Dr Samuel Johnson PhD

Dr Samuel Johnson

School of Mathematics
Lecturer in Applied Mathematics

Contact details

Address
School of Mathematics
University of Birmingham
Edgbaston
B15 2TT

Sam's research focuses on complex systems, and in particular on the relationship between structure and dynamics. Many of the questions his work addresses relate to ecology, neuroscience or society.

Qualifications

  • PhD in Physics (Interplay between Network Topology and Dynamics in Neural Systems), Univeristy of Granada, 2011
  • Certificate of Teaching Aptitude in Mathematics, University of Granada, 2008.
  • MSc in Physics and Mathematics (specialising in mathematical biology), University of Granada, 2008
  • BSc in Physics, University of Granada, 2006

Biography

Sam Johnson studied Physics and Mathematics at the University of Granada, Spain, where he did a PhD entitled 'Interplay between Network Topology and Dynamics in Neural Systems', under the supervision of Joaquin Torres and Joaquin Marro. He was a postdocat the University of Oxford working with Nick Jones before taking up a Marie Curie research fellowship at Imperial College London. After a brief period in a joint position between DNV GL and the University of Bath, he became a Warwick Zeeman Lecturer at the University of Warwick in 2014. In 2017 he took up his current position at the University of Birmingham as Lecturer in Applied Mathematics.

Postgraduate supervision

  • PhD students at the University of Warwick:
    Janis Klaise
    Guillem Mosquera Doñate

Research

Sam has many research interests, most of which can be placed under the umbrella of 'complex systems'. Some of the topics he is currently working on are:

  • Trophic structure of directed networks: Together with colleagues in Granada, Sam recently studied a network property called 'trophic coherence', (Johnson et al, PNAS, 2014). This and subsequent work (with colleagues Miguel Ángel Muñoz, Virginia Dominguez, Janis Klaise and Nick Jones) has shown that trophic coherence is related to many aspects of complex systems, including the prevalence of cycles and feedback loops, ecological stability, motif distributions and spreading processes such as epidemics and neuronal avalanches. It has also opened several questions, such as: Does trophic coherence account for the existence of large, complex ecosystems? Can trophic structure be used to identify node function in systems like gene regulatory networks? is there a general theory relating feedback and stability in complex, dynamical systems.
  • Human ecology: Work with Weisi Guo, Xueke Lu and Guillem Mosquera has show that the prevalence of violence around the world is related to the spatial distribution of cities according to a remarkably simple and robust law. We are currently looking into the causes of this effect though a combination of data analysis and agent based modelling and looking for ways in which our results can be applied.
  • Brain development: The neural network underlying all mental activity comes into being in a curious way: at birth it has a great many synapses (connections between neurons), about half of which are 'pruned' throughout infancy. Recent work with Ana Paula Millán, Joaquin Torres and Joaquin Marro describes a mechanism which could explain this phenomenon with a simple neural network model. We are now studying this process with more realistic neural modelling, looking into its effects in other complex systems. 

Other activities

  • Advisor to Polymaths R&D Ltd
  • Member of the Conflict Research Society

Publications

  • S. Johnson and N.S. Jones, “Looplessness in networks is linked to trophic coherence”, PNAS 114, 5618 (2017) (arXiv:1505.07332)
  • A.P. Millán, J.J. Torres, S. Johnson, and J. Marro, “The concurrence of form and function in developing networks: An explanation for synaptic pruning”, submitted (2017) (arXiv:1705.02773)
  • J. Klaise and S. Johnson, “The origin of motif families in food webs”, to appear in Scientific Reports (2017) (arXiv:1609.04318)
  • W. Guo, X. Lu, and S. Johnson, “The spatial ecology of war and peace”, submitted (2017) (arXiv:1604.01693)
  • J. Klaise and S. Johnson, “From neurons to epidemics: How trophic coherence affects spreading processes”, Chaos 26, 065310 (2016) (arXiv:1603.00670)
  • V. Domínguez-García, S. Johnson, and M.A. Muñoz, “Internality and coherence in complex networks”, Chaos 26, 065308 (2016) (arXiv:1603.03767)
  • S. Johnson, “Escaping the tragedy of the commons through targeted punishment”, Royal Society Open Science 2, 150223 (2015) (open access)
  • A.P. Millán, J.J. Torres, S. Johnson, and J. Marro, “Evolution of brain network structure under a critical condition as induced by local currents”, Int. J. Complex Systems in Science 5, 43-47 (2015) (open access)
  • S. Johnson, V. Domínguez-García, L. Donetti, and M.A. Muñoz, “Trophic coherence determines food-web stability”, PNAS 111, 17923 (2014) (open access)H.L. Mills, S. Johnson, M. Hickman, N.S. Jones, and C. Colijn, “Errors in reported degrees and Respondent Driven Sampling: Implications for bias”, Drug and Alcohol Dependence 142, 120 (2014) (open access)

  • H.L. Mills, S. Johnson, M. Hickman, N.S. Jones, and C. Colijn, “Errors in reported degrees and Respondent Driven Sampling: Implications for bias”, Drug and Alcohol Dependence 142, 120 (2014) (open access)
  • S. Johnson, V. Domínguez-García, and M.A. Muñoz, “Factors determining nestedness in complex networks”, PLOS ONE 8(9), e74025 (2013) (open access)
  • S. Johnson, J.J. Torres, and J. Marro, “Robust short-term memory without synaptic learning”, PLOS ONE 8(1), e50276 (2013) (open access)
  • S. de Franciscis, S. Johnson, and J.J. Torres, “Enhancing neural network performance via assortativity”, Physical Review E 83, 036114 (2011) (arXiv:1012.1813)
  • S. Johnson, “Interplay between Network Topology and Dynamics in Neural Systems”, PhD thesis (2011) (arXiv:1302.3943)
  • S. Johnson, J.J. Torres, J. Marro, and M.A. Muñoz, “Entropic origin of disassortativity in complex networks”, Physical Review Letters 104, 108702 (2010) (arXiv:1002.3286)

  • S. Johnson, J. Marro, and J.J. Torres, “Evolving networks and the development of neural systems”, Journal of Statistical Mechanics (2010) P03003 (arXiv:0905.3759)

  • J.J. Torres, S. de Franciscis, S. Johnson, and J. Marro, “Excitable networks: Nonequilibrium criticality and optimum topology”, International Journal of Bifurcation and Chaos 20, 869-75 (2010)

  • S. Johnson, J.J. Torres, and J. Marro, “Nonlinear preferential rewiring in fixed-size networks as a diffusion process”, Physical Review E 79, 050104(R) (2009) (arXiv:0905.1666)
  • S. Johnson, J. Marro, J.F. Mejias, and J.J. Torres, “Development of neural network structure with biological mechanisms”, Lecture Notes in Computer Science 5517, 228 (2009)
  • J.F. Mejias, J.J. Torres, S. Johnson, and H.J. Kappen, “Switching dynamics of neural systems in the presence of multiplicative colored noise”, Lecture Notes in Computer Science 5517, 17 (2009)
  • S. Johnson, J. Marro, and J.J. Torres, “Functional optimization in complex excitable networks”, EPL (Europhysics Letters) 83, 46006 (2008) (arXiv:0805.1309)