publications

2017

  • Plankton: the paradox and the power law
    Richard Law, José A. Cuesta, and Gustav W. Delius
    arXiv.org/q-bio/1705.05327 (2017)
  • Disentangling the effects of selection and loss bias on gene dynamics
    Jaime Iranzo, José A. Cuesta, Susanna Manrubia, Mikhail I. Katsnelson, and Eugene V. Koonin
    Proceedings of the National Academy of Sciences (USA) 114, E5616-E5624 (2017)
    DOI: 10.1073/pnas.1704925114
  • Sheldon Spectrum and the Plankton Paradox: Two Sides of the Same Coin—a trait-based plankton size-spectrum model
    José A. Cuesta, Gustav W. Delius, and Richard Law
    Journal of Mathematical Biology, Early Edition (2017)
    DOI: 10.1007/s00285-017-1132-7
    arXiv.org/q-bio/1607.04158
  • Distribution of genotype networks sizes in sequence-to-structure genotype-phenotype maps
    Susanna Manrubia and José A. Cuesta
    Journal of the Royal Society Interface 14, 20160976 (2017)
    DOI: 10.1098/rsif.2016.0976
    arXiv.org/q-bio/1702.00351
  • Enumerating secondary structures and structural moieties for circular RNAs
    José A. Cuesta and Susanna Manrubia
    Journal of Theoretical Biology 419, 375-382 (2017)
    DOI: 10.1016/j.jtbi.2017.02.024
    arXiv.org/q-bio/1607.04435
  • Adaptive multiscapes: an up-to-date metaphor to visualize molecular adaptation
    Pablo Catalán, Clemente F. Arias, José A. Cuesta, and Susanna Manrubia
    Biology Direct 12, 7 (2017)
    DOI: 10.1186/s13062-017-0178-1
  • 2016

  • Fair linking mechanisms for resource allocation with correlated player types
    Agustín Santos, Antonio Fernández Anta, José A. Cuesta, and Luis López Fernández
    Computing 8, 777-801 (2016)
  • 2015

  • The growth threshold conjecture: a theoretical framework for understanding T-cell tolerance
    Clemente F. Arias, Miguel A. Herrero, José A. Cuesta, Francisco J. Acosta, and Cristina Fernández-Arias
    Royal Society Open Science 2, 150016 (2015)
  • General approach for dealing with dynamical systems with spatiotemporal periodicities
    Jesus Casado-Pascual, José A. Cuesta, Niurka R. Quintero, and Renato Alvarez-Nodarse
    Physical Review E 91, 022905 (2015)
  • Reputation drives cooperative behaviour and network formation in human groups
    José A. Cuesta, Carlos Gracia-Lázaro, Alfredo Ferrer, Yamir Moreno, and Angel Sánchez
    Scientific Reports 5, 7843 (2015)
  • Evolution on neutral networks accelerates the ticking rate of the molecular clock
    Susanna Manrubia and José A. Cuesta
    Journal of the Royal Society Interface 12, 20141010 (2015)
  • 2014

  • toyLIFE: a computational framework to study the multi-level organization of the genotype-phenotype map
    Clemente F. Arias, Pablo Catalán, Susanna Manrubia, and José A. Cuesta
    Scientific Reports 4, 7549 (2014)
  • Fair linking mechanisms for resource allocation with correlated player types
    Agustín Santos, Antonio Fernández Anta, José A. Cuesta, and Luis López Fernández
    Proceedings of International Conference on NETworked sYStems (NETYS) 2014
    Lecture Notes in Computer Science 8593, 70-83 (Springer, 2014)
  • Spreading of intolerance under economic stress: results from a model with reputation
    Luis Martinez-Vaquero and José A. Cuesta,
    Physical Review E 90, 022805 (2014)
  • A comparative analysis of spatial Prisoner's Dilemma experiments: Conditional cooperation and payoff irrelevance
    Jelena Grujić, Carlos Gracia-Lázaro, Manfred Milinski, Dirk Semmann, Arne Traulsen, José A. Cuesta, Yamir Moreno, and Angel Sánchez
    Scientific Reports 4, 4615 (2014)
  • 2013

  • Gender differences in cooperation: experimental evidence on high school students
    José A. Molina, Carlos Gracia-Lázaro, J. Ignacio Jiménez-Nadal, Yamir Moreno, José A. Cuesta, and Angel Sánchez
    PLoS ONE 8, e83700 (2013)
  • Comment on "Ratchet universality in the presence of thermal noise"
    Niurka R. Quintero, Renato Alvarez-Nodarse and José A. Cuesta,
    Physical Review E 88, 066101 (2013)
  • Time-shift invariance determines the functional shape of the current in dissipative rocking ratchets
    José A. Cuesta, Niurka R. Quintero and Renato Alvarez-Nodarse
    Physical Review X 3, 041014 (2013)
  • Evolutionary stability and resistance to cheating in an indirect reciprocity model based on reputation
    Luis A. Martinez-Vaquero and José A. Cuesta
    Physical Review E 87, 052810 (2013)
  • 2012

  • Three is a crowd in iterated prisoner's dilemmas: experimental evidence on reciprocal behavior
    Jelena Grujić, Burcu Eke, Antonio Cabrales, José A. Cuesta and Angel Sánchez
    Scientific Reports 2, 638 (2012)
  • Local-based semantic navigation on a networked representation of information
    José A. Capitán, Javier Borge-Holthoefer, Sergio Gómez, Juan Martinez-Romo, Lourdes Araujo, José A. Cuesta and Alex Arenas
    PLoS ONE 7, e43694 (2012)
  • Stability and robustness analysis of cooperation cycles driven by destructive agents in finite populations
    Rubén J. Requejo, Juan Camacho, José A. Cuesta and Alex Arenas
    Physical Review E 86, 026105 (2012)
  • Heterogeneous networks do not promote cooperation when humans play a Prisoner's Dilemma
    Carlos Gracia-Lázaro, Alfredo Ferrer, Gonzalo Ruiz, Alfonso Tarancón, José A. Cuesta, Yamir Moreno and Angel Sánchez
    Proceedings of the National Academy of Sciences (USA) 109 12922-12926 (2012)
    Comment by Dirk Semmann in PNAS: Conditional cooperation can hinder network reciprocity
  • Generosity pays in the presence of direct reciprocity: A comprehensive study of 2 x 2 repeated games
    Luis A. Martínez-Vaquero, José A. Cuesta and Angel Sánchez
    PLoS ONE 7, e35135 (2012)
  • Human behavior in Prisoner's Dilemma experiments suppresses network reciprocity
    Carlos Gracia-Lázaro, José A. Cuesta, Angel Sánchez and Yamir Moreno
    Scientific Reports 2, 325 (2012)
  • On the coexistence of cooperators, defectors and conditional cooperators in the multiplayer iterated Prisoner's Dilemma
    Jelena Grujić, José A. Cuesta and Angel Sánchez
    Journal of Theoretical Biology 300, 299-308 (2012)
  • Individual strategy update and emergence of cooperation in social networks
    Carlos P. Roca, Angel Sánchez and José A. Cuesta
    Journal of Mathematical Sociology 36, 1-21 (2012)
  • 2011

  • Disentangling categorical relationships trough a graph of co-occurrences
    Juan Martinez-Romo, Lourdes Araujo, Javier Borge-Holthoefer, Alex Arenas, José A. Capitán and José A. Cuesta
    Physical Review E 84, 046108 (2011)
  • Ratchet effect on a relativistic particle driven by external forces
    Niurka R. Quintero, Renato Alvarez-Nodarse and José A. Cuesta
    Journal of Physics A: Mathematical and General 44, 425205 (2011)
  • Severe hindrance of viral infection propagation in spatially extended hosts
    José A. Capitán, José A. Cuesta, Susanna C. Manrubia and Jacobo Aguirre
    PLoS ONE 6, e23358 (2011)
  • Huge progeny production during the transient of a quasi-species model of viral infection, reproduction and mutation
    José A. Cuesta
    Mathematical and Computer Modelling 54, 1676-1681 (2011)
  • Crossed-ratchet effects and domain wall geometrical pinning
    V. I. Marconi, A. B. Kolton, J. A. Capitán, J. A. Cuesta, A. Pérez-Junquera, M. Vélez, J. I. Martín and J. M. R. Parrondo
    Physical Review B 83, 214403 (2011)
  • The Joker effect: cooperation driven by destructive agents
    Alex Arenas, Juan Camacho, J. A. Cuesta, and Rubén Requejo
    Journal of Theoretical Biology 279, 113-119 (2011)
  • Struggle for space: Viral extinction through competition for cells
    José A. Cuesta, Jacobo Aguirre, José A. Capitán and Susanna C. Manrubia
    Physical Review Letters 106, 028104 (2011)
  • Species assembly in model ecosystems, II: Results of the assembly process
    José A. Capitán, José A. Cuesta and Jordi Bascompte
    Journal of Theoretical Biology 269, 344-355 (2011)
  • Species assembly in model ecosystems, I: Analysis of the population model and the invasion dynamics
    José A. Capitán and José A. Cuesta
    Journal of Theoretical Biology 269, 330-343 (2011)
  • 2010

  • Neutral networks of genotypes: Evolution behind the curtain
    Susanna C. Manrubia and José A. Cuesta
    ARBOR, 186, 1051-1064 (2010)
    (color version)
  • Social experiments in the mesoscale: Humans playing a spatial Prisoner's Dilemma
    Jelena Grujić, Constanza Fosco, Lourdes Araujo, José A. Cuesta and Angel Sánchez
    PLoS ONE 5, e13749 (2010)
    Highlighed by Nature Physics in the 'Research highlights' section of its January 2011 issue
  • Catastrophic regime shifts in model ecological communities are true phase transitions
    José A. Capitán and José A. Cuesta
    Journal of Statistical Mechanics: Theory and Experiment 10, P10003 (2010)
  • Mathematics of evolution
    José A. Cuesta
    Newsletter of the EMS 76, 28-37 (2010)
  • Symmetries shape the current in ratchets induced by a bi-harmonic force
    Niurka R. Quintero, José A. Cuesta and Renato Alvarez-Nodarse
    Physical Review E 81, 030102R (2010)
    Supplementary Material
  • 2009

  • Las matemáticas de la evolución
    José A. Cuesta
    La Gaceta de la RSME 12, 667-686 (2009)
  • Statistical mechanics of ecosystem assembly
    José A. Capitán, José A. Cuesta and Jordi Bascompte
    Physical Review Letters 103, 168101-4 (2009)
    Selected for the October 15, 2009 issue of Virtual Journal of Biological Physics Research
  • The effect of spatial structure on the emergence of cooperation
    Carlos P. Roca, José A. Cuesta and Angel Sánchez
    Physical Review E 80, 046106-16 (2009)
    Selected for the October 15, 2009 issue of Virtual Journal of Biological Physics Research
  • Phase diagram of a two-dimensional lattice gas model of a ramp system
    Noé G. Almarza, José A. Capitán, José A. Cuesta and Enrique Lomba
    Journal of Chemical Physics 131, 124506-12 (2009)
  • Evolutionary game theory: temporal and spatial effects beyond replicator dynamics
    Carlos P. Roca, José A. Cuesta and Angel Sánchez
    Physics of Life Reviews 6, 208-249 (2009)
  • Imperfect imitation can enhance cooperation
    Carlos P. Roca, José A. Cuesta and Angel Sánchez
    Europhysics Letters 87, 47005-5 (2009)
  • Promotion of cooperation on networks? The myopic best response case
    Carlos P. Roca, José A. Cuesta and Angel Sánchez
    European Physical Journal B 71 587-595 (2009)
  • The Shared Reward Dilemma on structured populations
    Raúl Jimenez, José A. Cuesta, Haydée Lugo and Angel Sánchez
    Journal of Economic Interaction and Coordination 4 183-193 (2009)
  • Smectic and columnar ordering in length-polydisperse fluids of parallel hard cylinders
    Yuri Martínez-Ratón and José A. Cuesta
    Molecular Physics 107, 415-422 (2009)
  • 2008

  • Density functional theories of hard particle systems
    Pedro Tarazona, José A. Cuesta and Yuri Martínez-Ratón
    Lecture Notes in Physics 753, 247-341 (2008)
  • Phase behavior of parallel hard cylinders
    José A. Capitán, Yuri Martínez-Ratón and José A. Cuesta
    Journal of Chemical Physics 128, 194901-8 (2008)
    Selected for the June 1, 2008 issue of Virtual Journal of Biological Physics Research
  • Fundamental-measure density functional for mixtures of parallel hard cylinders
    Yuri Martínez-Ratón, José A. Capitán and José A. Cuesta
    Physical Review E 77, 051205-9 (2008)
  • The Shared Reward Dilemma
    José A. Cuesta, Raúl Jimenez, Haydée Lugo and Angel Sánchez
    Journal of Theoretical Biology 251, 253-263 (2008)
  • Emergence and resilience of cooperation in the spatial Prisoner's Dilemma via a reward mechanism
    Raúl Jimenez, Haydée Lugo, José A. Cuesta and Angel Sánchez
    Journal of Theoretical Biology 250, 475-483 (2008)
  • 2007

  • Fundamental-measure density functional for the fluid of aligned hard hexagons: New insights in fundamental measure theory
    José A. Capitán and José A. Cuesta
    Physical Review E 76, 011403-9 (2007)
  • The importance of selection rate in the evolution of cooperation
    Carlos P. Roca, José A. Cuesta and Angel Sánchez
    European Physical Journal Special Topics 143, 51-58 (2007)
  • 2006

  • La entropía como creadora de orden
    José A. Cuesta
    Revista Española de Física 20(4), 13-19 (2006)
  • First-principles derivation of density functional formalism for quenched-annealed systems
    Luis Lafuente and José A. Cuesta
    Physical Review E 74, 041502-9 (2006)
  • Time scales in evolutionary dynamics
    Carlos P. Roca, José A. Cuesta and Angel Sánchez
    Physical Review Letters 97, 159701-4 (2006)
  • A resistivity model for electrophoretic deposition
    Begoña Ferrari, Rodrigo Moreno and José A. Cuesta
    Key Engineering Materials 314, 175-180 (2006)
  • Genetic algorithm for burst detection and activity tracking in event streams
    Lourdes Araujo, José A. Cuesta and Juan J. Merelo
    PPSN IX, Lecture Notes in Computer Science 4193, 302-311 (Springer-Verlag, 2006)
  • 2005

  • Lattice density functional for colloid-polymer mixtures: Comparison of two fundamental measure theories
    José A. Cuesta, Luis Lafuente and Matthias Schmidt
    Physical Review E 72, 031405-9 (2005)
  • Altruistic behavior pays, or the importance of fluctuations in evolutionary game theory
    Angel Sánchez, José A. Cuesta and Carlos P. Roca
    Modeling Cooperative Behavior in the Social Sciences: Eigth Granada Lectures, P. L. Garrido, J. Marro and M. A. Muñoz eds. (AIP Proceedings Series, 2005)
  • Cluster density functional theory for lattice models based on the theory of Mobius functions
    Luis Lafuente and José A. Cuesta
    Journal of Physics A: Mathematical and General 38, 7461-7482 (2005)
  • Altruism may arise from individual selection
    Angel Sánchez and José A. Cuesta
    Journal of Theoretical Biology 235, 233-240 (2005)
  • 2004

  • Density functional theory for general hard-core lattice gases
    Luis Lafuente and José A. Cuesta
    Physical Review Letters 93, 130603-4 (2004)
  • General nonexistence theorem for phase transitions in one-dimensional systems with short range interactions, and physical examples of such transitions
    José A. Cuesta and Angel Sánchez
    Journal of Statistical Physics 115, 869-893 (2004)
    Erratum: 137, 593-594 (2009)
  • 2003

  • Density functional theory for nearest-neighbor exclusion lattice gases in two and three dimensions
    Luis Lafuente and José A. Cuesta
    Physical Review E 68, 066120-12 (2003)
  • Instabilities in complex mixtures with a large number of components
    Richard P. Sear and José A. Cuesta
    Physical Review Letters 91, 245701 (2003)
    Selected for the December 15, 2003 issue of Virtual Journal of Biological Physics Research
  • Phase behavior of hard-core lattice gases: A fundamental measure approach
    Luis Lafuente and José A. Cuesta
    Journal of Chemical Physics 119, 10832-10843 (2003)
  • Freezing in the presence of disorder: A lattice study
    Matthias Schmidt, Luis Lafuente and José A. Cuesta
    Journal of Physics: Condensed Matter 15, 4695-4708 (2003)
  • Overcomplete free energy functional for D=1 particle systems with next neighbor interactions
    Christian Tutschka and José A. Cuesta
    Journal of Statistical Physics 111, 1125-1148 (2003)
  • Phase diagrams of Zwanzig models: The effect of polydispersity
    Yuri Martínez-Ratón and José A. Cuesta
    Journal of Chemical Physics 118, 10164-10173 (2003)
  • Apparent phase transitions in finite one-dimensional sine-Gordon lattices
    Saúl Ares, José A. Cuesta, Angel Sánchez y Raúl Toral
    Physical Review E 67, 046108-6 (2003)
  • 2002

  • Fundamental measure theory for lattice fluids with hard core interactions
    Luis Lafuente and José A. Cuesta
    Journal of Physics: Condensed Matter 14 12079-12097 (2002)
  • Close to the edge of Fundamental Measure Theory: density functional for hard sphere mixtures
    José A. Cuesta, Yuri Martínez-Ratón and Pedro Tarazona
    Journal of Physics: Condensed Matter 14 11965-11980 (2002)
  • Enhancement by polydispersity of the biaxial nematic phase in a mixture of hard rods and plates
    Yuri Martínez-Ratón and José A. Cuesta
    Physical Review Letters 89 185701-4 (2002)
  • Elusiveness of fluid-fluid demixing in additive hard-core mixtures
    Luis Lafuente and José A. Cuesta
    Physical Review Letters 89 145701-4 (2002)
  • A theorem on the absence of phase transitions in one-dimensional growth models with onsite periodic potentials
    José A. Cuesta and Angel Sánchez
    Journal of Physics A: Mathematical and General 35, 2373-2377 (2002)
  • Phase transition analogous to Bose-Einstein condensation in systems of noninteracting surfactant aggregates
    José A. Cuesta and Richard P. Sear
    Physical Review E 65, 031406-13 (2002)
  • 2001

  • Continuous phase transition in polydisperse hard-sphere mixture
    Ronald Blaak and José A. Cuesta
    Journal of Chemical Physics 115, 963-969 (2001)
  • What do emulsification failure and Bose-Einstein condensation have in common?
    Richard P. Sear and José A. Cuesta
    Europhysics Letters 55, 451-457 (2001)
  • 2000

  • Phase equilibria in the polydisperse Zwanzig model of hard rods
    Nigel Clarke, José A. Cuesta, Richard Sear, Peter Sollich and Alessandro Speranza
    Journal of Chemical Physics 113, 5817-5829 (2000)
  • Phase behaviour of very asymmetric binary mixtures
    José A. Cuesta and Yuri Martínez-Ratón
    Journal of Physics: Condensed Matter 12A, 109-114 (2000)
  • 1999

  • Density functional approach to depletion interaction
    José A. Cuesta and Yuri Martínez-Ratón
    Journal of Physics: Condensed Matter 11, 10107-10118 (1999)
  • Fundamental-measure theory for mixtures of parallel hard cubes. II. Phase behaviour of the one-component fluid and of the binary mixture
    Yuri Martínez-Ratón and José A. Cuesta
    The Journal of Chemical Physics 111, 317-327 (1999)
  • Demixing in a single-peak distributed polydisperse mixture of hard spheres
    José A. Cuesta
    Europhysics Letters 46, 197-203 (1999)
  • Phase transitions in simple models of rod-like and disc-like micelles
    José A. Cuesta and Richard P. Sear
    European Physical Journal B 8, 233-244 (1999)
  • Optimal packing in polydisperse hard-sphere fluids
    Junfang Zhang, Ronald Blaak, Emmanuel Trizak, José A. Cuesta and Daan Frenkel
    The Journal of Chemical Physics 110, 5318-5324 (1999)
  • Analytical solution to a non-separable model for a one-dimensional fluid of anisotropic molecules near a hard wall
    Bruno Martínez-Haya, Juan M. Pastor, and José A. Cuesta
    Physical Review E 59, 1957-1967 (1999)
  • 1998

  • Phase behaviour of additive binary mixtures in the limit of infinite asymmetry
    Yuri Martínez-Ratón and José A. Cuesta
    Physical Review E 58, R4080-R4083 (1998)
  • 1997

  • Fundamental-measure theory for mixtures of parallel hard cubes. I. General formalism
    José A. Cuesta and Yuri Martínez-Ratón
    The Journal of Chemical Physics 107, 6379-6389 (1997)
  • Dimensional crossover of the fundamental-measure functional for parallel hard cubes
    José A. Cuesta and Yuri Martínez-Ratón
    Physical Review Letters 78, 3681-3684 (1997)
  • 1996

  • Fluid mixtures of parallel hard cubes
    José A. Cuesta
    Physical Review Letters 76, 3742-3745 (1996)
  • 1995

  • Random versus deterministic two-dimensional traffic flow models
    Froilán C. Martínez, José A. Cuesta, Juan M. Molera, and Ricardo Brito
    Physical Review E 51, R835-R838 (1995)
  • Theoretical approach to two-dimensional traffic flow models
    Juan M. Molera, Froilán C. Martínez, José A. Cuesta, and Ricardo Brito
    Physical Review E 51, 175-187 (1995)
  • Domain-wall kinetics and tunneling-induced instabilities in superlattices
    S. H. Kwok, T. B. Norris, L. L. Bonilla, J. Galán, J. A. Cuesta, F. C. Martínez, J. M. Molera, H. T. Grahn, K. Ploog, and R. Merlin
    Physical Review B 51, 10171-10174 (1995)
  • Self-consistent analysis of electric field effects on Si delta-doped GaAs
    José A. Cuesta, Angel Sánchez and Francisco Domínguez-Adame
    Semiconductor Science and Technology 10, 1303-1309 (1995)
  • 1994

  • Dynamics of electric-field domains and oscillations of the photocurrent in a simple superlattice model
    L. L. Bonilla, J. Galán, J. A. Cuesta, F. C. Martínez, and J. M. Molera
    Physical Review B 50, 8644-8657 (1994)
  • 1993

  • Phase transitions in two-dimensional traffic flow models
    José A. Cuesta, Froilán C. Martínez, Juan M. Molera, and Angel Sánchez
    Physical Review E 48, R4175-R4178 (1993)
  • Hard-sphere and hard-disk freezing from the differential formulation of the generalized effective liquid approximation
    Carlos F. Tejero and José A. Cuesta
    Physical Review E 47, 490-495 (1993)
  • On one-dimensional fluids of anisotropic molecules near a hard wall
    F. S. Herrero, B. Martínez-Haya, J. M. Pastor, J. A. Cuesta and C. F. Tejero
    Molecular Physics 79, 709-720 (1993)
  • 1992

  • Isotropic-nematic transition of D-dimensional hard convex bodies within the effective-liquid approach
    José A. Cuesta, Carlos F. Tejero, and Marc Baus
    Physical Review A 45, 7395-7412 (1992)
  • 1991

  • Effective-liquid approach to the generalized Onsager theories of the isotropic-nematic transition of hard convex bodies
    José A. Cuesta, Carlos F. Tejero, Hong Xu, and Marc Baus
    Physical Review A 44, 5306-5309 (1991)
  • Second virial coefficient of the D-dimensional hard Gaussian overlap model
    J. A. Cuesta and C. F. Tejero
    Physics Letters A 152, 15-18 (1991)
  • 1990

  • Monte Carlo simulation of two-dimensional hard ellipses
    José A. Cuesta and Daan Frenkel
    Physical Review A 42, 2126-2136 (1990)
  • Direct correlation function of a one-dimensional nematic fluid
    C. F. Tejero and J. A. Cuesta
    Physica A 168, 942-956 (1990)
  • 1989

  • Isotropic-nematic transition of hard ellipses
    José A. Cuesta, Carlos F. Tejero, and Marc Baus
    Physical Review A 39, 6498-6506 (1989)
  • Long-range inverse two-spin correlations in one-dimensional Potts lattices
    C. F. Tejero, J. A. Cuesta and R. Brito
    Journal of Statistical Physics 56, 33-42 (1989)
  • 1989

  • Absence of dissipative solutions of the Schroedinger and Klein-Gordon equations with logarithmic nonlinearity
    Ricardo Brito, José A. Cuesta and Antonio Fernández Rañada
    Physics Letters A 128, 360-366 (1988)
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