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Publications

Publications

2017

Richard Hinze, Peter Dittrich, Bashar Ibrahim (2017)
A Dynamical Model for Activating and Silencing the Mitotic Checkpoint.
Scientific Reports (Nature PG) 7.

Bashar Ibrahim (2017)
A Mathematical Framework for Kinetochore-Driven Activation Feedback in the Mitotic Checkpoint.
Bulletin of Mathematical Biology. 79 (5): 1183-1200. 

2017

Richard Henze, Peter Dittrich, Bashar Ibrahim (2017)
A Dynamical Model for Activating and Silencing the Mitotic Checkpoint
Scientific Reports 7

Bashar Ibrahim (2017)
A Mathematical Framework for Kinetochore-Driven Activation Feedback in the Mitotic Checkpoint
Bulletin of Mathematical Biology 79(5): 1183-1200

2016

Konrad Gizynski, Gerd Grünert, Peter Dittrich, Jerzy Gorecki (2016)
Evolutionary design of classifiers made of droplets containing a nonlinear chemical medium
Evolutionary Computation

Chunyang Mu, Peter Dittrich, Dave Parker, John Rowe (2016)
Formal Quantitative Analysis of Reaction Networks Using Chemical Organisation Theory
International Conference on Computational Methods in Systems Biology, 232-251

Jan Huwald, Stephan Richter, Bashar Ibrahim, Peter Dittrich (2016)
Compressing molecular dynamics trajectories: Breaking the one‐bit‐per‐sample barrier
Journal of Computational Chemistry 37 (20), 1897–1906

2015

Bashar Ibrahim (2015)
In silico spatial simulations reveal that MCC formation and excess BubR1 are required for tight inhibition of the anaphase-promoting complex
Molecular BioSystems. 12: 2867 - 2877

Bashar Ibrahim (2015)
Systems Biology Modeling of Five Pathways for Regulation and Potent Inhibition of the Anaphase-Promoting Complex (APC/C): Pivotal Roles for MCC and BubR1
OMICS: A Journal of Integrative Biology. May 2015, 19(5): 294-305. doi:10.1089/omi.2015.0027

Bashar Ibrahim (2015)
Spindle assembly checkpoint is sufficient for complete Cdc20 sequestering in mitotic control
Computational and Structural Biotechnology Journal 13, 320 - 328

Stephan Richter, Ingo Fetzer, Martin Thullner, Florian Centler, Peter Dittrich (2015)
Towards rule-based metabolic databases - a requirement analysis based on KEGG
International Journal of Data Mining and Bioinformatics (in press)

Bashar Ibrahim (2015)
Toward a systems-level view of mitotic checkpoints
Progress in biophysics and molecular biology 117(2–3), 217–224

Jakob Fischer, Axel Kleidon, Peter Dittrich (2015)
Thermodynamics of Random Reaction Networks
PloS one 10 (2), e0117312

Richard Henze, Jan Huwald, Nelly Fernanda Mostajo Berrospi, Peter Dittrich, Bashar Ibrahim (2015)
Structural analysis of in silico mutant experiments of human inner-kinetochore structure
Biosystems 127, 47-59

2014

Bashar Ibrahim, Richard Henze (2014)
Active Transport Can Greatly Enhance Cdc20: Mad2 Formation
International journal of molecular sciences 15 (10), 19074-19091

Andrew Adamatzky, B. De Lacy Costello, Peter Dittrich, Jerzy Gorecki, Klaus-Peter Zauner (2014)
On logical universality of Belousov-Zhabotinsky vesicles
International Journal of General Systems 43 (7), 757-769

Peter Kreyßig, Christian Wozar, Stephan Peter, Tomas Veloz, Bashar Ibrahim, Peter Dittrich (2014)
Effects of Small Particle Numbers on Long-Term Behaviour in Discrete Biochemical Systems
Bioinformatics 2014 Sep;30(17):i475-81

Gabi Escuela, Gerd Grünert, Peter Dittrich (2014)
Symbol representations and signal dynamics in evolving droplet computers
Natural Computing, 13(2): 247-256

Dennis Görlich, Gabi Escuela, Gerd Grünert, Peter Dittrich, Bashar Ibrahim (2014)
Molecular Codes Through Complex Formation in a Model of the Human Inner Kinetochore
Biosemiotics, 1-25

Konrad Gizynski, Gabi Escuela, Gerd Grünert, Peter Dittrich, Bashar Ibrahim (2014)
Strategy of teaching for a chemical classifier constructed with photosensitive droplets
IEEE Transactions on Evolutionary Computation, in review, 2014

Gerd Grünert, Konrad Gizynski, Gabi Escuela, Bashar Ibrahim, Peter Dittrich (2014)
Understanding networks of computing chemical droplet neurons based on information flow
Int. J. Neur. Syst. DOI: 10.1142/S0129065714500324
other links:
Thomas Hinze, Jörn Behre, Christian Bodenstein, Gabi Escuela, Gerd Grünert, Petra Hofstedt, Peter Sauer, Sikander Hayat, Peter Dittrich (2014)
Membrane systems and tools combining dynamical structures with reaction kinetics for applications in chronobiology
In Applications of Membrane Computing in Systems and Synthetic Biology, pages 133-173. Springer International Publishing, 2014

2013

Bashar Ibrahim, Richard Henze, Gerd Grünert, Matthew Egbert, Jan Huwald, Peter Dittrich (2013)
Spatial Rule-Based Modeling: A method and its application to the human mitotic kinetochore
Cells, 2:506-544

Matthew Egbert, Gerd Grünert, Gabi Escuela, Peter Dittrich (2013)
Synthetic signalling protocell networks as models of neural computation
Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems

Dennis Görlich, Gabi Escuela, Gerd Grünert, Peter Dittrich, Bashar Ibrahim (2013)
Molecular Codes Through Complex Formation in a Model of the Human Inner Kinetochore.
Biosemiotics, pages 223-247, 2013

Sergej Tschernyschkow, Sabine Herda, Gerd Grünert, Volker Döring, Dennis Görlich, Antje Hofmeister, Christian Hoischen, Stephan Diekmann, Peter Dittrich, Bashar Ibrahim (2013)
Rule-based Modeling and Simulations of the Inner Kinetochore Structure
Progress in Biophysics and Molecular Biology, 113(1):33 - 45, 2013

Christian Knüpfer, Clemens Beckstein, Peter Dittrich, Nicolas Le Novère (2013)
Structure, function, and behaviour of computational models in systems biology
BMC Systems Biology, 7:43

Dennis Görlich, Peter Dittrich (2013)
Molecular codes in biological and chemical reaction networks
PLoS ONE, 8(1): e54694

Gerd Grünert, Jan Szymanski, Julian Holley, Gabi Escuela, Alexandra Diem, Bashar Ibrahim, Andrew Adamatzky, Jerzy Gorecki, Peter Dittrich (2013)
Multi-scale Modelling of Computers made from Excitable Chemical Droplets
International Journal of Unconventional Computing, 9(3-4)

2012

Lutz R. Gehlen, Gerd Grünert, M. Beatrix Jones, Chris D. Rodley, Jörg Langowski, J.M .O'Sullivan (2012)
Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions
Nucleus (Austin, Tex.), 3(4):370

Ayse Koca Caydasi, Maiko Lohel, Gerd Grünert, Peter Dittrich, Gislene Pereira, Bashar Ibrahim (2012)
A Dynamical Model of the Spindle Position Checkpoint
Molecular Systems Biology, 8(582)

Peter Kreyßig, Gabi Escuela, Bryan Reynaert, Tomas Veloz, Bashar Ibrahim, Peter Dittrich (2012)
Cycles and the Qualitative Evolution of Chemical Systems
PLoS ONE, 7(10): e45772

Andrew Adamatzky, Julian Holley, Peter Dittrich, Jerzy Gorecki, B. De Lacy Costello, Klaus-Peter Zauner, L. Bull (2012)
On architectures of circuits implemented in simulated Belousov–Zhabotinsky droplets
Biosystems, 109(1):72-77 (2012)

G. Bergner, S. Schlücker, B. Kampe, Peter Dittrich, B. Dietzek1, J. Popp (2012)
Optimal control of coherent anti-Stokes Raman scattering image contrast
Appl. Phys. Lett., 100, 261106 (2012)

Tomas Veloz, Pablo Razeto Barry, Peter Dittrich, Alejandro Fajardo (2012)
Reaction networks and evolutionary game theory
Journal of mathematical biology 68 (1-2), 181-206

Gerd Grünert, Gabi Escuela, Peter Dittrich (2012)
Symbol representations in Evolving Droplet Computers
J. Durand-Lose, N. Jonoska (Eds.): Unconventional Computation and Natural Computation - 11th International Conference, UCNC 2012, Orlean, France, Sept. 3-7, 2012. Proceedings. LNCS 7445, Springer, 2012

Alexandra Diem, Gerd Grünert, Peter Dittrich (2012)
Evolution and growth of molecular networks for disease classification
In Book of Abstracts, European Conference on Complex Systems, page 44, Brussels, September 2012

2011

Dennis Görlich, Stefan Artman, Peter Dittrich (2011)
Cells as Semantic Systems
BBA General Subjects, Special Issue "Systems Biology of Microorganisms", 1810(10), 914-923, 2011

Dennis Görlich, Peter Dittrich (2011)
Identifying Molecular Organic Codes in Reaction Networks
Proceedings of ECAL2009, LNCS, Springer, Berlin, 2011

Pietro Speroni di Fenizio, Naoki Matsumaru, Peter Dittrich (2011)
Flying Over Mount Improbable
Proceedings of ECAL2009, LNCS, Springer, Berlin, 2011

Gerd Grünert, Gabi Escuela, Peter Dittrich, Thomas Hinze (2011)
Morphological Algorithms: Membrane Receptor-ligand Interactions and Rule-based Molecule Graph Evolution for Exact Set Cover Problem
Proceedings of CMC12, France, 2011

Peter Kreyßig, Peter Dittrich (2011)
Reaction Flow Artificial Chemistries
Advances in Artificial Life, ECAL 2011, pages 431-437, MIT Press, 2011

Peter Kreyßig, Peter Dittrich (2011)
Fragments and Chemical Organisations
Electronic Notes in Theoretical Computer Science, 272:19-41, Proceedings SASB 2010, 2011

Peter Kreyßig, Peter Dittrich (2011)
Emergent Control
Organic Computing - A Paradigm Shift for Complex Systems, pages 67-78, Springer Basel, 2011

Naoki Matsumaru, Peter Kreyßig, Peter Dittrich (2011)
Organisation-oriented Chemical Programming
Organic Computing - A Paradigm Shift for Complex Systems, pages 207-220, Springer Basel, 2011

Peter Kreyßig, Peter Dittrich (2011)
On the Future of Chemistry-inspired Computing
Organic Computing - A Paradigm Shift for Complex Systems, pages 583-585, Springer Basel, 2011

Stephan Peter, Peter Dittrich (2011)
On the Relation between Organizations and Limit Sets in Chemical Reaction Systems
Advances in Complex Systems, 14, 77-96, 2011

Stephan Peter, Tomas Veloz, Peter Dittrich (2011)
Feasibility of Organizations - A Refinement of Chemical Organization Theory with Application to P Systems
Membrane Computing, LNCS, Germany, 2011

Tomas Veloz, Bryan Reynaert, David Rojas-Camaggi, Peter Dittrich (2011)
A Decomposition Theorem in Chemical Organizations
Advances in Artificial Life, ECAL 2011, pages 820-827, MIT Press, 2011

Gerd Grünert, Peter Dittrich (2011)
Using the SRSim Software for Spatial and Rule-Based Modeling of Combinatorially Complex Biochemical Reaction Systems
Membrane Computing, LNCS, Springer Berlin, 2011

Gerd Grünert, Peter Dittrich, Klaus-Peter Zauner (2011)
Artificial wet neuronal networks from compartmentalised excitable chemical media
ERCIM News, 85(85):30-32, 2011

2010

Gabi Escuela, Thomas Hinze, Peter Dittrich, Stefan Schuster, Mario Moreno-Alvarez (2010)
Modelling Modified Atmosphere Packaging for Fruits and Vegetables using Membrane Systems
In A. Fred, J. Filipe, H. Gamboa (Eds.), Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing (BIOSIGNALS), INSTICC press, 2010

Ayse Koca Caydasi, Bashar Ibrahim, Gislene Pereira (2010)
Monitoring spindle orientation: spindle position checkpoint in charge.
Cell Div., 5:28

Ayse Koca Caydasi, Bahtiyar Kurtulmus, Maria I.L. Orrico, Astrid Hofmann, Bashar Ibrahim, Gislene Pereira (2010)
Elm1 kinase activates the spindle position checkpoint kinase Kin4.
J. Cell Biol., 190(6):975-989
Comment in: Leslie , M. (2010) Elm1 sparks the SPOC, J. Cell Biol., 190 (6): 944.


Gerd Grünert, Bashar Ibrahim, Thorsten Lenser, Maiko Lohel, Thomas Hinze, Peter Dittrich (2010)
Rule-based spatial modeling with diffusing, geometrically constrained molecules
BMC Bioinformatics, 11:307

Thomas Hinze, Thorsten Lenser, Gabi Escuela, I. Heiland, Stefan Schuster (2010)
Modelling Signalling Networks with Incomplete Information about Protein Activation States: A P System Framework of the KaiABC Oscillator
In G. Paun, M.J. Perez-Jimenez, A. Riscos-Nunez, G. Rozenberg, A. Salomaa (Eds.), Proceedings Tenth International Workshop on Membrane Computing (WMC10), Springer Verlag, 2010

2009

Maiko Lohel, Bashar Ibrahim, Stephan Diekmann, Peter Dittrich (2009)
The role of localization in the operation of the mitotic spindle assembly checkpoint
Cell Cycle 8(16), 2009

Dennis Görlich, Peter Dittrich (2009)
Identifying Molecular Organic Codes in Reaction Networks
LNCS, Springer, Berlin, 2009 (in print)

Pietro Speroni di Fenizio, Naoki Matsumaru, Peter Dittrich (2009)
Flying Over Mount Improbable
Proc. ECAL2009, LNCS, Springer, Berlin, 2009 (in print)

Christoph Kaleta, Stephan Richter, Peter Dittrich (2009)
Using Chemical Organization Theory for Model-Checking
Bioinformatics, 25 May 2009 (advanced access)
other links:
Peter Dittrich (2009)
Artificial Chemistry
In: Bob Meyers et al. (Eds.); Encyclopedia of Complexity and System Science, Springer, ISBN: 978-0-387-75888-6 (in print)

Bashar Ibrahim, Eberhard Schmidt, Peter Dittrich, Stephan Diekmann (2009)
MCC Assembly is not Combined With Full Cdc20 Sequestering
Biosystems, 95(1):35-50, 2009

Bashar Ibrahim, Eberhard Schmitt, Peter Dittrich, Stephan Diekmann (2009)
In-silico study of kinetochore control, amplification, and inhibition effects in MCC assembly
Biosystems, 95(1), 35-50.

Thorsten Lenser, Günter Theissen, Peter Dittrich (2009)
Developmental Robustness by Obligate Interaction of Class B Floral Homeotic Genes and Proteins
PLoS Comput. Biol., 5(1):e1000264, 2009.

Thomas Hinze, Raphael Fassler, Thorsten Lenser, Peter Dittrich (2009)
Register Machine Computations on Binary Numbers by Oscillating and Catalytic Chemical Reactions Modelled Using Mass-Action Kinetics
Int. J. Found. Comput. Sci., 20(3): 411-426. (in print)

Thomas Hinze, Raphael Fassler, Gabi Escuela, Bashar Ibrahim, Stefan Schuster (2009)
Computation by Synthetic Cell Signaling and Oscillating Processes Modelled using Mass-Action Kinetics
In K. Ambos-Spies, B. Löwe, W. Merkle (Eds.), Proceedings Booklet Fifth Conference on Computability in Europe (CiE2009), pp. 186-195, University of Heidelberg, Germany

Gill Benkoe, Florian Centler, Peter Dittrich, Baerbel M. R. Stadler, Peter F. Stadler (2009)
A Topological Approach to Chemical Organizations
Artif. Life, 15(1):71-88, 2009

Hideaki Suzuki, Peter Dittrich (2009)
Artificial Chemistry (Editorial Introduction to Special Issue)
Artif. Life, 15(1):1-3, 2009

2008

Stefanie Weidtkamp-Peters, Thorsten Lenser, Dmitri Negorev, Norman Gerstner, Thomas G. Hofmann, Georg Schwanitz, Christian Hoischen, Gerd Maul, Peter Dittrich, Peter Hemmerich (2008)
Dynamics of Component Exchange at PML Nuclear Bodies
J. Cell Sci., Online since 29 July 2008
other links:
Bashar Ibrahim, Stephan Diekmann, Eberhard Schmidt, Peter Dittrich (2008)
In-Silico Modeling of the Mitotic Spindle Assembly Checkpoint
PLoS ONE 3(2):e1555, 2008
other links:
Bashar Ibrahim, Peter Dittrich, Stephan Diekmann, Eberhard Schmidt (2008)
Mad2 binding is not sufficient for complete Cdc20 sequestering in mitotic transition control (an in silico study)
Biophysical Chemistry, 134(1-2), 93-100, 2008

Christoph Kaleta, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich (2008)
Phenotype prediction in regulated metabolic networks
BMC Systems Biology, 2:37
other links:
Sikander Hayat, Thomas Hinze (2008)
Toward integration of in vivo molecular computing devices: successes and challenges
HFSP Journal, 1(1):60-64, 2008
ISSN 1955-2068


Thomas Hinze, Raphael Fassler, Thorsten Lenser, Naoki Matsumaru, Peter Dittrich (2008)
Event-Driven Metamorphoses of P Systems
In P. Frisco, D.W. Corne, G. Paun (Eds.), Proceedings Ninth International Workshop on Membrane Computing (WMC9), pp. 209-225, Heriot-Watt University, accepted for publication in Series Lecture Notes in Computer Science, Springer Verlag, 2008

Thomas Hinze, Sikander Hayat, Thorsten Lenser, Naoki Matsumaru, Peter Dittrich (2008)
Biosignal-Based Computing by AHL Induced Synthetic Gene Regulatory Networks.
In P. Encarnacao, A. Veloso (Eds.), Proceedings of the First International Conference on Bio-Inspired Systems and Signal Processing, Vol. 1, pp. 162-169, IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, INSTICC press, 2008
ISBN 978-989-8111-18-0


Florian Centler, Christoph Kaleta, Pietro Speroni di Fenizio, Peter Dittrich (2008)
Computing Chemical Organizations in Biological Networks
Bioinformatics, 24(14), 1611 - 1618, 2008
other links:
Raphael Fassler, Thomas Hinze, Thorsten Lenser, Peter Dittrich (2008)
Construction of Oscillating Chemical Register Machines on Binary Numbers using Mass-Action Kinetics.
In O.H. Ibarra, P. Sosik (Eds.), Preliminary Proceedings Prague International Workshop on Membrane Computing in conjunction with DNA14 (PIWMC2008), pp. 11-22, Silesian University Press, 2008
ISBN 978-80-7248-468-3


Hendrik Rohn, Bashar Ibrahim, Thorsten Lenser, Thomas Hinze, Peter Dittrich (2008)
Enhancing Parameter Estimation of Biochemical Networks by Exponentially Scaled Search Steps
In: E. Marchiori, J.H. Moore (Eds.), Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Proceedings EvoBio 2008, Naples, Series Lecture Notes in Computer Science, Vol. 4973, pp. 177-187, Springer Verlag, 2008

Peter Dittrich, Lars Winter (2008)
Chemical Organizations in a Toy-Model of the Political System
Advances in Complex Systems 11(4), 609-627

2007

Bashar Ibrahim, Peter Dittrich, Stephan Diekmann, Eberhard Schmidt (2007)
Stochastic effects in a compartmental model for mitotic checkpoint regulation
Journal of Integrative Bioinformatics, 4(3), 66, 2007
other links:
Thomas Hinze, Sikander Hayat, Thorsten Lenser, Naoki Matsumaru, Peter Dittrich (2007)
Hill Kinetics Meets P Systems.
In G. Eleftherakis, P. Kefalas, G. Paun, G. Rozenberg, A. Salomaa (Eds.) Membrane Computing, Series Lecture Notes in Computer Science, Vol. 4860, pp. 320-335, Springer Verlag, 2007

Thomas Hinze, Raphael Fassler, Thorsten Lenser, Naoki Matsumaru, Peter Dittrich (2007)
Efficient Chemical Computing using Deterministic Reaction Systems with Prioritisation of Rules.
In M. Droste, M. Lohrey (Eds.) Proceedings 17. Theorietag Automaten und Formale Sprachen, pp. 68-73, University of Leipzig, 2007 (partially in German)

Thomas Hinze, Sikander Hayat, Thorsten Lenser, Naoki Matsumaru, Peter Dittrich (2007)
Hill Kinetics Meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents in silico and in vivo.
In: G. Eleftherakis, P. Kefalas, G. Paun (Eds.), Proceedings Eight Workshop on Membrane Computing (WMC8), Thessaloniki, pp. 363-381, SEERC Publishers, 2007

Peter Dittrich, Pietro Speroni di Fenizio (2007)
Chemical Organization Theory
Bull. Math. Biol., 69(4):1199-1231, 2007
other links:
Florian Centler, Peter Dittrich (2007)
Chemical organizations in atmospheric photochemistries: a new method to analyze chemical reaction networks
Planet. Space Sci. , 55(4): 413-428, 2007
other links:
Peter Dittrich, Pietro Speroni di Fenizio (2007)
Chemical Organization Theory
In: M. Al-Rubeai, M. Fussenegger (Eds.); Cell Engineering, Volume 5: Systems Biology, p. 361-393, Springer
other links:
Naoki Matsumaru, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich (2007)
Chemical Organization Theory as a Theoretical Base for Chemical Computing
International Journal of Unconventional Computing, 3(4), 285-309
other links:
Thorsten Lenser, Thomas Hinze, Bashar Ibrahim, Peter Dittrich (2007)
Towards Evolutionary Network Reconstruction Tools for Systems Biology
In: E. Marchiori, J.H. Moore, J.C. Rajapakse (Eds.), Proceedings EvoBio 2007, Valencia, Series Lecture Notes in Computer Science, Vol. 4447, pp. 132-142, Springer Verlag, 2007

Naoki Matsumaru, Thorsten Lenser, Thomas Hinze, Peter Dittrich (2007)
Designing a chemical program using chemical organization theory
BMC Systems Biology, 1(Suppl 1):P26, 2007 - poster presentation, doi:10.1186/1752-0509-1-S1-P26
other links:
Naoki Matsumaru, Thorsten Lenser, Thomas Hinze, Peter Dittrich (2007)
Toward Organization-Oriented Chemical Programming: A Case Study with the Maximal Independent Set Problem
In: F. Dressler, I. Carreras (Eds.), Advances in Biologically Inspired Information Systems, (Series: Studies in Computational Intelligence, Vol. 69), p. 147-163, Springer, Berlin, doi: 10.1007/978-3-540-72693-7_8

Pietro Speroni di Fenizio, Peter Dittrich (2007)
Chemical Organizations at Different Spatial Scales
In: Proc. European Conference on Artificial Life (ECAL 2007), LNCS 4648, p. 1-11, Springer, Berlin, ISBN: 978-3-540-74912-7
other links:
Peter Dittrich, Lars Winter (2007)
A Toy-Model of the Political System
In: Proc. of European Conference on Complex Systems (ECCS 2007), Dresden October 1-5, 2007 (accepted)

Peter Dittrich, Naoki Matsumaru (2007)
Organization-Oriented Chemical Programming
Hybrid Intelligent Systems, 2007. HIS 2007. 7th International Conference on (HIS 2007), 17-19 Sept. 2007, pages 8-23, IEEE DL
other links:
Peter Dittrich, Bashar Ibrahim, Thomas Hinze, Thorsten Lenser, Naoki Matsumaru (2007)
Hierarchically Evolvable Components for Complex Systems: Biologically Inspired Algorithmic Design.
In J. Jost, D. Helbing, H. Kantz, A. Deutsch (Eds.) Proceedings of the European Conference on Complex Systems (ECCS2007), p. 85, Dresden University of Technology, 2007

Christian Knüpfer, Clemens Beckstein, Peter Dittrich (2007)
How to Formalise the Meaning of a Bio-Model: A Case Study
BMC Systems Biology 1 (Suppl 1), BioSysBio 2007: Systems Biology, Bioinformatics, Synthetic Biology - Meeting abstracts. Manchester, UK. 11-13 January 2007, p.28.
other links:

2006

Thomas Hinze, Thorsten Lenser, Peter Dittrich (2006)
A Protein Substructure Based P System for Description and Analysis of Cell Signalling Networks
In: H.J. Hoogeboom, G. Paun, G. Rozenberg (Eds.), Proceedings Seventh Workshop on Membrane Computing (WMC7), Leiden, Series Lecture Notes in Computer Science, Vol. 4361, pp. 409-423, Springer Verlag, 2006

James Decraene, Peter Dittrich, Thomas Hinze, Thorsten Lenser (2006)
A Protein Substructure Based P System for Description and Analysis of Cell Signalling Networks
In: H.J. Hoogeboom, G. Paun, G. Rozenberg (Eds.), Proceedings Seventh Workshop on Membrane Computing (WMC7), Leiden, Series Lecture Notes in Computer Science, Vol. 4361, pp. 409-423, Springer Verlag, 2006

Thomas Hinze, Thorsten Lenser, Peter Dittrich (2006)
Zellsignalnetzwerke - Biologische Computer mit universeller Berechnungsstärke
In: R. Freund, M. Oswald (Eds.), Proc. 16. Theorietag Automaten und Formale Sprachen, p. 73--77, TU Wien, 2006

Christoph Schmidt, Thomas Hinze, Thorsten Lenser, Peter Dittrich (2006)
Selected Public Databases and Software Tools with Relevance to the ESIGNET Project
Technical Report on Computer Science 06-24, 64 pp., FSU Jena, 2006

Naoki Matsumaru, Peter Dittrich (2006)
Organization-oriented chemical programming for the organic design of distributed computing systems
Proc. of BIONETICS'06, Cavalese, December 11-13, IEEE
other links:
Anne Kupczok, Peter Dittrich (2006)
Determinants of Simulated RNA Evolution
J. Theor. Biol., 238(3), 726-735
other links:
Christoph Kaleta, Florian Centler, Peter Dittrich (2006)
Analyzing Molecular Reaction Networks: From Pathways to Chemical Organizations
Mol. Biotechnol., 34(2): 117-123

Naoki Matsumaru, Pietro Speroni di Fenizio, Florian Centler, Peter Dittrich (2006)
On the Evolution of Chemical Organizations
in: S. Artmann, P. Dittrich (Eds.), Proc. 7th German Workshop on Artificial Life, p. 135-146
other links:
Stefan Artman, Peter Dittrich (2006)
Explorations in the Complexity of Possible Life: Abstracting and Synthesizing the Principles of Living Systems, Proceedings of the 7th German Workshop on Artificial Life
IOS Press, Amsterdam

Naoki Matsumaru, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich (2006)
Chemical organization theory applied to virus dynamics
it - Information Technology, 48(3), 154-160
other links:
Peter Dittrich, Pietro Speroni di Fenizio (2006)
Chemical Organization Theory
In: M. Al-Rubeai, M. Fussenegger (Eds.); Cell Engineering, Volume 5: Systems Biology, p. 361-393, Springer
other links:
Naoki Matsumaru, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich (2006)
Chemical Organization Theory as a Theoretical Base for Chemical Computing
International Journal of Unconventional Computing, 3(4), 285-309
other links:
Florian Centler, Pietro Speroni di Fenizio, Naoki Matsumaru, Peter Dittrich (2006)
Chemical organizations in the central sugar metabolism of Escherichia Coli
In: Modeling and Simulation in Science Engineering and Technology, Post-proceedings of ECMTB 2005 (in print)

Christian Knüpfer, Clemens Beckstein, Peter Dittrich (2006)
Towards a Semantic Description of Bio-Models: Meaning Facets -- A Case Study
In Ananiadou, S., Fluck, J. (eds.): Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM 2006), Jena, April 9-12, 2006. CEUR-WS, Aachen, RWTH University, pp.97-100 (2006)
other links:
Clemens Beckstein, Peter Dittrich, Christian Erfurth, Dietmar Fey, Birgitta König-Ries, Martin Mundhenk, Harald Sack (2006)
SOGOS - Distributed Meta Level Architecture for the Self-Organizing Grid of Services
In: Mobile Services and Ontologies (MoSO 2006), 9 May 2006, Nara, Japan, p. 1-8, IEEE DL (in print)

2005

Peter Dittrich, Pietro Speroni di Fenizio (2005)
Chemical Organization Theory: Towards a Theory of Constructive Dynamical Systems
arXiv:q-bio.MN/0501016 (supplement available on request)
other links:
Naoki Matsumaru, Pietro Speroni di Fenizio, Florian Centler, Peter Dittrich (2005)
A Case Study of Chemical Organization Theory Applied to Virus Dynamics
in: J. T. Kim (Ed.), Systems Biology Workshop at ECAL 2005, Workshop Proceedings CD-ROM, 5-9 Septmebner 2005, Kent, UK
other links:
Naoki Matsumaru, Florian Centler, Peter Dittrich (2005)
Chemical Organization Theory as a Theoretical Base for Chemical Computing
in: C. Teuscher, A. Adamatzky (Eds.), Workshop on Unconventional Computing, p. 71-82, Luniver Press, Beckington.
other links:
Peter Dittrich (2005)
The Chemical Information Processing Metaphor as a Programming Paradigm for Organic Computing
In: Proc. of the Workshop Self-Organization and Emergence, 18th International Conference on Architecture of Computing Systems (ARCS 2005), U. Brinkschulte et al. (Eds.), VDE Verlag, Innsbruck, Austria, March 14-17, p. 95-100, 2005.
other links:
Peter Dittrich (2005)
Chemical Computing
in: J.-P. Banatre, J.-L. Giavitto, P. Fradet, O. Michel (Eds.), Unconventional Programming Paradigms (UPP 2004), LNCS 3566, p. 19 - 32, Springer, Berlin, 2005

Peter Dittrich, Lars Winter (2005)
Reaction Networks as a Formal Mechanism to Explain Social Phenomena
in: H. Deguchi, K. Kijima, T. Terano, H. Kita (Eds.), Proceeding of The Fourth International Workshop on Agent-based Approaches in Economics and Social Complex Systems (AESCS 2005), July 9-13, 2005, Tokyo Institute of Technology, p. 433-446

2004

Christian Knüpfer, Peter Dittrich, Clemens Beckstein (2004)
Artificial Gene Regulation: A Data Source for Validation of Reverse Bioengineering
in: H. Schaub, F. Detje, U. Brüggemann (Eds), Proceedings of the 6th German Workshop on Artificial Life (GWAL6), April 14-16, 2004, Bamberg, Germany, pp. 66-75, Akademische Verlagsgesellschaft Aka, Berlin.

Naoki Matsumaru, Florian Centler, Klaus-Peter Zauner, Peter Dittrich (2004)
Self-adaptive Scouting - Autonomous Experimentation for Systems Biology
in: Raidl, G. R. et al. (Eds.) Applications of Evolutionary Computing, EvoWorkshops 2004. LNAI 3005:52-62, Springer, Berlin

Christian Lasarczyk, Peter Dittrich, Wolfgang Banzhaf (2004)
Topology Based Training Set Selection
Evolutionary Computation, 12(2):223-242
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2003

Peter Dittrich, Thomas Kron, Wolfgang Banzhaf (2003)
On the Scalability of Social Order: Modeling the Problem of Double and Multi Contingency Following Luhmann
Journal of Artificial Societies and Social Simulation, 6(1)
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Wolfgang Banzhaf, Thomas Christaller, Peter Dittrich, kim, Jens Ziegler (2003)
Advances in Artificial Life - 7th European Conference, ECAL 2003, Dortmund, Germany September 2003, Proceedings
LNAI 2801, Springer, Berlin

Florian Centler, Peter Dittrich, Lawrence Ku, Naoki Matsumaru, Jeffrey Pfaffmann, Klaus-Peter Zauner (2003)
Artificial Life as an Aid to Astrobiology: Testing Life Seeking Techniques
W. Banzhaf et al., Advances in Artificial Life, ECAL 2003, LNAI 2801, pp. 31-40, Springer, Berlin, 2003

Peter Dittrich, kim (2003)
Workshop and Tutorials - European Conference for Artificial Life, September 14-17, 2003, Dortmund
University of Dortmund, 2003

2002

Peter Dittrich, Thomas Kron (2002)
Complex Reflexive Agents as Models of Social Actors
Proc. of the SICE Workshop on Artificial Society/Organization/Economy, 25th Meeting of System Engineering. 20 March 2002, Gakujutso Sougou Center, Tokyo, Japan. pp. 79-88.

Pietro Speroni di Fenizio, Peter Dittrich (2002)
Artificial Chemistry's Global Dynamics. Movement in the Lattice of Organisation
The Journal of Three Dimensional Images, 16(4):160-163.

Thomas Kron, Peter Dittrich (2002)
Doppelte Kontingenz nach Luhmann - Ein Simulationsexperiment
T. Kron (Ed.), Luhmann modelliert, Leske+Budrich, Opladen, pp. 209-251

Wolfgang Banzhaf, Peter Dittrich (2002)
Morphogenetic Programming (MGP)
Series "SYS Report", Technical Report of Systems Analysis Research Group, University of Dortmund, Department of Computer Science, D-44221 Dortmund, Germany, No. SYS-2/02, ISSN 0941-4568,, Univ. of Dortmund, 1998

2001

Peter Dittrich, Jens Ziegler, Wolfgang Banzhaf (2001)
Artificial Chemistries - A Review
Artificial Life, 7(3):225-275

Peter Dittrich, Wolfgang Banzhaf (2001)
Survival of the Unfittest? - The Seceder Model and its Fitness Landscape
J. Kelemen and P. Sosik (Eds.), Advances in Artificial Life (Proc. 6th European Conference on Artificial Life), LNCS 2159, pp. 100-109, Prague, September 10-14, 2001. Springer, Berlin

Pietro Speroni di Fenizio, Peter Dittrich, Wolfgang Banzhaf (2001)
Spontaneous Formation of Proto-Cells in an Universal Artificial Chemistry on a Planar Graph
J. Kelemen and P. Sosik (Eds.), Advances in Artificial Life (Proc. 6th European Conference on Artificial Life), LNCS 2159, pp. 206-215, Prague, September 10-14, 2001. Springer, Berlin

Pietro Speroni di Fenizio, Peter Dittrich, Jens Ziegler, Wolfgang Banzhaf (2001)
Towards a Theory of Organizations
German Workshop on Artificial Life (GWAL 2000), Bayreuth, April 5-7, 2000 (in print)
other links:
Thomas Kron, Peter Dittrich (2001)
Doppelte Kontingenz und Strukturbildung
T. Kron, K Junge, S. Papendick (Hrsg.): Luhmann modelliert. Ansätze zur Simulation von Kommunikationssystemen. Opladen. Leske + Budrich (accepted, in German)

Peter Dittrich (2001)
On Artificial Chemistries
Doctoral thesis, University of Dortmund, Department of Computer Science, D-44221 Dortmund, Germany, January 25, 2001

Peter Dittrich, Thomas Kron, Christian Kuck, Wolfgang Banzhaf (2001)
Iterated Mutual Observation with Genetic Programming
Sozionik Aktuell 2/2001
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2000

Peter Dittrich, Fredrik Liljeros, Arne Soulier, Wolfgang Banzhaf (2000)
Spontaneous Group Formation in the Seceder Model
Phys. Rev. Lett., 84:3205-3208
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Peter Dittrich (2000)
The Seceder Effect in Bounded Space
InterJournal Complex Systems, 363
other links:
Peter Dittrich, Mathias Wulf, Wolfgang Banzhaf (2000)
A Vital 2-D Assembler Automaton
Artificial Life VII Workshop Proceedings, C. C. Maley and E. Boudreau (Eds.), 2000
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Andre Skusa, Wolfgang Banzhaf, Jens Busch, Peter Dittrich, Jens Ziegler (2000)
Künstliche Chemie
Künsliche Intelligenz, 1/00: 12-19
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Thomas Kron, Peter Dittrich (2000)
Der komplexe Agent - Eine algorithmische Formalisierung von Akteurmodellen
30. Kongress der Deutschen Gesellschaft für Soziologie, "Gute Gesellschaft ?", Abstract-Band, September 26-29, 2000, Köln, Germany, pp. 169-170. Full paper in german available on request

1999

Wolfgang Banzhaf, Peter Dittrich, Burkhard Eller (1999)
Topological Interactions in a Binary String System
Physica D, 125 (1999) 85 - 104
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Peter Dittrich (1999)
Artificial Chemistries
(tutorial material) Tutorial held at ECAL'99, 13-17 September 1999, Lausanne, CH
other links:
Peter Dittrich, Andre Skusa, Wolfgang Kantschik, Wolfgang Banzhaf (1999)
Dynamical Properties of the Fitness Landscape of a GP Controlled Random Morphology Robot
Proceedings of the Genetic and Evolutionary Computation Conference, W. Banzhaf and Jason Daida and A. E. Eiben and M. H. Garzon and V. Honavar and Mark Jakiela and Robert E. Smith (Eds.), vol. 2, p. 1002-1008, Morgan Kaufmann, San Francisco, CA, 1999
other links:
Wolfgang Kantschik, Peter Dittrich, Markus Brameier, Wolfgang Banzhaf (1999)
Empirical Analysis of Different Levels of Meta-Evolution
Congress on Evolutionary Computation (CEC99), July 6-9, 1999, Washington DC, USA, vol. 3, p. 2086-2093, IEEE, 1999

Wolfgang Kantschik, Peter Dittrich, Markus Brameier, banhaf (1999)
Meta-Evolution in Graph GP
Genetic Programming, Second European Workshop (EuroGP'99), Proceedings, R. Poli, P. Nordin, W.B. Langdon, T.C. Fogarty (eds.), LNCS 1598, p. 15-28, Springer, Berlin, 1999
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Wolfgang Banzhaf, Dirk Banscherus, Peter Dittrich (1999)
Hierarchical Genetic Programming using Local Modules
Series "Computational Intelligence ", Internal Report of SFB 531, No. 56/99, ISSN 1433-3325, Univ. of Dortmund, D-44221 Dortmund, Germany, 1999

1998

Peter Dittrich, Wolfgang Banzhaf (1998)
Self-Evolution in a Constructive Binary String System
Artificial Life 4(2), pp. 203-220, 1998
other links:
Peter Dittrich, Andreas Buergel, Wolfgang Banzhaf (1998)
Learning to Move a Robot with Random Morphology
Evolutionary Robotics, First European Workshop, EvoRob98, Paris, France, April 1998, Proceedings, Phil Husbands and Jean-Arcady Meyer (eds.), LNCS 1468, pp. 165-178 Springer, Berlin, 1998
other links:
Peter Dittrich, Jens Ziegler, Wolfgang Banzhaf (1998)
Mesoscopic Analysis of Self-Evolution in an Artificial Chemistry
Proc. of ''Artificial Life VI'', Los Angeles, June 26-29, 1998; C. Adami, R. Belew, H. Kitano, and C. Taylor, eds., MIT Press, pages 95-103
other links:
Peter Dittrich, Jens Ziegler, Wolfgang Banzhaf (1998)
Mesoscopic Analysis of an Artificial Chemistry with Self-Organizing Topology
Third German Workshop on Artificial Life, C. Wilke and S. Altmeyer and T. Martinetz (eds.), pp. 155-170, Verlag Harri Deutsch, Frankfurt a. M., 1998
other links:
Peter Dittrich (1998)
Real Evolution in Artificial Chemistries
The Right Stuff: Appropriate Mathematics for Evolutionary and Developmenta Biology, Chrystopher L. Nehaniv and Günter P. Wagner (Eds.), Technical Report, Computer Science, University of Hertfordshire, School of Information Science, No. 315, p. 27-31

Peter Dittrich, Jens Ziegler (1998)
Artificial Chemistries (workgroup proposal)
Third German Workshop on Artificial Life, C. Wilke and S. Altmeyer and T. Martinetz (Eds.), p. 249-258 Verlag Harri Deutsch, Frankfurt a. M.

Peter Dittrich, Wolfgang Banzhaf, Hilmar Rauhe, Jens Ziegler (1998)
Macroscopic and Microscopic Computation in an Artificial Chemistry
Proceedings of the Second German Workshops on Artificial Life (GWAL'97), P. Dittrich, H. Rauhe, and W. Banzhaf (Eds.), SYS Report, No. SYS-5/98, ISSN 0941-4568, Univ. of Dortmund, p. 19-22, 1998
other links:
Wolfgang Banzhaf, Dirk Banscherus, Peter Dittrich (1998)
Hierarchical Genetic Programming using Local Modules
InterJournal Complex Systems, no. 228
other links:
Markus Brameier, Wolfgang Kantschik, Peter Dittrich, Wolfgang Banzhaf (1998)
SYSGP - A C ++ library of different GP variants
Series "Computational Intelligence", Internal Report of SFB 531, No. 48/98, ISSN 1433-3325, Univ. of Dortmund, D-44221 Dortmund, Germany, 1998

Peter Dittrich, Hilmar Rauhe, Wolfgang Banzhaf (1998)
Proceedings of the Second German Workshop on Artificial Life
Series "SYS Report", Technical Report of Systems Analysis Research Group, University of Dortmund, Department of Computer Science, D-44221 Dortmund, Germany, No. SYS-5/98, ISSN 0941-4568,, Univ. of Dortmund, 1998
other links:

1997

Peter Dittrich, Wolfgang Banzhaf (1997)
A Topological Structure Based on Hashing - Emergence of a "Spatial" Oranization
Fourth European Conference on Artificial Life (ECAL97), Brighton 1997
other links:
Jens Ziegler, Peter Dittrich, Wolfgang Banzhaf (1997)
Towards a Metabolic Robot Controller
Information Processing in Cells and Tissues, Mike Holcombe and Ray Paton (eds.), Plenum Press, New York, pp. 305-318
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1996

Wolfgang Banzhaf, Peter Dittrich, Hilmar Rauhe (1996)
Emergent Computation by Catalytic Reactions
Nanotechnology, 7 (1996) pp. 307 - 314
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1995

Peter Dittrich (1995)
Selbstorganisation in einem System von Binärstrings mit algorithmischen Sekundärstrukturen
Diplomarbeit im Fachbereich Informatik der Universität Dortmund, Lehrstul fuer Systemanalyse (LS XI) (Diplomathesis, Dept. of Computer Science, University of Dortmund)
other links:
Peter Dittrich, Wolfgang Banzhaf (1995)
Selbstevolution in einem Binärstringsystem
Proceedings des Workshops "Artificial Life", GMD-Studien Nr. 271, Kersin Dautenhahn et al., Sankt Augustin 1995
other links:
Peter Dittrich, Wolfgang Banzhaf (1995)
The chemical computation metaphor and robot control
Third European Conf. Artificial Life (ECAL'95) - Abstracts, page 45, Granada, Spain, June 4-6, 1995.