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The variational implicit-solvent model (VISM) is an efficient approach to biomolecular interactions, where electrostatic interactions are crucial. The total VISM free energy of a dielectric boundary (i.e. solute–solvent interface) consists of the interfacial energy, solute–solvent interaction energy and dielectric electrostatic energy. The last part is the maximum value of the classical and concave Poisson–Boltzmann (PB) energy functional of electrostatic potentials, with the maximizer being the equilibrium electrostatic potential governed by the PB equation. For the consistency of energy minimization and computational stability, here we propose alternatively to minimize the convex Legendre-transformed Poisson–Boltzmann (LTPB) electrostatic energy functional of all dielectric displacements constrained by Gauss' Law in the solute region. Both integrable and discrete solute charge densities are treated, and the duality of the LTPB and PB functionals is established. A penalty method is designed for the constrained minimization of the LTPB functional. In application to biomolecular interactions, we minimize the total VISM free energy iteratively, while in each step of such iteration, minimize the LTPB energy. Convergence of such a min–min algorithm is shown. Our numerical results on the solvation of a single ion indicate that the LTPB performs better than the PB formulation, providing possibilities for efficient biomolecular simulations. [ABSTRACT FROM AUTHOR]

A large number of experimental studies have demonstrated that globular proteins can be absorbed from the solution by both polycationic and polyanionic brushes when the net charge of protein globules is of the same or of the opposite sign with respect to that of brush-forming polyelectrolyte chains. Here, we overview the results of experimental studies on interactions between globular proteins and polycationic or polyanionic brushes, and present a self-consistent field theoretical model that allows us to account for the asymmetry of interactions of protein-like nanocolloid particles comprising weak (pH-sensitive) cationic and anionic groups with a positively or negatively charged polyelectrolyte brush. The position-dependent insertion free energy and the net charge of the particle are calculated. The theoretical model predicts that if the numbers of cationic and anionic ionizable groups of the protein are approximately equal, then the interaction patterns for both cationic and anionic brushes at equal offset on the "wrong side" from the isoelectric point (IEP), i.e., when the particle and the brush charge are of the same sign, are similar. An essential asymmetry in interactions of particles with polycationic and polyanionic brushes is predicted when fractions of cationic and anionic groups differ significantly. That is, at a pH above IEP, the anionic brush better absorbs negatively charged particles with a larger fraction of ionizable cationic groups and vice versa. [ABSTRACT FROM AUTHOR]

We develop a comprehensive continuum model capable of treating both electrostatic and structural interactions in liquid dielectrics. Starting from a two-order parameter description in terms of charge density and polarization, we derive a field-theoretic model generalizing previous theories. Our theory explicitly includes electrostatic and structural interactions in the bulk of the liquid and allows for polarization charges within a Drude model. In particular we provide a detailed description of the boundary conditions which include the charge regulation mechanism and surface polarization, which is explained both in general terms and analyzed for an exemplary model case. Future applications of our theory to predict and validate experimental results are outlined. [ABSTRACT FROM AUTHOR]

We construct a mean-field variational model to study how the dependence of dielectric coefficient (i.e., relative permittivity) on local ionic concentrations affects the electrostatic interaction in an ionic solution near a charged surface. The electrostatic free-energy functional of ionic concentrations, which is the key object in our model, consists mainly of the electrostatic potential energy and the ionic ideal-gas entropy. The electrostatic potential is determined by Poisson's equation in which the dielectric coefficient depends on the sum of concentrations of individual ionic species. This dependence is assumed to be qualitatively the same as that on the salt concentration for which experimental data are available and analytical forms can be obtained by the data fitting. We derive the first and second variations of the free-energy functional, obtain the generalized Boltzmann distributions, and show that the free-energy functional is in general nonconvex. To validate our mathematical analysis, we numerically minimize our electrostatic free-energy functional for a radially symmetric charged system. Our extensive computations reveal several features that are significantly different from a system modeled with a dielectric coefficient independent of ionic concentration. These include the non-monotonicity of ionic concentrations, the ionic depletion near a charged surface that has been previously predicted by a one-dimensional model, and the enhancement of such depletion due to the increase of surface charges or bulk ionic concentrations.

A phase-field free-energy functional for the solvation of charged molecules (e.g., proteins) in aqueous solvent (i.e., water or salted water) is constructed. The functional consists of the solute volumetric and solute-solvent interfacial energies, the solute-solvent van der Waals interaction energy, and the continuum electrostatic free energy described by the Poisson-Boltzmann theory. All these are expressed in terms of phase fields that, for low free-energy conformations, are close to one value in the solute phase and another in the solvent phase. A key property of the model is that the phase-field interpolation of dielectric coefficient has the vanishing derivative at both solute and solvent phases. The first variation of such an effective free-energy functional is derived. Matched asymptotic analysis is carried out for the resulting relaxation dynamics of the diffused solute-solvent interface. It is shown that the sharp-interface limit is exactly the variational implicit-solvent model that has successfully captured capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states of underlying biomolecular systems as found in experiment and molecular dynamics simulations. Our phase-field approach and analysis can be used to possibly couple the description of interfacial fluctuations for efficient numerical computations of biomolecular interactions.

The electrostatic screening phenomena on a macroion in 1:1 concentrated electrolytes are investigated in an underscreening regime. Using the primitive model, we obtained the density profile of microions near a macroion through Monte Carlo simulations. Beyond a critical electrolyte concentration, the density of both coions and counterions is at a maximum near a macroion. Consequently, the behaviour of microions in concentrated electrolyte solutions cannot be explained by the traditional picture of electric double layers. Additionally, we investigated the dependence of this phenomenon on the size of microions. These results shed light on the anomalous microion distribution of electrolytes due to the ion–ion correlations in the underscreening regime. [ABSTRACT FROM AUTHOR]

Charge descriptors of aquatic nanoparticles (NPs) are evaluated from proton titration curves measured at different salt concentrations and routinely analysed by the Non-Ideal Competitive Adsorption-Donnan (NICAD) model. This model, however, suffers from approximations regarding particle electrostatics, which may bias particle charge estimation. Implementation of Poisson-Boltzmann (PB) theory within consistent treatment of NPs protolytic data is expected to address NICAD shortcomings. An alternative to NICAD is elaborated on the basis of nonlinearized PB equation for soft particle electrostatics to properly unravel the electrostatic and chemical components of proton binding to NPs. A numerical package is developed for automated analysis of proton titration curves and proton affinity spectra at different salt concentrations. The performance of the method is illustrated for humic matter nanoparticles with different charge and size, and compared to that of NICAD. Unlike NICAD, PB-based treatment successfully reproduces particle charge dependence on pH for practical salt concentrations from the thin to thick electric double layer limit. Donnan representation in NICAD leads to moderate to dramatic misestimations of proton affinity and binding heterogeneity depending on particle size to Debye layer thickness ratio. Interpretation of NPs protolytic properties with PB theory further avoids adjustment of the 'particle Donnan volume' empirically introduced in NICAD. [ABSTRACT FROM AUTHOR]

The electrostatic properties of the ionic cloud, or electrical double layer, neutralizing a charged electrode are relevant to improve the storage of electrical energy and the efficiency of supercapacitors and/or batteries using coulombic fluids. In this work, we study the microscopic profiles of charged particles, integrated surface charge density, and the mean electrostatic potential associated to a pair of infinite parallel plates uncharged or, else, with opposite charge, in the presence of a salt-free aqueous solution constituted by big positive macroions and small anions, which interact via an explicit electrostatic coulombic potential and are dissolved in an implicit solvent. The particle profiles and the integrated surface charge density associated to Monte Carlo simulations and integral equations theory display an oscillatory or non-monotonic behaviour producing the phenomena of charge inversion and charge reversal. These phenomena are not predicted by the non-linear Poisson-Boltzmann equation, which highlights the importance of ion correlations and ionic volume excluded effects. The phenomenon of surface charge amplification is observed near the point of zero charge, which is yielded by the particle size-asymmetry. For a fixed concentration of macroions, a monotonic increase of the mean electrostatic potential difference between the charged parallel plates is predicted by simulations and theories as a function of the electrodes' charge. For a fixed surface charge density, the capacitance of the parallel plates capacitor increases when the ionic strength of the macroion's solution increases. A concavity inversion and an augment of the differential capacitance is also observed for an electrode near the point of zero charge as function of the macroion's concentration. • Simulations and theory are used to model an electrical double layer supercapacitor. • Aqueous solutions of multivalent macroions increase significantly the capacitance. • Charge inversion and charge reversal are observed at high macroions' concentrations. • Surface charge amplification is observed near the point of zero charge. • A concavity inversion of the differential capacitance is seen at high concentrations. [ABSTRACT FROM AUTHOR]

Electric potential distribution in nanoscale electroosmosis has been investigated using the nonequilibrium molecular dynamics ( NEMD), whose results are compared with the continuum based Poisson-Boltzmann (PB) theory. If the bin size of the MD simulation is no smaller than a molecular diameter and the focusing region is limited to the diffusion layer, the ionic density profiles on the bins of the MD results agree well with the predictions based on the PB theory for low and moderate bulk ionic concentrations. The PB equation breaks down at high bulk ionic concentrations, which is also consistent with the macroscopic description.

In this paper, we consider the Poisson‐Boltzmann theory to model the electrostatic potential of a bulk electrolyte containing a single planar charged surface. In the case of a constant surface charge density, we address the problem as a ODE system by using the stability theory for autonomous dynamical systems. By stating that the surface charge density and the surface potential are non‐linearly related through the Grahame equation, we give a description of the stable manifold of the system. To solve the Grahame equation and obtain an approximation for the stable manifold, we propose a smoothing collocation method based on cubic splines, including implementation details and numerical results. [ABSTRACT FROM AUTHOR]

In the study of colloidal, biological and electrochemical systems, it is customary to treat surfaces, macromolecules and electrodes as homogeneously charged. This simplified approach is proven successful in most cases, but fails to describe a wide range of heterogeneously charged surfaces commonly used in experiments. For example, recent experiments have revealed a long-range attraction between overall neutral surfaces, locally charged in a mosaic-like structure of positively and negatively charged domains (“patches”). Here, we review experimental and theoretical studies addressing the stability of heterogeneously charged surfaces, their effect on ionic profiles in solution, and the interaction between two such surfaces. We focus on electrostatics, and highlight the important new physical parameters appearing in the heterogeneous case, such as the largest patch size and inter-surface charge correlations. [ABSTRACT FROM AUTHOR]

Nucleic acids are biopolymers that carry genetic information and are also involved in various gene regulation functions such as gene silencing and protein translation. Because of their negatively charged backbones, nucleic acids are polyelectrolytes. To adequately understand nucleic acid folding and function, we need to properly describe its i) polymer/polyelectrolyte properties and ii) associating ion atmosphere. While various theories and simulation models have been developed to describe nucleic acids and the ions around them, many of these theories/simulations have not been well evaluated due to complexities in comparison with experiment. In this review, I discuss some recent experiments that have been strategically designed for straightforward comparison with theories and simulation models. Such data serve as excellent benchmarks to identify limitations in prevailing theories and simulation parameters. [ABSTRACT FROM AUTHOR]

Over recent years, the supposedly universal Hofmeister series has been replaced by a diverse spectrum of direct, partially altered and reversed series. This review aims to provide a detailed understanding of the full spectrum by combining results from molecular dynamics simulations, Poisson–Boltzmann theory and AFM experiments. Primary insight into the origin of the Hofmeister series and its reversal is gained from simulation-derived ion–surface interaction potentials at surfaces containing non-polar, polar and charged functional groups for halide anions and alkali cations. In a second step, the detailed microscopic interactions of ions, water and functional surface groups are incorporated into Poisson–Boltzmann theory. This allows us to quantify ion-specific binding affinities to surface groups of varying polarity and charge, and to provide a connection to the experimentally measured long-ranged electrostatic forces that stabilize colloids, proteins and other particles against precipitation. Based on the stabilizing efficiency, the direct Hofmeister series is obtained for negatively charged hydrophobic surfaces. Hofmeister series reversal is induced by changing the sign of the surface charge from negative to positive, by changing the nature of the functional surface groups from hydrophobic to hydrophilic, by increasing the salt concentration, or by changing the pH. The resulting diverse spectrum reflects that alterations of Hofmeister series are the rule rather than the exception and originate from the variation of ion-surface interactions upon changing surface properties. [ABSTRACT FROM AUTHOR]

Electrostatic correlations and fluctuations in ionic systems can be described within an extended Poisson–Boltzmann theory using a Gaussian variational form. The resulting equations are challenging to solve because they require the solution of a high-dimensional nonlinear partial differential equation for the pair correlation function. This has limited existing studies to simple approximations or to one-dimensional geometries. In this paper we show that the numerical solution of the equations is greatly simplified by the use of selective inversion of a finite difference operator which occurs in the theory. This selective inversion preserves the sparse structure of the problem and leads to substantial savings in computer effort. In one and two dimensions further simplifications are made by using a mixture of selective inversion and Fourier techniques. With the help of numerical examples, we validate the accuracy of the numerical method and show that electrostatic correlations and fluctuations could lead to a large deviation from the classical Poisson–Boltzmann equation with the increase of the coupling parameter. [ABSTRACT FROM AUTHOR]

For the development of ultra-sensitive electrical bio/chemical sensors based on nanowire field effect transistors (FETs), the influence of the ions in the solution on the electron transport has to be understood. For this purpose we establish a simulation platform for nanowire FETs in the liquid environment by implementing the modified Poisson-Boltzmann model into Landauer transport theory. We investigate the changes of the electric potential and the transport characteristics due to the ions. The reduction of sensitivity of the sensors due to the screening effect from the electrolyte could be successfully reproduced. We also fabricated silicon nanowire Schottky-barrier FETs and our model could capture the observed reduction of the current with increasing ionic concentration. This shows that our simulation platform can be used to interpret ongoing experiments, to design nanowire FETs, and it also gives insight into controversial issues such as whether ions in the buffer solution affect the transport characteristics or not. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Abstract: To describe Donnan equilibrium at the membrane–solution interface, the simplest approach uses the classical Boltzmann equation, based on a mean-field description of ions as ideal point charges, in combination with the assumption of fully overlapped electrical double layers in the membrane pores. We test the Boltzmann equation by measurement of the equilibrium counterion and co-ion concentration in densely charged membranes equilibrated with various NaCl solutions (0.01–3M). To obtain a good fit of data it was found necessary to express the membrane charge and ion concentration per volume of aqueous solution phase in the membrane, and to include a volume-exclusion term in the Boltzmann relation. A discrepancy between theory and experiment data is found at low external NaCl concentrations. Similar deviations from the Donnan model have been reported for over half a century, but do not yet have a convincing explanation. Agreement between experiment data and theory at low external NaCl concentrations is obtained when we model the desorption experiment taking into account the role of H+ and OH− ions in closing the charge balance, and postulating the presence in the membrane of a tiny amount of fixed groups with a charge opposite to overall fixed membrane charge. [Copyright &y& Elsevier]

Abstract: In aqueous solutions, dissolved ions interact strongly with the surrounding water and surfaces, thereby modifying solution properties in an ion-specific manner. These ion-hydration interactions can be accounted for theoretically on a mean-field level by including phenomenological terms in the free energy that correspond to the most dominant ion-specific interactions. Minimizing this free energy leads to modified Poisson-Boltzmann equations with appropriate boundary conditions. Here, we review how this strategy has been used to predict some of the ways ion-specific effects can modify the forces acting within and between charged interfaces immersed in salt solutions. [Copyright &y& Elsevier]

Abstract: Polyelectrolyte gels are intelligent materials that undergo large reversible volume changes for a range of environmental stimuli. Although the strength of electrostatic interactions have a strong influence on the gel response, these interactions are not properly accounted in the classical mean-field theories that assume a homogeneous charge-neutral gel. Using Poisson–Boltzmann theory and theoretically informed coarse-grained simulations, we emphasize the importance of charge inhomogeneities and the associated Coulomb interactions in determining the response of gels. Our analysis reveals that nanometer-sized gels, collapsed gels, and gels in media with low salinity or high dielectric constant, have large regions of excess charge. We also observe that the addition of salt can induce collapse in swollen gels by compensating the polymer charge. [Copyright &y& Elsevier]

Abstract: These lecture notes describe ionic screening of liquid-immersed charged surfaces within the linear and the nonlinear Poisson–Boltzmann theory. The classic Gouy–Chapman description of a single charged planar surface is extensively described, as well as its linearised version and the connection with charge renormalisation. We also consider effective ion-mediated electrostatic interactions between suspended colloidal particles in some detail, and in addition we study Debye–Hückel theory for bulk electrolytes. We argue that relatively straightforward extensions of these basic notions can be used to describe systems of recent interest, e.g. patchy surfaces, oil–water interfaces, and Pickering emulsions. A number of references to recent literature is included. [ABSTRACT FROM AUTHOR]

Abstract: The Poisson–Boltzmann (PB) theory is extensively used to gain insight on charged colloids and biological systems as well as to elucidate fundamental properties of intermolecular forces. Many works have been devoted in the past to study PB-related features and to confirm them experimentally. In this work we explore the properties of inter-plate forces in terms of different boundary conditions. We treat the cases of constant surface charge, constant surface potential and mixed boundaries. The interplay between electrostatic interactions, attractive counter-ion release, and repulsive van ’t Hoff contribution is discussed separately for each case. Finally, we discuss how the crossover between attractive and repulsive interactions for constant surface charge case is influenced by the presence of multivalent counter-ions, where it is shown that the range of the attractive interaction grows with the valency. [Copyright &y& Elsevier]

The interaction between two parallel charged plates in ionic solution is a general starting point for studying colloidal complexes. An intuitive expression of the pressure exerted on the plates is usually proposed, which includes an electrostatic plus an osmotic contribution. We present here an explicit and self-consistent derivation of this formula in the only framework of the Poisson-Boltzmann (PB) theory. We also show that, depending on external constraints, the correct thermodynamic potential can differ from the usual PB free energy. For asymmetric, oppositely charged plates, the resulting expression predicts a non-trivial equilibrium position with the plates separated by a finite distance. The depth of this energy minimum is decisive for the stability of the complex. It is therefore crucial to obtain its explicit dependence on the charge densities of the plates and on the ion concentration. Analytic expressions for the position and depth of the energy minimum were derived in 1975 by Ohshima [Colloid Polym. Sci. 253, 150 (1975)] but, surprisingly, these important results seem to have been overlooked. We retrieve these expressions in a simpler formalism, more familiar to the physics community, and give a physical interpretation of the observed behavior. [ABSTRACT FROM AUTHOR]

Catalytic potential of linear polyelectrolyte solutions in presence of +2:-2 salts, as evidenced through ionic correlations in the inhomogeneous atmosphere around a polyion, is studied using Monte Carlo simulation techniques and the traditional non-linear Poisson-Boltzmann approach. The simulations are performed on the cylindrical cell model where a uniformly charged hard cylinder mimics the linear polyion caged in a cylindrical cell containing divalent counterions and co-ions. Cell (volume) average of the inter-ionic correlations, as reflected in the pair-correlation functions, is presented as function of the polyion concentration, the low-molecular electrolyte concentration, and the ion radius. The volume average of the doublet pair distribution function between counterions is found to be sensitive to variation of model parameters. The results indicate large enhancement in the reaction rate between the counterions, while a decrease in the coion-coion and the coion-counterion reaction rate is noted, all in comparison with pure electrolyte solutions. The agreement between the predictions of the Poisson-Boltzmann theory and the simulation results is merely qualitative in most instances. [ABSTRACT FROM AUTHOR]

The distribution of ions between charged cylindrical micropores modeling an adsorbing material and a bulk electrolyte was calculated. For this purpose the Grand Canonical Monte Carlo method and the method based on solution of the nonlinear Poisson-Boltzmann equation were utilized. The focus was on the effect of the solvent, characterized here merely by its dielectric constant. The Donnan exclusion coefficient and mean activity coefficient of an electrolyte confined in a microcapillary were calculated as functions of the electrolyte concentration and the dielectric constant of the solvent. The exclusion coefficient was found to decrease with increasing electrolyte concentration and with decreasing dielectric constant of the solvent. In other words, the desalination mechanism becomes very inefficient in solvents with dielectric constant lower than that of water. In comparison with Monte Carlo simulations the Poisson-Boltzmann theory was able to predict correct trends for the Donnan exclusion coefficient, but it grossly overestimated Monte Carlo results. The microscopic picture which emerged on the basis of the distributions of small ions in the microcapillary was helpful in explaining these results. [ABSTRACT FROM AUTHOR]

Electric potential distribution in nanoscale electroosmosis has been investigated using the nonequilibrium molecular dynamics (NEMD), whose results are compared with the continuum based Poisson-Boltzmann (PB) theory. If the bin size of the MD simulation is no smaller than a molecular diameter and the focusing region is limited to the diffusion layer, the ionic density profiles on the bins of the MD results agree well with the predictions based on the PB theory for low and moderate bulk ionic concentrations. The PB equation breaks down at high bulk ionic concentrations, which is also consistent with the macroscopic description. [ABSTRACT FROM AUTHOR]

Abstract: When a monolayer of negatively charged surfactant molecules is brought in contact with an aqueous solution containing mixtures of counterions of different size and valency, very large deviations from Poisson–Boltzmann theory (PBT) develop at a high surface charge, with the smaller counterion outcompeting the larger one (even if divalent) near the interface, leading to counterion segregation [V.L. Shapovalov, G. Brezesinski, J. Phys. Chem. B 110 (2006) 10032]. We use a modified PBT that empirically includes an extended Carnahan–Starling equation-of-state to describe hard-sphere interactions in electrical double layers containing ions of different size and charge. Model calculations are made for ion concentration profiles, free energies, surface pressures, and differential capacities. At high surface charge, volume interactions become important, leading to significant deviations from PBT. In contrast to PBT, at high surface charge, contributions to energy and pressure are no longer mainly entropic, but instead volume and electrostatic field effects now dominate. When the hydrated size of the divalent ion is used as an adjustable parameter, the theory is in good agreement with the experimental data. [Copyright &y& Elsevier]

Abstract: We extend the classical Gouy–Chapman model of two planar parallel interacting double layers, which is used as a first approximation to describe the force between colloidal particles, by considering the finite thickness of the colloids. The formation of two additional double layers due to this finite thickness modifies the interaction force compared to the Gouy–Chapman case, in which the colloids are semi-infinite objects. In this paper we calculate this interaction force and some other size-dependent properties using a mean-field level of description, based on the Poisson–Boltzmann (PB) equation. We show that in the case of finite-size colloids, this equation can be set in a closed form depending on the geometrical parameters and on their surface charge. The corresponding linear (Debye–Hückel) theory and the well-known results for semi-infinite colloids are recovered from this formal solution after appropriate limits are taken. We use a density functional corresponding to the PB level of description to show how in the case where the total colloidal charge is fixed, it redistributes itself on their surfaces to minimize the energy of the system depending on the aforementioned parameters. We study how this charge relaxation affects the colloidal interactions. [Copyright &y& Elsevier]

The problem of how ions influence the folding of RNA into specific tertiary structures is being addressed from both thermodynamic (by how much do different salts affect the free energy change of folding) and structural (how are ions arranged on or near an RNA and what kinds of environments do they occupy) points of view. The challenge is to link these different approaches in a theoretical framework that relates the energetics of ion-RNA interactions to the spatial distribution of ions. This review distinguishes three different kinds of ion environments that differ in the extent of direct ion-RNA contacts and the degree to which the ion hydration is perturbed, and summarizes the current understanding of the way each environment relates to the overall energetics of RNA folding. [ABSTRACT FROM AUTHOR]

Proteins, including ion channels, often are described in terms of some average structure and pictured as rigid entities immersed in a featureless solvent continuum. This simplified view, which provides for a convenient representation of the protein's overall structure, incurs the risk of deemphasizing important features underlying protein function, such as thermal fluctuations in the atom positions and the discreteness of the solvent molecules. These factors become particularly important in the case of ion movement through narrow poles, where the magnitude of the thermal fluctuations may be comparable to the ion pore atom separations, such that the strength of the ion channel interactions may vary dramatically as a function of the instantaneous con figuration of the ion and the surrounding protein and pore water. Descriptions of ion permeation through narrow pores, which employ static protein structures and a macroscopic continuum dielectric solvent, thus face fundamental difficulties, We illustrate this using simple model calculations based on the gramicidin A and KcsA potassium channels, which show that thermal atomic fluctuations lead to energy profiles that vary by tens of kcal/mol. Consequently, within the framework of a rigid pore model, ion-channel energetics is extremely sensitive to the choice of experimental structure and how the space-dependent dielectric constant is assigned. Given these observations, the significance of any description based on a rigid structure appears limited. Creating a conducting channel model from one single structure requires substantial and arbitrary engineering of the model parameters, making it difficult for such approaches to contribute to our understanding of ion permeation at a microscopic level. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations have been carried out for simple electrolyte systems to study the electrokinetically driven osmotic flow in parallel-plate channels of widths ∼10-120 nm. The results are compared with the classical theory predictions based on the solution to the Poisson-Boltzmann equation. We find that despite some of the limitations in the Poisson-Boltzmann equation, such as assumption of the Boltzmann distribution for the ions, the classical theory captures the general trend of the variations of the osmotic flow with channel width, as characterized by the mobility of the fluid in channels between ∼10 and 120 nm at moderate to low ion concentration. At moderate concentration (corresponding to relatively low surface potential), the classical theory is almost quantitative. The theory and simulation show more disagreement at low concentration, primarily caused by the high surface potential where the assumption of Boltzmann distribution becomes inaccurate. We discuss the limitations of the Poisson-Boltzmann equation as applied to the nanoscale channels. [ABSTRACT FROM AUTHOR]

A structural view of DNA association/hybridization to a target oligonucleotide molecule near a surface has been developed. Recent experiments have showed a kinetically rapid hybridization between large target DNA fragments and oligonucleotides electrostatically immobilized (untethered) to a surface. Theory and computer simulations have been used to investigate the nature of the specificity and affinity in such a system. Simulations were performed for a modified silicon dioxide surface with positively charged groups at neutral pH. The dosing of a surface with unattached oligonucleotide was simulated. The oligonucleotide was found to associate with the surface in salt water in a way that some of the bases remained stacked, and most of the bases near the surface on average pointed preferentially toward the solution, away from the surface. Use of an analytic solution to the linear Poisson-Boltzmann (PB) theory of the electric double layer interaction between DNA and a hard surface predicts tight binding in this system. The simulation thus gives a mechanism for specificity and the theory a mechanism for affinity. The geometry is such that only non-helical base pairs would be accommodated with an irregular backbone. [ABSTRACT FROM AUTHOR]