José A. Cuesta Ruiz
Scientific Publications
2018
- Statistical theory of phenotype abundance distributions: A test through exact enumeration of genotype spaces
Juan Antonio García-Martín, Pablo Catalán, Susanna Manrubia, and José A. Cuesta,
Europhysics Letters 123, 28001 (2018)
DOI: 10.1209/0295-5075/123/28001 - Cognitive resource allocation determines the organization of personal networks
Ignacio Tamarit, José A. Cuesta, Robin I. M. Dunbar, and Angel Sánchez
Proceedings of the National Academy of Sciences (USA) 115, 8316-8321 (2018) DOI: 10.1073/pnas.1719233115 - On the networked architecture of genotype spaces and its critical effects on molecular evolution
Jacobo Aguirre, Pablo Catalán, José A. Cuesta, and Susanna Manrubia
Open Biology 8, 180069 (2018)
DOI: 10.1098/rsob.180069 - Adding levels of complexity enhances robustness and evolvability in a multilevel genotype-phenotype map
Pablo Catalán, Andreas Wagner, Susanna Manrubia, and José A. Cuesta
Journal of the Royal Society Interface 15, 20170516 (2018)
DOI: 10.1098/rsif.2017.0516 - 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 76, 67-96 (2018)
DOI: 10.1007/s00285-017-1132-7
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) - Fair linking mechanisms for resource allocation with correlated player types
Agustín Santos, Antonio Fernández Anta, José A. Cuesta, and Luis López Fernández
Computing 91 (2015) DOI:10.1007/s00607-015-0461-x - 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 102, 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 Martínez-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 Martínez-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
Sicentific 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, e43684 (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, Afredo Ferrera, Gonzalo Ruiz, Alfonso Tarancón, José A. Cuesta, Yamir Moreno and Angel Sánchez
Proceedings of the National Academy of Sciences USA 109, 12922-12926 (2012) - 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) - The 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, 028104-1-4 (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) - 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)