Target Search Kinetics Of Self-propelled Particles And Controlled DNA Chain Translocation Dynamics

Using Langevin dynamics,we have investigated the target search dynamics of self-propelled particles and ssDNA translocation dynamics under driving force.First,we present a numerical investigation of the search kinetics of self-propelled particles(SPPs)to a target located at the center or at the boundary of a confining domain.When searching a target located at the center of a circular confining domain,the search efficiency of SPPs is improved compared to that of Brownian particles if the rotational diffusion is not too slow.In this case,the mean search time τ could be minimized with proper combinations of the characteristic rotation time τθ and the self-propulsion velocity v0.It is further shown to be a consequence of the interplay between the enhanced diffusion and the thigmotactism(boundary-following behavior)of SPPs due to the self-propulsion.However,for a target located at the boundary of the circular confining domain,we find that the search process is continuing to be accelerated with increasing τ0 or v0.Our results highlight the role of the target position in the search kinetics,and open up new opportunities to optimize the search process of SPPs by taking accurate controls over their motions.Next,a numerical investigation of the target search dynamics of self-propelled particles(SPPs)in heterogeneous environments is presented in this work.We show that the spatial heterogeneity has a dramatic effect on the target search dynamics of SPPs.The relative magnitude of the self-propulsion length lp and the radius of the circular domain Rc determines how the mean search time of SPPs τ depends on the area fraction of fixed obstacles φob.For lp<Rc,the target search process is diffusion-dominated so that a monotonic increase in τ with increasing φob is observed.For lp>Rc,τ is shown to be a non-monotonic convex function as a function of φob due to the interplay of the distribution-dominated and diffusion-dominated dynamic regimes.Furthermore,at fixed φob,τ shows a minimum upon increasing the self-propulsion velocity vo of a SPP of a slow rotational diffusion when it searches for a target at low φob,while it decreases monotonically at high φob.The present work highlights that the introduction of spatial heterogeneity causes rich dynamic behaviors of a SPP searching for a target,and deepens our understanding of the transport of active matter in heterogeneous media.Last,we reveal the fact that the speed of ssDNA translocation through biopore was nearly two orders of magnitude slower than that of solid-state nanopore is attributed by the much larger drag coefficient in a narrow channel comparable to the monomer size.Compare to solid state nanopore in which we know translocation time distribution is caused by conformation fluctuation of polymer chain,the variance of translocation time in biopore is primarily due to the Brownian motion of the polymer chain inside nanopore.More importantly,we provide a conception that further slowing down DNA translocation speed is essentially a successive position clamping process of each nucleotide by energy well.By using Langevin dynamic simulations,specific height and breadth of the interaction energy well and the magnitude of driving force have been presented to demonstrate how to make an irregular fast DNA translocation process become a regulated slow process appropriate for DNA sequencing applications.