Pressure-induced transport of DNA confined in narrow capillary channels

Pressure-induced transport of double-stranded DNA (dsDNA) from 10 base pairs (bp) to 1.9 mega base pairs (Mbp) confined in a 750-nm-radius capillary was studied using a hydrodynamic chromatographic technique and four distinct length regions (rod-like, free-coiled, constant mobility, and transition regions) were observed. The transport behavior varied closely with region changes. The rod-like region consisted of DNA shorter than the persistence length (～150 bp) of dsDNA, and these molecules behaved like polymer rods. Free-coiled region consisted of DNA from ～150 bp to ～2 kilo base pairs (kbp), and the effective hydrodynamic radius R(HD) of these DNA scaled to L(0.5) (L is the DNA length in kbp), a characteristic property of freely coiled polymers. Constant mobility region consisted of DNA longer than ～100 kbp, and these DNA had a constant hydrodynamic mobility and could not be resolved. Transition region existed between free-coiled and constant mobility regions. The transport mechanism of DNA in this region was complicated, and a general empirical equation was established to relate the mobility with DNA length. Understanding of the fundamental principles of DNA transport in narrow capillary channels will be of great interest in the development of "lab-on-chip" technologies and nongel DNA separations.     

Rheology of dilute polyelectrolyte solutions in narrow channels

The shear flow of dilute polyelectrolyte solutions bounded by either neutral or repulsive walls is modeled using a nonlinear dumbbell with conformation-dependent friction. Assuming that the configurational probability density function depends on the internal coordinates (r) and the distance of the center of mass of the molecule to the walls, coupled differential equations for the tensor moments <rr> are obtained. Coulombic repulsion between beads is considered to simulate the charge repulsion between ionized sites distributed along the backbone of a real polyelectrolyte. The repulsive interaction between the polyelectrolyte molecule and the charged walls is that of the DLVO model and the molecule is considered to be a charged sphere. Numerical solutions for the components of the tensor <rr> are worked out with the preaverage approach, and only when neutral walls considered are exact solutions obtained. Viscosity results show that in the limit of very wide channels, the corresponding viscosity in the bulk is obtained. The wall repulsion on the charged molecules produces migration of molecules towards the center of the channel resulting in a depleted layer with lower viscosity next to the walls. The calculated slip phenomenon using the method employed by Grisafi and Brunn is dependent on the beads repulsion and the shear rate. The slip velocity obtained with the Mooney method shows similarities with available experimental results for polyelectrolyte solutions. Birefringence calculations are performed in narrow and wide channels for different bead repulsions, with interesting results for both flexible and rigid molecules. Received: 26 September 1998 Accepted in revised form: 11 March 1999     

Quasi-static liquid-air drainage in narrow channels with variations in the gap

This paper studies the shape of an air bubble quasi-statically flowing in the longitudinal direction of narrow channels. Two bottom topographies are treated, i.e., linear and quadratic variations of the gap along the transverse direction. This work analyses the main characteristics of the gas-liquid interface with respect to the wedge aspect ratio. From the convergence of asymptotic, numerical and experimental analyses, we found simple dependences for the finger width and total curvature as a function of channel aspect ratio. These results provide simple and general expressions for the pressure drop needed to overcome capillary forces and push the air finger inside the channel.     

Quantifying barriers to monovalent anion transport in narrow non-polar pores

The transport of anionic drinking water contaminants (fluoride, chloride, nitrate and nitrite) through narrow pores ranging in effective radius from 2.5 to 6.5 ? was systematically evaluated using molecular dynamics simulations to elucidate the magnitude and origin of energetic barriers encountered in nanofiltration. Free energy profiles for ion transport through the pores show that energy barriers depend on pore size and ion properties and that there are three key regimes that affect transport. The first is where the ion can fit in the pore with its full inner hydration shell, the second is where the pore size is between the bare ion and hydrated radius, and the third is where the ion size approaches that of the pore. Energy barriers in the first regime are relatively small and due to rearrangement of the inner hydration shell and/or displacement of further hydration shells. Energy barriers in the second regime are due to partial dehydration and are larger than barriers seen in the first regime. In the third regime, the pore becomes too small for bare ions to fit regardless of hydration and thus energy barriers are very high. In the second regime where partial dehydration controls transport, the trend in the slopes of the change in energy barrier with pore size corresponds to the hydration strength of the anions.     

Scaling of electrokinetic transport in nanometer channels

Electrokinetic transport is a popular transport mechanism used in nanofluidic systems, and understanding its scaling behavior is important for the design and optimization of nanofluidic devices. In this article, we report on the scaling of electroosmotic flow and ionic conductivity in positively charged slit nanochannels by using continuum and atomistic simulations. The effects of confinement and surface charge are discussed in detail. In particular, we found that the viscosity of the interfacial water increases substantially as the surface charge density increases and the electrophoretic mobility of the interfacial ions decreases. We show that such effects can influence the scaling of the electrokinetic transport in confined nanochannels significantly.     

Luminescence and electrification in a flow of dielectric liquids through narrow channels

Blue-violet luminescence was observed in a mineral oil, which appeared under hydrodynamic cavitation conditions in a channel orifice 1 mm in diameter in a transparent throttling device at inlet pressures higher than 2 MPa. The appearance of electric pulses when a dielectric liquid flew through a thin channel orifice was observed much earlier than luminescence arose. A device for continuously scanning electric potential along a flow without disturbing it was developed. According to the oscillograms obtained, the electric signal was high-frequency, could not be synchronized, and its separate peaks reached 1000 mV. Light emission flux decreased as the temperature of the liquid increased to 30–35°C and inlet pressure grew. The appearance of luminescence and its intensity depended on the sharpness of the entrance edge of the throttle. Studies of hydrodynamic luminescence revealed hysteresis of light emission. A mechanism of localized light emission based on an important role played by electrokinetic phenomena was suggested.     

Modeling of electrokinetic transport in silica nanofluidic channels

We present a theoretical and numerical modeling study of the multiphysicochemical process in electrokinetic transport in silica nanochannels. The electrochemical boundary condition is solved by considering both the chemical equilibrium on solid-liquid interfaces and the salt concentration enrichment caused by the double layer interaction. The transport behavior is modeled numerically by solving the governing equations using the lattice Poisson-Boltzmann method. The framework is validated by good agreements with the experimental data for all range of ionic concentrations. The modeling results suggest that when the double layers interact, the bulk salt concentration enrichment results in the saturation of conductances for low ionic concentrations. Both the streaming conductance and the electrical conductance are enhanced by the double layer interaction, and such enhancements diminish when the channel size is larger than 10 times of the Debye length. The streaming conductance increases with pH almost linearly when pH < 8, while the electrical conductance increases with pH exponentially.     

Molecular arrangements and conformations of liquid unbranched alkanes in narrow slits

Realistic, atomistic models of liquid tridecane in broad slits (>3 nm) and in narrow slits of thickness 1,2 nm and 1,0 nm have been obtained using the Monte Carlo technique. The setup of the models is such that the molecules in the slits are in equilibrium with the bulk liquid. The surfaces of the plates are modelled as two-dimensional arrays of hexagonally packed units having the same size and interaction parameters of a methylene group. The regions adjacent to the plates in slits with thickness > 3 nm are characterized by a well defined tendency to form partially ordered layer structures, while molecules at a distance from the plates larger than 1,5 nm are unperturbed. The simultaneous presence of two plates increases the tendency to form layer structures when their distance is 1,2 nm, while this tendency is almost totally destroyed when the slit is squeezed down to a thickness of 1,0 nm. This is also associated with a 10% decrease of the density in the latter slit.     

The special features of molecular transport in nanosized channels

The molecular theory of the transport of pure substances and mixtures of molecules of different shapes in narrow slit-like pores, in which the potential of surface forces creates a strongly anisotropic distribution of molecules across pores and thereby makes the hydrodynamics equation inapplicable, is considered. The new microhydrodynamic approach is based on the lattice gas model, which takes into account the intrinsic volume of molecules and intermolecular interactions in the quasi-chemical approximation. Self-consistent calculations of dissipative coefficients taking nonlocal fluid properties into account were performed on the basis of the transition state model including information about equilibrium adsorbate distribution. Changes in fluid concentrations from the gaseous to liquid state and a broad temperature range, including the critical region, are analyzed. This allows vapor, liquid, and vapor-liquid fluid flows to be considered in the presence of capillary condensation. An increase in the size of pores transforms the equations of the theory into hydrodynamic transfer equations for gas or liquid flows, while preserving the relation of transfer coefficients to intermolecular potentials. The use of microhydrodynamic approach equations in numerical calculations and the possibility of applying this approach are discussed.     

Communication: Driven Brownian transport in eccentric septate channels

In eccentric septate channels the pores connecting adjacent compartments are shifted off-axis, either periodically or randomly, so that straight trajectories parallel to the axis are not allowed. Driven transport of a Brownian particle in such a channel is characterized by a strong suppression of the current and its dispersion. For large driving forces, both quantities approach an asymptotic value, which can be analytically approximated in terms of the stationary distribution of the particle exit times out of a single channel compartment.     

Parametrical studies of electroosmotic transport characteristics in submicrometer channels

Spatially two-dimensional nonequilibrium mathematical model describing electroosmotic flow through a submicrometer channel with an electric charge fixed on the channel walls is presented. This system is governed by the hydrodynamic, electrostatic, and mass transport phenomena. The model is based on the coupled mass balances, Poisson, Navier-Stokes, and Nernst-Planck equations. Nonslip boundary conditions are employed. The effect of an imposed electric field on the system behavior is studied by means of a numerical analysis of the model equations. We have obtained the following findings. If the channel width is comparable to the thickness of the electric double layer, the system behaves as an ion-exchange membrane and the dependence of the electric current passing through the channel on the applied voltage is strongly nonlinear. In the case of negatively (positively) charged walls, a narrow region of very low conductivity (so-called ionic gate) is formed in the free electrolyte near the channel entry facing the anode (cathode) side. For a wide channel, the electric current is proportional to the applied voltage and the velocity of electrokinetic flow is linearly proportional to the electric field strength. Complex hydrodynamics (eddy formation and existence of ionic gates) is the most interesting characteristics of the studied system. Hence, current-voltage and velocity-voltage curves and the corresponding spatial distributions of the model variables at selected points are studied and described in detail.     

Dark channels in resonant tunneling transport through artificial atoms

We investigate sequential tunneling through a multilevel quantum dot confining multiple electrons in the regime where several channels are available for transport within the bias window. By analyzing solutions to the master equations of the reduced density matrix, we give general conditions on when the presence of a second transport channel in the bias window quenches transport through the quantum dot. These conditions are in terms of distinct tunneling anisotropies which may aid in explaining the occurrence of negative differential conductance in quantum dots in the nonlinear regime.     

Construction of biomimetic proton transport channels in metal-organic framework

Construction of proton transport channels in metal-organic frameworks(MOFs) with simple synthesis processes, high proton conductivities and good performance stabilities has been of great interest for proton exchange membrane fuel cell(PEMFC). Herein, we mimic the proton transport behavior of amino acid residues in bacteriorhodopsin, select UiO-66-COOH as the host, glycine and aspartic acid as the functional guest molecules, and then functionalize the MOF framework with amino acids to obtain biom...     

Concentration dependences of the transport coefficients of rod-like molecules in narrow slit-shaped pores

The concentration dependences of the label transport and shear viscosity coefficients for rod-like molecules in slit-shaped pores were studied. The calculations were carried out using the lattice gas model, which describes a broad range of fluid concentrations (from the gaseous to the liquid state) and temperatures (including the critical region). In the calculation of the local distributions of mixture components in the equilibrium states, lateral interactions were taken into account. The translational and rotational motions of molecules were described in terms of the transition state theory for nonideal reaction systems, which took into account the influence of neighboring molecules on the height of the activation barrier. The model equations reflect the pronounced anisotropy of the distribution of system components along the normal to the pore wall surface and ordering effects of molecules along various directions. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1485–1494, September, 2006.     

The mechanism of the appearance of luminescence and electrification in liquid flows through narrow channels

The mechanism of the effects observed in hydrodynamic unit throttles was studied. These effects included luminescence in the visible range localized in a microscopic toroidal volume and electric pulses when a dielectric liquid flew through a narrow passage orifice. Equations for charging and conduction currents were obtained. The stationary electric charge, potential, and field strength on the internal surface of a passage orifice were calculated. It was shown theoretically that the appearance of luminescence most probably occurred in electrical breakdowns in cavitation bubbles in the initial flow section inside the passage orifice. Electric charge formed not only during hydrodynamic cavitation but also in a laminar throttle in the absence of cavitation in the liquid; the electrokinetic mechanism applied to this phenomenon too. It was shown experimentally that electric charges appeared not only in plastic but also in metallic throttles. The suggested mechanism of light emission and electric charge appearance was in agreement with the experimental results.     

Molecular dynamics simulations of polymer transport in nanocomposites

Molecular dynamics simulations on the Kremer-Grest bead-spring model of polymer melts are used to study the effect of spherical nanoparticles on chain diffusion. We find that chain diffusivity is enhanced relative to its bulk value when polymer-particle interactions are repulsive and is reduced when polymer-particle interactions are strongly attractive. In both cases chain diffusivity assumes its bulk value when the chain center of mass is about one radius of gyration R(g) away from the particle surface. This behavior echoes the behavior of polymer melts confined between two flat surfaces, except in the limit of severe confinement where the surface influence on polymer mobility is more pronounced for flat surfaces. A particularly interesting fact is that, even though chain motion is strongly speeded up in the presence of repulsive boundaries, this effect can be reversed by pinning one isolated monomer onto the surface. This result strongly stresses the importance of properly specifying boundary conditions when the near surface dynamics of chains are studied.     

Molecular transfer and transport in noncovalent microcontact printing

Microcontact printing is commonly used to create patterned films of molecules covalently bonded to substrates (e.g., thiols on gold). Here we describe microcontact printing of several types of noncovalently bonding molecules on mica. Due to the weaker interaction of the molecules with the substrate, environmental factors such as temperature and relative humidity play an important role. The vapor pressure of the inks also had a large impact on the fidelity of the stamped patterns. Fingering instabilities were observed for monolayers of octadecanol, docosanol, stearylamine, and stearic acid stamped at moderate relative humidity. The fidelity of the stamped pattern generally increased with the headgroup-surface interaction strength. These stamped monolayer films shed light on molecular transfer and two-dimensional spreading mechanisms.     

Molecular transport in nanopores: a theoretical perspective

Molecular transport in nanopores plays a central role in many emerging nanotechnologies for gas separation and storage, as well as in nanofluidics. Theories of the transport provide an understanding of the mechanisms that influence the transport and their interplay, and can lead to tractable models that can be used to advance these nanotechnologies through process analysis and optimisation. We review some of the most influential theories of fluid transport in small pores and confined spaces. Starting from the century old Knudsen formulation, the dusty gas model and several other related approaches that share a common point of departure in the Maxwell-Stefan diffusion equations are discussed. In particular, the conceptual basis of the models and the validity of the assumptions and simplifications necessary to obtain their final results are analysed. It is shown that the effect of adsorption is frequently either neglected, or treated on an ad hoc basis, such as through the division of the pore flux into gas-phase and surface diffusion contributions. Furthermore, while it is commonplace to assume that cross-sectional pressure is uniform, it is demonstrated that this violates the Gibbs-Duhem relation and that it is the chemical potential that essentially remains constant in the cross-section, as near-equilibrium density profiles are preserved even during transport. The Dusty Gas model and Maxwell-Stefan model for surface diffusion are analysed, and their strengths and weaknesses discussed, illustrating the use of conflicting choices of frames of reference in the former case, and the importance of assigning appropriate values for the binary diffusivity in the latter case. The oscillator model, developed in this laboratory, which is exact in the low density limit under diffuse reflection conditions, is shown to represent an advance on the classical Knudsen formula, although the latter frequently appears as a fundamental part of many transport models. The distributed friction model, also developed in this laboratory for the study of multi-component transport at any Knudsen number is discussed and compared with previous approaches. Finally, the outlook for theory and future research needs are discussed.     

Molecular identification of Ca2+ channels in human sperm

The acrosome reaction is a Ca(2+)-dependent exocytotic process that is a prerequisite step for fertilization. External calcium entry through voltage-activated Ca(2+) channels is known to be essential in inducing the acrosome reaction of mammalian spermatozoa. Due to their complex geometry, however, electrophysiological identification of sperm Ca(2+) channels has been limited. Here we identified Ca(2+) channel mRNAs expressed in motile human sperm using RT-PCR and their levels were compared using RNase protection assays. L-type, non- L-type, and T-type Ca(2+) channel mRNAs were detected by RT-PCR using degenerate primers. Cloning and sequencing of the PCR products revealed alpha1B, alpha1C, alpha1E, alpha1G, and alpha1H sequences. RT-PCR using specific primers repeatedly detected alpha1B, alpha1C, alpha1E, alpha1G, and alpha1H mRNAs, and additionally alpha1I mRNA. But alpha1A and alpha1D messages were not detected. Relative expression levels of the detected Ca(2+) channel subtypes were compared by RNase protection assays. The abundance of detected mRNA messages was in the following order: alpha1H alpha1G alpha1E alpha1B alpha1C alpha1I. These findings indicated that human motile sperm express multiple voltage-activated Ca(2+) channel RNAs among which T-type and non-L-type channel messages are likely to be predominantly expressed. Based on their relative expression levels, we propose that not only T-type but also non-L-type calcium channels may be major gates for the external calcium influx, required for the acrosome reaction.