Cao García, Francisco Javier

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First Name
Francisco Javier
Last Name
Cao García
Universidad Complutense de Madrid
Faculty / Institute
Ciencias Físicas
Estructura de la Materia, Física Térmica y Electrónica
Física Aplicada
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Now showing 1 - 6 of 6
  • Publication
    Noncooperative thermodynamics and kinetic models of ligand binding to polymers: Connecting McGhee-von Hippel model with the Tonks gas model
    (American Physical Society, 2020-07-20) García Villaluenga, Juan Pedro; Vidal, Jules; Cao García, Francisco Javier
    Ligand binding to polymers modifies the physical and chemical properties of the polymers, leading to physical, chemical, and biological implications. McGhee and von Hippel obtained the equilibrium coverage as a function of the ligand affinity, through the computation of the possible binding sites for the ligand. Here, we complete this theory deriving the kinetic model for the ligand-binding dynamics and the associated equilibrium chemical potential, which turns out to be of the Tonks gas model type. At low coverage, the Tonks chemical potential becomes the Fermi chemical potential and even the ideal gas chemical potential. We also discuss kinetic models associated with these chemical potentials. These results clarify the kinetic models of ligand binding, their relations with the chemical potentials, and their range of validity. Our results highlight the inaccuracy of ideal and simplified kinetic approaches for medium and high coverages.
  • Publication
    Cooperative kinetics of ligand binding to linear polymers
    (Elsevier, 2022) García Villaluenga, Juan Pedro; Cao García, Francisco Javier
    Ligands change the chemical and mechanical properties of polymers. In particular, single strand binding protein (SSB) non-specifically bounds to single-stranded DNA (ssDNA), modifying the ssDNA stiffness and the DNA replication rate, as recently measured with single-molecule techniques. SSB is a large ligand presenting cooperativity in some of its binding modes. We aim to develop an accurate kinetic model for the cooperative binding kinetics of large ligands. Cooperativity accounts for the changes in the affinity of a ligand to the polymer due to the presence of another bound ligand. Large ligands, attaching to several binding sites, require a detailed counting of the available binding possibilities. This counting has been done by McGhee and von Hippel to obtain the equilibrium state of the ligands-polymer complex. The same procedure allows to obtain the kinetic equations for the cooperative binding of ligands to long polymers, for all ligand sizes. Here, we also derive approximate cooperative kinetic equations in the large ligand limit, at the leading and next-to-leading orders. We found cooperativity is negligible at the leading-order, and appears at the next-to-leading order. Positive cooperativity (increased affinity) can be originated by increased binding affinity or by decreased release affinity, implying different kinetics. Nevertheless, the equilibrium state is independent of the origin of cooperativity and only depends on the overall increase in affinity. Next-to-leading approximation is found to be accurate, particularly for small cooperativity. These results allow to understand and characterize relevant ligand binding processes, as the binding kinetics of SSB to ssDNA, which has been reported to affect the DNA replication rate for several SSB-polymerase pairs. (C) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
  • Publication
    Virtualización del Laboratorio de Física General
    (2021-12-23) López Moya, Marcos; Cao García, Francisco Javier; Contreras González, José Luis; Dinis Vizcaino, Luis Ignacio; Domínguez Díaz, Alberto; Muñoz Muñoz, Laura; Nieto Castaño, Daniel; Rouco Gómez, Víctor; Ruíz Martínez, Vicente Carlos; Sánchez Parcerisa, Daniel; Rodríguez Pérez, Oscar; Zarco Moreno, Manuel
    Creación de material audiovisual para adaptar los contenidos del Laboratorio de Física General de la Facultad de Ciencias Físicas a los nuevos escenarios docentes. El material creado es de utilidad para los diferentes grados e ingenierías que utilizan este laboratorio, como los de Física, Química, Biología y Geología entre otros.
  • Publication
    ENSO coupling to the equatorial Atlantic: analysis with an extended improved recharge oscillator model
    (Frontiers Media, 2023-01-13) Crespo Miguel, Rodrigo; Polo Sánchez, Irene; Mechoso, Carlos R.; Rodríguez Fonseca, María Belén; Cao García, Francisco Javier
    Introduction: Observational and modeling studies have examined the interactions between El Niño-Southern Oscillation (ENSO) and the equatorial Atlantic variability as incorporated into the classical charge-recharge oscillator model of ENSO. These studies included the role of the Atlantic in the predictability of ENSO but assumed stationarity in the relationships, i.e., that models’ coefficients do not change overtime. Arecentworkbytheauthors has challenged the stationarity assumption in the ENSO framework but without considering the equatorial Atlantic influence on ENSO. Methods: The present paper addresses the changing relationship between ENSO and the Atlantic El Niño using an extended version of the recharge oscillator model. The classical two-variable model of ENSO is extended by adding a linear coupling on the SST anomalies in the equatorial Atlantic. The model’s coefficients are computed for different periods. This calculation is done using two methods tofitthemodel tothe data: (1) the traditional method (ReOsc), and (2) a novel method (ReOsc+) based on fitting the Fisher’s Z transform of the auto and cross-correlation functions. Results: Weshowthat, duringthe 20th century, the characteristic dampingrate of the SST and thermocline depth anomalies in the Pacific have decreased in time by a factor of 2 and 3, respectively. Moreover, the damping time of the ENSO fluctuations has doubled from 10 to 20 months, and the oscillation period of ENSO has decreased from 60-70 months before the 1960s to 50 months afterward. These two changes have contributed to enhancing ENSO amplitude. The results also show that correlations between ENSO and the Atlantic SST strengthened after the 70s and the way in which the impact of the equatorial Atlantic is added to the internal ENSO variability. Conclusions: The remote effects of the equatorial Atlantic on ENSO must be considered in studies of ENSO dynamics and predictability during specific time-periods. Our results provide further insight into the evolution of the ENSO dynamics anditscoupling to the equatorial Atlantic, as well as an improved tool to study the coupling of climatic and ecological variables.
  • Publication
    Tecnología paRa docenciA eN eScenarios de discapacidad basada en inteligencia artiFicial en tiempO-Real: Interprete de Signos Multicanal (TRANSFORM)
    (2020-07-21) Botella Juan, Guillermo; del Barrio García, Alberto; Clemente Barreira, Juan Antonio; Lopez Alonso, José Manuel; Ezquerro Rodriguez, José Miguel; Piquer Otero, Andrés; Carrascal de la Heras, Ginés; Roa Romero, Carlos; Mas Aguilar, Juan; Fahmy Amin, Hesham Ahmed; García Moreno, Daniel; Aguilera Calle, Iván; Sierra López, Angel; Cao García, Francisco Javier
    Desarrollar un intérprete de signos en tiempo real mediante técnicas de aprendizaje profundo, aceleradores y procesado de video inteligente con objeto de desarrollar tiflotecnología barata, portable y accesible para toda la universidad.
  • Publication
    Spatial scales of population synchrony in Predator-Prey Systems
    (The University of Chicago Press Chicago, IL, 2020-02) Jarillo Díaz, Javier; Sæther, Bernt-Erik; Engen, Steinar; Cao García, Francisco Javier
    Many species show synchronous fluctuations in population size over large geographical areas, which are likely to increase their regional extinction risk. Here we examine how the degree of spatial synchrony in population dynamics is affected by trophic interactions using a two-species predator-prey model with spatially correlated environmental noise. We show that the predator has a larger spatial scale of population synchrony than the prey if the population fluctuations of both species are mainly determined by the direct effect of stochastic environmental variations in the prey. This result implies that in ecosystems regulated from the bottom up, the spatial scale of synchrony of the predator population increases beyond the scale of the spatial autocorrelation in the environmental noise and in the prey fluctuations. Harvesting the prey increases the spatial scale of population synchrony of the predator, while harvesting the predator reduces the spatial scale of the population fluctuations of its prey. Hence, the development of sustainable harvesting strategies should also consider the impact on unharvested species at other trophic levels as well as human perturbations of ecosystems, whether the result of exploitation or an effect on dispersal processes, as they can affect food web structures and trophic interactions over large geographical areas.