solutions for different scientific and technological purposes.Special emphasis isgiven to publicationsdiscussing novel theories and practical solutions that, by overcoming the limitations of traditional methods, may successfully address modern scientific challenges, thus promoting scientificandtechnologicalprogress.Theseriespublishesmonographs,contributed volumes and conference proceedings, as well as advanced textbooks. The main targetsoftheseriesaregraduatestudents,researchersandprofessionalsworkingat the forefront of their fields. More information about this series at http://www.springer.com/series/10577 ⋅ Junichi Suzuki Tadashi Nakano Michael John Moore Editors Modeling, Methodologies and Tools for Molecular and Nano-scale Communications Modeling, Methodologies and Tools 123 Editors JunichiSuzuki Michael John Moore Department ofComputer Science PennsylvaniaState University University of Massachusetts State College, PA Boston, MA USA USA Tadashi Nakano Graduate Schoolof Biological Sciences Osaka University Osaka Japan ISSN 2196-7326 ISSN 2196-7334 (electronic) Modeling andOptimization inScience andTechnologies ISBN978-3-319-50686-9 ISBN978-3-319-50688-3 (eBook) DOI10.1007/978-3-319-50688-3 LibraryofCongressControlNumber:2016959967 ©SpringerInternationalPublishingAG2017 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission orinformationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfrom therelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authorsortheeditorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinor foranyerrorsoromissionsthatmayhavebeenmade. Printedonacid-freepaper ThisSpringerimprintispublishedbySpringerNature TheregisteredcompanyisSpringerInternationalPublishingAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface Nanoscalecommunicationhasemergedasanewresearchtopicincommunications engineering. The term “nano” typically refers to the dimensions from a nanometer to hundred nanometers, and nanoscale communication is loosely defined as com- municationthatmayoccur inthatrange. Communicationengineers havestartedto investigate two distinct forms of nanoscale communication: molecular communi- cation and electromagnetic-based nanoscale communication. In molecular com- munication, chemical signals are used for communication among nano- or microscaledevices,while inEM-basednanoscalecommunication,electromagnetic waves are used. As nanoscale communication further develops, it may enable new applications in medicine, environment, and industry. It may also enable the inte- gration of nano- or microscale devices into currently available communication networks to form future communication networks. The research area of nanoscale communication is rapidly growing as evidenced by an increasing number of papers that have been published in recent years. In editing this book, our goal was to collect, from leading experts of nanoscale communication, comprehensive summary articles with recent research results on nanoscale communication. Toward this goal, this book consists of 24 articles col- lectively covering (cid:129) Fundamentals of Molecular Communication (Chapters “Concentration- Encoded Molecular Communication in Nanonetworks. Part 1: Fundamentals, Issues, and Challenges”–“An Architecture of Calcium Signaling for Molecular Communication Based Nano Network”), in which signal processing, commu- nication theory, architectures, and protocols for molecular communication are presented, (cid:129) Molecular Communication in Biology (Chapters “On Regulation of Neuro- spikeCommunicationforHealthyBrain”–“QuantifyingRobustnessinBiological NetworksUsingNS-2”),inwhichsignalpropagationinthebrain,inter-molecule interactions,generegulatorynetworks,andcellcommunicationarestudied, v vi Preface (cid:129) Electromagnetic–Based Nano-scale Communication (Chapters “Fundamentals of Graphene-Enabled Wireless On-Chip Networking”– NanoscaleCommunicationsBasedonFluorescenceResonanceEnergyTransfer (FRET)”), in which system design and methods of electromagnetic-based nanoscale communication are presented, (cid:129) NanomaterialandNanostructure(Chapters“Ultrasonics—AnEffectiveNon- invasiveTooltoCharacterizeNanofluids”–“ReliableDesignforCrossbarNano- architectures”), in which nanotechnology for applied purposes such as security and computing is discussed, (cid:129) Medical Applications of Nanoscale Communication (Chapters “Effect of Aging, Disease Versus Health Conditions in the Design of Nano- communications in Blood Vessels”–“Computational Biosensors: Molecules, Algorithms, and Detection Platforms”), in which disease diagnosis, drug delivery, and biomolecular sensing are presented. Webelievethisbookservesasapointofreferencesforstudentsandresearchers who are interested in this emerging area of nanoscale communication as well as those who are working in the area. Finally, we thank all chapters’ authors and reviewers who made this book possible. Boston, MA, USA Junichi Suzuki Osaka, Japan Tadashi Nakano State College, PA, USA Michael John Moore Contents Part I Fundamentals of Molecular Communication Concentration-Encoded Molecular Communication in Nanonetworks. Part 1: Fundamentals, Issues, and Challenges .... .... .... ..... .... 3 Mohammad Upal Mahfuz, Dimitrios Makrakis and Hussein T. Mouftah Concentration-Encoded Molecular Communication in Nanonetworks. Part 2: Performance Evaluation ... .... .... .... .... .... ..... .... 35 Mohammad Upal Mahfuz, Dimitrios Makrakis and Hussein T. Mouftah Physical Channel Model for Molecular Communications.... ..... .... 57 Humaun Kabir and Kyung Sup Kwak Modulation in Molecular Communications: A Look on Methodologies .. .... .... ..... .... .... .... .... .... ..... .... 79 Ecehan Berk Pehlivanoglu, Bige Deniz Unluturk and Ozgur Baris Akan Modulation Techniques for Molecular Communication via Diffusion..... . 99 H. Birkan Yilmaz, Na-Rae Kim and Chan-Byoung Chae The Use of Coding and Protocols Within Molecular Communication Systems .. .... .... .... .... ..... .... .... .... .... .... ..... .... 119 MarkS.Leeson,MatthewD.Higgins,ChenyaoBai,YiLu,XiayangWang and Ruixiao Yu Understanding Communication via Diffusion: Simulation Design and Intricacies .... .... .... .... ..... .... .... .... .... .... ..... .... 139 Bilal Acar, Ali Akkaya, Gaye Genc, H. Birkan Yilmaz, M. Şükrü Kuran and Tuna Tugcu An Architecture of Calcium Signaling for Molecular Communication Based Nano Network ... .... ..... .... .... .... .... .... ..... .... 165 Amitava Mukherjee, Sushovan Das and Soumallya Chatterjee vii viii Contents Part II Molecular Communication in Biology On Regulation of Neuro-spike Communication for Healthy Brain . .... 207 Mladen Veletić, Pål Anders Floor, Rié Komuro and Ilangko Balasingham Molecular Dynamics Simulations of Biocorona Formation .. ..... .... 241 Rongzhong Li, Cody A. Stevens and Samuel S. Cho Modeling Cell Communication by Communication Engineering... .... 257 Jian-Qin Liu and Wuyi Yue Quantifying Robustness in Biological Networks Using NS-2 . ..... .... 273 Bhanu K. Kamapantula, Ahmed F. Abdelzaher, Michael Mayo, Edward J. Perkins, Sajal K. Das and Preetam Ghosh Part III Electromagnetic-Based Nano-scale Communication Fundamentals of Graphene-Enabled Wireless On-Chip Networking....... 293 Sergi Abadal, Ignacio Llatser, Albert Mestres, Josep Solé-Pareta, Eduard Alarcón and Albert Cabellos-Aparicio Energy Harvesting in Nanonetworks.... .... .... .... .... ..... .... 319 Shahram Mohrehkesh, Michele C. Weigle and Sajal K. Das NanoscaleCommunicationsBasedonFluorescenceResonanceEnergy Transfer (FRET)... .... .... ..... .... .... .... .... .... ..... .... 349 Murat Kuscu and Ozgur B. Akan Part IV Nanomaterial and Nanostructure Ultrasonics—An Effective Non-invasive Tool to Characterize Nanofluids .... .... .... .... ..... .... .... .... .... .... ..... .... 379 M. Nabeel Rashin and J. Hemalatha RF Nanostructured Security.. ..... .... .... .... .... .... ..... .... 401 Mohamed Kheir, Heinz Kreft, Iris Hölken and Reinhard Knöchel Reliable Design for Crossbar Nano-architectures.. .... .... ..... .... 421 Masoud Zamani and Mehdi B. Tahoori Part V Medical Applications of Nanoscale Communication Effect of Aging, Disease Versus Health Conditions in the Design of Nano-communications in Blood Vessels ... .... .... .... ..... .... 447 Luca Felicetti, Mauro Femminella, Pietro Liò and Gianluca Reali Electromagnetic Nanonetworks for Sensing and Drug Delivery ... .... 473 Renato Iovine, Valeria Loscrì, Sara Pizzi, Richard Tarparelli and Anna Maria Vegni Contents ix CommunicationofDrugLoadedNanogelswithCancerCellReceptors for Targeted Delivery... .... ..... .... .... .... .... .... ..... .... 503 Govind Soni and Khushwant S. Yadav Modeling, Analysis and Design of Bio-hybrid Micro-robotic Swarms for Medical Applications .... ..... .... .... .... .... .... ..... .... 517 Guopeng Wei, Paul Bogdan and Radu Marculescu Computational Biosensors: Molecules, Algorithms, and Detection Platforms. .... .... .... .... ..... .... .... .... .... .... ..... .... 541 Elebeoba E. May, Jason C. Harper and Susan M. Brozik Digital Body... .... .... .... ..... .... .... .... .... .... ..... .... 579 Aftab Ahmad
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