Transition between Two Regimes Describing Internal Fluctuation of DNA in a Nanochannel

We measure the thermal fluctuation of the internal segments of a piece of DNA confined in a nanochannel about 50100 nm wide. This local thermodynamic property is key to accurate measurement of distances in genomic analysis. For DNA in 100 nm channels, we observe a critical length scale 10 m for the mean extension of internal segments, below which the de Gennes' theory describes the fluctuations with no fitting parameters, and above which the fluctuation data falls into Odijk's deflection theory regime. By analyzing the probability distributions of the extensions of the internal segments, we infer that folded structures of length 150250 nm, separated by 10 m exist in the confined DNA during the transition between the two regimes. For 50 nm channels we find that the fluctuation is significantly reduced since the Odijk regime appears earlier. This is critical for genomic analysis. We further propose a more detailed theory based on small fluctuations and incorporating the effects of confinement to explicitly calculate the statistical properties of the internal fluctuations. Our theory is applicable to polymers with heterogeneous mechanical properties confined in non-uniform channels. We show that existing theories for the end-to-end extension/fluctuation of polymers can be used to study the internal fluctuations only when the contour length of the polymer is many times larger than its persistence length. Finally, our results suggest that introducing nicks in the DNA will not change its fluctuation behavior when the nick density is below 1 nick per kbp DNA

Mechanosensitive channel activation by diffusio-osmotic force.

For ion channel gating, the appearance of two distinct conformational states and the discrete transitions between them are essential, and therefore of crucial importance to all living organisms. We show that the physical interplay between two structural elements that are commonly present in bacterial mechanosensitive channels--namely, a charged vestibule and a hydrophobic constriction--creates two distinct conformational states, open and closed, as well as the gating between them. We solve the nonequilibrium Stokes-Poisson-Nernst-Planck equations, extended to include a molecular potential of mean force, and show that a first order transition between the closed and open states arises naturally from the diffusio-osmotic stress caused by the ions and the water inside the channel and the elastic restoring force from the membrane

Mechanosensitive channel activation by diffusio-osmotic force.

For ion channel gating, the appearance of two distinct conformational states and the discrete transitions between them are essential, and therefore of crucial importance to all living organisms. We show that the physical interplay between two structural elements that are commonly present in bacterial mechanosensitive channels--namely, a charged vestibule and a hydrophobic constriction--creates two distinct conformational states, open and closed, as well as the gating between them. We solve the nonequilibrium Stokes-Poisson-Nernst-Planck equations, extended to include a molecular potential of mean force, and show that a first order transition between the closed and open states arises naturally from the diffusio-osmotic stress caused by the ions and the water inside the channel and the elastic restoring force from the membrane

Unraveling the combined effects of dielectric and viscosity profiles on surface capacitance, electro-osmotic mobility, and electric surface conductivity.

We calculate the electro-osmotic mobility and surface conductivity at a solid-liquid interface from a modified Poisson-Boltzmann equation, including spatial variations of the dielectric function and the viscosity that where extracted previously from molecular dynamics simulations of aqueous interfaces. The low-dielectric region directly at the interface leads to a substantially reduced surface capacitance. At the same time, ions accumulate into a highly condensed interfacial layer, leading to the well-known saturation of the electro-osmotic mobility at large surface charge density regardless of the hydrodynamic boundary conditions. The experimentally well-established apparent excess surface conductivity follows from our model for all hydrodynamic boundary conditions without additional assumptions. Our theory fits multiple published sets of experimental data on hydrophilic and hydrophobic surfaces with striking accuracy, using the nonelectrostatic ion-surface interaction as the only fitting parameter

Beyond the continuum: how molecular solvent structure affects electrostatics and hydrodynamics at solid-electrolyte interfaces.

Standard continuum theory fails to predict several key experimental results of electrostatic and electrokinetic measurements at aqueous electrolyte interfaces. In order to extend the continuum theory to include the effects of molecular solvent structure, we generalize the equations for electrokinetic transport to incorporate a space dependent dielectric profile, viscosity profile, and non-electrostatic interaction potential. All necessary profiles are extracted from atomistic molecular dynamics (MD) simulations. We show that the MD results for the ion-specific distribution of counterions at charged hydrophilic and hydrophobic interfaces are accurately reproduced using the dielectric profile of pure water and a non-electrostatic repulsion in an extended Poisson-Boltzmann equation. The distributions of Na(+) at both surface types and Cl(-) at hydrophilic surfaces can be modeled using linear dielectric response theory, whereas for Cl(-) at hydrophobic surfaces it is necessary to apply nonlinear response theory. The extended Poisson-Boltzmann equation reproduces the experimental values of the double-layer capacitance for many different carbon-based surfaces. In conjunction with a generalized hydrodynamic theory that accounts for a space dependent viscosity, the model captures the experimentally observed saturation of the electrokinetic mobility as a function of the bare surface charge density and the so-called anomalous double-layer conductivity. The two-scale approach employed here-MD simulations and continuum theory-constitutes a successful modeling scheme, providing basic insight into the molecular origins of the static and kinetic properties of charged surfaces, and allowing quantitative modeling at low computational cost

Profile of the static permittivity tensor of water at interfaces: consequences for capacitance, hydration interaction and ion adsorption.

We derive the theoretical framework to calculate the dielectric response tensor and determine its components for water adjacent to hydrophilic and hydrophobic surfaces using molecular dynamics simulations. For the nonpolarizable water model used, linear response theory is found to be applicable up to an external perpendicular field strength of ∼2 V/nm, which is well beyond the experimental dielectric breakdown threshold. The dipole contribution dominates the dielectric response parallel to the interface, whereas for the perpendicular component it is essential to keep the quadrupole and octupole terms. Including the space-dependent dielectric function in a mean-field description of the ion distribution at a single charged interface, we reproduce experimental values of the interfacial capacitance. At the same time, the dielectric function decreases the electrostatic part of the disjoining pressure between two charged surfaces, unlike previously thought. The difference in interfacial polarizability between hydrophilic and hydrophobic surfaces can be quantized in terms of the dielectric dividing surface. Using the dielectric dividing surface and the Gibbs dividing surface positions to estimate the free energy of a single ion close to an interface, ion-specific adsorption effects are found to be more pronounced at hydrophobic surfaces than at hydrophilic surfaces, in agreement with experimental trends

Dielectric profile of interfacial water and its effect on double-layer capacitance.

The framework for deriving tensorial interfacial dielectric profiles from bound charge distributions is established and applied to molecular dynamics simulations of water at hydrophobic and hydrophilic surfaces. In conjunction with a modified Poisson-Boltzmann equation, the trend of experimental double-layer capacitances is well reproduced. We show that the apparent Stern layer can be understood in terms of the dielectric profile of pure water

Nanoscale pumping of water by AC electric fields.

Using molecular dynamics simulations we demonstrate pumping of water through a carbon nanotube by time-dependent electric fields. The fields are generated by electrodes with oscillating charges in a broad gigahertz frequency range that are attached laterally to the tube. The key ingredient is a phase shift between the electrodes to break the spatiotemporal symmetry. A microscopic theory based on a polarization-dragging mechanism accounts quantitatively for our numerical findings

Electrokinetics at aqueous interfaces without mobile charges.

We theoretically consider the possibility of using electric fields in aqueous channels of cylindrical and planar geometry to induce transport in the absence of mobile ionic charges. Using the Navier-Stokes equation, generalized to include the effects of water spinning, dipole orientation and relaxation, we show analytically that pumping of a dipolar liquid through an uncharged hydrophobic channel can be achieved by injecting torque into the liquid, based on the coupling between molecular spinning and fluid vorticity. This is possible using rotating electric fields and suitably chosen interfacial boundary conditions or transiently by suddenly switching on a homogeneous electric field. A static electric field, however, does not induce a steady state flow in channels, irrespective of the geometry. Using molecular dynamics (MD) simulations, we confirm that static fields do not lead to any pumping, in contrast to earlier publications. The pumping observed in MD simulations of carbon nanotubes and oil droplets in a static electric field is tracked down to an imprudent implementation of Lennard-Jones interaction truncation schemes