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Former Research Group

Structure of Evolution - Publications

Explore the scholarly works of the "Structure of Evolution" group. Browse journal articles, contributions in books and conference proceedings, academic theses, or discover our research through preprints.


inJournal
2025 Journal Open Access
Camille N. Lambert, Vaitea Opuu, Francesco Calvanese, Francesco Zamponi, Eric Hayden, Martin Weigt, Matteo Smerlak and Philippe Nghe

Exploring the space of self-reproducing ribozymes using probabilistic generative models

In: Nature communications, 16 (2025), p. 7836
inJournal
2024
Ian A. Hatton, Onofrio Mazzarisi, Ada Altieri and Matteo Smerlak

Diversity begets stability : sublinear growth and competitive coexistence across ecosystems

In: Science, 383 (2024) 6688, eadg8488
inJournal
2023 Journal Open Access
Maria Alejandra Ramirez, Matteo Smerlak, Arne Traulsen and Jürgen Jost

Diversity enables the jump towards cooperation for the Traveler's Dilemma

In: Scientific reports, 13 (2023), p. 1441
inJournal
2023 Journal Open Access
Mohammad Salahshour

Evolution as a result of resource flow in ecosystems : Ecological dynamics can drive evolution

In: PLOS ONE, 18 (2023) 10, e0286922
Academic
2023 Repository Open Access
Cyrille Merleau Nono

From RNA folding to inverse folding : a computational study

Dissertation, Universität Leipzig, 2023
inJournal
2023 Repository Open Access
Kuang-Yu Chen, Jayaprakash Karuppusamy, Mary B. O'Neill, Vaitea Opuu, Mathieu Bahin, Sophie Foulon, Pablo Ibanez, Tatsuhiko Ozawa, Sylvie van der Werf, Philippe Nghe, Nadia Naffakh, Andrew Griffiths and Catherine Isel

High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing

In: Proceedings of the National Academy of Sciences of the United States of America, 120 (2023) 6, e2211098120
inJournal
2023 Journal Open Access
Mohammad Salahshour

Interaction between games give rise to the evolution of moral norms of cooperation

In: PLoS computational biology, 18 (2023) 9, e1010429
inJournal
2023 Journal Open Access
Mohammad Salahshour

Predator-prey power laws : trophic interactions give rise to scale-invariant ecosystems

In: New journal of physics, 25 (2023) 12, p. 123012
inJournal
2023 Repository Open Access
Lorenzo Fant, Onofrio Mazzarisi, Emanuele Panizon and Jacopo Grilli

Stable cooperation emerges in stochastic multiplicative growth

In: Physical review / E, 108 (2023) 1, L012401
inJournal
2023 Journal Open Access
Ian A. Hatton, Eric D. Galbraith, Cyrille Merleau Nono, Teemu P. Miettinen and Benjamin McDonald Smith

The human cell count and size distribution

In: Proceedings of the National Academy of Sciences of the United States of America, 120 (2023) 39, e2303077120
inJournal
2023 Repository Open Access
Aleksander Klimek and Tommaso Cornelis Rosati

The spatial Λ-Fleming-Viot process in a random environment

In: The annals of applied probability, 33 (2023) 3, pp. 2426-2492
inJournal
2023 Journal Open Access
Stefano Ippolito, Francesca Urban, Wenhao Zheng, Onofrio Mazzarisi, Cataldo Valentini, Adam G. Kelly, Sai Manoj Gali, Mischa Bonn, David Beljonne, Federico Corberi, Jonathan N. Coleman and Paolo Samori

Unveiling charge transport mechanisms in electronic devices based on defect-engineered MoS\(_2\) covalent networks

In: Advanced materials, 35 (2023) 15, p. 221157
inJournal
2022 Repository Open Access
Maseim Kenmoe, Ronald Kriemann, Matteo Smerlak and Anton Zadorin

A fast iterative algorithm for near-diagonal eigenvalue problems

In: SIAM journal on matrix analysis and applications, 43 (2022) 4, pp. 1573-1598
Preprint
2022 Repository Open Access
Cyrille Merleau Nono and Matteo Smerlak

An evolutionary algorithm for inverse RNA folding inspired by Levy flights

inJournal
2022 Journal Open Access
Cyrille Merleau Nono and Matteo Smerlak

aRNAque : an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights

In: BMC bioinformatics, 23 (2022), p. 335
inJournal
2022 Journal Open Access
Daniel M. Perkins, Ian A. Hatton, Benoit Gauzens, Andrew D. Barnes, David Ott, Benjamin Rosenbaum, Catarina Vinagre and Ulrich Brose

Consistent predator-prey biomass scaling in complex food webs

In: Nature communications, 13 (2022), p. 4990
inJournal
2022 Repository Open Access
Camila Bräutigam and Matteo Smerlak

Diffusion approximations in population genetics and the rate of Muller's ratchet

In: Journal of theoretical biology, 550 (2022), p. 111236
inJournal
2022 Repository Open Access
Anton Zadorin

Exact travelling solution for a reaction-diffusion system with a piecewise constant production supported by a codimension-1 subspace

In: Communications on pure and applied analysis, 21 (2022) 5, pp. 1567-1580
inJournal
2022 Journal Open Access
Joseph R. Burger, Jordan G. Okie, Ian A. Hatton, Vanessa P. Weinberger, Munik Shrestha, Kyra J. Liedtke, Tam Be, Austin R. Cruz, Xiao Feng, Cesar Hinojo-Hinojo, Abu S. M. G. Kibria, Kacey C. Ernst and Brian J. Enquist

Global city densities : re-examining urban scaling theory

In: Frontiers in conservation science, 3 (2022), p. 879934
inJournal
2022 Repository Open Access
Federico Corberi, Leticia F. Cugliandolo, Marco Espositio, Onofrio Mazzarisi and Marco Picco

How many phases nucleate in the bidimensional Potts model?

In: Journal of statistical mechanics, 2022 (2022) 7, p. 073204
Preprint
2022 Repository Open Access
Vaitea Opuu and Hélène Bret

Investigating graph neural network for RNA structural embedding

inJournal
2022 Repository Open Access
Matteo Smerlak

Perturbation theory without power series : iterative construction of non-analytic operator spectra

In: epl, 140 (2022) 3, p. 32001
Preprint
2022 Repository Open Access
Mohammad Salahshour

Predator-prey interactions give rise to scale-invariant ecosystems

inJournal
2022
Matteo Smerlak and Carlo Rovelli

Put defence money into planetary emergencies, urge Nobel winners

In: Nature, 601 (2022), pp. 318-318
inJournal
2022 Journal Open Access
Vaitea Opuu, Cyrille Merleau Nono, Vincent Messow and Matteo Smerlak

RAFFT : Efficient prediction of RNA folding pathways using the fast Fourier transform

In: PLoS computational biology, 18 (2022) 8, e1010448
inJournal
2022 Journal Open Access
Mohammad Salahshour, Vincent Oberhauser and Matteo Smerlak

The cost of noise : stochastic punishment falls short of sustaining cooperation in social dilemma experiments

In: PLOS ONE, 17 (2022) 3, e0263028
inBook
2021 Journal Open Access
Cyrille Merleau Nono and Matteo Smerlak

A simple evolutionary algorithm guided by local mutations for an efficient RNA design

In: GECCO '21 : proceedings of the genetic and evolutionary computation conference ; Lille France 10 July, 2021- 14 July, 2021 / Francisco Chicano (ed.)
New York : ACM, 2021. - pp. 1027-1034
inJournal
2021 Journal Open Access
Mohammad Salahshour and Shahin Rouhani

Collective movement and collective information acquisition with signaling

In: Frontiers in physics, 9 (2021), p. 668283
inJournal
2021 Journal Open Access
Mohammad Salahshour

Evolution of cooperation and consistent personalities in public goods games

In: Scientific reports, 11 (2021), p. 23708
inJournal
2021 Journal Open Access
Mohammad Salahshour

Evolution of cooperation in costly institutions exhibits Red Queen and Black Queen dynamics in heterogeneous public goods

In: Communications biology, 4 (2021), p. 1340
inJournal
2021 Journal Open Access
Mohammad Salahshour

Evolution of prosocial punishment in unstructured and structured populations and in the presence of antisocial punishment

In: PLOS ONE, 16 (2021) 8, e0254860
inJournal
2021 Journal Open Access
Mohammad Salahshour

Freedom to choose between public resources promotes cooperation

In: PLoS computational biology, 17 (2021) 2, e1008703
inJournal
2021 Repository Open Access
Matteo Smerlak

Intermittency as metastability : a predictive approach to evolution in disordered environments

In: epl, 134 (2021) 2, p. 28002
Book
2021
Matteo Smerlak

Les trous noirs

2e édition. - Paris : PUF, 2021. - p. 126
(Que sais-je? ; 4003)
ISBN: 978-2-7154-0738-1, ISBN: 978-2-7154-0740-4
inJournal
2021 Journal Open Access
Onofrio Mazzarisi, Amanda de Azevedo-Lopes, Jeferson J. Arenzon and Federico Corberi

Maximal diversity and Zipf's law

In: Physical review letters, 127 (2021) 12, p. 128301
inJournal
2021 Journal Open Access
Sylvain Charlat, André Ariew, Pierrick Bourrat, Maria Ferreira Ruiz, Thomas Heams, Philippe Huneman, Sandeep Krishna, Michael Lachmann, Nicolas Lartillot, Loius Le Sergeant d'Hendecourt, Christope Malaterre, Philippe Nghe, Etienne Rajon, Olivier Rivoire, Matteo Smerlak and Zorana Zeravcic

Natural selection beyond life? A workshop report

In: Life : open access journal, 11 (2021) 10, p. 1051
inJournal
2021 Journal Open Access
Matteo Smerlak

Neutral quasispecies evolution and the maximal entropy random walk

In: Science advances, 7 (2021) 16, eabb2376
inJournal
2021 Journal Open Access
Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Remi Monasson, Clément Nizak and Olivier Rivoire

Parameters and determinants of responses to selection in antibody libraries

In: PLoS computational biology, 17 (2021) 3, e1008751
Preprint
2021 Repository Open Access
Mohammad Salahshour

Playing soft with cooperators emerges as a moral norm and promotes cooperation in evolutionary games

inJournal
2021 Repository Open Access
Matteo Smerlak

Quasi-species evolution maximizes genotypic reproductive value (not fitness or flatness)

In: Journal of theoretical biology, 522 (2021), p. 110699
inJournal
2021 Repository Open Access
Anton Zadorin and Olivier Rivoire

Sex as information processing : optimality and evolution

In: Physical review / E, 103 (2021) 6, p. 062413
inJournal
2021 Journal Open Access
Ian A. Hatton, Ryan F. Heneghan, Yinon M. Bar-On and Eric D. Galbraith

The global ocean size spectrum from bacteria to whales

In: Science advances, 7 (2021) 46, eabh3732
inJournal
2021 Journal Open Access
Niloy Biswas, Alison Etheridge and Aleksander Klimek

The spatial Lambda-Fleming-Viot process with fluctuating selection

In: Electronic journal of probability, 26 (2021), p. 25
inJournal
2021 Journal Open Access
Cyrille Merleau Nono, Sophie Pénisson, Philip J. Gerrish, Santiago F. Elena and Matteo Smerlak

Why are viral genomes so fragile? The bottleneck hypothesis

In: PLoS computational biology, 17 (2021) 7, e1009128
inJournal
2020 Journal Open Access
Omri Tal and Tat Dat Tran

Adaptive bet-hedging revisited : considerations of risk and time horizon

In: Bulletin of mathematical biology, 82 (2020) 4, p. 50
inJournal
2020 Journal Open Access
Mohammad Salahshour

Coevolution of cooperation and language

In: Physical review / E, 102 (2020) 4, p. 042409
inJournal
2020 Journal Open Access
Ian A. Hatton and Eric D. Galbraith

Commentary on ''Key ecological parameters of immotile versus locomotive life'' by Gorshkov and Makarieva

In: Russian journal of ecosystem ecology, 5 (2020) 2, p. 5
Preprint
2020 Repository Open Access
Maseim Kenmoe, Matteo Smerlak and Anton Zadorin

Dynamical perturbation theory for eigenvalue problems

inBook
2020 Repository Open Access
Ivan P. Yamshchikov, Cyrille Merleau Nono, Igor Samenko and Jürgen Jost

It means more if it sounds good : yet another hypothesis concerning the evolution of polysemous words

In: Proceedings of the 5th international conference on complexity, future information systems and risk : COMPLEXIS 2020 ; May 8-9, 2020 ; Volume 1 / Reinhold Behringer... (eds.)
Setúbal (Portugal) : SCITEPRESS, 2020. - pp. 143-148
Preprint
2020 Repository Open Access
Matteo Smerlak

Localization of neutral evolution : selection for mutational robustness and the maximal entropy random walk

Preprint
2020 Repository Open Access
Mohammad Salahshour

The evolution of punishing institutions

inBook
2020
Ian A. Hatton

What regulates growth across levels of organization?

In: Unsolved problems in ecology / Andrew Dobson... (eds.)
Princeton : Princeton University Press, 2020. - pp. 203-217
inJournal
2019 Repository Open Access
Federico Corberi, Onofrio Mazzarisi and Andrea Gambassi

Dynamics of fluctuations in the Gaussian model with conserved dynamics

In: Journal of statistical mechanics, 2019 (2019) 10, p. 104001
Preprint
2019 Repository Open Access
Matteo Smerlak

Effective potential reveals evolutionary trajectories in complex fitness landscapes

inJournal
2019
Igor Haman Tchappi, Stéphane Galland, Vivient Corneille Kamla, Jean-Claude Kamgang, Cyrille Merleau Nono and Hui Zhao

Holonification model for a multilevel agent-based system : application to road traffic

In: Personal and ubiquitous computing, 23 (2019) 5/6, pp. 633-651
inJournal
2019 Journal Open Access
Ian A. Hatton, Andy P. Dobson, David Storch, Eric D. Galbraith and Michel Loreau

Linking scaling laws across eukaryotes

In: Proceedings of the National Academy of Sciences of the United States of America, 116 (2019) 43, pp. 21616-21622
inJournal
2019
Mohammad Salahshour

Phase diagram and optimal information use in a collective sensing system

In: Physical review letters, 123 (2019) 6, p. 068101
Preprint
2019 Repository Open Access
Jonathan Chetwynd-Diggle and Aleksander Klimek

Rare mutations in the spatial Lambda-Fleming-Viot model in a fluctuating environment and SuperBrownian Motion

inJournal
2018 Repository Open Access
Matteo Smerlak

Natural selection as coarsening

In: Journal of statistical physics, 172 (2018) 1, pp. 105-113
inJournal
2018 Repository Open Access
Omri Tal and Tat Dat Tran

New perspectives on multilocus ancestry informativeness

In: Mathematical biosciences, 306 (2018), pp. 60-81
inJournal
2017 Journal Open Access
Matteo Smerlak and Bapu Vaitla

A non-equilibrium formulation of food security resilience

In: Royal Society Open Science, 4 (2017) 1, p. 160874
inJournal
2017 Repository Open Access
Omri Tal, Tat Dat Tran and Jacobus W. Portegies

From typical sequences to typical genotypes

In: Journal of theoretical biology, 419 (2017), pp. 159-183
inJournal
2017 Repository Open Access
Matteo Smerlak and Ahmed Youssef

Limiting fitness distributions in evolutionary dynamics

In: Journal of theoretical biology, 416 (2017), pp. 68-80
inBook
2017
Matteo Smerlak

The relational interpretation of quantum mechanics and the EPR paradox

In: The quantum world : philosophical debates on quantum physics / Bernard d' Espagnat... (eds.)
Cham : Springer, 2017. - pp. 195-223
(The frontiers collection)
inJournal
2017 Repository Open Access
Matteo Smerlak and Ahmed Youssef

Universal statistics of selected values

In: epl, 117 (2017) 5, p. 50003
Book
2016
Matteo Smerlak

Les trous noirs

Paris : PUF, 2016. - p. 126
(Que sais-je? ; 4003)
ISBN: 978-2-13-063009-8
inJournal
2016 Repository Open Access
Matteo Smerlak

Minimum relative entropy distributions with a large mean are Gaussian

In: Physical review / E, 94 (2016) 6, p. 062107
inJournal
2016 Journal Open Access
Yaron Granot, Omri Tal, Saharon Rosset and Karl Skorecki

On the apportionment of population structure

In: PLOS ONE, 11 (2016) 8, e0160413
inJournal
2016 Repository Open Access
Matteo Smerlak

Thermodynamics of inequalities : from precariousness to economic stratification

In: Physica / A, 441 (2016), pp. 40-50
inJournal
2015 Journal Open Access
Eugenio Bianchi, Tommaso De Lorenzo and Matteo Smerlak

Entanglement entropy production in gravitational collapse : covariant regularization and solvable models

In: Journal of high energy physics, 2015 (2015) 6, p. 180
inJournal
2015 Repository Open Access
Omri Tal

From typical sequences to typical genotype

In: Human heredity, 80 (2015) 3, pp. 122-122
inJournal
2015 Journal Open Access
Matteo Smerlak, Brady Stoll, Agam Gupta and James S. Magdanz

Mapping systemic risk : critical degree and failures distribution in financial networks

In: PLOS ONE, 10 (2015) 7, e0130948
inJournal
2015 Repository Open Access
Ian A. Hatton, Kevin S. McCann, John M. Fryxell, T. Jonathan Davies, Matteo Smerlak, Anthony R. E. Sinclair and Michel Loreau

The predator-prey power law : biomass scaling across terrestrial and aquatic biomes

In: Science, 349 (2015) 6252, aac6284
inJournal
2014 Repository Open Access
Eugenio Bianchi and Matteo Smerlak

Entanglement entropy and negative energy in two dimensions

In: Physical review / D, 90 (2014) 4, p. 041904
inJournal
2014 Repository Open Access
Eugenio Bianchi and Matteo Smerlak

Last gasp of a black hole : unitary evaporation implies non-monotonic mass loss

In: General relativity and gravitation, 46 (2014) 10, p. 1809
inJournal
2014 Repository Open Access
Aristide Baratin, Sylvain Carrozza, Daniele Oriti, James Ryan and Matteo Smerlak

Melonic phase transition in group field theory

In: Letters in mathematical physics, 104 (2014) 8, pp. 1003-1017
inBook
2014
Omri Tal

Quantifying the high-dimensional information of population structure

In: 42nd European Mathematical Genetics Meeting (EMGM) 2014, April 1-2, 2014, Cologne, Germany : Abstracts
Basel : Karger, 2014. - p. 110
(Human Heredity ; 76 (2013) 2)
inBook
2014
Matteo Smerlak

Séance VII : l'interprétation relationnelle de la mécanique quantique et le paradoxe EPR

In: Le monde quantique : les débats philosophiques de la physique quantique / Bernard d' Espagnat... (eds.)
Paris : ÔEditions matériologiques, 2014. - pp. 299-336
inBook
2013
Matteo Smerlak

Einstein\(\mathscr {}^2\) : Brownian motion meets general relativity

In: Analogue gravity phenomenology / Daniele Faccio... (eds.)
Cham : Springer, 2013. - pp. 385-398
(Lecture notes in physics ; 870)
inJournal
2013 Repository Open Access
Matteo Smerlak and Suprit Singh

New perspectives on Hawking radiation

In: Physical review / D, 88 (2013) 10, p. 104023
inJournal
2013 Repository Open Access
Matteo Smerlak

The two faces of Hawking radiation

In: International journal of modern physics / D, 22 (2013) 12, p. 1342019
inJournal
2013 Journal Open Access
Valentin Bonzom, Razvan Gurau and Matteo Smerlak

Universality in \(p\)-spin glasses with correlated disorder

In: Journal of statistical mechanics, 2013 (2013) 2, L02003
inJournal
2012 Repository Open Access
Valentin Bonzom and Matteo Smerlak

Bubble divergences : sorting out topology from cell structure

In: Annales Henri Poincaré, 13 (2012) 1, pp. 185-208
inJournal
2012 Repository Open Access
Valentin Bonzom and Matteo Smerlak

Bubble divergences from twisted cohomology

In: Communications in mathematical physics, 312 (2012) 2, pp. 399-426
inJournal
2012 Journal Open Access
Matteo Smerlak

Diffusion in curved spacetimes

In: New journal of physics, 14 (2012) 2, p. 023019
Preprint
2012
Matteo Smerlak

Divergences in spinfoam models : powercounting and resummation in the flat model

Preprint
2012 Repository Open Access
Matteo Smerlak

Divergences in spinfoam quantum gravity

inJournal
2012 Repository Open Access
Valentin Bonzom and Matteo Smerlak

Gauge symmetries in spin-foam gravity : the case for ''cellular quantization''

In: Physical review letters, 108 (2012) 24, p. 241303
inJournal
2012 Repository Open Access
Carlo Rovelli and Matteo Smerlak

In quantum gravity, summing is refining

In: Classical and quantum gravity, 29 (2012) 5, p. 055004
Preprint
2012 Repository Open Access
Matteo Smerlak

Metadiffusion

inJournal
2012 Repository Open Access
Matteo Smerlak

On the inertia of heat

In: The European physical journal plus, 127 (2012) 7, p. 72
Preprint
2012 Repository Open Access
Matteo Smerlak and Ahmed Youssef

Self-organization without heat : the geometric ratchet effect

inJournal
2012 Journal Open Access
Matteo Smerlak and Carlo Rovelli

Spinfoams : summing or refining?

In: Journal of physics / Conference series, 360 (2012) 1, p. 012053
Preprint
2012 Repository Open Access
Matteo Smerlak

Stochastic thermodynamics of entropic transport

inJournal
2012 Repository Open Access
Matteo Smerlak

Tailoring diffusion in analog spacetimes

In: Physical review / E, 85 (2012) 4, p. 041134
inJournal
2012 Repository Open Access
Carlo Rovelli and Matteo Smerlak

Unruh effect without trans-horizon entanglement

In: Physical review / D, 85 (2012) 12, p. 124055
inJournal
2011 Repository Open Access
Matteo Smerlak

A blackbody is not a blackbox

In: European journal of physics, 32 (2011) 5, pp. 1143-1153
inJournal
2011 Repository Open Access
Matteo Smerlak

Comment on 'Lost in translation : topological singularities in group field theory'

In: Classical and quantum gravity, 28 (2011) 17, p. 178001
inJournal
2011 Repository Open Access
Carlo Rovelli and Matteo Smerlak

Thermal time and Tolman-Ehrenfest effect : 'temperature as the speed of time'

In: Classical and quantum gravity, 28 (2011) 7, p. 075007
inJournal
2010 Journal Open Access
Caroline Derec, Matteo Smerlak, Jacques Servais and Jean-Claude Bacri

Anomalous diffusion in microchannel under magnetic field

In: Physics procedia, 9 (2010), pp. 109-112
inJournal
2010 Repository Open Access
Valentin Bonzom and Matteo Smerlak

Bubble divergences from cellular cohomology

In: Letters in mathematical physics, 93 (2010) 3, pp. 295-305
inJournal
2009 Repository Open Access
Jacques Magnen, Karim Noui, Vincent Rivasseau and Matteo Smerlak

Scaling behavior of three-dimensional group field theory

In: Classical and quantum gravity, 26 (2009) 18, p. 185012
inJournal
2008
Carlo Rovelli and Matteo Smerlak

Le monde quantique, une question de perspective

In: La recherche : revue mensuelle, 418 (2008), pp. 42-45
inJournal
2008 Repository Open Access
Valentin Bonzom, Etera R. Livine, Matteo Smerlak and Simone Speziale

Towards the graviton from spinfoams : the complete perturbative expansion of the 3d toy model

In: Nuclear physics / B, 804 (2008) 3, pp. 507-526
inJournal
2007 Repository Open Access
Matteo Smerlak and Carlo Rovelli

Relational EPR

In: Foundations of physics, 37 (2007) 3, pp. 427-445
Preprint
2006
Matteo Smerlak

Relational quantum mechanics