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I. Santamaria-Holek

Publications and source records attributed to I. Santamaria-Holek.

At least 19 recordsLinked to original sources

Generalized Rényi Entropy Production Rate in Non-equilibrium Systems: From Markov Processes to Chaotic Dynamics

A generalization of the entropy production rate is proposed $Π_q$ in non-equilibrium systems by extending the formalism of classical stochastic thermodynamics to regimes with non-Gaussian fluctuations. Through the Rényi entropy $S_q$ , where entropic parameter $q$ modulates critical fluctuations, it is defined $Π_q$ and the postulated generalized $q$-affinity ${\cal A}_q$ for Markov processes, where it is demonstrated that $Π_q \geq 0$, generalizing the second thermodynamics law.The derived formal framework was applied to the Rössler model, a nonlinear dynamical system exhibiting chaos. Numerical simulations show that the entropy production rate $Π_q$ can be used as an index of robustness and complexity by quantitatively corroborating the greater robustness of funnel-type chaos compared to spiral-type chaos. Our results reveal limitations of Gibbs-Shannon entropy in capturing non-Gaussian fluctuations induced by nonlinearity. On the contrary, it is found that $Π_q$ it can be a suitable magnitude to measure the intensity of chaotic dynamics through the entropy parameter $q$ , indicating a plausible link with Lyapunov exponents. The proposed formal framework extends the scope of stochastic thermodynamics to complex systems, integrating chaotic dynamics and the role of the entropic index q as a source of irreversibility and in capturing non-Gaussian contributions to entropy production.

cond-mat.stat-mech

Multiscale modeling of exocytosis in the fertilization process

We discuss the implementation of a multiscale biophysico-chemical model able to cope with the main mechanisms underlying cumulative exocytosis in cells. The model is based on a diffusion equation in the presence of external forces that links calcium signaling and the biochemistry associated to the activity of cytoskeletal-based protein motors. This multiscale model offers an excellent quantitative spatio-temporal description of the cumulative exocytosis measured by means of fluorescence experiments. We also review pre-existing models reported in the literature on calcium waves, protein motor activation and dynamics, and intracellular directed transport of vesicles. As an example of the proposed model, we analyze the formation of the shield against polyspermy in the early events of fertilization in sea urchin eggs.

q-bio.SC

Non-linear irreversible thermodynamics of single-molecule experiments

Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the non-linear case of systems under non-equilibrium external constraints, we are able to calculate the entropy production and the general non-linear kinetic equations for the variables involved. In particular, we analyze the case of RNA stretching protocols obtaining critical oscillations between different configurational states when forced by external means to remain in the unstable region of its free-energy landscape, as observed in experiments. We also calculate the entropy produced during these hopping events, and show how resonant phenomena in stretching experiments of single RNA macromolecules may arise. We also calculate the hopping rates using Kramer's approach obtaining a good comparison with experiments.

physics.bio-ph

Reconstructing the free-energy landscape associated to molecular motors processivity

We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and considers the presence of a competitive inhibition reaction by ADP. We first reconstruct a continuous free-energy landscape of the cycle catalyst process that allows us to calculate the number of steps given by a single molecular motor. Then, we calculate an analytical expression associated to the translational velocity and the stopping time of the molecular motor in terms of time and ATP concentration. An energetic interpretation of motor processivity is discussed in quantitative form by using experimental data. We also predict a time duration of collective processes that agrees with experimental reports.

q-bio.SC

A non-equilibrium thermodynamics model for combined adsorption and diffusion processes in micro- and nanopores

A non-equilibrium thermodynamics model able to analyze the combined effect of diffusion and adsorption in porous materials is proposed. The model considers the coupled dynamics of the diffusive phase, described by a diffusion type equation, and the adsorbed phase governed by a generalized Langmuir equation. It is shown that the combination of diffusion and adsorption can be treated as diffusion in an effective medium, with an effective diffusion coefficient depending on the characteristics of the adsorption kinetics. The interplay between these effects leads to the appearance of different regimes in which the effective diffusion coefficient exhibits peculiar behaviours such as a decrease due to the presence of the adsorption process and a non-monotonous behavior resulting from particle interactions. We outline applications of the model developed to diffusion in porous materials such as zeolites and bentonites, and to engineered highly porous materials.

cond-mat.mtrl-sci

Controlling protein crystal growth rate by means of temperature

We have proposed a model to analyze the growth kinetics of lysozyme crystals/aggregates under non-isothermal conditions. The model was formulated through an analysis of the entropy production of the growth process which was obtained by taking into account the explicit dependence of the free energy on the temperature. We found that the growth process is coupled with temperature variations resulting in a novel Soret-type effect. We identified the surface entropy of the crystal/aggregate as a decisive ingredient controlling the behavior of the average growth rate as a function of temperature. The behavior of the Gibbs free energy as a function of temperature is also analyzed. The agreement between theory and experiments is very good in the range of temperatures considered.

cond-mat.mtrl-sci

The rheology of concentrated suspensions of arbitrarily-shaped particles

We propose an improved effective-medium theory to obtain the concentration dependence of the viscosity of particle suspensions at arbitrary volume fractions. Our methodology can be applied, in principle, to any particle shape as long as the intrinsic viscosity is known in the dilute limit and the particles are not too elongated. The procedure allows to construct a continuum-medium model in which correlations between the particles are introduced through an effective volume fraction. We have tested the procedure using spheres, ellipsoids, cylinders, dumbells, and other complex shapes. In the case of hard spherical particles, our expression improves considerably previous models like the widely used Krieger-Dougherty relation. The final expressions obtained for the viscosity scale with the effective volume fraction and show remarkable agreement with experiments and numerical simulations at a large variety of situations.

cond-mat.soft

Mesoscopic non-equilibrium thermodynamics approach to non-Debye dielectric relaxation

Mesoscopic non-equilibrium thermodynamics is used to formulate a model describing non-homogeneous and non-Debye dielectric relaxation. The model is presented in terms of a Fokker-Planck equation for the probability distribution of non-interacting polar molecules in contact with a heat bath and in the presence of an external time-dependent electric field. Memory effects are introduced in the Fokker-Planck description through integral relations containing memory kernels, which in turn are used to establish a connection with fractional Fokker-Planck descriptions. The model is developed in terms of the evolution equations for the first two moments of the distribution function. These equations are solved by following a perturbative method from which the expressions for the complex susceptibilities are obtained as a functions of the frequency and the wave number. Different memory kernels are considered and used to compare with experiments of dielectric relaxation in glassy systems. For the case of Cole-Cole relaxation, we infer the distribution of relaxation times and its relation with an effective distribution of dipolar moments that can be attributed to different segmental motions of the polymer chains in a melt.

cond-mat.stat-mech

Statistical Mechanical Theory of a Closed Oscillating Universe

Based on Newton's laws reformulated in the Hamiltonian dynamics combined with statistical mechanics, we formulate a statistical mechanical theory supporting the hypothesis of a closed oscillating universe. We find that the behaviour of the universe as a whole can be represented by a free entropic oscillator whose lifespan is nonhomogeneous, thus implying that time is shorter or longer according to the state of the universe itself given through its entropy. We conclude that time reduces to the entropy production of the universe and that a nonzero entropy production means that local fluctuations could exist giving rise to the appearance of masses and to the curvature of the space.

cond-mat.stat-mech

Improved viscosity-concentration equation for emulsions of nearly spherical droplets

We propose an improved viscosity model accounting for experiments of emulsions of two immiscible liquids at arbitrary volume fractions and low shear rates. The model is based on a recursive-differential method formulated in terms of the appropriate scaling variable which emerges from an analysis of excluded volume effects in the system. This variable, called the effective filling fraction, incorporates the geometrical information of the system which determines the maximum packing and reduces to the bare filling fraction for infinitely diluted emulsions. The agreement of our model for the viscosity with experiments is remarkable for all the range of volume fractions and viscosity ratio.

cond-mat.soft

Protein motors induced enhanced diffusion in intracellular transport

Diffusion of transported particles in the intracellular medium is described by means of a generalized diffusion equation containing forces due to the cytoskeleton network and to the protein motors. We find that the enhanced diffusion observed in experiments depends on the nature of the force exerted by the protein motors and on parameters characterizing the intracellular medium which is described in terms of a generalized Debye spectrum for the noise density of states.

cond-mat.soft

Fluctuation Theorems for Systems under Fokker-Planck dynamics

We study Brownian motion driven with both conservative and nonconservative external forces. By using the thermodynamic approach of the theory of Brownian motion we obtain the Fokker-Planck equation and derive expressions for the Fluctuation Theorem in local equilibrium and in quasi-equilibrium. In local equilibrium the expressions we obtain coincide with previous results.

cond-mat.stat-mech

Anomalous Diffusion In Microrheology: A Comparative Study

We present a comparative study on two theoretical descriptions of microrheological experiments. Using a generalized Langevin equation (GLE), we analyze the origin of the power-law behavior of the main properties of a viscoelastic medium. Then, we discuss the equivalence of the GLE with a generalized Fokker-Planck equation (GFPE), and how more general GFPE's can be derived from a thermo-kinetic formalism. These complementary theories lead to a justification for the physical nature of the Hurst exponent of fractional kinetics. Theory is compared with experiments.

cond-mat.stat-mech

Superstatistics of Brownian motion: A comparative study

The dynamics of temperature fluctuations of a gas of Brownian particles in local equilibrium with a nonequilibrium heat bath, are described using an approach consistent with Boltzmann-Gibbs statistics (BG). We use mesoscopic nonequilibrium thermodynamics (MNET) to derive a Fokker-Planck equation for the probability distribution in phase space including the local intensive variables fluctuations. We contract the description to obtain an effective probability distribution (EPD) from which the mass density, van Hove's function and the dynamic structure factor of the system are obtained. The main result is to show that in the long time limit the EPD exhibits a similar behavior as the superstatistics distribution of nonextensive statistical mechanics (NESM), therfore implying that the coarse-graining procedure is responsible for the so called nonextensive effects.

cond-mat.stat-mech

Thermo-kinetic approach of single-particles and clusters involving anomalous diffusion under viscoelastic response

We present a thermo-kinetic description of anomalous diffusion of single-particles and clusters in a viscoelastic medium in terms of a non-Markovian diffusion equation involving memory functions. The scaling behaviour of these functions is analyzed by considering hydrodynamics and cluster-size space random walk arguments. We explain experimental results on diffusion of Brownian particles in the cytoskeleton, in cluster-cluster aggregation and in a suspension of micelles.

cond-mat.stat-mech

Generalized hydrodynamics of a dilute finite-sized particles suspension: Dynamic viscosity

We present a mesoscopic hydrodynamic description of the dynamics of colloidal suspensions. We consider the system as a gas of Brownian particles suspended in a Newtonian heat bath subjected to stationary non-equilibrium conditions imposed by a velocity field. Using results already obtained in previous studies in the field by means of a generalized Fokker-Planck equation, we obtain a set of coupled differential equations for the local diffusion current and the evolution of the total stress tensor. We find that the dynamic shear viscosity of the system contains contributions arising from the finite size of the particles.

cond-mat.stat-mech

Finite-size effects in intracellular microrheology

We propose a model to explain finite-size effects in intracellular microrheology observed in experiments. The constrained dynamics of the particles in the intracellular medium, treated as a viscoelastic medium, is described by means of a diffusion equation in which interactions of the particles with the cytoskeleton are modelled by a harmonic force. The model reproduces the observed power-law behavior of the mean-square displacement in which the exponent depends on the ratio between particle-to-cytoskeleton-network sizes.

cond-mat.soft