Skip to main content
SpringerLink
Log in
Book cover

Dynamics of Complex Interconnected Systems: Networks and Bioprocesses pp 1–28Cite as

STRUCTURE AND COMMUNICATION IN COMPLEX NETWORKS

  • Conference paper

  • 665 Accesses

Part of the book series: NATO Science Series II ((NAII,volume 232))

Abstract

Networks is tool to describe systems composed of many different units which each typically interact with a few of the other units. Networks thus used to quantify complex systems from the intricate interactions of proteins inside a living cell, to ecosystems, social systems and computer networks. In most cases the network quantify communication channels in the system. Thus directly connected nodes communicates easy, while more distant nodes only obtain exchange information through a number of intermediate steps. In fact already in 1982 a detailed study of social networks within university departments revealed that mutual information of one member about another one was decaying exponentially with their distance, and increased linearly with number of common friends (degenerate paths). We will take this viewpoint and consider a Network as a description of who get direct information from who, and which parts that has to resort to second hand or even more inaccurate information: networks quantify the extent to which complex systems operate under the constraints of a limited information horizon.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • K.B. Arnvig, S. Pedersen and K. Sneppen (2000). “Thermodynamics of Heat Shock Response”. Phys. Rev. Lett. 84 3005 (cond-mat/9912402)

    Article  ADS  Google Scholar 

  • E. Aurell, K. Sneppen (2002). Epigenetics as a first passage problem, Phys. Rev. Letters. 88, 048101–1.

    Article  ADS  Google Scholar 

  • E. Aurell, S. Brown and K. Sneppen (2002). Stability puzzles in phage λ, Physical Review E 65, 051914.

    Article  ADS  Google Scholar 

  • A.-L. Barabasi, R. Albert (1999). Emergence of scaling in random networks, Science, 286, 509.

    Article  MathSciNet  Google Scholar 

  • J. Bock and K. Sneppen (2004). Quantifying the Benefits of Translation Regulation in the Unfolded Protein Response. To appear in Physical Biology.

    Google Scholar 

  • S. Bornholdt & K. H.Ebel (2001). World Wide Web scaling from Simon’s 1955 model, Phys. Rev. E. 035104(R).

    Google Scholar 

  • S. Bornholdt and K. Sneppen (2000). “Robustness as an evolutionary principle”, Proc Roy. Soc. London, B 267 2281.

    Article  Google Scholar 

  • A. Broder et al. (2000). Graph Structure in the Web, Computer Networks 33, 309–320.

    Article  ADS  Google Scholar 

  • K.T. Bæk, S. Svenningsen, H. Eisen, K. Sneppen & S. Brown (2003). “Single-cell analysis of lambda immunity regulation”, J. Mol. Biol. 334 363.

    Article  Google Scholar 

  • G. Caldarelli, A. Capocci, P. De Los Rios, and M. A. Muoz (2002) Scale-Free Networks from Varying Vertex Intrinsic Fitness. Phys. Rev. Lett. 89 258702.

    Article  ADS  Google Scholar 

  • J.S. Cox and P. Walter. (1996). A Novel Mechanism for Regulating Activity of a Transcription Factor That Controls the Unfolded Protein Response. Cell. 87:391–404.

    Article  Google Scholar 

  • Davidson et al. (2002). A Genomic Regulatory Network for Development. Science 295 (5560): 1669–2002.

    Article  ADS  Google Scholar 

  • S.F. Elena & R.E. Lenski (1999). Test of synergetic interactions among deleterious mutations in bacteria Nature 390, 395.

    Article  ADS  Google Scholar 

  • P. Erdös & A. Rényi (1960). On the evolution of random graphs. Publ. Math. Inst. Hung. Acad. Sci. 5, 1760.

    Google Scholar 

  • J.E. Ferrell Jr. (2000). What do Scaffold Proteins Really Do, Science STKE, www. stke.sciencemag.org/cgi/content/full/sigtrans;2000/52/pe1

    Google Scholar 

  • G.B. Field and W.C. Saslow (1965). Astrophys. J. 142 568.

    Article  ADS  Google Scholar 

  • A.-C. Gavin, et al. (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147.

    Article  ADS  Google Scholar 

  • L.H. Hartwell, J.J. Hopfield, S. Leibler, and A.W. Murray, (1999). From molecular to modular cell biology, Nature 402 (6761 Suppl), C47.

    Article  Google Scholar 

  • A.M. Huerta, H. Salgado, D. Thieffry & J. Collado-Vides (1998). RegulonDB: A database on transcriptional regulation in Escherichia coli Nucleic Acid Res. 26, 55. (see also http:// www.smi.stanford.edu/ projects/ helix/ psb98/ thieffry.pdf

    Article  Google Scholar 

  • D. Hughes, M. Paczuski, R.O. Dendy, P. Helander and K.G. McClements. Physical Rev. Letters 90 131101 (2003).

    Article  ADS  Google Scholar 

  • M. Paczuski and D. Hughes, cond-mat/0311304 (2003).

    Google Scholar 

  • T. Ito, et al. (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome, Proc. Natl. Acad. Sci. USA 98, 4569.

    Article  ADS  Google Scholar 

  • H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai & A.-L. Barabasi (2000). The large scale organization of metabolic networks. Nature, 407, 651–654.

    Article  ADS  Google Scholar 

  • H. Jeong, S. Mason, A.-L. Barabasi, Z.N. Oltvai (2001). Centrality and lethality of protein networks. Nature 411, 41–42.

    Article  ADS  Google Scholar 

  • B.J. Kim, A. Trusina, P. Minhagen and K. Sneppen (2003). Scale free networks from merging and creation. Submitted to Physical Review Letters.

    Google Scholar 

  • B.J. Kim, A. Trusina, P. Minnhagen and K. Sneppen (2004). Self Organized Scale-Free Networks from Merging and Regeneration. nlin.AO/0403006.

    Google Scholar 

  • D.E. Koshland, Jr., A. Goldbeter, and J.B. Stock (1978). Amplification and adaptation in regulatory and sensory systems. Science. 217 220

    Article  ADS  Google Scholar 

  • S. Maslov and K. Sneppen (2002). Specificity and stability in topology of protein networks, Science 296 910.

    Article  ADS  Google Scholar 

  • S. Maslov and K. Sneppen (2002). “Pattern Detection in Complex Networks: Correlation Profile of the Internet” Submitted to Phys. Rev. Lett., cond-mat/0205379

    Google Scholar 

  • S. Maslov and K. Sneppen (2004). Computational Architecture of the Yeast regulatory network. Preprint.

    Google Scholar 

  • P. Minnhagen, M. Rosvall, K. Sneppen, A. Trusina (2004). Self-organization of structures and networks from merging and small-scale fluctuations. cond-mat/- 0406752.

    Google Scholar 

  • M. E. J. Newman, S. H. Strogatz, and D. J. Watts (2001). Random graphs with arbitrary degree distributions and their applications, Phys. Rev. E, 64, 026118, 1.

    Article  ADS  Google Scholar 

  • E.van Nimwegen (2003). Scaling Laws in the functional content of genomes. Trends in Genetics bf 19 479

    Google Scholar 

  • K.J. Peterson and E.H. Davidson, Regulatory evolution and the origin of the bilaterians. Proc. Natl. Acad. Sci. USA 97, 4430–4433, 2000

    Article  ADS  Google Scholar 

  • D.J. de S. Price (1965). Networks of scientic papers. Science 149, 510.

    Article  ADS  Google Scholar 

  • D.J. de S. Price (1976). A general theory of bibliometric and other cumulative advantage processes. J. Amer. Soc. Inform. Sci. 27 292.

    Article  Google Scholar 

  • M. Ptashne & A. Gann (1997). Nature 386 569.

    Article  ADS  Google Scholar 

  • N. Rosenfeld, M. Elowitz & U. Alon (2002). Negative Autoregulation Speeds the Response Times of Transcription Networks. JMB, 323 785–793.

    Article  Google Scholar 

  • M. Rosvall & K. Sneppen (2003). Modeling Dynamics of Information Networks. cond-mat/0308399.

    Google Scholar 

  • M. Rosvall, A. Trusina, P. Minnhagen and K. Sneppen (2004). Networks and Cities: An Information Perspective. cond-mat/0407054.

    Google Scholar 

  • S.S. Shen-Orr, R. Milo, S. Mangan and U. Alon (2002). Network motifs in the transcriptional regulation of Escherichia coli Nature Genetics, Published online: 22 April 2002, DOI:10. 1038/ng881

    Google Scholar 

  • C. Sidrauski, J. Cox, & P. Walter. 1997. tRNA Ligase Is Required for Regulated mRNA Splicing in the Unfolded Protein Response. Cell 87 405–413.

    Article  Google Scholar 

  • H. Simon (1955). Biometrika 42 (1955) 425.

    Article  MathSciNet  MATH  Google Scholar 

  • K. Sneppen, M. Rosvall, A. Trusina and P. Minhagen (2004). A simple model for self-organization of bipartite networks Europhysics letters 67 349.

    Article  ADS  Google Scholar 

  • K. Sneppen, M. Rosvall, A. Trusina, P. Minnhagen. A simple model for self organization of bipartite networks. Europhys. Lett. 67 (2004) 349

    Article  ADS  Google Scholar 

  • K. Sneppen, A. Trusina and M. Rosvall (2004). Hide and seek on complex networks. cond-mat/0407055

    Google Scholar 

  • C.K.Stover et al. (2000), Complete genome sequence of Pseudomonas Aeruginosa PA01, an opportunistic pathogen Nature 406, 959.

    Article  ADS  Google Scholar 

  • G. Tiana, M. H. Jensen, K. Sneppen (2002). Time delay as a key to Apoptosis Induction in the p53 Network. Eur. Phys. J. B 29 135.

    Article  ADS  Google Scholar 

  • A. Trusina, S. Maslov, P. Minnhagen & K. Sneppen (2003). Hierarchy and Anti- Hierarchy in Real and Scale Free networks. cond-mat/0308339.

    Google Scholar 

  • A. Vazquez, A. Flammini, A. Maritan, and A. Vespignani (2001). Modelling of protein interaction networks arXiv:cond-mat/0108043.

    Google Scholar 

  • P. Uetz, et al. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisia. Nature 403, 623.

    Article  ADS  Google Scholar 

  • D. J. Watts and S. H. Strogatz (1998). Collective dynamics of “small-world” networks. Nature, 393 440.

    Article  ADS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Center for Models of Life Niels Bohr Institute, Blegdamsvej 17, Copenhagen, 2100

    KIM SNEPPEN

Authors
  1. KIM SNEPPEN
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Institute for Energy Technology, Kjeller, Norway

    Arne T. Skjeltorp

  2. Frank Laboratory of Neutron Physics, Dubna, Russia

    Alexander V. Belushkin

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer

About this paper

Cite this paper

SNEPPEN, K. (2006). STRUCTURE AND COMMUNICATION IN COMPLEX NETWORKS. In: Skjeltorp, A.T., Belushkin, A.V. (eds) Dynamics of Complex Interconnected Systems: Networks and Bioprocesses. NATO Science Series II, vol 232. Springer, Dordrecht. https://doi.org/10.1007/1-4020-5030-5_1

Download citation

Publish with us

Policies and ethics

Search

Navigation