Jonathan Naylor

Jonathan Naylor

Doctor of Philosophy

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7
Publications
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56
Citations

Publications

Publications (7)
Article
Full-text available
Many complex behaviors in biological systems emerge from large populations of interacting molecules or cells, generating functions that go beyond the capabilities of the individual parts. Such collective phenomena are of great interest to bioengineers due to their robustness and scalability. However, engineering emergent collective functions is dif...
Preprint
Full-text available
Many complex behaviours in biological systems emerge from large populations of interacting molecules or cells, generating functions that go beyond the capabilities of the individual parts. Such collective phenomena are of great interest to bioengineers due to their robustness and scalability. However, engineering emergent collective functions is di...
Article
Motivation: 3D physical modelling is a powerful computational technique that allows for the simulation of complex systems such as consortia of mixed bacterial species. The complexities in physical modelling reside in the knowledge intensive model building process and the computational expense in calculating their numerical solutions. These models...
Preprint
Full-text available
Motivation: 3D physical modelling is a powerful computational technique that allows for the simulation of complex systems such as consortia of mixed bacterial species. The complexities in physical modelling reside in the knowledge intensive model building process and the computational expense in calculating their numerical solutions. These models c...
Article
Full-text available
Autocatalytic sets are self-sustaining and collectively catalytic chemical reaction networks which are believed to have played an important role in the origin of life. Simulation studies have shown that autocatalytic sets are, in principle, evolvable if multiple autocatalytic subsets can exist in different combinations within compartments, i.e., so...
Article
Full-text available
uthors and contributions as published: Jonathan Naylor, Harold Fellermann, Yuchun Ding, Waleed K. Mohammed, Nicholas S. Jakubovics, Joy Mukherjee, Catherine A. Biggs, Phillip C. Wright, and Natalio Krasnogor. JN wrote the manuscript, developed the software and models and performed data analysis. HF supervised the work, designed the overall study, s...
Article
Simbiotics is a spatially explicit multi-scale modeling platform for the design, simulation and analysis of bacterial populations. Systems ranging from planktonic cells and colonies, to biofilm formation and development may be modeled. Representation of biological systems in Simbiotics is flexible, user-defined processes may be in a variety of form...

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