TOPIC: Advanced readings

We have identified a set of specific papers in molecular communications, able to provide a more focused contribution on specific aspects of molecular communications. Up to now, we have identified the following topics

• Specificity:
• Perturbation
• Field
• Motion
• Message Carrier
• Medium
• Molecular absorptions
• Molecular flow and feedbacks

Specificity
Contributions focused upon the service of enabling a nanoscale Message Carrier to convey its information to a desired receiver or class of receivers while avoiding loss of message carriers along the way from reception by other receivers or classes of receivers.

• T.A. Sanders, E. Llagostera, and M. Barna, “Specialized Filopodia Direct Long-range Transport of SHH During Vertebrate Tissue Patterning,” Nature, vol. 497, no. 7451, pp. 628–632, 30 May 2013.
• S. Roy, H. Huang, S. Liu, and T.B. Kornberg, “Cytoneme-Mediated Contact-Dependent Transport of the Drosophila Decapentaplegic Signaling Protein,” Science, vol. 343, no. 6173, 21 February 2014.
• L. Bardwell, X. Zou, Q. Nie, and N. L. Komarova, “Mathematical Models of Specificity in Cell Signaling,” Biophysical Journal, vol. 92, no. 10, pp. 3425-3441, 15 May 2007.

Perturbation
Contributions focused upon novel ideas involving nanoscale encoding, signaling, and modulation.

• M.J. Moore, T. Suda, and K. Oiwa, “Molecular Communication: Modeling Noise Effects on Information Rate,” IEEE Transactions on NanoBioscience, vol. 8, no. 2, pp. 169-180, June 2009.

Field
Contributions emphasizing directionality and coordinated control of Message Carriers at the nanoscale.

• I.V. Dokukina, M.E. Gracheva, E.A. Grachev, and J.D. Gunton, “Role of Network Connectivity in Intercellular Calcium Signaling,” Physica D: Nonlinear Phenomena, vol. 237, no. 6, pp. 745-754, 15 May 2008.
• S. Schuster, M. Marhl, and T. Hofer, “Modelling of Simple and Complex Calcium Oscillations,” European Journal of Biochemistry, vol. 269, no. 5, pp. 1333-1355, March 2002.
• Y. Tang and H.G. Othmer, “Frequency Encoding in Excitable Systems with Applications to Calcium Oscillations,” Proceedings of the National Academy of Sciences, vol. 29, no. 17, pp. 7869-7873, 15 August 1995.

Motion
Contributions related to understanding and engineering basic Message Carrier movement at the nanoscale.

• W.H. Bossert, and E.O. Wilson, “The Analysis of Olfactory Communication Among Animals,” Journal of Theoretical Biology, vol. 5, no. 3, pp. 443–469, November 1963.
• I. Llatser, A. Cabellos-Aparicio, and E. Alarcon, “Networking Challenges and Principles in Diffusion-Based Molecular Communication,” IEEE Wireless Communications, vol. 19, no. 5, pp. 36-41, October 2012.
• S. Kadloor, R.S. Adve, and A.W. Eckford, “Molecular Communication Using Brownian Motion with Drift,” IEEE Transactions on NanoBioscience, vol. 11, no. 2, pp. 89-99, June 2012.
• K. Francis and B.O. Palsson, “Effective Intercellular Communication Distances are Determined by the Relative Time Constants for Cyto/Chemokine Secretion and Diffusion,” Proceedings of the National Academy of Sciences, vol. 94, no. 23, pp. 12258-12262, 11 November 1997.
• S. Klumpp, T.M. Nieuwenhuizen, and R. Lipowsky, “Self-Organized Density Patterns of Molecular Motors in Arrays of Cytoskeletal Filaments,” Biophysical Journal, vol. 88, no. 5, pp. 3118-32, May 2005.
• N. Farsad, A.W. Eckford, and S. Hiyama, “A Markov Chain Channel Model for Active Transport Molecular Communication,” IEEE Transactions on Signal Processing, vol. 62, no. 9, pp. 2424-2436, May 2014.
• S. Balasubramaniam and P. Lio, “Multi-Hop Conjugation Based Bacteria Nanonetworks,” IEEE Transactions on NanoBioscience, vol. 12, no. 1, pp. 47-59, March 2013.

Message Carrier
Contributions regarding the design and construction of Message Carriers at the nanoscale.

• S. Hiyama, T. Inoue, T. Shima, Y. Moritani, T. Suda, and K. Sutoh, “Autonomous Loading, Transport, and Unloading of Specified Cargoes by Using DNA Hybridization and Biological Motor-Based Motility,” Small, vol. 4, no. 4, pp. 410-415, April 2008.
• Frank Walsh, Sasitharan Balasubramaniam, "Reliability and Delay Analysis of Multi-hop Virus-based Nanonetworks," IEEE Transactions on Nanotechnology, 12: 5. pp. 674-684, September 2013.

Medium
Contributions emphasizing novel media in which nanoscale Message Carriers reside.

• Y. Chahibi, M. Pierobon, S.O. Song, and I.F. Akyildiz, “A Molecular Communication System Model for Particulate Drug Delivery Systems,” IEEE Transactions on Biomedical Engineering, vol. 60, no. 12, pp. 3468-3483, December 2013.
• N. Farsad, A.W. Eckford, S. Hiyama, and Y. Moritani, “On-Chip Molecular Communication: Analysis and Design,” IEEE Transactions on NanoBioscience, vol. 11, no. 3, pp. 304-314, September 2012.

Molecular absorptions
Contributions regarding mechanisms and models about absorption of Message Carriers and their temporal statistics.

• H. Yilmaz, A. Heren, T. Tugcu, and C.-B. Chae. Three-dimensional channel characteristics for molecular communications with an absorbing receiver. IEEE Communications Letters, 18(6):929–932, June 2014.
• A. Akkaya, H. Yilmaz, C. Chae, and T. Tugcu. Effect of receptor density and size on signal reception in molecular communication via diffusion with an absorbing receiver. IEEE Communications Letters, 19(2):155–158, Feb 2015.
• L. Felicetti, M. Femminella, G. Reali, J. Daigle, M. Malvestiti, and P. Gresele. Modeling CD40-based molecular communications in blood vessels. IEEE Transactions on NanoBioscience, 13(3):230–243, 2014.

Molecular flows and feedbacks
Contributions regarding mechanisms for regulating continuous molecular flow, with special focus on drug delivery applications.

• T. Nakano, Y. Okaie, and A. V. Vasilakos. Transmission rate control for molecular communication among biological nanomachines. IEEE Journal on Selected Areas in Communications, 31(12, supplement):835-846, 2013.
• L. Felicetti, M. Femminella, G. Reali, T. Nakano, and A. V. Vasilakos. TCP-like molecular communications. IEEE Journal on Selected Areas in Communications, 32(12):2354-2367, 2014.