Output

Members of the centre regularly publish articles on various Complex Systems Science topics and here we only list the research output in which the CCSS activities played a role (in the order of dates of available online). * indicates the author is affiliated to the Centre for Complex Systems Studies.

2024

  • Otilia Boldea, Amir Alipoor, Sen Pei, Jeffrey Shaman, Ganna Rozhnova*. Age-specific transmission dynamics of SARS-CoV-2 during the first 2 years of the pandemic. PNAS Nexus, 31 January 2024, https://doi.org/10.1093/pnasnexus/pgae024
  • Michiel van Boven*, Christiaan H. van Dorp, Ilse Westerhof, Vincent Jaddoe, Valerie Heuvelman, Liesbeth Duijts, Elandri Fourie, Judith Sluiter-Post, Marlies A. van Houten, Paul Badoux, Sjoerd Euser, Bjorn Herpers, Dirk Eggink, Marieke de Hoog, Trisja Boom, Joanne Wildenbeest, Louis Bont, Ganna Rozhnova*, Marc J. Bonten, Mirjam E. Kretzschmar*, Patricia Bruijning-Verhagen. Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study. PLOS Computational Biology, 29 January 2024, https://doi.org/10.1371/journal.pcbi.1011832 
  • Ana Macanovic*, Milena Tsvetkova, Wojtek Przepiorka, Vincent Buskens*. Signals of Belonging: Emergence of Signalling Norms as Facilitators of Trust and Parochial Cooperation. Philosophical Transactions of the Royal Society B, 22 January 2024, https://doi.org/10.1098/rstb.2023.0029

2023

  • Phillip P. A. Staniczenko, Debabrata Panja*. Temporal origin of nestedness in interaction networks. PNAS Nexus, 24 November, 2023 https://doi.org/10.1093/pnasnexus/pgad412

  • Martijn Wehrens, Laurens H.J. Krah*, Benjamin D. Towbin, Rutger Hermsen*, Sander J Tans. The interplay between metabolic stochasticity and cAMP-CRP regulation in single E. coli cells. Cell Reports, 20 October 2023, https://doi.org/10.1016/j.celrep.2023.113284

  • Nico Wunderling, Anna von der Heydt*, Yevgeny Aksenov, Stephen Barker, Robbin Bastiaansen*, Victor Brovkin, Maura Brunetti, Victor Couplet, Thomas Kleinen, Caroline H. Lear, Johannes Lohmann, Rosa Maria Roman-Cuesta, Sacha Sinet*, Didier Swingedouw, Ricarda Winkelmann, Pallavi Anand, Jonathan Barichivich, Sebastian Bathiany, Mara Baudena*, John T. Bruun, Cristiano M. Chiessi, Helen K. Coxall, David Docquier, Jonathan Donges, Swinda K.J. Falkena, Ann Kristin Klose, David Obura, Juan Rocha, Stefanie Rynders, Norman Julius Steinert, Matteo Willeit. Climate tipping point interactions and cascades: A review. EGUsphere (preprint), 1 Augustus 2023, https://doi.org/10.5194/egusphere-2023-1576

  • Marta Magnani*, Rubén Díaz-Sierra, Luke Sweeney, Antonello Provenzale, Mara Baudena*. Fire responses shape plant communities in a minimal model for fire ecosystems across the world, The American Naturalist, 28 July 2023, https://doi.org/10.1086/725391

  • Andrea Di Benedetto*, Claudia E. Wieners*, Henk A. Dijkstra*, Henk T.C. Stoof*. Media preference increases polarization in an agent-based election model. Physica A: Statistical Mechanics and its Applications, 4 July 2023, https://doi.org/10.1016/j.physa.2023.129014

  • Igor M. Rouzine, Ganna Rozhnova*. Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies. Communications Medicine, 19 June 2023, https://doi.org/10.1038/s43856-023-00320-x 

  • Ahmad Ahmadi Yazdi, Mahdi Shafiee Kamalabad*, Daniel L. Oberski, Marco Grzegorczyk. Bayesian multivariate control charts for multivariate profiles monitoring. Quality Technology & Quantitative Management, 27 May 2023, https://doi.org/10.1080/16843703.2023.2214386  

  • Mahdi Shafiee Kamalabad*, Roger Leenders, Joris Mulder. What is the Point of Change? Change Point Detection in Relational Event Models. Social Networks, 4 April 2023, https://doi.org/10.1016/j.socnet.2023.03.004
  • Mark M. Dekker*, Luc E. Coffeng, Frank P. Pijpers, Debabrata Panja*, Sake J. de Vlas. Reducing societal impacts of SARS-CoV-2 interventions through subnational implementation. eLife, 7 March 2023, https://doi.org/10.7554/eLife.80819
  • Silja Zimmermann*, Brian J. Dermody*, Bert Theunissen*, Martin J. Wassen, Lauren M. Divine, Veronica M. Padula, Henrik von Wehrden, Ine Dorresteijn*. A leverage points perspective on Arctic Indigenous food systems research: a systematic review. Sustainability Science, 31 January 2023, https://doi.org/10.1007/s11625-022-01280-2
  • Peter D. Nooteboom*, Joe Scutt Phillips, Christian Kehl, Simon Nicol, Erik van Sebille*. Modelling of tuna around fish aggregating devices: The importance of ocean flow and prey. Ecological Modelling, January 2023, https://doi.org/10.1016/j.ecolmodel.2022.110188

2022

  • Otilia Boldea, Amir Alipoor, Sen Pei, Jeffrey Shaman, Ganna Rozhnova*. Age-specific transmission dynamics of SARS-CoV-2 during the first two years of the pandemic (preprint). arXiv preprint, 27 December 2022, https://doi.org/10.48550/arXiv.2212.13470
  • Ilse Westerhof, Marieke de Hoog, Margareta Ieven, Christine Lammens, Janko van Beek, Ganna Rozhnova*, Dirk Eggink, Sjoerd Euser, Joanne Wildenbeest, Liesbeth Duijts, Marlies van Houten, Herman Goossens, Carlo Giaquinto, Patricia Bruijning‑Verhagen. The impact of variant and vaccination on SARS-CoV-2 symptomatology; three prospective household cohorts. International Journal of Infectious Diseases, 23 December 2022, https://doi.org/10.1016/j.ijid.2022.12.018 
  • Kim A. G. J. Romijnders, Laura de Groot, Sigrid C. J. M. Vervoort, Maartje Basten, Berend J. van Welzen, Mirjam E. Kretzschmar*, Peter Reiss, Udi Davidovich, Maarten F. Schim van der Loef, Ganna Rozhnova*. The experienced positive and negative influence of HIV on quality of life of people with HIV and vulnerable to HIV in the Netherlands. Scientific Reports, 19 December 2022, https://doi.org/10.1038/s41598-022-25113-5
  • Alexandra Teslya, Ganna Rozhnova*, Thi Mui Pham, Daphne A. van Wees, Hendrik Nunner*, Noortje G. Godijk, Martin Bootsma*, Mirjam E. Kretzschmar*. The importance of sustained compliance with physical distancing during COVID-19 vaccination rollout. Communications Medicine, 19 November 2022, https://doi.org/10.1038/s43856-022-00207-3 
  • Rutger Hermsen*. Emergent multilevel selection in a simple spatial model of the evolution of altruism. PLoS Computational Biology, 25 October 2022, https://doi.org/10.1371/journal.pcbi.1010612 
  • Alje van Dam*, Andres Gomez-Lievano, Frank Neffke, Koen Frenken*. An information-theoretic approach to the analysis of location and colocation patterns. Journal of Regional Science, 8 September 2022, https://doi.org/10.1111/jors.12621
  • Peter D. Nooteboom*, Michiel Baatsen, Peter K. Bijl, Michael A. Kliphuis, Erik van Sebille*, Appy Sluijs, Henk A. Dijkstra*, Anna S. von der Heydt*. Improved Model-Data Agreement With Strongly Eddying Ocean Simulations in the Middle-Late Eocene. Paleoceanography and Paleoclimatology, 6 August 2022, https://doi.org/10.1029/2021PA004405
  • Sebastiaan Tieleman*. Model Transfer and Universal Patterns: Lessons from the Yule Process. Synthese, 17 June 2022,  https://link.springer.com/content/pdf/10.1007/s11229-022-03737-4.pdf
  • Reint Fischer, Delphine Lobelle, Merel Kooi, Albert Koelmans, Victor Onink, Charlotte Laufkötter, Linda Amaral-Zettler, Andrew Yool, Erik van Sebille*. Modelling submerged biofouled microplastics and their vertical trajectories. Biogeosciences, 25 April 2022, https://doi.org/10.5194/bg-19-2211-2022
  • Peter D. Nooteboom*, Peter K. Bijl, Christian Kehl, Erik van Sebille*, Martin Ziegler, Anna S. von der Heydt*, Henk A. Dijkstra*. Sedimentary microplankton distributions are shaped by oceanographically connected areas. Earth System Dynamics, 15 February 2022, https://doi.org/10.5194/esd-13-357-2022
  • Mirjam E. Kretzschmar, Ashby B, Fearon E, Overton CE, Panovska-Griffiths J, Pellis L, Quaife M, Ganna Rozhnova, Scarabel F, Stage HB, Swallow B, Thompson RN, Tildesley MJ, Villela D. Challenges for modelling interventions for future pandemics. Epidemics, 11 February 2022, https://doi.org/10.1016/j.epidem.2022.100546
  • Addison Rice, Peter D. Nooteboom*, Erik van Sebille*, Francien Peterse, Martin Ziegler, Appy Sluijs. Limited Lateral Transport Bias During Export of Sea Surface Temperature Proxy Carriers in the Mediterranean Sea. Geophysical Research Letters, 10 February 2022, https://doi.org/10.1029/2021GL096859

  • Adriana D. Correia*, L. Leestmaker*, Henk T.C Stoof*, Joris Broere*. Physica A: Statistical Mechanics and its Applications, 29 January 2022, https://doi.org/10.1016/j.physa.2022.126972

  • Adriana D. Correia*, Michael Moortgat*, Henk T.C Stoof*. Grover's Algorithm for Question Answering. arXiv preprint, 27 January 2022, https://doi.org/10.48550/arXiv.2106.05299

  • Giacomo Rapisardi, Ivan Kryven*, Alex Arenas. Percolation in networks with local homeostatic plasticity. Nature Communications, 10 January 2022, https://doi.org/10.1038/s41467-021-27736-0

2021

  • Hilje M. Doekes, Rutger Hermsen*. Multiscale selection in spatially structured populations (Preprint). bioRxiv, 12 December 2021,  https://doi.org/10.1101/2021.12.21.473617
  • Hendrik Nunner*, Vincent Buskens*, Mirjam Kretzschmar*. A Model for the Co-Evolution of Dynamic Social Networks and Infectious Disease Dynamics. Computational Social Networks, 7 October 2021, 10.1186/s40649-021-00098-9
  • Sebastiaan Tieleman*. Towards a Validation Methodology of Macroeconomic Agent-Based Models. Computational Economics, 12 September 2021, https://doi.org/10.1007/s10614-021-10191-w
  • Alje van Dam*, Mark Dekker*, Ignacio Morales‑Castilla, Miguel Á. Rodríguez, David Wichmann*, Mara Baudena*. Correspondence analysis, spectral clustering and graph embedding: applications to ecology and economic complexity. Scientific Reports, 26 April 2021, https://doi.org/10.1038/s41598-021-87971-9
  • Ariana Torres-Knoop, Verena Schamboeck, Nitish Govindarajan, Pieter D. Iedema, Ivan Kryven*. Effect of different monomer precursors with identical functionality on the properties of the polymer network. Communications Materials, 21 May 2021, https://doi.org/10.1038/s43246-021-00154-x
  • Ariana Torres-Knoop, Ivan Kryven*. Learning heterogenous reaction rates from stochastic simulations. Physical Review E, 4 May 2021, https://doi.org/10.1103/PhysRevE.103.052402
  • Delphine Lobelle, Merel Kooi, Albert A. Koelmans, Charlotte Laufkötter, Cleo E. Jongedijk, Christian Kehl, Erik van Sebille*. Global Modeled Sinking Characteristics of Biofouled Microplastic. Journal of Geophysical Research: Oceans, 20 March 2021, https://doi.org/10.1029/2020JC017098
  •  Rebeca de la Fuente, Gábor Drótos, Emilio Hernández-García, Cristóbal López, Erik van Sebille*.  Sinking microplastics in the water column: simulations in the Mediterranean Sea. Ocean Science, 9 March 2021, https://doi.org/10.5194/os-17-431-2021
  • Yuliia Orlova, Alessa A. Gambardella, Ivan Kryven*, Katrien Keune, Piet D. Iedema. Generative Algorithm for Molecular Graphs Uncovers Products of Oil Oxidation. Journal of Chemical Information and Modeling, 21 February 2021, https://doi.org/10.1021/acs.jcim.0c01163
  • Ivan Kryven*, Clara Stegehuis. Contact tracing in configuration models. Journal of Physics: Complexity, 2 February 2021, https://doi.org/10.1088/2632-072X/abd3ad
  • Mark M. Dekker*, Debabrata Panja*. Cascading dominates large-scale disruptions in transport over complex networks. PLoS ONE, 25 January 2021, https://doi.org/10.1371/journal.pone.0246077
  • David Wichmann*, Christian Kehl, Henk A. Dijkstra*, Erik van Sebille*. Ordering of trajectories reveals hierarchical finite-time coherent sets in Lagrangian particle data: detecting Agulhas rings in the South Atlantic Ocean. Nonlinear Processes in Geophysics, 19 January 2021, https://doi.org/10.5194/npg-28-43-2021
  • Dawid Walentek*, Joris Broere*, Matteo Cinelli, Mark M. Dekker*, Jonas M. B. Haslbeck. Success of economic sanctions threats: coercion, information and commitment. International Interactions, 7 January 2021, https://doi.org/10.1080/03050629.2021.1860034

2020

  • Sámuel G Balogh, Gergely Palla, Ivan Kryven*. Networks with degree–degree correlations are special cases of the edge-coloured random graph. Journal of Complex Networks, 31 December 2020, https://doi.org/10.1093/comnet/cnaa045
  • Claudia E.Wieners*. Haze, Hunger, Hesitation: Disaster aid after the 1783 Laki eruption. Journal of Volcanology and Geothermal Research, 15 November 2020, https://doi.org/10.1016/j.jvolgeores.2020.107080
  • David Wichmann*, Christian Kehl, Henk A. Dijkstra*, Erik van Sebille*. Detecting flow features in scarce trajectory data using networks derived from symbolic itineraries: an application to surface drifters in the North Atlantic. Nonlinear Processes in Geophysics, 14 November 2020, https://doi.org/10.5194/npg-27-501-2020
  • Sven Baars, Daniele Castellana,  Fred W. Wubs, Henk A. Dijkstra*. Application of Adaptive Multilevel Splitting to High-Dimensional Dynamical Systems, Journal of Computational Physics. 30 September 2020, https://doi.org/10.1016/j.jcp.2020.109876. 
  • Adriana D. Correia*, Michael Moortgat*, Henk T. C. Stoof*. Density matrices with metric for derivational ambiguity. Journal of Applied Logics. 14 September 2020, http://collegepublications.co.uk/ifcolog/?00041
  • Peter D. Nooteboom*, Philippe Delandmeter, Erik van Sebille*, Peter K. Bijl, Henk A. Dijkstra*, Anna S. von der Heydt*. Resolution dependency of sinking Lagrangian particles in ocean general circulation models, PLOS ONE. 10 September 2020, https://doi.org/10.1371/journal.pone.0238650
  • Ann Kristin Klose, Rene van Westen, Henk A. Dijkstra*.  Phase synchronization of the Kuroshio Current System, Ocean Science. 4 September 2020, https://doi.org/10.5194/os-2019-96
  • Verena Schamboeck, Piet D. Iedema, Ivan Kryven*. Coloured random graphs explain the structure and dynamics of cross-linked polymer networks. Scientific Reports. 3 September 2020, https://doi.org/10.1038/s41598-020-71417-9
  • Yuliia Orlova, Alessa A. Gambardella, Rebecca E.Harmona, Ivan Kryven*, Piet D.Iedema. Finite representation of reaction kinetics in unbounded biopolymer structures. Chemical Engineering Journal. 8 August 2020, https://doi.org/10.1016/j.cej.2020.126485
  • Juste Raimbault, Joris Broere*, Marius Somveille, Jesus Mario Serna, Evelyn Strombom, Christine Moore, Ben Zhu, Lorraine Sugar. A spatial agent based model for simulating and optimizing networked eco-industrial systems. Resources, Conservation and Recycling, April 2020, https://doi.org/10.1016/j.resconrec.2019.104538
  • Alje van Dam*, Koen Frenken. Variety, complexity and economic development. Research Policy, 18 March 2020, https://doi.org/10.1016/j.respol.2020.103949
  • Paul Petersik, Henk A. Dijkstra*.  Probabilistic forecasting of El Niño using neural network models, Geophysical Research Letters. 13 March 2020, https://doi.org/10.1029/2019GL086423

2019

2018

  • Mark M. Dekker*, Anna S. von der Heydt*, Henk A. Dijkstra*. Cascading transitions in the climate system. Earth System Dynamics, 6 November 2018, https://doi.org/10.5194/esd-9-1243-2018
  • Matthias Aengenheyster, Qing Yi Feng*, Rick van der Ploeg, Henk A. Dijkstra*. The point of no return for climate action: effects of climate uncertainty and risk tolerance. Earth System Dynamics, 30 August 2018, https://doi.org/10.5194/esd-9-1085-2018 (News article)
  • Peter D. Nooteboom*, Qing Yi Feng*, Cristóbal López, Emilio Hernández-García, Henk A. Dijkstra*. Using network theory and machine learning to predict El Niño. Earth System Dynamics, 23 July 2018, https://doi.org/10.5194/esd-9-969-2018 (News article)
  • Michiel Rhoen, Qing Yi Feng*. Why the ‘Computer says no’: illustrating big data’s discrimination risk through complex systems science. International Data Privacy Law, 25 June 2018, https://doi.org/10.1093/idpl/ipy005 (News article)
  • Brian J. Dermody*, Murugesu Sivapalan, Elke Stehfest, Detlef P. van Vuuren, Martin J. Wassen, Marc F. P. Bierkens, Stefan C. Dekker. A framework for modelling the complexities of food and water security under globalisation. Earth System Dynamics, 31 January 2018, https://doi.org/10.5194/esd-9-103-2018 (News article)