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                              NOISE in MOLECULAR COMMUNICATIONS

Even today a good many distinguished minds seem unable to accept or even to understand that from

a source of noise natural selection could quite unaided have drawn all the music of the biosphere

(Jacques Monod)

  1. Movahednasab M., Soleimanifar M., Gohari A., et al.: Adaptive Transmission Rate With a Fixed Threshold Decoder for Diffusion-Based Molecular Communication. IEEE Trans on Communications, Vol. 64, no. 1, 2016, pp. 236 – 248. DOI 10.1109/TCOMM.2015.2501823

  2. Tiwari S.K., Upadhyay P.K.: Maximum Likelihood Estimation of SNR for Diffusion-Based Molecular Communication. IEEE Wireless Communications Lett., Vol. 5, no. 3, 2016, pp. 320 – 323. DOI 10.1109/LWC.2016.2553034

  3. Damrath M., Hoeher P.A.: Low-Complexity Adaptive Threshold Detection for Molecular Communication. IEEE Trans on NanoBioscience, Vol. 15, no. 3, 2016, pp. 200 – 208. DOI 10.1109/TNB.2016.2520566

  4. Li Bin, Sun Mengwei, Wang Siyi, et al.: Low-Complexity Noncoherent Signal Detection for Nanoscale Molecular Communications. IEEE Trans on NanoBioscience, Vol. 15, no. 1, 2016, pp. 3 – 10. DOI 10.1109/TNB.2015.2504542

  5. Abd El-atty, Saied M., Gharsseldien Z.M.: Influence of inter-nanoparticle interaction on nanonetworks-based molecular communications. Optik, Vol. 127, no. 5, 2016, pp. 2959 – 2968. DOI 10.1016/j.ijleo.2015.10.067

  6. Wang Xiayang, Higgins M.D., Leeson M.S.: Relay Analysis in Molecular Communications With Time-Dependent Concentration. IEEE Communications Lett., Vol. 19, no. 11, 2015, pp. 1977 – 1980. DOI 10.1109/LCOMM.2015.2478780

  7. Wang Xiayang, Higgins M.D., Leeson M.S.: Distance Estimation Schemes for Diffusion Based Molecular Communication Systems. IEEE Communications Lett., Vol. 19, no. 3, 2015, pp. 399 – 402. DOI 10.1109/LCOMM.2014.2387826

  8. Maham Behrouz: A Communication Theoretic Analysis of Synaptic Channels Under Axonal Noise. IEEE Communications Lett., Vol. 19, no. 11, 2015, pp. 1901 – 1904. DOI 10.1109/LCOMM.2015.2478006

  9. Qiu Song, Wang Siyi, Guo Weisi: Experimental Nakagami distributed noise model for molecular communication channels with no drift. Electronics Lett., Vol. 51, no. 8, 2015, pp. 612 – 613. DOI 10.1049/el.2014.4460

  10. Bicen A.O., Austin C.M., Akyildiz I.F., et al.: Efficient Sampling of Bacterial Signal Transduction for Detection of Pulse-Amplitude Modulated Molecular Signals. IEEE Trans. on Biomedical Circuits and Systems, Vol. 9, no. 4, 2015, pp. 505 – 517. DOI 10.1109/TBCAS.2015.2465182

  11. Unluturk B.D., Bicen A.O., Akyildiz I.F.: Genetically Engineered Bacteria-Based BioTransceivers for Molecular Communication. IEEE Trans on Communications, Vol. 63, no. 4, 2015, pp. 1271 – 1281. DOI 10.1109/TCOMM.2015.2398857

  12. Bicen A.O., Akyildiz I.F.: Interference Modeling and Capacity Analysis for Microfluidic Molecular Communication Channels. IEEE Trans on Nanotechnology, Vol. 14, no. 3, 2015, pp. 570 – 579. DOI 10.1109/TNANO.2015.2418175

  13. Farsad N., Eckford A.W., Hiyama Satoshi: Design and Optimizing of On-Chip Kinesin Substrates for Molecular Communication. IEEE Trans on Nanotechnology, Vol. 14, no. 4, 2015, pp. 699 – 708. DOI 10.1109/TNANO.2015.2431995

  14. Chou Chun Tung: Impact of Receiver Reaction Mechanisms on the Performance of Molecular Communication Networks. IEEE Trans on Nanotechnology, Vol. 14, no. 2, 2015, pp. 304 – 317. DOI 10.1109/TNANO.2015.2393866

  15. Jiang Chunxiao, Chen Yan, Liu K., Ray J.: Nanoscale molecular communication networks: a game-theoretic perspective. EURASIP Journal on Advances in Signal Processing, 2015, Article # 5. DOI 10.1186/s13634-014-0188-4

  16. Shashkova S., Welkenhuysen N., Hohmann S.: Molecular communication: crosstalk between the Snf1 and other signaling pathways. FEMS Yeast Research, Vol. 15, no. 4, 2015, Article # fov026. DOI 10.1093/femsyr/fov026

  17. Mahfuz M.U., Makrakis D., Mouftah H.T.: A Comprehensive Analysis of Strength-Based Optimum Signal Detection in Concentration-Encoded Molecular Communication With Spike Transmission. IEEE Trans on NanoBioscience, Vol. 14, no. 1, 2015, pp. 67 – 83. DOI 10.1109/TNB.2014.2368593

  18. Aijaz A., Aghvami A.-H.: Error Performance of Diffusion-Based Molecular Communication Using Pulse-Based Modulation. IEEE Trans on NanoBioscience, Vol. 14, no. 1, 2015, pp. 146 – 151. DOI 10.1109/TNB.2014.2364182

  19. Lin Lin, Chengfeng Yang, Maode Ma, Shiwei Ma: Diffusion-Based Clock Synchronization for Molecular Communication Under Inverse Gaussian Distribution. IEEE Sensors Journal, Vol. 15, no. 9, 2015, pp. 4866 – 4874. DOI 10.1109/JSEN.2015.2429673

  20. Yilmaz H.B., Chan-Byoung Chae, Tepekule Burcu, Pusane Ali E.: Arrival modelling for molecular communication via diffusion. Electronics Lett., Vol. 50, no. 23, 2014, pp. 1667 – 1669. DOI 10.1049/el.2014.2943

  21. Kabir M.H., Kwak K.S.: Effect of memory on BER in molecular communication. Electronics Lett., Vol. 50, no. 2, 2014, pp. 71 – 72. DOI 10.1049/el.2013.2757

  22. Bicen A.O., Akyildiz I.F.: End-to-End Propagation Noise and Memory Analysis for Molecular Communication over Microfluidic Channels. IEEE Trans on Communications, Vol. 62, no. 7, 2014, pp. 2432 – 2443. DOI 10.1109/TCOMM.2014.2323293

  23. Mahfuz M.U., Makrakis D., Mouftah H.T.: A Comprehensive Study of Sampling-Based Optimum Signal Detection in Concentration-Encoded Molecular Communication. IEEE Trans on NanoBioscience, Vol. 13, no. 3, 2014, pp. 208 – 222. DOI 10.1109/TNB.2014.2341693

  24. Noel A., Cheung K.C., Schober R.: Optimal Receiver Design for Diffusive Molecular Communication With Flow and Additive Noise. IEEE Trans on NanoBioscience, Vol. 13, no. 3, 2014, pp. 350 – 362. DOI 10.1109/TNB.2014.2337239

  25. Hui Li, Moser S.M., Dongning Guo: Capacity of the Memoryless Additive Inverse Gaussian Noise Channel. IEEE Journal on Selected Areas in Communications, Vol. 32, no. 12, 2014, pp. 2315 – 2329. DOI 10.1109/JSAC.2014.2367673

  26. Guopeng Wei, Marculescu R.: Miniature Devices in the Wild: Modeling Molecular Communication in Complex Extracellular Spaces. IEEE Journal on Selected Areas in Communications, Vol. 32, no. 12, 2014, pp. 2344 – 2353. DOI 10.1109/JSAC.2014.2367711

  27. Felicetti L., Femminella M., Reali G., Nakano T., Vasilakos A.V.: TCP-Like Molecular Communications. IEEE Journal on Selected Areas in Communications, Vol. 32, no. 12, 2014, pp. 2354 – 2367. DOI 10.1109/JSAC.2014.2367653

  28. Mosayebi R., Arjmandi H., Gohari A., Nasiri-Kenari M., Mitra U.: Receivers for Diffusion-Based Molecular Communication: Exploiting Memory and Sampling Rate. IEEE Journal on Selected Areas in Communications, Vol. 32, no. 12, 2014, pp. 2368 – 2380. DOI 10.1109/JSAC.2014.2367732

  29. Chieh Lo, Yao-Jen Liang, Kwang-Cheng Chen: A Phase Locked Loop for Molecular Communications and Computations. IEEE Journal on Selected Areas in Communications, Vol. 32, no. 12, 2014, pp. 2381 – 2391. DOI 10.1109/JSAC.2014.2367661

  30. A.C. Heren, F.N. Kilicli, G. Genc, T. Tugcu: Effect of Messenger Molecule Decomposition in Communication via Diffusion. ACM Int. Conf. on Nanoscale Computing & Communication (ACM NANOCOM), 2014, Aricle # 12. DOI 10.1145/2619955.2619969

  31. Voliotis M., Perrett R.M., McWilliams C., McArdle C.A., Bowsher C.G: Information transfer by leaky, heterogeneous, protein kinase signaling systems. Proc. of the National Acad. of Sciences of the United States of America, Vol. 111, no. 3, 2014, pp. E326 – E333. DOI 10.1073/pnas.1314446111

  32. Pierobon M., Akyildiz I.F.: A Statistical–Physical Model of Interference in Diffusion-Based Molecular Nanonetworks. IEEE Trans on Communications, Vol. 62, no. 6, 2014, pp. 2085 – 2095. DOI 10.1109/TCOMM.2014.2314650

  33. A. Noel, K.C. Cheung, R. Schober: Improving Receiver Performance of Diffusive Molecular Communication With Enzymes. IEEE Trans on NanoBioscience, Vol. 13, no. 1, 2014, pp. 1536 – 1541. DOI 10.1109/TNB.2013.2295546

  34. A. Noel, K.C. Cheung, R. Schober: A Unifying Model for External Noise Sources and ISI in Diffusive Molecular Communication. arXiv:1310.5930, 2014.

  35. Su Yinghan, Li Xiaoya, Ji Weidan, Sun Bin, Xu Can, Li Zhaoshen, Qian Guojun, Su Changqing: Small molecule with big role: MicroRNAs in cancer metastatic microenvironments. Cancer Lett., Vol. 344, no. 2, 2014, pp. 147 – 156. DOI 10.1016/j.canlet.2013.10.024

  36. Akkaya A., Genc G., Tugcu T.: HLA based architecture for molecular communication simulation. Simulation Modelling Practice and Theory, Vol. 42, Special no. SI, 2014, pp. 163 – 177. DOI 10.1016/j.simpat.2013.12.012

  37. Wang Xiayang, Higgins M.D., Leeson M.S.: Simulating the performance of SW-ARQ schemes within molecular communications. Simulation Modelling Practice and Theory, Vol. 42, Special no. SI, 2014, pp. 178 – 188. DOI 10.1016/j.simpat.2013.12.006

  38. Mahfuz M.U., Makrakis D., Mouftah H.T.: Strength-based optimum signal detection in concentration-encoded pulse-transmitted OOK molecular communication with stochastic ligand-receptor binding. Simulation Modelling Practice and Theory, Vol. 42, Special no. SI, 2014, pp. 189 – 209. DOI 10.1016/j.simpat.2013.11.005

  39. Llatser I., Demiray D., Cabellos-Aparicio A., Altilar D.T., Alarcon E.: N3Sim: Simulation framework for diffusion-based molecular communication nanonetworks. Simulation Modelling Practice and Theory, Vol. 42, Special no. SI, 2014, pp. 210 – 222. DOI 10.1016/j.simpat.2013.11.004

  40. Ciulla M.M., De Marco F., Montelatici E., Lazzari L., Perrucci G.L , Magrini F.: Assessing cytokines' talking patterns following experimental myocardial damage by applying Shannon's information theory. Journal of Theoretical Biology, Vol. 343, 2014, pp. 25 – 31. DOI 10.1016/j.jtbi.2013.10.019

  41. Das M., Ithychanda S.S., Qin Jun, Plow E.F.: Mechanisms of talin-dependent integrin signaling and crosstalk. Biochimica & Biophysica Acta-Biomembranes, Vol. 1838, no. 2, Special no. SI, 2014, pp. 579 – 588. DOI 10.1016/j.bbamem.2013.07.017

  42. Kleppe Rune, Ghorbani S., Martinez A., Haavik J.: Modelling cellular signal communication mediated by phosphorylation dependent interaction with 14-3-3 proteins. FEBS Lett., Vol. 588, no. 1, 2014, pp. 92 – 98. DOI 10.1016/j.febslet.2013.11.012

  43. N. Farsad, N.-R. Kim, A.W. Eckford, C.-B. Chae: Channel and noise models for nonlinear molecular communication systems. arXiv:1311.6208, 2013.

  44. A.C. Heren, M.S. Kuran, H.B. Yilmaz, T. Tugcu: Channel capacity of calcium signalling based on inter-cellular calcium waves in astrocytes. IEEE Int. Conf. on Communications (ICC), 2013, pp.792 – 797. DOI 10.1109/ICCW.2013.6649341

  45. M.S. Kuran, H.B. Yilmaz, T. Tugcu: A Tunnel-based Approach for Signal Shaping in Molecular Communication. IEEE Int. Workshop on Molecular and Nano-scale Communications (MONACOM), 2013. DOI 10.1109/ICCW.2013.6649338

  46. M. Pierobon, I.F. Akyildiz: Capacity of a diffusion-based molecular communication system with channel memory and molecular noise. IEEE Trans on. Information Theory, Vol. 59, no. 2, 2013, pp. 942 – 954. DOI 10.1109/TIT.2012.2219496

  47. C.T. Chou: Noise Properties of Linear Molecular Communication Networks. Nano Communication Networks, Vol. 4, no. 3, 2013, pp. 87 – 97. ArXiv: 1312.1375v1

  48. A. Noel, K.C. Cheung, R. Schober: Optimal Receiver Design for Diffusive Molecular Communication with Flow and Additive Noise. ArXiv: 1308.0109v2, 2013.

  49. Iakhiaev M.A., Iakhiaev A.V.: Mapping the intramolecular signal propagation pathways in protein using Bayesian change point analysis of atomic motions. Computational Biology and Chemistry, Vol. 47, 2013, pp. 89 – 95. DOI 10.1016/j.compbiolchem.2013.08.004

  50. Chun Tung Chou: Extended Master Equation Models for Molecular Communication Networks. IEEE Trans on NanoBioscience, Vol.12, no. 2, 2013, pp 79 – 92. DOI 10.1109/TNB.2013.2237785

  51. G. Genc, H.B. Yilmaz, T. Tugcu: Reception enhancement with protrusions in
    communication via diffusion.
    First Int. Black Sea Conf. on Communications & Networking (BlackSeaCom), 2013, pp. 89 – 93. DOI 10.1109/BlackSeaCom.2013.6623387

  52. Kadloor S., Adve R.S., Eckford A.W.: Molecular Communication Using Brownian Motion With Drift. IEEE Trans on NanoBioscience, Vol. 11, no. 2, 2012, pp 89 – 99. DOI 10.1109/TNB.2012.2190546

  53. K. Srinivas, A.W. Eckford, R.S. Adve: Molecular communication in fluid media: The additive inverse gaussian noise channel. IEEE Trans on Information Theory, Vol. 58, no. 7, 2012, pp. 4678 – 4692. DOI 10.1109/TIT.2012.2193554

  54. M.S. Kuran, H.B. Yilmaz, T. Tugcu, I.F. Akyildiz: Interference Effects on Modulation Techniques in Diffusion Based Nanonetworks. Elsevier Nano Communication Networks, Vol. 3, no. 1, 2012, pp. 65 – 73.

  55. H. ShahMohammadian, G.G. Messier, S. Magierowski: Optimum receiver for molecule shift keying modulation in diffusion-based molecular communication channels. Nano Communication Networks, Vol. 3, no. 3, 2012, pp. 183 – 195. DOI 10.1016/j.nancom.2012.09.006

  56. Malak D., Akan O.B.: Molecular communication nanonetworks inside human body. Nano Communication Networks, Vol. 3, 2012, pp. 19 – 35. DOI 10.1016/j.nancom.2011.10.002

  57. Eckford A.W., Srinivas K.V., Adve R.S.: The peak constrained additive inverse Gaussian noise channel. Proc of IEEE Int Symp on Information Theory, 2012, pp 2973 – 2977. DOI 10.1109/ISIT.2012.6284105

  58. P. Rué, N. Domedel-Puig, J. Garcia-Ojalvo, A.J. Pons: Integration of cellular signals in chattering environments. Progress in Biophysics and Molecular Biology, Vol. 110, no. 1, 2012, pp. 106 – 112. DOI 10.1016/j.pbiomolbio.2012.05.003

  59. M.U. Mahfuz, D. Makrakis, H. Mouftah: Characterization of Intersymbol Interference in Concentration-Encoded Unicast Molecular Communication. Proc. 24th IEEE Canadian Conf. on Electrical and Computer Eng. (IEEE CCECE-2011), Niagara Falls, ON, 2011, pp. 164 – 168. DOI 10.1109/CCECE.2011.6030431

  60. Pierobon M., Akyildiz I.F.: Noise Analysis in Ligand-Binding Reception for Molecular Communication in Nanonetworks. IEEE Trans. on Signal Processing, Vol. 59, no. 9, 2011, pp. 4168 – 4182. DOI 10.1109/TSP.2011.2159497

  61. M.S. Kuran, T. Tugcu: Co-channel Interference for Communication via Diffusion System in Molecular Communication. Int. ICST Conf. on Bio-Inspired Models of Network, Information, and Computing Systems (BIONETICS), 2011, pp. 199 – 212. DOI 10.1007/978-3-642-32711-7_19

  62. Miorandi D.: A stochastic model for molecular communications. Nano Communication Networks, Vol. 2, no. 4, 2011, pp. 205 – 212. DOI 10.1016/j.nancom.2011.04.005

  63. M. Pierobon, I.F. Akyildiz : Diffusion-based noise analysis for molecular communication in nanonetworks. IEEE Trans. Signal Process., Vol. 59, no. 6, 2011,  pp. 2532 – 2547. DOI 10.1109/TSP.2011.2114656

  64. M. Pierobon, I.F. Akyildiz: A physical end-to-end model for molecular communication in nanonetworks. IEEE Journal on Selected Areas in Communications, Vol. 28, no. 4, 2010, pp. 602 – 611. DOI 10.1109/JSAC.2010.100509

  65. M. J. Moore, T. Suda, K. Oiwa : Molecular communication: Modeling noise effects on information rate. IEEE Trans. Nanobiosci., Vol. 8, no. 2, 2009, pp. 169 – 180. DOI 10.1109/TNB.2009.2025039

  66. Hornung G., Barkai N.: Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback. PLoS Computational Biology, Vol. 4, no 1, 2008, DOI 10.1371/journal.pcbi.0040008

  67. J. Rung: Signals and Noise in Complex Biological Systems. PhD dissertation, Uppsala University, 2007, ISBN 978-91-554-6888-0

  68. T. Zhou, L. Chen, K. Aihara: Molecular communication through stochastic synchronization induced by extracellular fluctuations. Phys. Rev. Lett., Vol. 95, 21 October 2005, pp 1783103 1 – 9. DOI 10.1103/PhysRevLett.95.178103 http://www.bio.davidson.edu/courses/genomics/2009/Ho_Shing/Articles/Zhou_2005.pdf

  69. M. Kollmann, L. Løvdok, K. Bartholomé, J. Timmer, V. Sourjik: Design principles of a bacterial signalling network. Nature, Vol 438, Letters to Editor, 2005, pp 504 – 507. DOI 10.1038/nature04228

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  72. A. J. Trewavasa, R. Malho: Signal Perception and Transduction: The Origin of the Phenotype. The Plant Cell, Vol. 9, July 1997, pp 1181 – 1195. DOI 10.1105/tpc.9.7.1181 http://www.plantcell.org/content/9/7/1181.full.pdf

 

Links:

http://www.nslij-genetics.org/wli/1fnoise/ (A bibliography on 1/f noise in biosystems)

http://papers.cnl.salk.edu/PDFs/

http://iopscience.iop.org/1742-5468/focus/extra.focus5


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