polymer translocation and packaging role of flickering pores time dependent driving and capsid shapes

Abstract

The translocation of biopolymers across nanopores is an ubiquitous process in bi- newlineology. Examples range from the transport of RNA through a nuclear membrane pore newlinecomplex, viral ejection of DNA into host cells, and protein transport through membrane newlinechannels. One of the principal reasons for studying polymer translocation is to create newlineeffective biosequencing methods, such as the detection of a DNA sequence. The poly- newlinemer is field-driven across the pore, and the translocating polymer segment is mapped newlinefrom the ionic current perturbations. In order to achieve precise control in the detection newlineprocess, we need to control the polymer-pore interactions and pore geometry. Within newlinethis framework, theoretical models have yielded significant insights into how polymer newlineproperties, pore characteristics, interactions between polymers, and external drive af- newlinefect translocation dynamics. Polymer translocation also plays a key role in gene therapy newlineand controlled drug delivery. newlineThere are various scenarios in biological nanopores, such as the twin pore complex in newlinethe inner membrane of mitochondria and the nuclear pore complex (NPC), where the newlinepore size can change during protein translocation. In the realm of synthetic nanopore newlinedesign, elastomeric nanochannel devices have been utilized to adjust the width of the newlinechannels by applying mechanical stresses. To replicate the behavior of these systems, newlineas in our first study, we investigated the driven translocation of a semiflexible polymer newlinethrough an attractive extended pore with a periodically oscillating width. Theoretical newlinestudies of polymer translocation through pores with dynamically changing widths have newlineshown that the translocation can be significantly improved compared to that of a static newlinepore. Comparing the average translocation time for an oscillating pore (and#964; osc ) with that newlineof a static pore (and#964; stat ), we showed that semiflexible polymers translocate more effi- newlineciently through oscillating pores than through static ones. However, the gain defined newlineas and#951; = and#964; stat /and#964; osc , is highly inf