Centre for Synthetic Biology and the Bioeconomy

Staff Profile

Dr Harold Fellermann

Lecturer

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 Systems Modeling, 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 and synthetic biology, as well as supramolecular chemistry and systems chemistry.

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 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 in-vitro and in-vivo molecular computing, the emergence of information in prebiotic chemical networks, as well as method development for stochastic simulation techniques.

Teaching

I am currently teaching the following modules

CSC8004 - Networks and Web Technologies

CSC8304 - Computing Environments for Bioinformatics

Publications

  • 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.
  • 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.
  • 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.
  • 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.
  • 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, 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.
  • Naylor J, Fellermann H, Krasnogor N. Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations. Bioinformatics 2019, 35(19), 3859-3860.
  • 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.
  • 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.
  • Fellermann H, Bacardit J, Goñi-Moreno A, Füchslin RM, ed. The 2019 Conference on Artificial Life. MIT Press, 2019.
  • 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.
  • 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.
  • Hordijk W, Naylor J, Krasnogor N, Fellermann H. Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World. Life 2018, 8(3), 33.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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, Tanaka S, Rasmussen S. Sequence selection by dynamical symmetry breaking in an autocatalytic binary polymer model. Physical Review E 2017, 96(6), 062407.
  • 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.
  • 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.
  • 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.
  • Fellermann H, Markovitch O, Gilfellon O, Madsen C, Phillips A. Toward Programmable Biology. ACS Synthetic Biology 2016, 5(8), 793-794.
  • Tangen U, Fellermann H, Rasmussen S. Simulating self-replicating chemically immersed microchip swarm structures. In: European Conference on Artificial Life. 2015, York, UK.
  • Fellermann H, Krasnogor N. Chemical Production and Molecular Computing in Addressable Reaction Compartments. Lecture Notes in Computer Science 2014, 8493, 173-182.
  • 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.
  • 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.
  • 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.
  • Fellermann H, Cardelli L. Programming Chemistry in DNA Adressable Bioreactors. Royal Society Interface 2014, 11(99), 1-12.
  • Corominas-Murtra B, Fellermann H. Protocell duplication as a thermodynamic cycle. In: European Conference on Complex Systems '14. 2014, Lucca, Italy: Springer.
  • 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.
  • Tanaka S, Fellermann H, Rasmussen S. Structure and Selection in an Autocatalytic Binary Polymer Model. Europhysics Letters 2014, 107(2), 28004.
  • 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.
  • 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, 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.
  • 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).
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Fellermann H, Rasmussen S. On the Growth Rate of Non-Enzymatic Molecular Replicators. Entropy 2011, 13(10), 1882–1903.
  • 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, Dörr M, Hanczy MM, Laursen L, Maurer SE, Merkle D, Monnard PA, Støy K, Rasmussen S, ed. Artificial Life XII. MIT Press, 2010.
  • 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 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.
  • 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. Spatially resolved artificial chemistry. In: Komosinski, Maciej, Adamatzky, Andrew, ed. Artificial Life Models in Software. Springer, 2009.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.