The Complex Systems lab focuses on understanding the evolutionary origins of complex systems, using both mathematical models and experimental approaches based on synthetic biology. This lab has proposed and developed the concept of Major Synthetic Transitions as a framework for exploring the origins of innovation in evolution using a parallel approach, namely our potential for building or simulating synthetic systems that can recreate past evolutionary events. This includes the origin of protocells, multicellular systems, symbiosis, cognition and language. Another research area addresses Unstable Evolutionary Dynamics, namely the dynamics of biological systems (particularly RNA viruses and cancer) that exhibit a tendency towards high genetic instability as part of their adaptation potential. The Complex Systems lab also introduced the concept of "Terraforming" endangered or human-made ecosystems to avoid catastrophic shifts. The success of this proposal will require the development of a new synthesis involving multiple scales and conceptual frameworks, ranging from synthetic biology and cellular circuits to ecological communities. Finally, it also studies the evolution of artificial systems, in both silico ecosystems and technological networks, in its search for a true definition of evolutionary dynamics and technological phylogenies.

Lab website: Complex Systems Lab

Ricard Solé Vicente

Solé Vicente, Ricard
ICREA Research Professor (UPF)
Complex Systems Lab

Núria Conde Pueyo

Conde Pueyo, Núria
Postdoctoral Researcher
Complex Systems

Victor Maull Miquel

Maull Miquel, Victor
Predoctoral researcher
Complex Sistems

Jordi Piñero Fernández

Piñero Fernández, Jordi
Predoctoral Researcher
Complex Systems

Pla Mauri, Jordi
Predoctoral Researcher
Complex Systems

Duran-Nebreda S, Bonforti A, Montañez R, Valverde S, Solé R. 2016. Emergence of proto-organisms from bistable stochastic differentiation and adhesion. Journal of the Royal Society Interface, 13(117). DOI:10.1098/rsif.2016.0108

Duran-Nebreda S, Solé R V. 2016. Toward Synthetic Spatial Patterns in Engineered Cell Populations with Chemotaxis. ACS Synthetic Biology, 5(7):654-661. DOI:10.1021/acssynbio.5b00254

de Lorenzo V, Marlière P, Solé R. 2016. Bioremediation at a global scale: from the test tube to planet Earth. Microbial Biotechnology, 9(5):618-625. DOI:10.1111/1751-7915.12399

Carbonell-Ballestero M, Garcia-Ramallo E, Montañez R, Rodriguez-Caso C, Macía J. 2016. Dealing with the genetic load in bacterial synthetic biology circuits: Convergences with the Ohm’s law. Nucleic Acids Research, 44(1):496-507. DOI:10.1093/nar/gkv1280

Bonforti A, Duran-Nebreda S, Montañez R, Solé R. 2016. Spatial self-organization in hybrid models of multicellular adhesion. Chaos, 26(10). DOI:10.1063/1.4965992

Valverde S, Sole RV. 2015. Punctuated equilibrium in the large-scale evolution of programming languages. Journal of the Royal Society Interface, 12(107). DOI:10.1098/rsif.2015.0249

Valverde S, Solé RV. 2015. A cultural diffusion model for the rise and fall of programming languages. Human Biology, 87(3):224-234. DOI:10.13110/humanbiology.87.3.0224

Valverde S, Ohse S, Turalska M, West BJ, Garcia-Ojalvo J. 2015. Structural determinants of criticality in biological networks. Frontiers in Physiology, 6(may):1-9. DOI:10.3389/fphys.2015.00127

Solé R. 2015. Bioengineering the biosphere? Ecological Complexity, 22:40-49. DOI:10.1016/j.ecocom.2015.01.005

Solé RV, Montañez R, Duran-Nebreda S. 2015. Synthetic circuit designs for earth terraformation. Biology Direct, 10(1):1-10. DOI:10.1186/s13062-015-0064-7

Shirt-Ediss B, Solé R V, Ruiz-Mirazo K. 2015. Emergent chemical behavior in variable-volume protocells. Life, 5(1):181-211. DOI:10.3390/life5010181

Seoane LF, Solé R. 2015. Phase transitions in Pareto optimal complex networks. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 92(3):1-12. DOI:10.1103/PhysRevE.92.032807

Sardanyés J, Bonforti A, Conde N, Solé R, Macia J. 2015. Computational implementation of a tunable multicellular memory circuit for engineered eukaryotic consortia. Frontiers in Physiology, 6(oct):1-13. DOI:10.3389/fphys.2015.00281

Sardanyés J, Rodrigues C, Januário C, Martins N, Gil-Gómez G, Duarte J. 2015. Activation of effector immune cells promotes tumor stochastic extinction: A homotopy analysis approach. Applied Mathematics and Computation, 252:484-495. DOI:10.1016/j.amc.2014.12.005

Guillamon A, Fontich E, Sardanyés J. 2015. Bifurcations analysis of oscillating hypercycles. Journal of Theoretical Biology, 387:23-30. DOI:10.1016/j.jtbi.2015.09.018

Duarte J, Rodrigues C, Januário C, Martins N, Sardanyés J. 2015. How Complex, Probable, and Predictable is Genetically Driven Red Queen Chaos?. Acta Biotheoretica, 63(4):341-361. DOI:10.1007/s10441-015-9254-z

Avena-Koenigsberger A, Goñi J, Soleeé R, Sporns O. 2015. Network morphospace. Journal of the Royal Society Interface, 12(103). DOI:10.1098/rsif.2014.0881

Solé R V., Valverde S, Rodriguez-Caso C, Sardanyés J. 2014. Can a minimal replicating construct be identified as the embodiment of cancer?. BioEssays, 36(5):503-512. DOI:10.1002/bies.201300098

Shirt-Ediss B, Ruiz-Mirazo K, Mavelli F, Solé R V. 2014. Modelling lipid competition dynamics in heterogeneous protocell populations. Scientific Reports, 4. DOI:10.1038/srep05675

Sardanyés J, Simó C, Martínez R, Solé R V., Elena SF. 2014. Variability in mutational fitness effects prevents full lethal transitions in large quasispecies populations. Scientific Reports, 4. DOI:10.1038/srep04625

Macia J, Sole R. 2014. How to make a synthetic multicellular computer. PLoS ONE, 9(2). DOI:10.1371/journal.pone.0081248

Hillung J, Cuevas JM, Valverde S, Elena SF. 2014. Experimental evolution of an emerging plant virus in host genotypes that differ in their susceptibility to infection. Evolution, 68(9):2467-2480. DOI:10.1111/evo.12458

Gautrais J, Buhl J, Valverde S, Kuntz P, Theraulaz G. 2014. The role of colony size on tunnel branching morphogenesis in ant nests. PLoS ONE, 9(10):1-11. DOI:10.1371/journal.pone.0109436

Corominas-Murtra B, Fortuny J, Solé R V. 2014. Towards a mathematical theory of meaningful communication. Scientific Reports, 4:1-8. DOI:10.1038/srep04587

Carbonell-Ballestero M, Duran-Nebreda S, Montañez R, Solé R, Macía J, Rodríguez-Caso C. 2014. A bottom-up characterization of transfer functions for synthetic biology designs: Lessons from enzymology. Nucleic Acids Research, 42(22):14060-14069. DOI:10.1093/nar/gku964

Azzurro E, Tuset VM, Lombarte A, Maynou F, Simberloff D, Rodríguez-Pérez A, Solé RV. 2014. External morphology explains the success of biological invasions. Ecology Letters, 17(11):1455-1463. DOI:10.1111/ele.12351

Amor DR, Solé R V. 2014. Catastrophic shifts and lethal thresholds in a propagating front model of unstable tumor progression. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 90(2):1-11. DOI:10.1103/PhysRevE.90.022710

Amor DR, Fort J. 2014. Cohabitation reaction-diffusion model for virus focal infections. Physica A: Statistical Mechanics and its Applications, 416:611-619. DOI:10.1016/j.physa.2014.08.023

Zwart MP, Pijlman GP, Sardanyés J, Duarte J, Januário C, Elena SF. 2013. Complex dynamics of defective interfering baculoviruses during serial passage in insect cells. Journal of Biological Physics, 39(2):327-342. DOI:10.1007/s10867-013-9317-9

Weitz JS, Poisot T, Meyer JR, Flores CO, Valverde S, Sullivan MB, Hochberg ME. 2013. Phage-bacteria infection networks. Trends in Microbiology, 21(2):82-91. DOI:10.1016/j.tim.2012.11.003

Valverde S, Solé R V. 2013. Networks and the city. Architectural Design, 83(4):112-119. DOI:10.1002/ad.1627

Solé R V., Valverde S. 2013. Before the Endless Forms: Embodied Model of Transition from Single Cells to Aggregates to Ecosystem Engineering. PLoS ONE, 8(4). DOI:10.1371/journal.pone.0059664

Solé R V., Valverde S. 2013. Macroevolution in silico: Scales, constraints and universals. Palaeontology, 56(6):1327-1340. DOI:10.1111/pala.12047

Solé R V., Macia J. 2013. Expanding the landscape of biological computation with synthetic multicellular consortia. Natural Computing, 12(4):485-497. DOI:10.1007/s11047-013-9380-y

Solé R V., Valverde S, Casals MR, Kauffman SA, Farmer D, Eldredge N. 2013. The evolutionary ecology of technological innovations. Complexity, 18(4):15-27. DOI:10.1002/cplx.21436

Seoane LF,  Solé RV. 2013. A multiobjective optimization approach to statistical mechanics. Cornell University Library

Rodríguez-Caso C. 2013. Can cell mortality determine division of labor in tissue organization?. Journal of Theoretical Biology, 332:161-170. DOI:10.1016/j.jtbi.2013.05.001

Otero-Espinar M V., Seoane LF, Nieto JJ, Mira J. 2013. An analytic solution of a model of language competition with bilingualism and interlinguistic similarity. Physica D: Nonlinear Phenomena, 264:17-26. DOI:10.1016/j.physd.2013.08.011

Fort J, Solé R V. 2013. Accelerated tumor invasion under non-isotropic cell dispersal in glioblastomas. New Journal of Physics, 15. DOI:10.1088/1367-2630/15/5/055001

Duarte J, Januário C, Rodrigues C, Sardanyés J. 2013. Topological complexity and predictability in the dynamics of a tumor growth model with Shilnikov’s chaos. International Journal of Bifurcation and Chaos, 23(7). DOI:10.1142/S0218127413501241

Corominas-Murtra B, Goñi J, Solé R V., Rodríguez-Caso C. 2013. On the origins of hierarchy in complex networks. Proceedings of the National Academy of Sciences of the United States of America, 110(33):13316-13321. DOI:10.1073/pnas.1300832110

Widder S, Solé R, Macía J. 2012. Evolvability of feed-forward loop architecture biases its abundance in transcription networks. BMC Systems Biology, 6. DOI:10.1186/1752-0509-6-7

Valverde S, Solé R V, Elena SF. 2012. Evolved modular epistasis in artificial organisms. Artificial Life 13: Proceedings of the 13th International Conference on the Simulation and Synthesis of Living Systems, ALIFE 2012. 111-115. DOI:10.7551/978-0-262-31050-5-ch016

Macía J, Posas F, Solé R V. 2012. Distributed computation: The new wave of synthetic biology devices. Trends in Biotechnology, 30(6):342-349. DOI:10.1016/j.tibtech.2012.03.006

Macía J, Solé R V., Elena SF. 2012. The causes of epistasis in genetic networks. Evolution, 66(2):586-596. DOI:10.1111/j.1558-5646.2011.01451.x

Regot S, Macia J, Conde N, Furukawa K, Kjellén J, Peeters T, Hohmann S, de Nadal E, Posas F, Solé R. 2011. Distributed biological computation with multicellular engineered networks. Nature, 469(7329):207-211. DOI:10.1038/nature09679

Flores CO, Meyer JR, Valverde S, Farr L, Weitz JS. 2011. Statistical structure of host-phage interactions. Proceedings of the National Academy of Sciences of the United States of America, 108(28):1-10. DOI:10.1073/pnas.1101595108

Corominas-Murtra B, Fortuny J, Solé R V. 2011. Emergence of Zipf’s law in the evolution of communication. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 83(3):1-7. DOI:10.1103/PhysRevE.83.036115

Corominas-Murtra B, Rodríguez-Caso C, Goñi J, Solé R. 2011. Measuring the hierarchy of feedforward networks. Chaos, 21(1). DOI:10.1063/1.3562548

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