arXiv subjects

Sahin Buyukdagli

Publications and source records attributed to Sahin Buyukdagli.

At least 37 records · Page 2Linked to original sources

arXiv2018

Theoretical modeling of polymer translocation: From the electrohydrodynamics of short polymers to the fluctuating long polymers

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.

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arXiv2018

Comment on "Nonlocal statistical field theory of dipolar particles in electrolyte solutions" by Y.A. Budkov

The article by Budkov introduces a nonlocal field-theoretic model of solvent-explicit electrostatics. Despite giving a detailed introduction to the early literature on the topic, the article misses out on a series of articles that we published several years ago. Consequently, the manuscript essentially rederives without mention several results that were derived by us for the first time.

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arXiv2018

Dielectric trapping of biopolymers translocating through insulating membranes

Sensitive sequencing of biopolymers by nanopore-based translocation techniques requires 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 $τ$ with the polymer length $L$. In the short polymer regime $L\lesssim10$ nm where the external drift force dominates electrostatic polymer interactions, the translocation is characterized by the drift behavior $τ\sim L^2$. In the intermediate length regime $10\;{\rm nm}\lesssim L\lesssimκ_{\rm b}^{-1}$ where $κ_{\rm b}$ 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 $L\gtrsimκ_{\rm b}^{-1}$ where salt screening leads to the saturation of the dielectric trap, the translocation time grows linearly as $τ\sim L$. This strong departure from the drift behavior highlights the essential role played by electrostatic interactions in polymer translocation.

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arXiv2018

pH-Mediated Regulation of Polymer Transport Through SiN Pores

We characterize the pH controlled polymer capture and transport thorough silicon nitride (SiN) pores subject to protonation. A charge regulation model able to reproduce the experimental zeta potential of SiN pores is coupled with electrohydrodynamic polymer transport equations. The formalism can quantitatively explain the experimentally observed non-monotonic pH dependence of avidin conductivity in terms of the interplay between the electroosmotic and electrophoretic drag forces on the protein. We also scrutinize the DNA conductivity of SiN pores. We show that in the low pH regime where the amphoteric pore is cationic, DNA-pore attraction acts as an electrostatic trap. This provides a favorable condition for fast polymer capture and extended translocation required for accurate polymer sequencing.

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arXiv2018

Enhanced polymer capture speed and extended translocation time in pressure-solvation traps

The efficiency of nanopore-based biosequencing techniques requires fast anionic polymer capture by like-charged pores followed by a prolonged translocation process. We show that this condition can be achieved by setting a pressure-solvation trap. Polyvalent cation addition to the KCl solution triggers the like-charge polymer-pore attraction. The attraction speeds-up the pressure-driven polymer capture but also traps the molecule at the pore exit, reducing the polymer capture time and extending the polymer escape time by several orders of magnitude. By direct comparison with translocation experiments [D. P. Hoogerheide et al., ACS Nano 8, 7384 (2014)], we characterize as well the electrohydrodynamics of polymers transport in pressure-voltage traps. We derive scaling laws that can accurately reproduce the pressure dependence of the experimentally measured polymer translocation velocity and time. We also find that during polymer capture, the electrostatic barrier on the translocating molecule slows down the liquid flow. This prediction identifies the streaming current measurement as a potential way to probe electrostatic polymer-pore interactions.

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arXiv2018

Facilitated polymer capture by charge inverted electroosmotic flow in voltage-driven polymer translocation

The optimal functioning of nanopore-based biosensing tools necessitates rapid polymer capture from the ion reservoir. We identify an ionic correlation-induced transport mechanism that provides this condition without the chemical modification of the polymer or the pore surface. In the typical experimental configuration where a negatively charged silicon-based pore confines a 1:1 electrolyte solution, anionic polymer capture is limited by electrostatic polymer-membrane repulsion and the electroosmotic (EO) flow. Added multivalent cations suppress the electrostatic barrier and revers the pore charge, inverting the direction of the EO flow that drags the polymer to the trans side. This inverted EO flow can be used to speed up polymer capture from the reservoir and to transport weakly or non-uniformly charged polymers that cannot be controlled by electrophoresis.

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arXiv2017

Multivalent cation induced attraction of anionic polymers by like-charged pores

The efficiency of nanopore-based polymer sensing devices depends on the fast capture of anionic polyelectrolytes by negatively charged pores. This requires the cancellation of the electrostatic barrier associated with repulsive polymer-pore interactions. We develop a correlation-corrected theory to show that the barrier experienced by the polymer can be efficiently overcome by the addition of multivalent cations into the electrolyte solution. Cation adsorption into the pore enhances the screening ability of the pore medium with respect to the bulk reservoir which translates into an attractive force on the polymer. Beyond a critical multivalent cation concentration, this correlation-induced attraction overcomes the electrostatic barrier and triggers the adsorption of the polymer by the like-charged pore. It is shown that like-charge polymer-pore attraction is suppressed by monovalent salt but enhanced by the membrane charge strength and the pore confinement. Our predictions may provide enhanced control over polymer motion in translocation experiments.

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arXiv2017

Controlling Polymer Capture and Translocation by Electrostatic Polymer-Pore Interactions

Polymer translocation experiments typically involve anionic polyelectrolytes such as DNA molecules driven through negatively charged nanopores. Quantitative modelling of polymer capture to the nanopore followed by translocation therefore necessitates the consideration of the electrostatic barrier resulting from like-charge polymer-pore interactions. To this end, in this work we couple mean-field level electrohydrodynamic equations with the Smoluchowski formalism to characterize the interplay between the electrostatic barrier, the electrophoretic drift, and the electro-osmotic liquid flow. In particular, we find that due to distinct ion density regimes where the salt screening of the drift and barrier effects occur, there exists a characteristic salt concentration maximizing the probability of barrier-limited polymer capture into the pore. We also show that in the barrier-dominated regime, the polymer translocation time increases exponentially with the membrane charge and decays exponentially fast with the pore radius and the salt concentration. These results suggest that the alteration of these parameters in the barrier-driven regime can be an efficient way to control the duration of the translocation process and facilitate more accurate measurements of the ionic current signal in the pore.

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arXiv2017

Like-charge attraction and opposite-charge decomplexation between polymers and DNA molecules

We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test charge theory to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for one-loop level electrostatic correlation effects such as the ionic cloud deformation around the strongly charged DNA molecule as well as image-charge forces induced by the low DNA permittivity. Our model can reproduce and explain various characteristics of the experimental phase diagrams for polymer solutions. First, the addition of polyvalent cations to the electrolyte solution results in the attraction of the negatively charged polymer by the DNA molecule. The glue of the like-charge attraction is the enhanced shielding of the polymer charges by the dense counterion layer at the DNA surface. Secondly, through the shielding of the DNA-induced electrostatic potential, mono- and polyvalent cations of large concentration both suppress the like-charge attraction. Within the same formalism, we also predict a new opposite-charge repulsion effect between the DNA molecule and a positively charged polymer. In the presence of polyvalent anions such as sulfate or phosphate, their repulsion by the DNA charges leads to the charge screening deficiency of the region around the DNA molecule. This translates into a repulsive force that results in the decomplexation of the polymer from DNA. This opposite-charge repulsion phenomenon can be verified by current experiments and the underlying mechanism can be beneficial to gene therapeutic applications where the control over polymer-DNA interactions is the key factor.

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arXiv2016

Correlation-induced DNA adsorption on like-charged membranes

The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates for further analysis, e.g., by force microscopy, or the pulling of polyelectrolytes into membrane nanopores, as in sequencing applications. In this paper, we present a theoretical analysis of such scenarios based on the self-consistent field theory approach, which allows us to address the important effect of charge correlations. We calculate the grand potential of a stiff polyelectrolyte immersed in an electrolyte in contact with a negatively charged dielectric membrane. For the sake of conciseness, we neglect conformational polymer fluctuations and model the molecule as a rigid charged line. At strongly charged membranes, the adsorbed counterions enhance the screening ability of the interfacial region. In the presence of highly charged polymers such as double-stranded DNA molecules close to the membrane, this enhanced interfacial screening dominates the mean-field level DNA-membrane repulsion and results in the adsorption of the DNA molecule to the surface. This picture provides a simple explanation for the recently observed DNA binding onto similarly charged substrates [G. L.-Caballero et al., Soft Matter 10, 2805 (2014)] and points out charge correlations as a non-negligible ingredient of polymer-surface interactions.

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arXiv2016

Beyond Poisson-Boltzmann: fluctuations and fluid structure in a self-consistent theory

Poisson-Boltzmann (PB) theory is the classic approach to soft matter electrostatics which has been applied to numerous problems of physical chemistry and biophysics. Its essential limitations are the neglect of correlation effects and of fluid structure. Recently, several theoretical insights have allowed the formulation of approaches that go beyond PB theory in a systematic way. In this topical review we provide an update on the developments achieved in self-consistent formulations of correlation-corrected Poisson-Boltzmann theory. We introduce the corresponding system of coupled nonlinear equations for both continuum electrostatics with a uniform dielectric constant and a structured solvent, a dipolar Coulomb fluid, including nonlocal effects. While the approach is only approximate and also limited to corrections in the so-called weak fluctuation regime, it allows to include physically relevant effects, as we show for a range of applications of these equations.

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arXiv2016

Electrostatics of polymer translocation events in electrolyte solutions

We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based membranes are driven by a competition between the repulsive DNA-image-charge interactions and the attractive coupling between the DNA segments on the trans and the cis sides of the membrane. The latter effect is induced by the reduction of the coupling by the dielectric membrane. In strong salt solutions where the repulsive image-charge effects dominate the attractive trans-cis coupling, the DNA molecule encounters a translocation barrier of ~10 kBT. In dilute electrolytes, the trans-cis coupling takes over image-charge forces and the membrane becomes a metastable attraction point that can trap translocating polymers over long time intervals. This mechanism can be used in translocation experiments in order to control the DNA motion by tuning the salt concentration of the solution.

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arXiv2015

Electrostatic energy barriers from dielectric membranes upon approach of translocating DNA molecules

We probe the electrostatic cost associated with the approach phase of DNA translocation events. Within an analytical theory at the Debye-Huckel level, we calculate the electrostatic free energy of a rigid DNA molecule interacting with a dielectric membrane. For carbon or silicon based low permittivity neutral membranes, the DNA molecule experiences a repulsive energy barrier between 10 kBT and 100 kBT. In the case of engineered membranes with high dielectric permittivity, the membrane surface attracts the DNA with an energy of the same magnitude. Both the repulsive and attractive interactions result from image-charge effects and their magnitude survive even for the thinnest graphene-based membranes of size d~6 A. For weakly charged membranes, the electrostatic free energy is always attractive at large separation distances but switches to repulsive close to the membrane surface. We also characterise the polymer length dependence of the interaction energy. For specific values of the membrane charge density, low permittivity membranes repel short polymers but attract long polymers. Our results can be used to control the strong electrostatic free energy of DNA-membrane interactions prior to translocation events by chemical engineering of the relevant system parameters.

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arXiv2015

Electrostatic interactions in charged nanoslits within an explicit solvent theory

Within a dipolar Poisson-Boltzmann theory including electrostatic correlations, we consider the effect of explicit solvent structure on solvent and ion partition confined to charged nanopores. We develop a relaxation scheme for the solution of this highly non-linear integro-differential equation for the electrostatic potential. The scheme is an extension of the approach previously introduced for simple planes (S. Buyukdagli and Ralf Blossey, J. Chem. Phys. 140, 234903 (2014)) to nanoslit geometry. We show that the reduced dielectric response of solvent molecules at the membrane walls gives rise to an electric field significantly stronger than the field of the classical Poisson-Boltzmann equation. This peculiarity associated with non-local electrostatic interactions results in turn in an interfacial counterion adsorption layer absent in continuum theories. The observation of this enhanced counterion affinity in the very close vicinity of the interface may have important impacts on nanofludic transport through charged nanopores. Our results indicate the quantitative inaccuracy of solvent implicit nanofiltration theories in predicting the ionic selectivity of membrane nanopores.

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arXiv2015

Dielectric anisotropy in polar solvents under external fields

We investigate dielectric saturation and increment in polar liquids under external fields. We couple a previously introduced dipolar solvent model to a uniform electric field and derive the electrostatic kernel of interacting dipoles. This procedure allows an unambiguous definition of the liquid dielectric permittivity embodying non-linear dielectric response and correlation effects.We find that the presence of the external field results in a dielectric anisotropy characterized by a two-component dielectric permittivity tensor. The increase of the electric field amplifies the permittivity component parallel to the field direction, i.e. dielectric increment is observed along the field. However, the perpendicular component is lowered below the physiological permittivity, indicating dielectric saturation perpendicular to the field. By comparison with Molecular Dynamics simulations from the literature, we show that the mean-field level dielectric response theory underestimates dielectric saturation. The inclusion of dipolar correlations at the weak-coupling level intensify the mean-field level dielectric saturation and improves the agreement with simulation data at weak electric fields. The correlation-corrected theory predicts as well the presence of a metastable configuration corresponding to the antiparallel alignment of dipoles with the field. This prediction can be verified by solvent-explicit simulations where solvent molecules are expected to be trapped transiently in this metastable state.

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arXiv2015

Ionic current inversion in pressure-driven polymer translocation through nanopores

We predict streaming current inversion with multivalent counterions in hydrodynamically driven polymer translocation events from a correlation-corrected charge transport theory including charge fluctuations around mean-field electrostatics. In the presence of multivalent counterions, electrostatic many-body effects result in the reversal of the DNA charge. The attraction of anions to the charge-inverted DNA molecule reverses the sign of the ionic current through the pore. Our theory allows for a comprehensive understanding of the complex features of the resulting streaming currents. The underlying mechanism is an efficient way to detect DNA charge reversal in pressure-driven translocation experiments with multivalent cations.

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arXiv2014

Controlling polymer translocation and ion transport via charge correlations

We develop a correlation-corrected transport theory in order to predict ionic and polymer transport properties of membrane nanopores in physical conditions where mean-field electrostatics breaks down. The experimentally observed low KCl conductivity of open alpha-Hemolysin pores is quantitatively explained by the presence of surface polarization effects. Upon the penetration of a DNA molecule into the pore, these polarization forces combined with the electroneutrality of DNA sets a lower boundary for the ionic current, explaining the weak salt dependence of blocked pore conductivities at dilute ion concentrations. The addition of multivalent counterions into the solution results in the reversal of the polymer charge and the direction of the electroosmotic flow. With trivalent spermidine or quadrivalent spermine molecules, the charge inversion is strong enough to stop the translocation of the polymer and to reverse its motion. This mechanism can be used efficiently in translocation experiments in order to improve the accuracy of DNA sequencing by minimizing the translocation velocity of the polymer.

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arXiv2014

Dipolar correlations in structured solvents under nanoconfinement

We study electrostatic correlations in structured solvents confined to nanoscale systems. We derive variational equations of Netz-Orland type for a model liquid composed of finite size dipoles. These equations are solved for both dilute solvents and solvents at physiological concentrations in a slit nanopore geometry. Correlation effects are of major importance for the dielectric reduction and anisotropy of the solvent resulting from dipole image interactions and also lead to a reduction of van der Waals attractions between low dielectric bodies. Finally, by comparison with other recently developed self-consistent theories and experiments, we scrutinize the effect of solvent-membrane interactions on the differential capacitance of the charged liquid in contact with low dielectric substrates. The interfacial solvent depletion driven by solvent-image interactions plays the major role in the observed low values of the experimental capacitance data, while non-locality associated with the extended charge structure of solvent molecules only brings a minor contribution.

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