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

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

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

Electrohydraulic power conversion in planar nanochannels.

We explore mechanisms for flow generation in water-filled nanochannels, employing the coupling between translational and rotational momentum. Using a generalized Navier-Stokes equation that includes dipolar polarization and relaxation, we show that static electric fields do not induce fluid flow in the planar geometry, while rotating electric fields efficiently convert electric into hydraulic power on the nanoscale. We also perform extensive molecular dynamics simulations of water in nanochannels and find that erroneous force truncation can give rise to spurious flow effects for static electric fields

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

Power generation by pressure-driven transport of ions in nanofluidic channels.

We report on the efficiency of electrical power generation in individual rectangular nanochannels by means of streaming currents, the pressure-driven transport of counterions in the electrical double layer. Our experimental study as a function of channel height and salt concentration reveals that the highest efficiency occurs when double layers overlap, which corresponds to nanoscale fluidic channels filled with aqueous solutions of low ionic strength. The highest efficiency of approximately 3% was found for a 75 nm high channel, the smallest channel measured. The data are well described by Poisson-Boltzmann theory with an additional electrical conductance of the Stern layer