Peculiarities of the Mean Transition Path Time Dependence on the Barrier Height in Entropy Potentials

Channel-facilitated transport under resetting dynamics

The transport of particles through channels holds immense significance in physics, chemistry, and biological sciences. For instance, the motion of solutes through biological membranes is facilitated by specialized proteins that create water-filled channels. Valuable insights can be obtained by studying the transition paths of particles through a channel and gathering information on their lifetimes inside the channel as well as their exit probabilities. In a similar vein, we consider a one-dimensional model of channel-facilitated transport where a diffusive particle is subject to attractive interactions with the walls of the channel. We study the statistics of conditional and unconditional escape times in the presence of resetting-an intermittent dynamics that brings the particle back to its initial coordinate stochastically. We determine analytically the physical conditions under which such a resetting mechanism becomes beneficial for the faster escape of the particles from the channel, thus enhancing transport. Our theory has been verified with the aid of Brownian dynamics simulations for various interaction strengths and extents. The overall results presented herein highlight the scope of resetting-based strategies to be universally promising for complex transport processes of single or long molecules through biological membranes.

Fick-Jacobs description and first passage dynamics for diffusion in a channel under stochastic resetting

The transport of particles through channels is of paramount importance in physics, chemistry, and surface science due to its broad real world applications. Much insight can be gained by observing the transition paths of a particle through a channel and collecting statistics on the lifetimes in the channel or the escape probabilities from the channel. In this paper, we consider the diffusive transport through a narrow conical channel of a Brownian particle subject to intermittent dynamics, namely, stochastic resetting. As such, resetting brings the particle back to a desired location from where it resumes its diffusive phase. To this end, we extend the Fick-Jacobs theory of channel-facilitated diffusive transport to resetting-induced transport. Exact expressions for the conditional mean first passage times, escape probabilities, and the total average lifetime in the channel are obtained, and their behavior as a function of the resetting rate is highlighted. It is shown that resetting can expedite the transport through the channel-rigorous constraints for such conditions are then illustrated. Furthermore, we observe that a carefully chosen resetting rate can render the average lifetime of the particle inside the channel minimal. Interestingly, the optimal rate undergoes continuous and discontinuous transitions as some relevant system parameters are varied. The validity of our one-dimensional analysis and the corresponding theoretical predictions is supported by three-dimensional Brownian dynamics simulations. We thus believe that resetting can be useful to facilitate particle transport across biological membranes-a phenomenon that can spearhead further theoretical and experimental studies.

Enhancing carrier flux for efficient drug delivery in cancer tissues

Ultrasound focused toward tumors in the presence of circulating microbubbles improves the delivery of drug-loaded nanoparticles and therapeutic outcomes; however, the efficacy varies among the different properties and conditions of the tumors. Therefore, there is a need to optimize the ultrasound parameters and determine the properties of the tumor tissue important for the successful delivery of nanoparticles. Here, we propose a mesoscopic model considering the presence of entropic forces to explain the ultrasound-enhanced transport of nanoparticles across the capillary wall and through the interstitium of tumors. The nanoparticles move through channels of variable shape whose irregularities can be assimilated to barriers of entropic nature that the nanoparticles must overcome to reach their targets. The model assumes that focused ultrasound and circulating microbubbles cause the capillary wall to oscillate, thereby changing the width of transcapillary and interstitial channels. Our analysis provides values for the penetration distances of nanoparticles into the interstitium that are in agreement with experimental results. We found that the penetration increased significantly with increasing acoustic intensity as well as tissue elasticity, which means softer and more deformable tissue (Young modulus lower than 50 kPa), whereas porosity of the tissue and pulse repetition frequency of the ultrasound had less impact on the penetration length. We also considered that nanoparticles can be absorbed into cells and to extracellular matrix constituents, finding that the penetration length is increased when there is a low absorbance coefficient of the nanoparticles compared with their diffusion coefficient (close to 0.2). The model can be used to predict which tumor types, in terms of elasticity, will successfully deliver nanoparticles into the interstitium. It can also be used to predict the penetration distance into the interstitium of nanoparticles with various sizes and the ultrasound intensity needed for the efficient distribution of the nanoparticles.

Effect of ligand binding on riboswitch folding: Theory and simulations

The effect of ligand binding on the conformational transitions of the add A-riboswitch in cellular environments is investigated theoretically within the framework of the generalized Langevin equation combined with steered molecular dynamics simulations. Results for the transition path time distribution provide an estimate of the transit times, which are difficult to determine experimentally. The time for the conformational transitions of the riboswitch aptamer is longer for the ligand bound state as compared to that of the unbound one. The transition path time of the riboswitch follows a counterintuitive trend as it decreases with an increase in the barrier height. The mean transition path time of either transitions of the riboswitch in the ligand bound/unbound state increases with an increase in the complexity of the surrounding environment due to the caging effect. The results of the probability density function, transition path time distribution, and mean transition path time obtained from the theory qualitatively agree with those obtained from the simulations and with earlier experimental and theoretical studies.