Background

Dr Harold Fellerman is a Lecturer for the School of Computing at University of Newcastle.

 Google Scholar Profile

Research

I am a Lecturer for Molecular Computing and Nanoscience, working in the Interdisciplinary Computing and Complex Biosystems Research Group. I have more than ten years of experience in developing and applying computational design, modeling, and analysis techniques to problems from molecular biology, synthetic biology, as well as DNA nanotechnology.

I received my PhD in Applied System Science in 2009 from the University of Osnabrück, Germany, and have worked as a Postdoctoral Research Associate at Los Alamos National Labs (NM, USA) and the University of Southern Denmark (Odense), before joining Newcastle University in 2014. I am a Fellow of the European Center for Living Technology in Venice Italy, and a Member of the Board of Directors of the International Society of Artificial Life.

My current research focuses on the design and analysis of in-vitro and in-vivo DNA computing systems applications.

Publications

• Articles

  • Braccini M, Collinson E, Roli A, Fellermann H, Stano P. Recurrent neural networks in synthetic cells: a route to autonomous molecular agents?. Frontiers in Bioengineering and Biotechnology 2023, 11, 1210334.
  • Konur S, Mierla L, Fellermann H, Ladroue C, Brown B, Wipat A, Twycross J, Dun BP, Kalvala S, Gheorghe M, Krasnogor N. Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation. ACS Synthetic Biology 2021, 10(8), 1931-1945.
  • Gorochowski TE, Hauert S, Kreft JU, Marucci L, Stillman NR, Dora Tang TY, Bandiera L, Bartoli V, Dixon DOR, Fedorec AJH, Fellermann H, Fletcher AG, Foster T, Giuggioli L, Matyjaszkiewicz A, McCormick S, Montes Olivas S, Naylor J, Denniss AR, Ward D. Toward engineering biosystems with emergent collective functions. Frontiers in Bioengineering and Biotechnology 2021, 8, 705.
  • Lopiccolo A, Shirt-Ediss B, Torelli E, Olulana AFA, Castronovo M, Fellermann H, Krasnogor N. A last-in first-out stack data structure implemented in DNA. Nature Communications 2021, 12(1), 4861.
  • Grozinger L, Amos M, Gorochowski TE, Carbonell P, Oyarzún DA, Stoof R, Fellermann H, Zuliani P, Tas H, Goñi-Moreno A. Pathways to cellular supremacy in biocomputing. Nature Communications 2019, 10, 5250.
  • Naylor J, Fellermann H, Krasnogor N. Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations. Bioinformatics 2019, 35(19), 3859-3860.
  • Fellermann H, Shirt-Ediss B, Kozyra J, Linsley M, Lendrem D, Isaacs J, Howard TP. Design of experiments and the virtual PCR simulator: An online game for pharmaceutical scientists and biotechnologists. Pharmaceutical Statistics 2019, 18(4), 402-406.
  • Hordijk W, Naylor J, Krasnogor N, Fellermann H. Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World. Life 2018, 8(3), 33.
  • Naylor J, Fellermann H, Ding Y, Mohammed W, Jakubovics N, Mukherjee J, Biggs C, Wright P, Krasnogor N. Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations. ACS Synthetic Biology 2017, 6(7), 1194-1210.
  • Fellermann H, Tanaka S, Rasmussen S. Sequence selection by dynamical symmetry breaking in an autocatalytic binary polymer model. Physical Review E 2017, 96(6), 062407.
  • Kozyra J, Ceccarelli A, Torelli E, Lopiccolo A, Gu JY, Fellermann H, Stimming U, Krasnogor N. Designing uniquely addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami. ACS Synthetic Biology 2017, 6(7), 1140-1149.
  • Tanaka S, Fellermann H, Rasmussen S. Structure and Selection in an Autocatalytic Binary Polymer Model. Europhysics Letters 2014, 107(2), 28004.
  • Fellermann H, Cardelli L. Programming Chemistry in DNA Adressable Bioreactors. Royal Society Interface 2014, 11(99), 1-12.
  • Fellermann H, Hadorn M, Fuchslin RM, Krasnogor N. Formalizing Modularization and Data Hiding in Synthetic Biology. ACM Journal on Emerging Technologies in Computing Systems (JETC) 2014, 11(3), 24.
  • Fellermann H, Krasnogor N. Chemical Production and Molecular Computing in Addressable Reaction Compartments. Lecture Notes in Computer Science 2014, 8493, 173-182.
  • Weyland M, Fellermann H, Hadorn M, Sorek D, Lancet D, Rasmussen S, Füchslin RM. The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers. Computational and Mathematical Methods in Medicine 2013, 2013, 467428.
  • Hadorn M, Bönzli E, Sørensen KT, Fellermann H, Eggenberger P, Hanczyc MM. Specific and Reversible DNA-directed Self-Assembly of Oil-in-Water Emulsion Droplets. Proceedings of the National Academy of Science USA 2012, 109(50), 20320–20325.
  • Svaneborg C, Fellermann H, Rasmussen S. DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model. Lecture Notes in Computer Science 2012, 7433(123).
  • Fellermann H, Rasmussen S. On the Growth Rate of Non-Enzymatic Molecular Replicators. Entropy 2011, 13(10), 1882–1903.
  • Füchslin R, Fellermann H, Eriksson A, Ziock HJ. Coarse-graining and scaling in dissipative particle dynamics. Journal of Chemical Physics 2009, 130(21), 214102.
  • Fellermann H, Solé R. Minimal model of self-replicating nanocells: A physically embodied, information-free scenario. Philosophical Transaction of The Royal Society B 2007, 362(1486), 1803–1811.
  • Fellermann H, Rasmussen S, Ziock HJ, Solé R. Life-cycle of a minimal protocell – a dissipative particle dynamics (DPD) study. Journal of Artificial Life 2007, 13(4), 319–345.

• Book Chapters

  • Konur S, Fellermann H, Mierla LM, Sanassy D, Ladroue C, Kalvala S, Gheorghe M, Krasnogor N. An integrated in silico simulation and biomatter compilation approach to cellular computation. In: Adamatzky A, ed. Advances in Unconventional Computing. Cham: Springer, 2017, pp.655-676.
  • Fellermann H. Wet artificial life: the creation of artificial living systems. In: Hildegard Meyer-Ortmanns, Stefan Thurner, ed. Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer, 2011.
  • Fellermann H. Spatially resolved artificial chemistry. In: Komosinski, Maciej, Adamatzky, Andrew, ed. Artificial Life Models in Software. Springer, 2009.
  • Solé R, Sardanyes J, Fellermann H, Valverde S, Macía J, Munteanu A. Models of protocell replication. In: Steen Rasmussen, Mark A. Bedau, Liaohai Chen, David Deamer, David C. Krakauer, Norman H. Packard and Peter F. Stadler, ed. Protocells. MIT Press, 2008.
  • Rasmussen S, Bailey J, Boncella J, Chen L, Collis G, Colgate S, DeClue M, Fellermann H, Goranovic G, Jiang Y, Knutson C, Monnard PA, Mouffouk F, Nielson M, Sen A, Shreve A, Tamulis A, Travis B, Weronski P, Zhang J, Zhou X, Ziock HJ, Woodruff W. Assembly of a minimal protocell. In: Steen Rasmussen, Mark A. Bedau, Liaohai Chen, David Deamer, David C. Krakauer, Norman H. Packard and Peter F. Stadler, ed. Protocells. MIT Press, 2008.

• Conference Proceedings (inc. Abstracts)

  • Scheidegger S, Barba SM, Fellermann H, Gaipl U. Influence of the Antigen Pattern Vector on the Dynamics in a Perceptron-Based Artificial Immune - Tumour- Ecosystem During and After Radiation Therapy. In: Artificial Life and Evolutionary Computation. WIVACE 2021. 2023, Winterthur, Swizterland: Springer.
  • Füchslin RM, Ambühl J, Faggian A, Fellermann H, Flumini D, Geller A, Hanczyc HH, Klinkert A, Krütli P, Matuttis H, Ott T, Scheidegger S, Schmid GB, Smieszek T, Schneider JJ, Steiner A, Weyland MS. Ethical Aspects of Computational Modelling in Science, Decision Support and Communication. In: Artificial Life and Evolutionary Computation. WIVACE 2021. 2021, Winterthur, Switzerland: Springer.
  • Flumini D, Weyland MS, Schneider JJ, Fellermann H, Füchslin RM. Towards programmable chemistries. In: Artificial Life and Evolutionary Computation. WIVACE 2019. 2020, Rende, Italy: Springer, Cham.
  • Scheidegger S, Mikos A, Fellermann H. Modelling Artificial Immune–Tumor Ecosystem Interaction During Radiation Therapy Using a Perceptron–Based Antigen Pattern Recognition. In: The 2020 Conference on Artificial Life (ALIFE 2020). 2020, Montreal, Canada: MIT Press.
  • Miniussi M, Ott T, Fellermann H. Impact of noise and network size in coupled maps with asymmetric influence amplification. In: 2020 International Symposium on Nonlinear Theory and its Applications. 2020. In Preparation.
  • Fellermann H, Penn AS, Füchslin RM, Bacardit J, Goñi-Moreno A. Towards Low-Carbon Conferencing: Acceptance of Virtual Conferencing Solutions and Other Sustainability Measures in the ALIFE Community. In: The 2019 Conference on Artificial Life. 2019, Newcastle-upon-Tyne: MIT Press. In Preparation.
  • Fellermann H, Penn AS, Fuchslin RM, Bacardit J, Goni-Moreno A. Towards low-carbon conferencing: Acceptance of virtual conferencing solutions and other sustainability measures in the ALIFE community. In: Proceedings of the 2019 Conference on Artificial Life: How Can Artificial Life Help Solve Societal Challenges, ALIFE 2019. 2019, Newcastle upon Tyne: MIT Press.
  • Scheidegger S, Fellermann H. Optimizing Radiation Therapy Treatments by Exploring Tumour Ecosystem Dynamics in–silico. In: The 2019 Conference on Artificial Life. 2019, Newcastle upon Tyne, UK: MIT Press.
  • Fellermann H, Bacardit J, Goñi-Moreno A, Füchslin RM. Artificial Life in a Challenged World. In: The 2019 Conference on Artificial Life. 2019, Newcastle-upon-Tyne: MIT Press. In Preparation.
  • Fellermann H, Bacardit J, Goni-Moreno A, Fuchslin RM. Artificial life in a challenged world. In: Proceedings of the 2019 Conference on Artificial Life: How Can Artificial Life Help Solve Societal Challenges, ALIFE 2019. 2019, Newcastle upon Tyne, UK: MIT Press.
  • Shirt-Ediss B, Krasnogor N, Fellermann H. The fittest, the common, and the dullest: Selection dynamics of exact autocatalytic replicators. In: The 2018 Conference on Artificial Life. 2018, Tokyo, Japan: MIT Press.
  • Ott T, Schüle M, Fellermann H, Uwate Y. Structural Evolution in Networks of Coupled Maps with Asymmetric Influence Amplification. In: 2018 International Symposium on Nonlinear Theory and Its Applications. 2018, Tarragona, Spain. In Preparation.
  • Kozyra J, Ceccarelli A, Torelli E, Lopiccolo A, Fellermann H, Shirt-Ediss B, Krasnogor N. Toward in vivo nanostructures: hybrid origami scaffolds on De Bruijn sequence. In: BioOrigami Workshop. 2017, Ljubljana, Slovenia.
  • Kozyra J, Fellermann H, Shirt-Ediss B, Lopiccolo A, Krasnogor N. Optimizing nucleic acid sequences for a molecular data recorder. In: GECCO'17 Genetic and Evolutionary Computation Conference. 2017, Berlin, Germany: ACM.
  • Fellermann H, Lopiccolo A, Kozyra J, Krasnogor N. In vitro implementation of a stack data structure based on DNA strand displacement. In: Unconventional Computation and Natural Computation: 15th International Conference, UCNC 2016. 2016, Manchester, UK: Springer.
  • Tangen U, Fellermann H, Rasmussen S. Simulating self-replicating chemically immersed microchip swarm structures. In: European Conference on Artificial Life. 2015, York, UK.
  • Tanaka S, Fellermann H, Rasmussen S. Random polymerization may not produce random copolymers. In: Open Questions on the Origin of Life Conference. 2014, Kyoto, Japan.
  • Corominas-Murtra B, Fellermann H. Protocell duplication as a thermodynamic cycle. In: European Conference on Complex Systems '14. 2014, Lucca, Italy: Springer.
  • Sanassy D, Fellermann H, Krasnogor N, Konur S, Mierla LM, Gheorghe M, Ladroue C, Kalvala S. Modelling and stochastic simulation of synthetic biological Boolean gates. In: 2014 IEEE International Conference on High Performance Computing and Communications. 2014, Paris: IEEE.
  • Konur S, Ladroue C, Fellermann H, Sanassy D, Mierla LM, Ipate F, Kalvala S, Gheorghe M, Krasnogor N. Modeling and Analysis of Genetic Boolean Gates using Infobiotics Workbench. In: Workshop on Verification of Engineered Molecular Devices and Programs 2014. 2014, Vienna, Austria.
  • Rasmussen S, Fellermann H, Tanaka S. Sequence selection and evolution in a binary polymer model. In: 12th European Conference on Artificial Life. 2013, Taormina, Italy: Springer. In Preparation.
  • Löffler PMG, Wieczorek R, Wamberg M, Dörr M, Pedersen PL, Svaneborg C, Fellermann H, Edson JB, Cape JL, Ziock JH, Boncella JM, Rasmussen S, Monnard PA. Towards protocellular embedded replication of nucleic acids. In: 13th Intl Conf o the Synthesis and Simulation of Artificial Life ALIFE13. 2012, East Lansing MI, USA: MIT Press.
  • Albertsen AN, Maurer SE, Cape J, Fellermann H, Boncella JM, Ziock HJ, Rasmussen S, Monnard PA. Protocellular energetics and autonomous functions. In: 13th Intl Conf o the Synthesis and Simulation of Artificial Life ALIFE13. 2012, East Lansing MI, USA: MIT Press.
  • Dörr M, Schmidt-Petersen S, Fellermann H, Laursen L, Rasmussen S. Mapping the collective intelligence of the Artificial Life XIII stakeholders. In: 13th Intl Conf o the Synthesis and Simulation of Artificial Life ALIFE13. 2012, East Lansing MI, USA: MIT Press.
  • Hadorn M, Gil B, Svaneborg C, Hanczyc MM, Fellermann H, Füchslin R, Eggenberger-Hotz P, Kunstmann-Olsen C, Lancet D, McCaskill J, Monnard PA, Kiedrowski G, Rasmussen S. A Minimal Artificial Subcellular Matrix. In: 13th Intl Conf o the Synthesis and Simulation of Artificial Life ALIFE13. 2012, East Lansing MI, USA: MIT Press.
  • Rasmussen S, Monnard PA, Hanczyc MMH, Albertsen AN, Bönzli E, Caschera F, Dörr M, Fellermann H, Jørgensen WH, Löffler P, Maurer SE, Nielsen K, Pedersen P, Svaneborg C, Wamberg M, Wieczorek R, Ziock JH. A review of one approach to bottom up assembly of minimal life. In: 11th European Conference on the Simulation and Synthesis of Living Systems. 2011.
  • Rasmussen S, Albertsen AN, Fellermann H, Pedersen P, Svaneborg C, Ziock HJ. Assembling living materials and engineering life-like technologies. In: 13th annual conference companion on Genetic and evolutionary computation. 2011, Dublin, Ireland: ACM.
  • Fellermann H, Rasmussen S. Physically Grounded Simulations of a Self-Replicating Chemical Agrgegate. In: 12th Intl Conf on Synthesis and Simulation of Artificial Life ALIFE 12. 2010, Odense, Denmark: MIT Press.
  • Corominas-Murtra B, Fellermann H, Solé R, Rasmussen S. On the Interplay of Thermodynamics, Kinetics, and Information in Simple Replicator Systems. In: 12th Inl Conf on Synthesis and Simulation of Artificial Life ALIFE 12. 2010, Odense, Denmark: MIT Press.
  • Fellermann F, Rasmussen S, Ziock HJ, Solé R. A simple model of self-replicating protocells. In: 4th Annual Meeting on Foundations of Nanoscience (FNANO 2007). 2007.

• Edited Books

  • Fellermann H, Bacardit J, Goñi-Moreno A, Füchslin RM, ed. The 2019 Conference on Artificial Life. MIT Press, 2019.
  • Fellermann H, Dörr M, Hanczy MM, Laursen L, Maurer SE, Merkle D, Monnard PA, Støy K, Rasmussen S, ed. Artificial Life XII. MIT Press, 2010.

• Editorials

  • Fellermann H, Füchslin RM. The 2019 Conference on Artificial Life Special Issue. Artificial Life 2022, 28(2), 171-172.
  • Fellermann H, Markovitch O, Gilfellon O, Madsen C, Phillips A. Toward Programmable Biology. ACS Synthetic Biology 2016, 5(8), 793-794.