Browsing by Author "Sarabadani, J."
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Item Open Access Dielectric trapping of biopolymers translocating through insulating membranes(MDPI AG, 2018) Büyükdağlı, Şahin; Sarabadani, J.; Ala-Nissila, T.Sensitive sequencing of biopolymers by nanopore-based translocation techniques requires an extension of the time spent by the molecule in the pore. We develop an electrostatic theory of polymer translocation to show that the translocation time can be extended via the dielectric trapping of the polymer. In dilute salt conditions, the dielectric contrast between the low permittivity membrane and large permittivity solvent gives rise to attractive interactions between the cis and trans portions of the polymer. This self-attraction acts as a dielectric trap that can enhance the translocation time by orders of magnitude. We also find that electrostatic interactions result in the piecewise scaling of the translocation time t with the polymer length L. In the short polymer regime L ≲ 10 nm where the external drift force dominates electrostatic polymer interactions, the translocation is characterized by the drift behavior τ ~ L2. In the intermediate length regime 10 nm. ≲ L ≲ kb -1 where kb is the Debye-Hückel screening parameter, the dielectric trap takes over the drift force. As a result, increasing polymer length leads to quasi-exponential growth of the translocation time. Finally, in the regime of long polymers L ≳ kb -1 where salt screening leads to the saturation of the dielectric trap, the translocation time grows linearly as τ ~ L. This strong departure from the drift behavior highlights the essential role played by electrostatic interactions in polymer translocation.Item Open Access Pulling a DNA molecule through a nanopore embedded in an anionic membrane: tension propagation coupled to electrostatics(Institute of Physics Publishing, 2020) Sarabadani, J.; Büyükdağlı, Şahin; Ala-Nissila, T.We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension propagation theory with electrostatics for a negatively charged biopolymer pulled through a nanopore embedded in a similarly charged anionic membrane. We show that in the realistic case of a single-stranded DNA molecule, dilute salt conditions characterized by weak charge screening, and a negatively charged membrane, the translocation dynamics is unexpectedly accelerated despite the presence of large repulsive electrostatic interactions between the polymer coil on the cis side and the charged membrane. This is due to the rapid release of the electrostatic potential energy of the coil during translocation, leading to an effectively attractive force that assists end-driven translocation. The speedup results in non-monotonic polymer length and membrane charge dependence of the exponent α characterizing the translocation time τ ∝ Nα 0 of the polymer with length N0. In the regime of long polymers N0 500, the translocation exponent exceeds its upper limit α = 2 previously observed for the same system without electrostatic interactions.Item Open Access Theoretical modeling of polymer translocation: from the electrohydrodynamics of short polymers to the fluctuating long polymers(MDPI AG, 2019) Büyükdağlı, Şahin; Sarabadani, J.; Ala-Nissila, T.The theoretical formulation of driven polymer translocation through nanopores is complicated by the combination of the pore electrohydrodynamics and the nonequilibrium polymer dynamics originating from the conformational polymer fluctuations. In this review, we discuss the modeling of polymer translocation in the distinct regimes of short and long polymers where these two effects decouple. For the case of short polymers where polymer fluctuations are negligible, we present a stiff polymer model including the details of the electrohydrodynamic forces on the translocating molecule. We first show that the electrohydrodynamic theory can accurately characterize the hydrostatic pressure dependence of the polymer translocation velocity and time in pressure-voltage-driven polymer trapping experiments. Then, we discuss the electrostatic correlation mechanisms responsible for the experimentally observed DNA mobility inversion by added multivalent cations in solid-state pores, and the rapid growth of polymer capture rates by added monovalent salt in α-Hemolysin pores. In the opposite regime of long polymers where polymer fluctuations prevail, we review the iso-flux tension propagation (IFTP) theory, which can characterize the translocation dynamics at the level of single segments. The IFTP theory is valid for a variety of polymer translocation and pulling scenarios. We discuss the predictions of the theory for fully flexible and rodlike pore-driven and end-pulled translocation scenarios, where exact analytic results can be derived for the scaling of the translocation time with chain length and driving force.