harold fellermann

Publications

Peer reviewed journal and conference proceedings articles

• Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World
  W. Hordijk, J. Naylor, N. Krasnogor & H. Fellermann
  Life 8(3), 33, 2018
• Sequence selection by dynamical symmetry breaking in an autocatalytic binary polymer model
  H. Fellermann, S. Tanaka & S. Rasmussen
  Physical Reviews E 96, 062407, 2017
• Simbiotics: a multi-scale integrative platform for 3D modeling of bacterial populations
  J. Naylor, H. Fellermann, Y. Ding, W. K. Mohammed, N. S. Jakubovics, J. Mukherjee, C. A. Biggs, P. C. Wright, & N. Krasnogor
  ACS Synthetic Biology, 2017
• Optimizing nucleic acid sequences for a molecular data recorder
  J. Kozyra, H. Fellermann, B. Shirt-Ediss, A. Lopiccolo & N. Krasnogor
  Proceedings of the Genetic and Evolutionary Computation Conference GECCO, 2017
• Designing uniquely addressable bio-orthogonal synthetic scaffolds for DNA and RNA origami
  J. Kozyra, A. Ceccarelli, E. Torelli, A. Lopiccolo, J. Gu, H. Fellermann, U. Stimming & N. Krasnogor
  ACS Synthetic Biology, 2017
• Toward Programmable Biology
  H. Fellermann, O. Markovitch, O. Gilfellon, C. Madsen & A. Phillips
  ACS Synthetic Biology 5(8):793-794, 2016
• In vitro implementation of a stack data structure based on DNA strand displacement
  H. Fellermann, A. Lopiccolo, J. Kozyra & N. Krasnogor
  Lect. Notes. Comp. Sci. 9726:87-98, 2016
• Modelling and stochastic simulation of synthetic biological Boolean gates
  D. Sanassy, H. Fellermann, N. Krasnogor, S. Konur, L. M. Mierla, M. Gheorghe, C. Ladroue & S. Kalvala
  Proceedings of the 2014 IEEE International Conference on High Performance Computing and Communications pp. 404-408, 2014
• Modeling and Analysis of Genetic Boolean Gates using Infobiotics Workbench
  S. Konur, C. Ladroue, H. Fellermann, D. Sanassy, L. Mierla, F. Ipate, S. Kalvala, M. Gheorghe, N. Krasnogor
  Proceedings of Workshop on Verification of Engineered Molecular Devices and Programs 2014, Vienna, Austria (CAV 2014), pp. 26-37, 2014.
• Formalising Modularisation and Data Hiding for Synthetic Biology
  H. Fellermann, M. Hadorn, R. Füchslin & N. Krasnogor
  ACM J. Emerg. Tech. Comp. Sys 11(3):24, 2014
• Programming Chemistry in DNA Adressable Bioreactors
  H. Fellermann & L. Cardelli
  Royal Society Interface 11(99), 2014
• Sequence Selection in an Autocatalytic Binary Polymer Model
  S. Tanaka, H. Fellermann & S. Rasmussen
  Europhys. Lett. 107(2), 28004, 2014
• Chemical Production and Molecular Computing in Addressable Reaction Compartments
  H. Fellermann & N. Krasnogor
  Lect. Notes Comp. Sci. 8493:173-182, 2014
• The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers
  M. Weyland, H. Fellermann, M. Hadorn, D. Sorek, D. Lancet, S. Rasmussen, & R. M. Füchslin
  Computational and Mathematical Methods in Medicine 467428, 2013
• Specific and Reversible DNA-directed Self-Assembly of Oil-in-Water Emulsion Droplets
  M. Hadorn, E. Bönzli, K. T. Sørensen, H. Fellermann, P. Eggenberger Hotz & M. Hanczyc
  Proc. Nat. Acad. Sci. USA 109(47), 2012
• DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model
  C. Svaneborg, H. Fellermann & S. Rasmussen
  Lect. Notes in Comput. Sc. 7433, 123, 2012
• On the Growth Rate of Non-Enzymatic Molecular Replicators
  H. Fellermann & S. Rasmussen
  Entropy 13(10):1882–1903, 2011
• Coarse-graining and scaling in dissipative particle dynamics
  R. Füchslin, H. Fellermann, A. Eriksson & H.-J. Ziock
  J. Chem. Phys. 130(21):214102, 2009
• A simple model of self-replicating protocells
  H. Fellermann, S. Rasmussen, H.-J. Ziock & R. Solé
  Proceedings of the 4th Annual Conference on Foundations of Nanoscience, pp. 136–139, 2007
• Life-cycle of a minimal protocell – a dissipative particle dynamics (DPD) study
  H. Fellermann, S. Rasmussen, H.-J. Ziock & R. Solé
  Artif. Life 13(4):319–345, 2007
• Minimal model of self-replicating nanocells: A physically embodied, information-free scenario
  H. Fellermann & R. Solé
  Philos. Trans. R. Soc. Ser. B 362(1486):1803–1811, 2007

Edited Volumes

• Toward Programmable Biology
  Harold Fellermann, Omer Markovitch, Curtis Madsen, Owen Gilfellon
  Special issue of the ACS Journal of Synthetic Biology, 2016
• Proceedings of the 12th International Conference on the Synthesis and Simulation of Artificial Life
  H. Fellermann, M. Dörr, M. M. Hanczyc, L. Ladegaard Laursen, S. Maurer, D. Merkle, P.-A. Monnard, K. Stoy and S. Rasmussen (Eds.)
  MIT Press Cambridge, 2010

Book chapters & Non-reviewed articles

• Wet artificial life: the creation of artificial living systems
  H. Fellermann
  in: H. Meyer-Ortmanns & S. Thurner, Principles of Evolution, Springer Heidelberg, 2010
• Spatially resolved artificial chemistry
  H. Fellermann
  in: A. Adamatzky and M. Komosinski (Eds.), Artificial Life Models in Software 2nd Edition, Springer Heidelberg, 2009
• Models of protocell replication
  R. Solé, J. Sardanyes, H. Fellermann, S. Valverde, J. Macía, and A. Munteanu
  in: S. Rasmussen, et al. (Eds.), Protocells: Bridging Nonliving and Living Matter, MIT Press Cambridge, 2008
• Seeing the net for the nodes: coarse-graining modular Boolean networks
  H. Fellermann, M. Davidich
  Santa Fe Institute Working paper. 2008
• Assembly of a minimal protocell
  S. Rasmussen, J. Bailey, J. Boncella, L. Chen, G. Collis, S. Colgate, M. DeClue, H. Fellermann, G. Goranovic, Y. Jiang, C. Knutson, P.-A. Monnard, F. Mouffouk, M. Nielson, A. Sen, A. Shreve, A. Tamulis, B. Travis, P. Weronski, J. Zhang, X. Zhou, H.-J. Ziock, and W. Woodruff
  in: S. Rasmussen, et al. (Eds.), Protocells: Bridging Nonliving and Living Matter, MIT Press Cambridge, 2008
• The search for universal measures of complexity
  H. Fellermann
  in: C. Pahl-Wostl, and E. Ebenhöh (Eds.), Komplexe adaptive Systeme 27 pp. 25–43, 2003
• Lyapunov-Exponenten kontinuierlicher Systeme
  H. Fellermann
  in: H. Malchow Introduction to Theoretical Systems Science II, 2002

Public Media and Outreach

• How the code of life passed through primitive kinds of cells
  NASA Astrobiology Magazine, January 15, 2015
• Fra syntetisk liv til levende teknologi
  C. Svaneborg, A. Albertsen, H. Fellermann, S. Rasmussen
  Aktuel Naturvidenskab, 12. 09. 2011

Selected Recent Oral Presentations

• Beyond Numbers: Physical Simulation with Complex States
  H. Fellermann
  invited talk at the Dagstuhl Seminar on Algorithmic Chemoinformatics, Dagstuhl Germany, November 2-7, 2014
• Emergence and selection of cooperative structures in a self-replicating binary polymer model
  H. Fellermann, S. Rasmussen & S. Tanaka
  invited talk at the 3rd Emergence in Chemical Systems Conference, Anchorage USA, June 17-22, 2013
• Integrating Molecular Computing and Material Production in an Artificial Subcellular Matrix
  H. Fellermann & L. Cardelli
  invited talk at NSF/DSRC Advances in Molecular Computing Workshop, Copenhagen Denmark, May 2-5, 2013
• Integrating Molecular Computation and Material Production in an Artificial Subcellular Matrix
  H. Fellermann, M. Hadorn, E. Bönzli & S. Rasmussen
  poster presentation at the 1st International Conference on Living Machines, Barcelona, Spain, July 9-12, 2012
• Approaches to Multi-Scale Modelling of Complex Systems
  H. Fellermann
  invited talk at Microsoft Research, Cambridge UK, March 20, 2012
• A Membrane Computing-like calculus for integrated computation and material production
  H. Fellermann
  Weizmann Institute of Science, Rehovot Israel, December 10, 2011
• Thermodynamics and kinetics of protocells : Toward a quantitative theory of early life
  H. Fellermann, B. Corominas-Murtra, R. Solé, S. Rasmussen
  invited talk at European Conference of Complex Systems, Vienna Austria, July 2011
• Physically grounded simulations of a self-replicating chemical agrgegate
  H. Fellermann, S. Rasmussen
  12th International Conference on the Synthesis and Simulation of Living Systems, Odense Denmark, August 2010
• Coarse-graining Modular Boolean Networks
  H. Fellermann
  invited talk at Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México City México, July 29, 2010
• Artificial life: on the construction of artificial living systems
  H. Fellermann
  invited talk at Jacobs University, Bremen Germany, July 3 and 4, 2009

Last modified: 2018-08-20,