Polymer translocation is a process where the polymer traverses sequentially through a nanoscale 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 the promise of a fast and cheap technique for DNA sequencing. For the past 30 years, the study in the field has been intensive and the problem has offered challenges to biologists and physicists alike. This thesis concerns physics of two different polymer translocations processes. In driven polymer translocation, a driving force inside the pore pushes monomers through the membrane. In chaperone-assisted translocation, the bias for the translocation is provided by binding particles on the receiving side of the membrane. We use Langevin dynamics simulations to study and obtain knowledge of these non-equilibrium statistical physics phenomena. Tension propagation theory has established an essential role in the general framework of driven polymer translocation physics. In this thesis, we study the propagation of tension computationally with accurate measurements of related quantities. We find and explain important bias dependent changes in tension and translocation dynamics. We find that small driving force leads to strong biased diffusion of the cis-side polymer segment toward the membrane. This speeds up translocation. Together with friction of the pore, the diffusion causes a finite-size effect in which the scaling exponent, describing dependence of translocation time τ with the polymer length N , τ ∼ N β , increases as a function of driving force. When hydrodynamics is included, we observe the diffusion toward the membrane to be enhanced even 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 effect of the trans-side polymer segment on the process is minimal even in the worst case scenario of extreme crowding. Moreover, we investigate the effect of polymer rigidity on translocation dynamics. For semiflexible polymers, we observe regimes in trans-side friction related to driving force, diffusion, and solvent viscosity. We study chaperone-assisted translocation of flexible polymers using the first ever three-dimensional simulation model. We observe great variation in dynamics when details of the binding model are changed. These changes become pivotal for flexible chains. Depending on the 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.
|Publication status||Published - 2018|
|MoE publication type||G5 Doctoral dissertation (article)|
- polymer, translocation, molecular dynamics, simulations, chaperone