Entropy production and rectification efficiency in colloid transport along a pulsating channel

Entropy Production in Reaction-Diffusion Systems Confined in Narrow Channels

This work analyzes the effect of wall geometry when a reaction-diffusion system is confined to a narrow channel. In particular, we study the entropy production density in the reversible Gray-Scott system. Using an effective diffusion equation that considers modifications by the channel characteristics, we find that the entropy density changes its value but not its qualitative behavior, which helps explore the structure-formation space.

Negative rectification and anomalous diffusion in nonlinear substrate potentials: Dynamical relaxation and information entropy

We numerically investigate the rectification of the probability flux and dynamical relaxation of particles moving in a system with and without noise. The system, driven by two external forces, consists of two substrate potentials that have identical shapes and different potential barriers with different friction coefficients. The deterministic model exhibits the perfect rectification of the probability flux, ratchet effect, and the dependence of the unpredictability of the dynamics on basin of attraction. In contrast, the stochastic model displays that the rectification is sensitive to the temperature and an external bias. They can induce kinetic phase transitions between no transport and a finite net transport. These transitions lead to an unexpected phenomenon, called negative rectification. The results are analyzed through the corresponding time-dependent diffusion coefficient, information entropy (IE), etc. At a low temperature, anomalous diffusions occur in system. For the occurrence of the flux in certain parameter regimes, the larger the diffusion is, the smaller the corresponding IE is, and vice versa. We also present the selected parameter regimes for the emergence of the rectification and negative rectification. Additionally, we study the rectification of the interacting particles in the system and find that the flux may depend on the coupling strength and the number of the interacting particles, and that collective motions occur for the forward flux. Our work provides not only a way of the rectification for the transport of various particles (e.g., ions, electrons, photons, phonons, molecules, DNA chains, nanoswimmers, dust particles, etc.) in physics, chemistry, biology, and material science, but also a design of various circuits.

Computational Model for Membrane Transporters. Potential Implications for Cancer

To explain the increased transport of nutrients and metabolites and to control the movement of drug molecules through the transporters to the cancer cells, it is important to understand the exact mechanism of their structure and activity, as well as their biological and physical characteristics. We propose a computational model that reproduces the functionality of membrane transporters by quantifying the flow of substrates through the cell membrane. The model identifies the force induced by conformational changes of the transporter due to hydrolysis of ATP, in ABC transporters, or by an electrochemical gradient of ions, in secondary transporters. The transport rate is computed by averaging the velocity generated by the force along the paths followed by the substrates. The results obtained are in accordance with the experiments. The model provides an overall framework for analyzing the membrane transport proteins that regulate the flows of ions, nutrients and other molecules across the cell membranes, and their activities.

Impact of Interparticle Interaction on Thermodynamics of Nano-Channel Transport of Two Species

Understanding the function and control of channel transport is of paramount importance for cell physiology and nanotechnology. In particular, if several species are involved, the mechanisms of selectivity, competition, cooperation, pumping, and its modulation need to be understood. What lacks is a rigorous mathematical approach within the framework of stochastic thermodynamics, which explains the impact of interparticle in-channel interactions on the transport properties of the respective species. To achieve this, stochastic channel transport of two species is considered in a model, which different from mean field approaches, explicitly conserves the spatial correlation of the species within the channel by analysis of the stochastic dynamics within a state space, the elements of which are the channel's spatial occupation states. The interparticle interactions determine the stochastic transitions between these states. Local flow and entropy production in this state space reveal the respective particle flows through the channel and the intensity of the Brownian ratchet like rectifying forces, which these species exert mutually on each other, together with its thermodynamic effectiveness and costs. Perfect coupling of transport of the two species is realized by an attractive empty channel and strong repulsive forces between particles of the same species. This confines the state space to a subspace with circular topology, in which the concentration gradients as thermodynamic driving forces act in series, and channel flow of both species becomes equivalent. For opposing concentration gradients, this makes the species with the stronger gradient the driving, positive entropy producing one; the other is driven and produces negative entropy. Gradients equal in magnitude make all flows vanish, and thermodynamic equilibrium occurs. A differential interparticle interaction with less repulsive forces within particles of one species but maintenance of this interaction for the other species adds a bypass path to this circular subspace. On this path, which is not involved in coupling of the two species, a leak flow of the species with less repulsive interparticle interaction emerges, which is directed parallel to its concentration gradient and, hence, produces positive entropy here. Different from the situation with perfect coupling, appropriate strong opposing concentration gradients may simultaneously parallelize the flow of their respective species, which makes each species produce positive entropy. The rectifying potential of the species with the bypass option is diminished. This implies the existence of a gradient of the other species, above which its flow and gradient are parallel for any gradient of the less coupled species. The opposite holds for the less coupled species. Its flow may always be rectified and turned anti-parallel to its gradient by a sufficiently strong opposing gradient of the other one.

Transport and escape in a deformable channel driven by fractional Gaussian noise

Fractional Gaussian noise (FGN) with the Hurst exponent H is an important tool to model various phenomena in biophysical systems, like subdiffusion in a single protein molecule. Considering that there also exists a confined structure which can be modeled as a channel in these systems, transport and escape driven by FGN in a deformable channel are investigated in this paper. By calculating the mean velocity, and the mean first passage time (MFPT) for crossing the nearest bottleneck and the probability distribution of the final position, effects of FGN and channel structure on the system dynamics are illustrated. Our results indicate that FGN has a complex influence mechanism under different combinations of H and the noise intensity. For a persistence case (H>0.5), the mean velocity decreases but MFPT increases with the increase of the noise intensity and H. While for an antipersistence case (H<0.5), when H is small, the relationships among the mean velocity, MFPT and the noise intensity are exactly the opposite to persistence cases. When H has a large value, the mean velocity tends to first decrease and then increase. Moreover, effects of the bottleneck and channel asymmetry are investigated. It is shown that a small H and a large channel width can lead to a large mean velocity and fast crossing. Besides, a channel asymmetry can affect the system dynamics by inducing asymmetric structure and adjusting the width of bottleneck. However, the effect of the bottleneck is the main factor. Therefore, a combination of channel with wide bottleneck and FGN in an antipersistence regime is the optimal choice to promote the transport and escape. These results provide a basis for the explanation of molecular activity in living organisms and the design of particle mixture separators.

Effect of particle size oscillations on drift and diffusion along a periodically corrugated channel

We study diffusive transport of a particle in a channel with periodically varying cross-section, occurring when the size of the particle periodically switches between two values. In such a situation, the entropy potential, which accounts for the area accessible for diffusion particle, varies both spatially (along the channel axis) and temporally. This underlies the complex interplay between different timescales of the system and leads to novel dynamic regimes. The most notable observations are: emergence of directed motion (in case of asymmetric channel) and resonant diffusion, both controlled by the switching frequency. Resonantlike behaviors of the drift velocity and the effective diffusion coefficient are shown and discussed. Based on heuristic arguments, an approximate analytical treatment of the transport process is proposed. As a comparison with the results obtained from Brownian dynamics simulations indicates, this approach provides a satisfactory way to handle the problem analytically.