arXiv subjects

J. M. Sancho

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

At least 19 recordsLinked to original sources

arXiv2024

Subconductance states in a semimicroscopic model for a tetrameric pore

A physical model for a structured tetrameric pore is studied. The pore is modeled as a device composed of four subunits, each one exhibiting two possible states (open and closed). The pore is located within a membrane that separates two reservoirs with ionic solutions. All variables of the model follow physical dynamical equations accounting for the internal structure of the pore, derived from a single energy functional and supplemented with thermal noises. An extensive study of the resulting ionic intensity is performed for different values of the control parameters, mainly membrane potential and reservoir ion concentrations. Two possible physical devices are studied: voltage-gated (including a voltage sensor in each subunit) and non-voltage-gated pores. The ionic flux through the pore exhibits several distinct dynamical configurations, in particular subconductance states, which indicate very different dynamical internal states of the subunits. Such subconductance states become much easier to observe in sensorless pores. These results are compared with available experimental data on tetrameric K channels and analytical predictions.

physics.bio-ph↗

arXiv2022

Theoretical analysis of thermophoretic experimental data

Thermophoresis is a transport phenomenon induced by a temperature gradient. Very small objects dispersed in a fluid medium and in a temperature gradient present a non homogeneous steady density. Analysing this phenomenon within the theoretical scenario of non interacting Brownian motion one can assume that those particles are driven by a spatially dependent mechanical force. This implies the existence of a potential which was derived in a previous work. From this potential the qualitative properties of the force and the Soret coefficient were obtained. Nevertheless a quantitative correlation between the theory and the experimental data were not consistently proved. Here it is presented a methodology to match this theory with the experimental data, which it is used to analyse the experimental information of sodium docecyl sulfate (SDS) micelles.

cond-mat.stat-mech↗

arXiv2013

Modeling the mechano-chemistry of the ϕ29 DNA translocation motor

We present a study of the DNA translocation of the bacteriophage ϕ29 packaging molecular motor. From the experimental available information we present a model system based in an stochastic fashing potential, which reproduces the experimental observations such as: detailed trajectories, steps and substeps, spatial correlation, and velocity. Moreover the model allows the evaluation of power and efficiency of this motor. We have found that the maximum power regime does not correspond with that of the maximum efficiency. These informations can stimulate further experiments.

physics.bio-ph↗

arXiv2012

Speeding chemical reactions by focusing

We present numerical results for a chemical reaction of colloidal particles which are transported by a laminar fluid and are focused by periodic obstacles in such a way that the two components are well mixed and consequently the chemical reaction is speeded up. The roles of the various system parameters (diffusion coefficients, reaction rate, obstacles sizes) are studied. We show that focusing speeds up the reaction from the diffusion limited rate (t to the power -1/2) to very close to the perfect mixing rate, (t to the power -1).

physics.chem-ph↗

arXiv2011

Brownian colloidal particles: Ito, Stratonovich or a different stochastic interpretation

Recent experiments on Brownian colloidal particles have been studied theoretically in terms of overdamped Langevin equations with multiplicative white noise using an unconventional stochastic interpretation. Complementary numerical simulations of the same system are well described using the conventional Stratonovich interpretation. Here we address this dichotomy from a more generic starting point: the underdamped Langevin equation and its corresponding Fokker--Planck equation.

cond-mat.stat-mech↗

arXiv2010

Weak disorder: anomalous transport and diffusion are normal yet again

Particles driven through a periodic potential by an external constant force are known to exhibit a pronounced peak of the diffusion around a critical force that defines the transition between locked and running states. It has recently been shown both experimentally and numerically that this peak is greatly enhanced if some amount of spatial disorder is superimposed on the periodic potential. Here we show that beyond a simple enhancement lies a much more interesting phenomenology. For some parameter regimes the system exhibits a rich variety of behaviors from normal diffusion to superdiffusion, subdiffusion and even subtransport.

cond-mat.soft↗

arXiv2009

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↗

arXiv2007

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↗

arXiv2007

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↗

arXiv2006

Dispersionless transport in a washboard potential

We study and characterize a new dynamical regime of underdamped particles in a tilted washboard potential. We find that for small friction in a finite range of forces the particles move essentially nondispersively, that is, coherently, over long intervals of time. The associated distribution of the particle positions moves at an essentially constant velocity and is far from Gaussian-like. This new regime is complementary to, and entirely different from, well-known nonlinear response and large dispersion regimes observed for other values of the external force.

cond-mat.stat-mech↗

arXiv2006

Kinesin as an electrostatic machine

Kinesin and related motor proteins utilize ATP fuel to propel themselves along the external surface of microtubules in a processive and directional fashion. We show that the observed step-like motion is possible through time varying charge distributions furnished by the ATP hydrolysis circle while the static charge configuration on the microtuble provides the guide for motion. Thus, while the chemical hydrolysis energy induces appropriate local conformational changes, the motor translational energy is fundamentally electrostatic. Numerical simulations of the mechanical equations of motion show that processivity and directionality are direct consequences of the ATP-dependent electrostatic interaction between the different charge distributions of kinesin and microtubule.

q-bio.BM↗

arXiv2006

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↗

arXiv2006

Noise-Induced Order in Extended Systems: A Tutorial

External fluctuations have a wide variety of constructive effects on the dynamical behavior of spatially extended systems, as described by stochastic partial differential equations. A set of paradigmatic situations exhibiting such effects are briefly reviewed in this paper, in an attempt to provide a concise but thorough introduction to this active field of research, and at the same time an overview of its current status. This work is dedicated to Lutz Schimansky-Geier on the occassion of his 50th anniversary. Through the years, Prof. Schimansky-Geier has made important contributions to the field of spatiotemporal stochastic dynamics, including seminal investigations in the early 1990's on noise effects in front propagation, and studies of noise-induced phase transitions and noise-sustained structures in excitable media, among others.

cond-mat.stat-mech↗

arXiv2006

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↗

arXiv2006

Dynamics of an inchworm nano-walker

An inchworm processive mechanism is proposed to explain the motion of dimeric molecular motors such as kinesin. We present here preliminary results for this mechanism focusing on observables like mean velocity, coupling ratio and efficiency versus ATP concentration and the external load F.

q-bio.BM↗

arXiv2005

An analytical approach to sorting in periodic potentials

There has been a recent revolution in the ability to manipulate micrometer-sized objects on surfaces patterned by traps or obstacles of controllable configurations and shapes. One application of this technology is to separate particles driven across such a surface by an external force according to some particle characteristic such as size or index of refraction. The surface features cause the trajectories of particles driven across the surface to deviate from the direction of the force by an amount that depends on the particular characteristic, thus leading to sorting. While models of this behavior have provided a good understanding of these observations, the solutions have so far been primarily numerical. In this paper we provide analytic predictions for the dependence of the angle between the direction of motion and the external force on a number of model parameters for periodic as well as random surfaces. We test these predictions against exact numerical simulations.

cond-mat.soft↗

arXiv2005

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↗

arXiv2005

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↗