Stefan Bornholdt Complex Systems Lab 


Institute for Theoretical Physics
University of Bremen
Otto-Hahn-Allee
D-28359 Bremen
Germany

Tel: +49-421-218-62060 (Secr. -62000)
Fax: +49-421-218-9104


Research: Physics of Complex Systems

Our living world is made up of simple elementary forces and constitutents. But how do these work together to make life, evolution, brains, genomes, immune systems, societies? We study general principles of complex systems in nature from the perspective of statistical physics, often reducing a system to the most simple working model for a particular phenomenon. We use methods from statistical and computational physics, and our main tool, the computer, allows for the new kind of "experimental" theoretical physics. Research topics are interdisciplinary with current emphasis on:  Complex Networks, Theoretical Systems Biology, Self-organized Criticality, Socio- and Econophysics.

Group members:

Complex Systems Group

Stefan Bornholdt (head)                      0421-218-62060     bornholdt email of institute

Juan Diaz Ochoa (Postdoc)                 0421-218-3416     diazochoa email of institute

Stefan Braunewell (PhD student)        0421-218-3195     braunewell email of institute

Maria Davidich (PhD student)            0421-218-3195      davidich email of institute

Fabian Zöhrer (Diploma student)        0421-218-3416      zoehrer email of institute

Matthias Rybarsch (Diploma student) 0421-218-62063      rybarsch email of institute

Gabriele Gerber (Secretary)                  0421-218-62061       gerber email of institute

Stanislaus Brachmann (Technician)    0421-218-62062     brachmann email of institute

Former members:

Felix Beyer, Holger Ebel (D-fine), Christel Kamp  (Paul-Ehrlich-Institut, Frankfurt), Konstantin Klemm (Univ. Leipzig), Lutz-Ingo Mielsch, Jörg Reichardt (Univ. Wuerzburg), Torsten Roehl (Univ. Kiel), Thimo Rohlf (Santa Fe Institute), Takuya Yamano.


Publications:

Discrete models of genetic networks

  • S. Bornholdt and K. Sneppen, Neutral mutations and punctuated equilibrium in evolving genetic networks, Phys. Rev. Lett. 81 (1998) 236-239. [PDF]
  •  S. Bornholdt and K. Sneppen, Robustness as an Evolutionary Principle, Proc. R. Soc. London B 267 (2000) 2281-2286. [PDF]
  • S. Bornholdt, Modeling Genetic Networks and Their Evolution: A Complex Dynamical Systems Perspective, Biological Chemistry 382 (2001) 1289-1299. [PDF]
  • K. Klemm and S. Bornholdt, Robust gene regulation: Deterministic dynamics from asynchronous networks with delay, (2003) q-bio/0309013. [preprint]
  • K. Klemm and S. Bornholdt, Topology of biological networks and reliability of information processing, Proc. Natl. Acad. Sci. USA 102 (2005) 18414. [PDF] 
  •  S. Bornholdt, Less is more in modeling large genetic networks, Science 310 (2005) 449. [Summary] [ Full text]
  •  S. Braunewell and S. Bornholdt,  Reliability of genetic networks is evolvable, Phys. Rev. E 77 (2008) 060902. [PDF]
  •  S. Bornholdt,  Boolean network models of cellular regulation: prospects and limitations, J. Roy. Soc. Interface 5 (2008) S85-S94. doi:10.1098/rsif.2008.0132.focus [PDF]

    • Boolean network models of yeast

  • S. Braunewell and S. Bornholdt, Superstability of the yeast cell-cycle dynamics: Ensuring causality in the presence of biochemical stochasticity, J. Theor. Biol. 245 (2007) 638-643. [PDF]
  •  Maria I. Davidich and S. Bornholdt, Boolean network model predicts cell cycle sequence of fission yeast, PLoS ONE 3 (2008) e1672. doi:10.1371/journal.pone.0001672. [PDF]
  •  Maria I. Davidich and S. Bornholdt, The transition from differential equations to Boolean networks: A case study in simplifying a regulatory network model, J. Theor. Biol. 255 (2008) 269-277. doi:10.1016/j.jtbi.2008.07.020 [PDF]

    • Physics of complex networks I: Boolean networks

  • S. Bornholdt and T. Rohlf, Topological evolution of dynamical networks: Global criticality from local dynamics, Phys. Rev. Lett. 84 (2000) 6114-6117. [PDF]
  •  T. Rohlf and S. Bornholdt, Criticality in Random Threshold Networks: Annealed Approximation and Beyond, Physica A 310 (2002) 245-259. [PDF]
  •  K. Klemm and S. Bornholdt, Stable and unstable attractors in Boolean networks, Phys. Rev. E 72 (2005) 055101(R). [PDF]

    • Physics of complex networks II: Community detection

  •  J. Reichardt and S. Bornholdt, Detecting fuzzy communities in complex networks with a Potts model, Phys. Rev. Lett. 93 (2004) 218701. [PDF]
  •  J. Reichardt and S. Bornholdt, Statistical Mechanics of Community Detection, Phys. Rev. E 74 (2006) 016110. [PDF]
  •  J. Reichardt and S. Bornholdt, When are networks truly modular? Physica D 224 (2006) 20-26. [PDF] 
  •  J. Reichardt and S. Bornholdt, Clustering of sparse data via network communities --- a prototype study of a large online market, J. Stat. Mech. (2007) P06016. [PDF]
  •  J. Reichardt and S. Bornholdt, Partitioning and Modularity of Graphs with arbitrary Degree Distribution, Phys. Rev. E (Rapid Communications), Phys. Rev. E 76 (2007) 015102(R). [PDF]

    • Biological networks and morphogenesis

  • T. Rohlf and S. Bornholdt, Self-organized pattern formation and noise-induced control from particle computation, JSTAT (2005) L12001. [PDF] [JAVA applet]
  • T. Rohlf and S. Bornholdt, Morphogenesis by coupled regulatory networks: Reliable control of positional information and proportion regulation, J. Theor. Biol. 261 (2009) 176-193. [PDF] [JAVA applet]

    • Neural networks: Development and learning

  • K. Klemm, S. Bornholdt, and H.G. Schuster, Beyond Hebb: Exclusive-OR and biological learning, Phys. Rev. Lett. 84 (2000) 3013-3016. [PDF]
  • S. Bornholdt and T. Roehl, Self-organized critical neural networks, Phys. Rev. E 67 (2003) 066118. [PDF]

    • Applying statistical physics to the immune system

  • C. Kamp and S. Bornholdt, Co-evolution of quasispecies: B-cell mutation rates maximize viral error catastrophes, Phys. Rev. Lett. 88 (2002) 068104. [PDF]
  • C. Kamp and S. Bornholdt, From HIV infection to AIDS: A dynamically induced percolation transition?, Proc. R. Soc. London B 269 (2002) 2035-2040. [PDF]
  • C. Kamp, C.O. Wilke, C. Adami, and S. Bornholdt, Viral evolution under the pressure of an adaptive immune system - optimal mutation rates for viral escape, Complexity 8(2) (2003) 28-33. [PDF] [Nature News and Views feature]
  • C. Kamp and S. Bornholdt, Critical percolation in self-organized media: A case study on random directed networks, (2002) cond-mat/0210410. [preprint]

    • Complex networks: Internet and society

  • S. Bornholdt and H. Ebel, World Wide Web Scaling Exponent from Simon's 1955 Model, Phys. Rev. E 64 (2001) 035104(R). [PDF]
  • J. Davidsen, H. Ebel, and S. Bornholdt, Emergence of a small world from local interaction: Modeling acquaintance networks, Phys. Rev. Lett. 88 (2002) 128701. [PDF]
  • H. Ebel, L.-I. Mielsch, and S. Bornholdt, Scale-free topology of e-mail networks, Phys. Rev. E 66 (2002) 035103(R). [PDF] [Data]
  • H. Ebel and S. Bornholdt, Coevolutionary games on networks, Phys. Rev. E 66 (2002) 056118. [PDF]
  • H. Ebel and S. Bornholdt, Evolutionary games and the emergence of complex networks, (2002) cond-mat/0211666. [preprint]
  • H. Ebel, J. Davidsen, and S. Bornholdt, Dynamics of social networks, Complexity 8(2) (2003) 24-27. [PDF]

    • Applying statistical physics to economy and finance

  • S. Bornholdt, Expectation bubbles in a spin model of markets: Intermittency from frustration across scales, Int. J. Mod. Phys. C, Vol. 12, No. 5 (2001) 667-674. [PDF] [JAVA applet]
  • T. Kaizoji, S. Bornholdt, and Y. Fujiwara, Dynamics of price and trading volume in a spin model of stock markets with heterogeneous agents, Physica A 316 (2002) 441-452. [PDF]
  • S. Bornholdt and F. Wagner, Stability of money: Phase transitions in an Ising economy, Physica A 316 (2002) 453-468. [PDF]
  • I. Simonsen, L. Buzna, K. Peters, S. Bornholdt, D. Helbing, Transient dynamics increasing network vulnerability to cascading failures, Phys. Rev. Lett. 100 (2008) 218701. doi:10.1103/ 218701 [PDF]

    • Dynamics of evolutionary algorithms

  • S. Bornholdt, Genetic algorithm dynamics on a rugged fitness landscape, Phys. Rev. E 57 (1998) 3853. [PDF]
  • S. Bornholdt, Annealing schedule from population dynamics, Phys. Rev. E 59 (1999) 3942. [PDF]

    • Complex natural systems

  • E. Moritz, S. Bornholdt, H. Westphal, and M. Meschede, Neural network interpretation of LWD data (ODP Leg 170) confirms complete sediment subduction at the Costa Rica convergent margin, Earth and Planetary Science Letters 174 (2000) 301-312. [PDF]
  • F. Böhm, H. Westphal, and S. Bornholdt, Required but disguised: Environmental signals in limestone-marl alternations. Palaeogeography, Palaeoclimatology, Palaeoecology 2987 (2003) 1-18. [PDF]
  • H. Westphal, F. Böhm, and S. Bornholdt, Orbital Frequencies in the Sedimentary Record: Distorted by Diagenesis? - Facies 50 (2004) 3-11. [PDF]
  • S. Bornholdt, K. Sneppen, and H. Westphal, Longevity of orders is related to the longevity of their constituent genera rather than genus richness, Theory in Biosciences, in press. doi:10.1007/s12064-008-0053-9 [PDF]

    • Books:    book

  •   S. Bornholdt and H. G. Schuster (Eds.), Handbook of Graphs and Networks - From the Genome to the Internet, Wiley-VCH, Berlin (2002). [ Buy ]  
      book
  •  S. Bornholdt and K. Klemm (eds.), Dynamical Networks in Complex Systems, Europhysics Conference Abstracts Vol. 25F (2001). Note: We have a few copies of this abstract book left over. For a free copy please send an email to Stefan Bornholdt. The corresponding  conference site can be found here: International Conference on Dynamical Networks in Complex Systems 2001.
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      book
  •   T. Gramss, S. Bornholdt, M. Gross, M. Mitchell, and T. Pellizari, Non-Standard Computation, VCH Verlag, Weinheim (1998).

    • book
  •  S. Bornholdt und P.H. Feindt (eds.), Komplexe adaptive Systeme, Verlag Josef Roell, Dettelbach (1996).
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