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A. Gomez-Marin

Publications and source records attributed to A. Gomez-Marin.

12 recordsLinked to original sources

Searching for behavioral homologies: Shared generative rules for expansion and narrowing down of the locomotor repertoire in Arthropods and Vertebrates

We use immobility as an origin and reference for the measurement of locomotor behavior; speed, the direction of walking and the direction of facing as the three degrees of freedom shaping fly locomotor behavior, and cocaine as the parameter inducing a progressive transition in and out of immobility. In this way we expose and quantify the generative rules that shape fruit fly locomotor behavior, which consist of a gradual narrowing down of the fly's locomotor freedom of movement during the transition into immobility and a precisely opposite expansion of freedom during the transition from immobility to normal behavior. The same generative rules of narrowing down and expansion apply to vertebrate behavior in a variety of contexts, Recent claims for deep homology between the vertebrate basal ganglia and the arthropod central complex, and neurochemical processes explaining the expansion of locomotor behavior in vertebrates could guide the search for equivalent neurochemical processes that mediate locomotor narrowing down and expansion in arthropods. We argue that a methodology for isolating relevant measures and quantifying generative rules having a potential for discovering candidate behavioral homologies is already available and we specify some of its essential features.

q-bio.NC

Two-state flashing molecular pump

Here we study a pumping device capable of maintaining a density gradient and a flux of particles across a membrane. Its driving mechanism is based on the flashing ratchet effect powered by the random telegraph process in the presence of thermal fluctuations. Unlike Brownian motors, the concentrations at both reservoir boundaries need to be implemented as boundary conditions. The residence transition rates of the dichotomic flashing are related to the binding and hydrolysis of ATP molecules. The model is exactly solved and explored. The pump energetics is discussed and the relevant parameter values are tuned within a biological scale.

cond-mat.stat-mech

Lower bounds on dissipation upon coarse graining

By different coarse-graining procedures we derive lower bounds on the total mean work dissipated in Brownian systems driven out of equilibrium. With several analytically solvable examples we illustrate how, when, and where the information on the dissipation is captured.

cond-mat.stat-mech

The "footprints'' of irreversibility

We reformulate the result for the entropy production given in Phys. Rev. Lett. 98, 080602 (2007) in terms of the relative entropy of microscopic trajectories. By a combination with the Crook's theorem, we identify the path variables that are sufficient to fully identify irreversibility. We show that work saturates the relative entropy, and derive the entropy production for stochastic descriptions.

cond-mat.stat-mech

Bounding dissipation in stochastic models

We generalize to stochastic dynamics the exact expression for average dissipation along an arbitrary non-equilibrium process, given in Phys. Rev. Lett. 98, 080602 (2007). We then derive lower bounds by various coarse-graining procedures and illustrate how, when and where the information on the dissipation is captured in models of over- and underdamped Brownian particles.

cond-mat.stat-mech

White noise flashing Brownian pump

A Brownian pump of particles powered by a stochastic flashing ratchet mechanism is studied. The pumping device is embedded in a finite region and bounded by particle reservoirs. In the steady state, we exactly calculate the spatial density profile, the concentration ratio between both reservoirs and the particle flux. A simple numerical scheme is presented allowing for the consistent evaluation of all such observable quantities.

cond-mat.stat-mech

Self-sustained spatiotemporal oscillations induced by membrane-bulk coupling

We propose a novel mechanism leading to spatiotemporal oscillations in extended systems that does not rely on local bulk instabilities. Instead, oscillations arise from the interaction of two subsystems of different spatial dimensionality. Specifically, we show that coupling a passive diffusive bulk of dimension d with an excitable membrane of dimension d-1 produces a self-sustained oscillatory behavior. An analytical explanation of the phenomenon is provided for d=1. Moreover, in-phase and anti-phase synchronization of oscillations are found numerically in one and two dimensions. This novel dynamic instability could be used by biological systems such as cells, where the dynamics on the cellular membrane is necessarily different from that of the cytoplasmic bulk.

cond-mat.other

Test of the fluctuation theorem for stochastic entropy production in a nonequilibrium steady state

We derive a simple closed analytical expression for the total entropy production along a single stochastic trajectory of a Brownian particle diffusing on a periodic potential under an external constant force. By numerical simulations we compute the probability distribution functions of the entropy and satisfactorily test many of the predictions based on Seifert's integral fluctuation theorem. The results presented for this simple model clearly illustrate the practical features and implications derived from such a result of nonequilibrium statistical mechanics.

cond-mat.stat-mech

Tight coupling in thermal Brownian motors

We study analytically a thermal Brownian motor model and calculate exactly the Onsager coefficients. We show how the reciprocity relation holds and that the determinant of the Onsager matrix vanishes. Such condition implies that the device is built with tight coupling. This explains why Carnot's efficiency can be achieved in the limit of infinitely slow velocities. We also prove that the efficiency at maximum power has the maximum possible value, which corresponds to the Curzon-Alhborn bound. Finally, we discuss the model acting as a Brownian refrigerator.

cond-mat.stat-mech

Heat Fluctuations in Brownian Transducers

Heat fluctuation probability distribution function in Brownian transducers operating between two heat reservoirs is studied. We find, both analytically and numerically, that the recently proposed Fluctuation Theorem for Heat Exchange [C. Jarzynski and D. K. Wojcik, Phys. Rev. Lett. 92, 230602 (2004)] has to be modified when the coupling mechanism between both baths is considered. We also extend such relation when external work is present. Our work fixes the domain of applicability of the theorem in more realistic operating systems.

cond-mat.stat-mech

Ratchet, pawl and spring Brownian motor

We present a model for a thermal Brownian motor based on Feynman's famous ratchet and pawl device. Its main feature is that the ratchet and the pawl are in different thermal baths and connected by an harmonic spring. We simulate its dynamics, explore its main features and also derive an approximate analytical solution for the mean velocity as a function of the external torque applied and the temperatures of the baths. Such theoretical predictions and the results from numerical simulations agree within the ranges of the approximations performed.

cond-mat.other

Symmetric Brownian motor

In this paper we present a model of a symmetric Brownian motor (SBM) which changes the sign of its velocity when the temperature gradient is inverted. The velocity, external work and efficiency are studied as a function of the temperatures of the baths and other relevant parameters. The motor shows a current reversal when another parameter (a phase shift) is varied. Analytical predictions and results from numerical simulations are performed and agree very well. Generic properties of this type of motors are discussed.

cond-mat.stat-mech