blue wonder

PD Dr. Thomas Hinze

blue wonder
Image: Dr. Thomas Hinze
Visiting researcher
  • About him

    PD Dr. Thomas Hinze

    Image: Dr. Thomas Hinze

    PD Dr.-Ing. habil. Thomas Hinze

    was born in Halle/Saale in 1971. He graduated from the Dresden University of Technology with Diploma degree in computer science in 1997. Afterwards, he was employed as a software developer within the field of SAP-based applications. Later, he returned to academic research equipped with a PhD scholarship by the Studienstiftung des Deutschen Volkes (German Academic Scholarship Foundation). He received the PhD at Dresden University of Technology with the level summa cum laude for his thesis entitled "Universal Models and Selected Algorithms of DNA Computing" in 2002. Subsequently, he moved to the Friedrich Schiller University Jena in 2006. Starting as a postdoctoral researcher in the BioSystems Analysis Group headed by apl. Prof. Peter Dittrich, he continued his stay as project leader at the Department of Bioinformatics headed by Prof. Stefan Schuster explorating principles of biological information processing from 2009. In 2012, he became a senior university lecturer at the Friedrich Schiller University Jena along with his professorial dissertation entitled "Molecular Computing". In the same year, he filled the position of a university lecturer at the Brandenburg University of Technology Cottbus and succeeded in self-dependent teaching and enhancing the research area of Membrane Computing. Since 2017, he acts as senior university lecturer and independent guest research fellow at Friedrich Schiller University Jena again. His list of publications comprises 78 records in total including two patents and two German-speaking textbooks ("Computing with DNA" and "Computers Found in Nature"). He is a steering committee member of the International Membrane Computing Society and editorial board member of the Springer Journal of Membrane Computing.

    Link: personal web page https://users.fmi.uni-jena.de/~hinze/index-en.htmlExternal link

  • Research interests
    • Biologically Inspired Computing (in vitro, in vivo, in silico)
    • Molecular Computing (DNA-, RNA-, Protein-Computing, Chemical Computing, Dynamical Structures)
    • Membrane-, Cell-Based, Neural, Amorphous, Evolutionary Computing, Artificial Life,       Organic Computing
    • Systems, Synthetic, and Algebraic Biology for Exploration of Biological Information Processing
  • Publications

    https://users.fmi.uni-jena.de/~hinze/publikationen.htmlExternal link

    2023

    B. Förster, P. Langendörfer, T. Hinze.
    A Novel Approach to a Plant Inspired Distributed Security Scheme for Wireless Sensor Networks.
    2023 IEEE International Conference on Communications (ICC): IoT and Sensor Networks Symposium, 2022, submitted

    2022

    B. Förster, P. Langendörfer, T. Hinze.
    Determining Distributions of Security Means for Wireless Sensor Networks based on the Model of a Neighbourhood Watch. International Journal of Information Security, Springer Verlag, 2022, accepted

    A. Henderson, R. Nicolescu, M.J. Dinneen, T. Chan, H. Happe, T. Hinze.
    Programmable and Parallel Water Computing.
    Journal of Membrane Computing 4(4):209-221, Springer Verlag, 2022, in print

    R. Starke, I. Vukorep, K. Frommelt, A. Melcher, T. Hinze.
    Towards Artificial Ossification for Boneinspired Technical Structures.
    In M.F. Hvejsel and P.J.S. Cruz (Eds.), Structures and Architecture, Vol. 2, ISBN 978-0-367-90281-0, pp. 1211-1218, CRC Press (Taylor and Francis Group), 2022

    2021

    A. Henderson, R. Nicolescu, M.J. Dinneen, T. Chan, H. Happe, T. Hinze.
    Turing Completeness of Water Computing.
    Journal of Membrane Computing 3(3):182-193, Springer Verlag, 2021

    Link: https://doi.org/10.1007/s41965-021-00081-3External link

    G. Zhang, M.J. Perez-Jimenez, A. Riscos-Nunez, S. Verlan, S. Konur, T. Hinze, M. Gheorghe.
    Membrane Computing Models: Implementations.
    Springer-Verlag, 301 p., 2021

    ISBN 978-981-16-1565-8 (print version)
    ISBN 978-981-16-1566-5 (eBook)

    Link: https://doi.org/10.1007/978-981-16-1566-5External link

    2020

    T. Hinze.
    Coping with Dynamical Reaction System Topologies using Deterministic P Modules: A Case Study of Photosynthesis. Journal of Membrane Computing 2(4):281-289, Springer Verlag, 2020

    T. Hinze, H. Happe, A. Henderson, R. Nicolescu.
    Membrane Computing with Water. Journal of Membrane Computing 2(2):121-136, Springer Verlag, 2020

    2019

    T. Hinze, G. Rozenberg, A. Salomaa, C. Zandron (Editors).
    Membrane Computing. 19th International Conference, CMC 2018, Dresden, Germany, September 4-7, 2018, Revised Selected Papers. Series Lecture Notes in Computer Science, Vol. 11399, ISBN 978-3-030-12797-8, Springer-Verlag Berlin, Heidelberg, 288 p., 2019

    B. Förster, T. Hinze.
    Towards Automated Analysis of Belousov-Zhabotinsky Reactions in a Petri Dish by Membrane Computing using Optic Flow. In T.Hinze, G. Rozenberg, A. Salomaa, C. Zandron (Eds.), Membrane Computing. 19th International Conference. Series Lecture Notes in Computer Science, ISBN 978-3-030-12797-8, Vol. 11399, pp. 131-141, Springer Verlag, 2019

    A. Melcher, I. Vukorep, T. Hinze.
    Construction of Stable and Lightweight Technical Structures Inspired by Ossification of Bones using Osteogenetic P Systems. In T.Hinze, G. Rozenberg, A. Salomaa, C. Zandron (Eds.), Membrane Computing. 19th International Conference. Series Lecture Notes in Computer Science, ISBN 978-3-030-12797-8, Vol. 11399, pp. 208-228, Springer Verlag, 2019, Best Paper Award

     

    2018

    T. Hinze, J. Behre (Editors).
    Preliminary Proceedings of the Nineteenth International Conference on Membrane Computing (CMC19).
    ISBN 978-3-96409-030-0, Verlag ProBusiness Berlin, 276 S., 2018

    T. Hinze. The Java Environment for Nature-inspired Approaches (JENA): A Workbench for BioComputing and BioModelling Enthusiasts. In C. Graciani, A. Riscos-Nunez, Gh. Paun, G. Rozenberg, A. Salomaa (Eds.), Enjoying Natural Computing, Series Lecture Notes in Computer Science, Vol. 11270, pp. 155-169, ISBN 978-3-030-00264-0, Springer Verlag, 2018, invited paper

    Thomas Hinze, Benjamin Förster
    Event-based Life in a Nutshell: How Evaluation of Individual Life Cycles Can Reveal Statistical Inferences using Action-accumulating P Systems
    Lecture Notes in Computer Science 10725, 2018, 129-150, In: M. Gheorghe, G. Rozenberg, A. Salomaa, C. Zandron (Eds.), Membrane Computing. 18th International Conference. ISBN 978-3-319-73358-6, Springer Verlag
    [ bibtexExternal link | abstractExternal link ]

    2017

    T. Hinze
    Interview with Gheorghe Paun
    Bulletin of the International Membrane Computing Society, 2017, to appear in issue December 2017
    [ bibtexExternal link ]

    T. Hinze
    Coping with Dynamical Structures for Interdisciplinary Applications of Membrane Computing
    Springer Series Lecture Notes in Computer Science 10105, 2017, 16-27
    [ bibtexExternal link | abstractExternal link |  doi External link ]

    T. Hinze, L. Weber, U. Hatnik
    Walking Membranes: Grid-exploring P Systems with Artificial Evolution for Multi-purpose Topological Optimisation of Cascaded Processes
    Lecture Notes in Computer Science 10105 , 2017, 251-271
    [ bibtexExternal link | abstractExternal link |  doi External link ]

    2016

    T. Hinze, J. Behre, K. Kirkici, Pa. Sauer, Pe. Sauer, S. Hayat
    Passion to P for Polymorphic Processes in Practice
    In: Multidisciplinary Creativity. Homage to Gheorghe Paun on His 65th Birthday (eds. M. Gheorghe, I. Petre, M.J. Perez-Jimenez, G. Rozenberg, A. Salomaa), ISBN 978-606-8401-63-8, Spandugino, 2016, ch. 7, 77-88
    [ bibtexExternal link | abstractExternal link ]

    T. Hinze, K. Kirkici, Pa. Sauer, Pe. Sauer, J. Behre
    Membrane Computing Meets Temperature: A Thermoreceptor Model as Molecular Slide Rule with Evolutionary Potential
    Springer Lecture Notes in Computer Science 9504, 2016, 215-235
    [ bibtexExternal link | abstractExternal link |  doi External link |  url External link ]

    2015

    P. Sauer, T. Hinze, P. Hofstedt
    Dynamic Ad-hoc Topologies for Mobile Robot Navigation Based on Non-Uniform Grid Maps
    International Journal of Mechanical and Mechatronics Engineering 2(6), 2015, 92-101
    [ bibtexExternal link | abstractExternal link ]

    T. Hinze, K. Grützmann, B. Höckner, P. Sauer, S. Hayat
    Categorised Counting Mediated by Blotting Membrane Systems for Particle-Based Data Mining and Numerical Algorithms
    Lecture Notes in Computer Science 8961, 2015, 241-257
    [ bibtexExternal link | abstractExternal link |  doi External link |  url External link ]

    2014

    T. Hinze, J. Behre, C. Bodenstein, G. Escuela, G. Grünert, P. Hofstedt, P. Sauer, S. Hayat, P. Dittrich
    Membrane Systems and Tools Combining Dynamical Structures with Reaction Kinetics for Applications in Chronobiology
    In: Applications of Membrane Computing in Systems and Synthetic Biology (eds. P. Frisco, M. Gheorghe, M.J. Perez-Jimenez), Springer Series Emergence, Complexity, and Computation, 2014, ch. 5, 133-173
    [ bibtexExternal link |  doi External link |  url External link ]

    2013

    T. Hinze
    Unraveling Oscillating Structures by Means of P Systems
    International Journal of Foundations of Computer Science 24(5), 2013, 605-607
    [ bibtexExternal link |  doi External link ]

    T. Hinze
    Computer der Natur
    T. Hinze, Verlag bookboon.com, ISBN 978-87-403-0378-0, 2013, eBook
    [ bibtexExternal link |  url External link ]

    T. Hinze, B. Schell, M. Schumann, C. Bodenstein
    Maintenance of Chronobiological Information by P System Mediated Assembly of Control Units for Oscillatory Waveforms and Frequency
    In: Membrane Computing. 13th International Conference (eds. E. Csuhaj-Varju, M. Gheorghe, G. Paun, G. Rozenberg, A. Salomaa, G. Vaszil), Vol. 7762, Springer Verlag, 2013, 208-227
    [ bibtexExternal link |  doi External link ]

    2012

    T. Hinze
    Unraveling Oscillating Structures by Means of P Systems
    In: Research Topics in Membrane Computing (eds. M. Gheorghe, G. Paun, M.J. Perez-Jimenez), University of Sevilla, 2012, 39-42
    [ bibtexExternal link |  pdf External link |  url External link ]

    I. Heiland, C. Bodenstein, T. Hinze, O. Weisheit, O. Ebenhoeh, M. Mittag and S. Schuster
    Modelling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii
    Journal of Biological Physics 38 (3), 2012, 449-464
    [ bibtexExternal link | abstractExternal link |  doi External link ]

    T. Hinze, C. Bodenstein, B. Schau, I. Heiland, S. Schuster
    Chemical Analog Computers for Clock Frequency Control Based on P Modules
    In: Membrane Computing. Proceedings of the 12th International Conference (CMC12) (eds. M. Gheorghe, G. Paun, R. Rozenberg, A. Salomaa, S. Verlan), Springer Verlag, Vol. 7184, 2012, 182-202
    [ bibtexExternal link | abstractExternal link |  doi External link ]

    G. Gruenert, G. Escuela, P. Dittrich, T. Hinze
    Morphological Algorithms: Membrane Receptor-ligand Interactions and Rule-based Molecule Graph Evolution for Exact Set Cover Problems
    In: Membrane Computing. Proceedings of the 12th International Conference (CMC12) (eds. M. Gheorghe, G. Paun, R. Rozenberg, A. Salomaa, S. Verlan), Springer Verlag, Vol. 7184, 2012, 160-181
    [ bibtexExternal link | abstractExternal link |  doi External link ]

    2011

    T. Hinze, M. Schumann, C. Bodenstein, I. Heiland, S. Schuster
    Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In-silico Study of Modules for Circadian Clock Systems.
    Computational Intelligence and Neuroscience, vol. 2011, 2011, ID 262189
    [ bibtexExternal link | abstractExternal link |  doi External link |  url External link |  PudMed-ID: 22046179External link ]

    T. Hinze, C. Bodenstein, I. Heiland, S. Schuster
    Capturing Biological Frequency Control of Circadian Clocks by Reaction System Modularization
    ERCIM News 85, 2011, 27-29
    [ bibtexExternal link | abstractExternal link ]

    T. Hinze, M. Schumann, S. Schuster
    Synchronisation of Biological Clock Signals: Capturing Coupled Repressilators from a Control Systems Perspective
    In: Proceedings of the Fourth International Conference on Bio-Inspired Systems and Signal Processing (BIOSIGNALS2011) (eds. F. Babiloni, A. Fred, J. Filipe, H. Gamboa), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, SciTePress, ISBN 978-989-8425-35-5, 2011, 101-106
    [ bibtexExternal link | abstractExternal link ]

    2010

    Membrane Computing. Eleventh International Conference, CMC 2010, Jena, Germany, August 24-27, 2010. Revised Selected Papers.
    M. Gheorghe, T. Hinze, G. Paun, G. Rozenberg, A. Salomaa (Eds.), Series: Lecture Notes in Computer Science (Vol. 6501), Subseries: Theoretical Computer Science and General Issues , Springer Verlag, Heidelberg 2010, 393, ISBN: 978-3642181221
    [ bibtexExternal link | abstractExternal link ]

    Proceedings Compendium of the Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC2010) and of the First Workshop on Applications of Membrane Computing, Concurrency, and Agent-based Modelling in Population Biology (AMCA-POP2010)
    J. Behre, G. Escuela, T. Hinze (Eds.), ProBusiness Verlag, Berlin 2010, 238, ISBN: 978-3-86805-767-6
    [ bibtexExternal link ]

    G. Escuela, T. Hinze, P. Dittrich, S. Schuster, M. Moreno
    Modelling Modified Atmosphere Packaging for Fruits and Vegetables using Membrane Systems
    In: Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing (BIOSIGNALS2010) (eds. ), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, INSTICC press, 2010, 306-311, ISBN: 978-989-674-018-4
    [ bibtexExternal link ]

    G. Grünert, B. Ibrahim, T. Lenser, M. Lohel, T. Hinze, P. Dittrich
    Rule-based spatial modeling with diffusing, geometrically constrained molecules
    BMC Bioinformatics 11, 2010, 307
    [ bibtexExternal link | abstractExternal link |  doi External link |  PudMed-ID: 20529264External link ]

    J. Decraene, T. Hinze
    A Multidisciplinary Survey of Computational Techniques for the Modelling, Simulation and Analysis of Biochemical Networks
    Journal of Universal Computer Science 16 (9), 2010, 1152-1175
    [ bibtexExternal link | abstractExternal link |  url External link ]

    M. Sturm, T. Hinze
    Verfahren zur Ausführung von mathematischen Operationen mittels eines DNA-Computers und DNA-Computer hierzu
    Deutsches Patent, DE 101 59 886 B4, IPC G06N 3/00 patent, Deutsches Patentamt München, 2010, granted 2010
    [ bibtexExternal link ]

    G. Escuela, T. Hinze, P. Dittrich, S. Schuster, M. Moreno-Alvarez
    Applying Membrane Systems in Food Engineering
    In: Eight Brainstorming Week on Membrane Computing (eds. M.A. Martinez-del-Amor, G. Paun, I. Perez-Hurtado, A. Riscos-Nunez), Fenix Editora, Sevilla 2010, 109-121, ISBN: 978-84-614-2357-6
    [ bibtexExternal link ]

    H. Bordihn, R. Freund, T. Hinze, M. Holzer, M. Kutrib, F. Otto
    Proceedings of the Second Workshop on Non-Classical Models for Automata and Applications - Vol. 263 (NCMA2)
    Austrian Computer Society 2010, ISBN: 978-3-85403-263-2
    [ bibtexExternal link ]

    M. Gheorghe T. Hinze, G. Paun
    Proceedings of the Eleventh International Conference on Membrane Computing (CMC11)
    ProBusiness Verlag, Berlin 2010, ISBN: 978-3-86805-721-8
    [ bibtexExternal link ]

    G. Gruenert, B. Ibrahim, T. Lenser, M. Lohel, T. Hinze, P. Dittrich
    Rule-based spatial modeling with diffusing, geometrically constrained molecules.
    BMC Bioinformatics 11, 2010, 307
    [ bibtexExternal link |  PudMed-ID: 20529264External link ]

    T. Hinze, J. Decraene, G.G. Mitchell, J. Behre, S. Schuster
    Towards a Unified Approach for the Modelling, Analysis, and Simulation of Cell Signalling Networks.
    In: Sequence and Genome Analysis: Methods and Applications (eds. Z. Zhao), iConcept Press, 2010, ch. 13, 227-257
    [ bibtexExternal link |  pdf External link ]

    T. Hinze, T. Lenser, G. Escuela, I. Heiland, S. Schuster
    Modelling Signalling Networks with Incomplete Information about Protein Activation States: A P System Framework of the KaiABC Oscillator
    In: Proceedings of the 10th International Workshop on Membrane Computing (WMC) (eds. G. Paun, M.J. Perez-Jimenez, A. Riscos-Nunez, A. Salomaa), Springer Verlag, 2010, 316-334
    [ bibtexExternal link ]

    2009

    R. Haberland, T. Hinze
    Prolog-based XML processing for compact representation and deductive evaluation of biological reaction networks
    In: Abstract Booklet, International Conference Biosystems Analysis and Engineering (BioSys) (eds. G. Antranikian, D. Chiu, F. Keil, A. Liese, T.Scheper, A.-P. Zeng), University of Technology Hamburg, 2009, 27
    [ bibtexExternal link ]

    T. Hinze, R. Faßler, G. Escuela, B. Ibrahim, S. Schuster
    Computation by Synthetic Cell Signaling and Oscillating Processes Modelled using Mass-Action Kinetics
    In: Proceedings Booklet Fifth Conference on Computability in Europe (CiE) (eds. K. Ambos-Spies, B. Löwe, W. Merkle), University of Heidelberg 2009, 186-195
    [ bibtexExternal link ]

    N. Matsumaru, T. Hinze, P. Dittrich
    Organization-Oriented Chemical Programming of Distributed Artifacts
    International Journal of Nanotechnology and Molecular Computation 1 (4), 2009, 54-70
    [ bibtexExternal link ]

    T. Hinze, R. Fassler, T. Lenser, P. Dittrich
    Register Machine Computations on Binary Numbers by Oscillating and Catalytic Chemical Reactions Modelled using Mass-Action Kinetics
    International Journal of Foundations of Computer Science 20, 2009, 411-426
    [ bibtexExternal link ]

    T. Hinze, R. Fassler, T. Lenser, N. Matsumaru, P. Dittrich
    Event-Driven Metamorphoses of P Systems
    Lecture Notes in Computer Science 5391, 2009, 231-245
    [ bibtexExternal link ]

    2008

    T. Hinze, S. Hayat, T. Lenser, N. Matsumaru, P. Dittrich
    Biosignal-Based Computing by AHL Induced Synthetic Gene Regulatory Networks
    In: Proceedings of the First International Conference on Bio-Inspired Systems and Signal Processing (BIOSIGNALS) (eds. ), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, 2008, 162-169
    [ bibtexExternal link ]

    T. Lenser, N. Matsumaru, T. Hinze, P. Dittrich
    Tracking the Evolution of Chemical Computing Networks
    In: Proceedings of Artificial Life XI (eds. ), 2008, 343-350
    [ bibtexExternal link ]

    S. Hayat, T. Hinze
    Toward integration of in vivo molecular computing devices: successes and challenges
    HFSP Journal 2, 2008, 239-243
    [ bibtexExternal link ]

    2007

    T. Hinze, S. Hayat, T. Lenser, N. Matsumaru, P. Dittrich
    Hill Kinetics Meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents in silico and in vivo
    Series Lecture Notes in Computer Science 4860, 2007, 320-335
    [ bibtexExternal link ]

  • Teaching at the university Jena

    Informations about " Vorlesung und Projektübung Molekulare Algorithmen" in the summer term:

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