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• W2887308511 abstract "Polymer translocation is a process where the polymer traverses sequentially through ananoscale pore from one side of a membrane to the other. The process is involved in trans-portation of DNA, RNA, and proteins through cellular membrane structures. It also offers thepromise of a fast and cheap technique for DNA sequencing. For the past 30 years, the study inthe field has been intensive and the problem has offered challenges to biologists and physicistsalike.This thesis concerns physics of two different polymer translocations processes. In drivenpolymer translocation, a driving force inside the pore pushes monomers through the membrane.In chaperone-assisted translocation, the bias for the translocation is provided by bindingparticles on the receiving side of the membrane. We use Langevin dynamics simulations tostudy and obtain knowledge of these non-equilibrium statistical physics phenomena.Tension propagation theory has established an essential role in the general framework ofdriven polymer translocation physics. In this thesis, we study the propagation of tensioncomputationally with accurate measurements of related quantities. We find and explainimportant bias dependent changes in tension and translocation dynamics. We find that smalldriving force leads to strong biased diffusion of the cis-side polymer segment toward themembrane. This speeds up translocation. Together with friction of the pore, the diffusioncauses a finite-size effect in which the scaling exponent, describing dependence of translocationtime τ with the polymer length N , τ ∼ N β , increases as a function of driving force. Whenhydrodynamics is included, we observe the diffusion toward the membrane to be enhancedeven further due to the larger diffusion coefficient together with solvent backflow.We also study other less understood aspects of driven translocation. We show that the effectof the trans-side polymer segment on the process is minimal even in the worst case scenarioof extreme crowding. Moreover, we investigate the effect of polymer rigidity on translocationdynamics. For semiflexible polymers, we observe regimes in trans-side friction related todriving force, diffusion, and solvent viscosity.We study chaperone-assisted translocation of flexible polymers using the first ever threedimensional simulation model. We observe great variation in dynamics when details of thebinding model are changed. These changes become pivotal for flexible chains. Depending onthe binding model, the dynamics of the process can be dominated either by the cis or the trans-side polymer segment. We also observe tension propagation on the cis-side polymer segment,showing that chaperone-assisted translocation is inherently a non-equilibrium process.; Polymeeritranslokaatio on prosessi, jossa polymeeri kulkee monomeeri kerrallaan nanometrikokoluokkaaolevan kanavan lapi kalvon puolelta toiselle. Monet biopolymeerit, kuten DNA, RNA ja proteiinit, kulkevat solun sisaisten kalvorakenteiden lapi talla tavalla. Polymeeritranslokaatiota hyodynnetaan myos uudessa DNA:n…" @default.
• W2887308511 created "2018-08-22" @default.
• W2887308511 creator A5084309361 @default.
• W2887308511 date "2018-01-01" @default.
• W2887308511 modified "2023-09-27" @default.
• W2887308511 title "Dynamical Aspects of Driven and Chaperone-Assisted Polymer Translocation" @default.
• W2887308511 hasPublicationYear "2018" @default.
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