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J. M. Rubi

Publications and source records attributed to J. M. Rubi.

At least 19 recordsLinked to original sources

Surface Excess Energy Governs the Non-Monotonic Behavior of Active Diffusivity with Activity

Self-propulsion of particles is typically explained by phoretic mechanisms driven by externally imposed chemical, electric, or thermal gradients. In contrast, chemical reactions can enhance particle diffusion even in the absence of such external gradients. We refer to this increase as active diffusivity, often attributed to self-diffusiophoresis or self-electrophoresis, although these mechanisms alone do not fully account for experimental observations. Here, we investigate active diffusivity in catalytic Janus particles immersed in reactive media without imposed gradients. We show that interfacial reactions generate excess surface energy and sustained interfacial stresses that supplement thermal energy, enabling diffusion beyond the classical thermal limit. We consistently quantify this contribution using both dissipative and non-dissipative approaches, assuming that the aqueous bath remains near equilibrium. Our framework reproduces experimentally observed trends in diffusivity versus activity, including the non-monotonic behaviors reported in some systems, and agrees with data for nanometric Janus particles catalyzing charged substrates as well as vesicles with membrane-embedded enzymes driven by ATP hydrolysis. These results demonstrate that chemical reactions can induce and sustain surface-tension gradients and surface excess energy, providing design principles for tuning mobility in synthetic active matter.

cond-mat.soft

Entropy facilitated active transport

We show how active transport of ions can be interpreted as an entropy facilitated process. In this interpretation, the pore geometry through which substrates are transported can give rise to a driving force. This gives a direct link between the geometry and the changes in Gibbs energy required. Quantifying the size of this effect for several proteins we find that the entropic contribution from the pore geometry is significant and we discuss how the effect can be used to interpret variations in the affinity at the binding site.

q-bio.BM

Heat and work distributions for mixed Gauss-Cauchy process

We analyze energetics of a non-Gaussian process described by a stochastic differential equation of the Langevin type. The process represents a paradigmatic model of a nonequilibrium system subject to thermal fluctuations and additional external noise, with both sources of perturbations considered as additive and statistically independent forcings. We define thermodynamic quantities for trajectories of the process and analyze contributions to mechanical work and heat. As a working example we consider a particle subjected to a drag force and two independent Levy white noises with stability indices $α=2$ and $α=1$. The fluctuations of dissipated energy (heat) and distribution of work performed by the force acting on the system are addressed by examining contributions of Cauchy fluctuations to either bath or external force acting on the system.

cond-mat.stat-mech

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

Double Entropic Stochastic Resonance

We demonstrate the appearance of a purely entropic stochastic resonance (ESR) occurring in a geometrically confined system, where the irregular boundaries cause entropic barriers. The interplay between a periodic input signal, a constant bias and intrinsic thermal noise leads to a resonant ESR-phenomenon in which feeble signals become amplified. This new phenomenon is characterized by the presence of two peaks in the spectral amplification at corresponding optimal values of the noise strength. The main peak is associated with the manifest stochastic resonance synchronization mechanism involving the inter-well noise-activated dynamics while a second peak relates to a regime of optimal sensitivity for intra-well dynamics. The nature of ESR, occurring when the origin of the barrier is entropic rather than energetic, offers new perspectives for novel investigations and potential applications. ESR by itself presents yet another case where one constructively can harvest noise in driven nonequilibrium systems.

cond-mat.stat-mech

Entropic stochastic resonance: the constructive role of the unevenness

We demonstrate the existence of stochastic resonance (SR) in confined systems arising from entropy variations associated to the presence of irregular boundaries. When the motion of a Brownian particle is constrained to a region with uneven boundaries, the presence of a periodic input may give rise to a peak in the spectral amplification factor and therefore to the appearance of the SR phenomenon. We have proved that the amplification factor depends on the shape of the region through which the particle moves and that by adjusting its characteristic geometric parameters one may optimize the response of the system. The situation in which the appearance of such entropic stochastic resonance (ESR) occurs is common for small-scale systems in which confinement and noise play an prominent role. The novel mechanism found could thus constitute an important tool for the characterization of these systems and can put to use for controlling their basic properties.

cond-mat.stat-mech

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

The transition to irreversibility in sheared suspensions: An analysis based on a mesoscopic entropy production

We study the shear-induced diffusion effect and the transition to irreversibility in suspensions under oscillatory shear flow by performing an analysis of the entropy production associated to the motion of the particles. We show that the Onsager coupling between different contributions to the entropy production is responsible for the scaling of the mean square displacement on particle diameter and applied strain. We also show that the shear-induced effective diffusion coefficient depends on the volume fraction and use Lattice-Boltzmann simulations to characterize the effect through the power spectrum of particle positions for different Reynolds numbers and volume fractions. Our study gives a thermodynamic explanation of the the transition to irreversibility through a pertinent analysis of the second law of thermodynamics.

cond-mat.stat-mech

Reply to Comment on "Failure of the work-Hamiltonian connection for free-energy calculations" by Horowitz and Jarzynski

We show that the Comment [arXiv:0808.1224] by Horowitz and Jarzynski obtains as a main result a general free energy change for a harmonic system that in the macroscopic limit does not recover the textbook expression for the energy change of a Hookean spring. The reason is that Horowitz and Jarzynski improperly identify work with parametric changes of the Hamiltonian instead of with the standard quantity, force times displacement.

cond-mat.stat-mech

Entropic Stochastic Resonance

We present a novel scheme for the appearance of Stochastic Resonance when the dynamics of a Brownian particle takes place in a confined medium. The presence of uneven boundaries, giving rise to an entropic contribution to the potential, may upon application of a periodic driving force result in an increase of the spectral amplification at an optimum value of the ambient noise level. This Entropic Stochastic Resonance (ESR), characteristic of small-scale systems, may constitute a useful mechanism for the manipulation and control of single-molecules and nano-devices.

cond-mat.stat-mech

Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension

We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yields the master equation of a recently proposed sequential-step model. Non-linear switching kinetics is found between open and closed states. Our theory unifies the thermodynamic and kinetic descriptions and offers a systematic procedure to characterize the dynamics of the unfolding process

cond-mat.stat-mech

Stochastic population dynamics in turbulent fields

The behavior of interacting populations typically displays irregular temporal and spatial patterns that are difficult to reconcile with an underlying deterministic dynamics. A classical example is the heterogeneous distribution of plankton communities, which has been observed to be patchy over a wide range of spatial and temporal scales. Here, we use plankton communities as prototype systems to present theoretical approaches for the analysis of the combined effects of turbulent advection and stochastic growth in the spatiotemporal dynamics of the population. Incorporation of these two factors into mathematical models brings an extra level of realism to the description and leads to better agreement with experimental data than that of previously proposed models based on reaction-diffusion equations.

q-bio.PE

Biased diffusion in confined media: Test of the Fick-Jacobs approximation and validity criteria

We study biased, diffusive transport of Brownian particles through narrow, spatially periodic structures in which the motion is constrained in lateral directions. The problem is analyzed under the perspective of the Fick-Jacobs equation which accounts for the effect of the lateral confinement by introducing an entropic barrier in a one dimensional diffusion. The validity of this approximation, being based on the assumption of an instantaneous equilibration of the particle distribution in the cross-section of the structure, is analyzed by comparing the different time scales that characterize the problem. A validity criterion is established in terms of the shape of the structure and of the applied force. It is analytically corroborated and verified by numerical simulations that the critical value of the force up to which this description holds true scales as the square of the periodicity of the structure. The criterion can be visualized by means of a diagram representing the regions where the Fick-Jacobs description becomes inaccurate in terms of the scaled force versus the periodicity of the structure.

cond-mat.stat-mech

Gaussian noise and time-reversal symmetry in non-equilibrium Langevin models

We show that in driven systems the Gaussian nature of the fluctuating force and time-reversibility are equivalent properties. This result together with the potential condition of the external force drastically restricts the form of the probability distribution function, which can be shown to satisfy time-independent relations. We have corroborated this feature by explicitly analyzing a model for the stretching of a polymer and a model for a suspension of non-interacting Brownian particles in steady flow.

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

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