Simulations of non-neutral slab systems with long-range electrostatic interactions in two-dimensional periodic boundary conditions

Thermodynamic driving forces in contact electrification between polymeric materials

Contact electrification, or contact charging, refers to the process of static charge accumulation after rubbing, or even simple touching, of two materials. Despite its relevance in static electricity, various natural phenomena, and numerous technologies, contact charging remains poorly understood. For insulating materials, even the species of charge carrier may be unknown, and the direction of charge-transfer lacks firm molecular-level explanation. Here, we use all-atom molecular dynamics simulations to investigate whether thermodynamics can explain contact charging between insulating polymers. Based on prior work suggesting that water-ions, such as hydronium and hydroxide ions, are potential charge carriers, we predict preferred directions of charge-transfer between polymer surfaces according to the free energy of water-ions within water droplets on such surfaces. Broad agreement between our predictions and experimental triboelectric series indicate that thermodynamically driven ion-transfer likely influences contact charging of polymers. Furthermore, simulation analyses reveal how specific interactions of water and water-ions proximate to the polymer-water interface explain observed trends. This study establishes relevance of thermodynamic driving forces in contact charging of insulators with new evidence informed by molecular-level interactions. These insights have direct implications for future mechanistic studies and applications of contact charging involving polymeric materials.

Electrical Chain Rearrangement: What Happens When Polymers in Brushes Have a Charge Gradient?

Under the influence of electric fields, the chains in polyelectrolyte brushes can stretch and collapse, which changes the structure of the brush. Copolymer brushes with charged and uncharged monomers display a similar behavior. For pure polyelectrolyte and random copolymer brushes, the field-induced structure changes only the density of the brush and not its local composition, while the latter could be affected if charges are distributed inhomogeneously along the polymer backbone. Therefore, we systematically study the switching behavior of gradient polyelectrolyte brushes in electric fields for different solvent qualities, grafting densities, and charges per chain via coarse-grained molecular dynamics simulations. Similar to random copolymers and pure polyelectrolytes, these brushes show a mixed-phase transition: intermediate states between fully stretched and collapsed are characterized by a bimodal chain-end distribution. Additionally, we find that the total charge of the brush plays a key role in the critical field required for a complete transition. Finally, we find that gradient polyelectrolyte brushes are charge-enriched at the brush-solvent interface under stretched conditions and charge-depleted under collapsed conditions, allowing for control over the local composition and thus the surface charge of the brush due to the inhomogeneous charge along the grafted chains.

Computer Simulation Insight into the Adsorption and Diffusion of Polyelectrolytes on Oppositely Charged Surface

In the present work, by means of computer simulation, we studied the adsorption and diffusion of polyelectrolyte macromolecules on oppositely charged surfaces. We considered the surface coverage and the charge of the adsorbed layer depending on the ionization degree of the macromolecules and the charge of the surface and carried out a computer experiment on the polymer diffusion within the adsorbed layers, taking into account its strong dependency on the surface coverage and the macromolecular ionization degree. The different regimes were distinguished that provided maximal mobility of the polymer chains along with a high number of charged groups in the layer, which could be beneficial for the development of the functional coatings. The results were compared with those of previous experiments on the adsorption of polyelectrolyte layers that may be applied as biocidal renewable coatings that can reversibly desorb from the surface.

Electron transparent nanotubes reveal crystallization pathways in confinement

The cylindrical pores of track-etched membranes offer excellent environments for studying the effects of confinement on crystallization as the pore diameter is readily varied and the anisotropic morphologies can direct crystal orientation. However, the inability to image individual crystals in situ within the pores in this system has prevented many of the underlying mechanisms from being characterized. Here, we study the crystallization of calcium sulfate within track-etched membranes and reveal that oriented gypsum forms in 200 nm diameter pores, bassanite in 25-100 nm pores and anhydrite in 10 nm pores. The crystallization pathways are then studied by coating the membranes with an amorphous titania layer prior to mineralization to create electron transparent nanotubes that protect fragile precursor materials. By visualizing the evolutionary pathways of the crystals within the pores we show that the product single crystals derive from multiple nucleation events and that orientation is determined at early reaction times. Finally, the transformation of bassanite to gypsum within the membrane pores is studied using experiment and potential mean force calculations and is shown to proceed by localized dissolution/reprecipitation. This work provides insight into the effects of confinement on crystallization processes, which is relevant to mineral formation in many real-world environments.

Electrostatic Fields Stimulate Absorption of Small Neutral Molecules in Gradient Polyelectrolyte Brushes

Molecules can partition from a solution into a polymer coating, leading to a local enrichment. If one can control this enrichment via external stimuli, one can implement such coatings in novel separation technologies. Unfortunately, these coatings are often resource intensive as they require stimuli in the form changes of bulk solvent conditions such as acidity, temperature, or ionic strength. Electrically driven separation technology may provide an appealing alternative, as this will allow local, surface-bound stimuli instead of system-wide bulk stimuli to induce responsiveness. Therefore, we investigate via coarse grained molecular dynamics simulations the possibility of using coatings with charged moieties, specifically gradient polyelectrolyte brushes, to control the enrichment of the neutral target molecules near the surface with applied electric fields. We find that targets which interact more strongly with the brush show both more absorption and a larger modulation by electric fields. For the strongest interactions evaluated in this work, we obtained absorption changes of over 300 % between the collapsed and extended state of the coating.

Polymer brushes for friction control: Contributions of molecular simulations

When polymer chains are grafted to solid surfaces at sufficiently high density, they form brushes that can modify the surface properties. In particular, polymer brushes are increasingly being used to reduce friction in water-lubricated systems close to the very low levels found in natural systems, such as synovial joints. New types of polymer brush are continually being developed to improve with lower friction and adhesion, as well as higher load-bearing capacities. To complement experimental studies, molecular simulations are increasingly being used to help to understand how polymer brushes reduce friction. In this paper, we review how molecular simulations of polymer brush friction have progressed from very simple coarse-grained models toward more detailed models that can capture the effects of brush topology and chemistry as well as electrostatic interactions for polyelectrolyte brushes. We pay particular attention to studies that have attempted to match experimental friction data of polymer brush bilayers to results obtained using molecular simulations. We also critically look at the remaining challenges and key limitations to overcome and propose future modifications that could potentially improve agreement with experimental studies, thus enabling molecular simulations to be used predictively to modify the brush structure for optimal friction reduction.

Software for Evaluating Long-Range Electrostatic Interactions Based on the Ewald Summation and Its Application to Electrochemical Energy Storage Materials

Electrochemical characteristics such as open-circuit voltage and ionic conductivity of electrochemical energy storage materials are easily affected, typically negatively, by mobile ion/vacancy ordering. Ordered phases can be identified based on the lattice gas model and electrostatic energy screening. However, the evaluation of long-range electrostatic energy is not straightforward because of the conditional convergence. The Ewald method decomposes the electrostatic energy into a real space part and a reciprocal space part, achieving a fast convergence in each. Due to its high computational efficiency, Ewald-based techniques are widely used in analyzing characteristics of electrochemical energy storage materials. In this work, we present software not only integrating Ewald techniques for two-dimensional and three-dimensional periodic systems but also combining the Ewald method with the lattice matching algorithm and bond valence. It is aimed to become a useful tool for screening stable structures and interfaces and identifying the ionic transport channels of cation conductors.

A General Method for Calculating Solid/Liquid Interfacial Free Energies from Atomistic Simulations: Application to CaSO4.xH2O

We present a general method for computing interfacial free energies from atomistic simulations, which is particularly suitable for solid/liquid interfaces. Our method uses an Einstein crystal as a universal reference state and is more flexible than previous approaches. Surfaces with dipoles, complex reconstructions, and partially dissolved species are all easily accommodated within the framework. It may also be extended to calculating the relative free energies of different phases and other types of defect. We have applied our method to interfaces of bassanite and gypsum with water and obtained interfacial free energies of the order of 0.15 J/m2, of which approximately 50 % is due to entropic contributions. Our calculations of the interfacial free energy of NaCl with water obtained a value of 0.13 J/m2 of which only 19 % is from entropic contributions. We have also predicted equilibrium morphologies for bassanite and gypsum that compare well with experiments and previous calculations.

Fully periodic, computationally efficient constant potential molecular dynamics simulations of ionic liquid supercapacitors

Molecular dynamics (MD) simulations of complex electrochemical systems, such as ionic liquid supercapacitors, are increasingly including the constant potential method (CPM) to model conductive electrodes at a specified potential difference, but the inclusion of CPM can be computationally expensive. We demonstrate the computational savings available in CPM MD simulations of ionic liquid supercapacitors when the usual non-periodic slab geometry is replaced with fully periodic boundary conditions. We show how a doubled cell approach, previously used in non-CPM MD simulations of charged interfaces, can be used to enable fully periodic CPM MD simulations. Using either a doubled cell approach or a finite field approach previously reported by others, fully periodic CPM MD simulations produce comparable results to the traditional slab geometry simulations with a nearly double speedup in computational time. Indeed, these savings can offset the additional cost of the CPM algorithm, resulting in periodic CPM MD simulations that are computationally competitive with the non-periodic, fixed charge equivalent simulations for the ionic liquid supercapacitors studied here.

Widom insertion method in simulations with Ewald summation

We discuss the application of the Widom insertion method for calculation of the chemical potential of individual ions in computer simulations with Ewald summation. Two approaches are considered. In the first approach, an individual ion is inserted into a periodically replicated overall charge neutral system representing an electrolyte solution. In the second approach, an inserted ion is also periodically replicated, leading to the violation of the overall charge neutrality. This requires the introduction of an additional neutralizing background. We find that the second approach leads to a much better agreement with the results of grand canonical Monte Carlo simulation for the total chemical potential of a neutral ionic cluster.

Capacitance and Structure of Electric Double Layers: Comparing Brownian Dynamics and Classical Density Functional Theory

We present a study of the structure and differential capacitance of electric double layers of aqueous electrolytes. We consider electric double layer capacitors (EDLC) composed of spherical cations and anions in a dielectric continuum confined between a planar cathode and anode. The model system includes steric as well as Coulombic ion-ion and ion-electrode interactions. We compare results of computationally expensive, but “exact” , Brownian Dynamics (BD) simulations with approximate, but cheap, calculations based on classical Density Functional Theory (DFT). Excellent overall agreement is found for a large set of system parameters, including variations in concentration, ionic size- and valency-asymmetries, applied voltages and electrode separation, provided the differences between the canonical ensemble of the BD simulations and the grand-canonical ensemble of DFT are properly taken into account. In particular, a careful distinction is made between the differential capacitance $$C_N$$ C N at fixed number of ions and $$C_\mu $$ C μ at fixed ionic chemical potential. Furthermore, we derive and exploit their thermodynamic relations. In the future these relations will also be useful for comparing and contrasting experimental data with theories for supercapactitors and other systems. The quantitative agreement between simulation and theory indicates that the presented DFT is capable of accounting accurately for coupled Coulombic and packing effects. Hence it is a promising candidate to cheaply study room temperature ionic liquids at much lower dielectric constants than that of water.

A fast spectral method for electrostatics in doubly periodic slit channels

We develop a fast method for computing the electrostatic energy and forces for a collection of charges in doubly periodic slabs with jumps in the dielectric permittivity at the slab boundaries. Our method achieves spectral accuracy by using Ewald splitting to replace the original Poisson equation for nearly singular sources with a smooth far-field Poisson equation, combined with a localized near-field correction. Unlike existing spectral Ewald methods, which make use of the Fourier transform in the aperiodic direction, we recast the problem as a two-point boundary value problem in the aperiodic direction for each transverse Fourier mode for which exact analytic boundary conditions are available. We solve each of these boundary value problems using a fast, well-conditioned Chebyshev method. In the presence of dielectric jumps, combining Ewald splitting with the classical method of images results in smoothed charge distributions, which overlap the dielectric boundaries themselves. We show how to preserve the spectral accuracy in this case through the use of a harmonic correction, which involves solving a simple Laplace equation with smooth boundary data. We implement our method on graphical processing units and combine our doubly periodic Poisson solver with Brownian dynamics to study the equilibrium structure of double layers in binary electrolytes confined by dielectric boundaries. Consistent with prior studies, we find strong charge depletion near the interfaces due to repulsive interactions with image charges, which points to the need for incorporating polarization effects in understanding confined electrolytes, both theoretically and computationally.

Spontaneous pattern formation in superconducting films

Superconducting films are usually regarded as type II superconductors even when they are made of a type I material. The reason is the presence of stray magnetic fields that stabilize the vortex matter by inducing long-range repulsive interactions between vortices. While very thin films indeed reach this limit, there is a large interval of thicknesses where magnetic properties of superconducting films cannot be classified as either of the two conventional superconductivity types. Recent calculations revealed that in this interval the system exhibits spontaneous formation of magnetic flux-condensate patterns and superstructures appearing due to the interplay between the long-range stray field effects and proximity to the Bogomolnyi self-duality point. These calculations were based on the periodic in-plane boundary conditions which, as is well known from classical electrodynamics, for systems with long-range interactions can lead to field distortions and considerable discrepancies between results of different calculation methods. Here we demonstrate that similar spontaneous patterns are obtained for superconducting films with open in-plane boundary conditions (vanishing in-plane currents perpendicular to the edges of the finite film) and thus the phenomenon is not an artefact of chosen boundary conditions.

Electrode polarization effects on interfacial kinetics of ionic liquid at graphite surface: An extended lagrangian-based constant potential molecular dynamics simulation study

Computational models including electrode polarization can be essential to study electrode/electrolyte interfacial phenomena more realistically. We present here a constant-potential classical molecular dynamics simulation method based on the extended Lagrangian formulation where the fluctuating electrode atomic charges are treated as independent dynamical variables. The method is applied to a graphite/ionic liquid system for the validation and the interfacial kinetics study. While the correct adiabatic dynamics is achieved with a sufficiently small fictitious mass of charge, static properties have been shown to be almost insensitive to the fictitious mass. As for the kinetics study, electrical double layer (EDL) relaxation and ion desorption from the electrode surface are considered. We found that the polarization slows EDL relaxation greatly whereas it has little impact on the ion desorption kinetics. The findings suggest that the polarization is essential to estimate the kinetics in nonequilibrium processes, not in equilibrium. © 2019 Wiley Periodicals, Inc.

Computational Approaches to Photoelectrode Design through Molecular Functionalization for Enhanced Photoelectrochemical Water Splitting

Photoelectrochemical water splitting is a promising carbon-free approach to produce hydrogen from water. A photoelectrochemical cell consists of a semiconductor photoelectrode in contact with an aqueous electrolyte. Its performance is sensitive to properties of the photoelectrode/electrolyte interface, which may be tuned through functionalization of the photoelectrode surface with organic molecules. This can lead to improvements in the photoelectrode's properties. This Minireview summarizes key computational investigations on using molecular functionalization to modify photoelectrode stability, barrier height, and catalytic activity. It is discussed how first-principles density functional theory, first-principles molecular dynamics, and device modeling simulations can provide predictive insights and complement experimental investigations of functionalized photoelectrodes. Challenges and future directions in the computational modeling of functionalized photoelectrode/electrolyte interfaces within the context of experimental studies are also highlighted.

Entropic selectivity in air separation via a bilayer nanoporous graphene membrane

Molecular dynamics simulations show that controlling the pore size and the pore shape via the bilayer nanoporous graphene membrane provides a novel way to enhance entropic selectivity for air separation via tumbling motion of the oxygen molecule.

Electrostatics of Nanoparticle-Wall Interactions within Nanochannels: Role of Double-Layer Structure and Ion-Ion Correlations

We perform computational investigations of the electrolyte-mediated interactions of charged nanoparticles with the walls of nanochannels. We investigate the role of discrete ion effects, valence, and electrolyte strength on nanoparticle-wall interactions. We find for some of the multivalent charge regimes that the like-charged nanoparticles and walls can have attractive interactions. We study in detail these interactions and the free-energy profile for the nanoparticle-wall separation. We find there are energy barriers and energy minima giving preferred nanoparticle locations in the channel near the center and at a distance near to but separated from the channel walls. We characterize contributions from surface overcharging, condensed layers, and overlap of ion double layers. We perform our investigations using coarse-grained particle-level simulations with Brownian dynamics, classical density functional theory, and the mean-field Poisson-Boltzmann theory. We discuss the implications of our results for phenomena in nanoscale devices.

Effect of pore density on gas permeation through nanoporous graphene membranes

Pore density is an important factor dictating gas separations through one-atom-thin nanoporous membranes, but how it influences the gas permeation is not fully understood. Here we use molecular dynamics (MD) simulations to investigate gas permeation through nanoporous graphene membranes with the same pore size (3.0 Å × 3.8 Å in dimensions) but varying pore densities (from 0.01 to 1.28 nm-2). We find that higher pore density leads to higher permeation per unit area of membrane for both CO2 and He, but the rate of the increase decreases greatly for CO2 at high pore densities. As a result, the per-pore permeance decreases for CO2 but remains relatively constant for He with the pore density, leading to a dramatic change in CO2/He selectivity. By separating the total flux into direct flux and surface flux, we find that He permeation is dominated by direct flux and hence the per-pore permeation rate is roughly constant with the pore density. In contrast, CO2 permeation is dominated by surface flux and the overall decreasing trend of the per-pore permeation rate of CO2 with the pore density can be explained by the decreasing per-pore coverage of CO2 on the feed side with the pore density. Our work now provides a complete picture of the pore-density dependence of gas permeation through one-atom-thin nanoporous membranes.

Local pH and effective pKA of weak polyelectrolytes - insights from computer simulations

In this work we study the titration behavior of weak polyelectrolytes by computer simulations. We analyze the local pH near the chains at various conditions and provide molecular-level insight which complements the recent experimental determination of this quantity. Next, we analyze the non-ideal titration behaviour of weak polyelectrolytes in solution, calculate the effective ionization constant and compare the simulation results with theoretical predictions. In contrast with the universal behaviour with respect to chain length, we find non-universality and deviations from theory with respect to polymer concentration and permittivity of the solvent. The latter we explain in terms of counterion condensation and ion correlation effects, which lead to reversal of the non-ideal titration behaviour at very low permittivities. We discuss the impact of these findings on the interpretation of experimental results.

Kaiser-Bessel basis for particle-mesh interpolation

In this work, we introduce the Kaiser-Bessel interpolation basis for the particle-mesh interpolation in the fast Ewald method. A reliable a priori error estimate is developed to measure the accuracy of the force computation in correlated charge systems, and is shown to be effective in optimizing the shape parameter of the Kaiser-Bessel basis in terms of accuracy. By comparing the optimized Kaiser-Bessel basis with the traditional B-spline basis, we demonstrate that the former is more accurate than the latter in part of the working parameter space, say, a relatively small real-space cutoff, a relatively small reciprocal space mesh, and a relatively large truncation of basis. In some cases, the Kaiser-Bessel basis is found to be more than one order of magnitude more accurate.

Effective pair potential between charged nanoparticles at high volume fractions

Simulations of charged colloidal dispersions are technically challenging. One possible workaround consists in reducing the system to the colloids only, whose interactions are described through an effective pair potential, w^f. Still, the determination of w^f is difficult mainly because it depends on the colloidal density, ϕ. Here we propose to calculate w^f from simulations of a pair of colloids placed in a cubic box with periodic boundary conditions. The variation in ϕ is mimicked by an appropriate change in the concentration of counterions neutralized by an homogeneous background charge. The method is tested at the level of the primitive model. A good description of the structure of the colloidal dispersion is obtained in the low and high coupling regimes, even at high ϕ (≈30%). Furthermore, the method can easily be used in popular molecular simulation program packages and extended to non-spherical objects.

Free Energies of Cavity and Noncavity Hydrated Electrons Near the Instantaneous Air/Water Interface

The properties of the hydrated electron at the air/water interface are computed for both a cavity and a noncavity model using mixed quantum/classical molecular dynamics simulation. We take advantage of our recently developed formalism for umbrella sampling with a restrained quantum expectation value to calculate free-energy profiles of the hydrated electron's position relative to the water surface. We show that it is critical to use an instantaneous description of the air/water interface rather than the Gibbs' dividing surface to obtain accurate potentials of mean force. We find that noncavity electrons, which prefer to encompass several water molecules, avoid the interface where water molecules are scarce. In contrast, cavity models of the hydrated electron, which prefer to expel water, have a local free-energy minimum near the interface. When the cavity electron occupies this minimum, its absorption spectrum is quite red-shifted, its binding energy is significantly lowered, and its dynamics speed up quite a bit compared with the bulk, features that have not been found by experiment. The surface activity of the electron therefore serves as a useful test of cavity versus noncavity electron solvation.

Effects of Confinement on the Dielectric Response of Water Extends up to Mesoscale Dimensions

The extent of confinement effects on water is not clear in the literature. While some properties are affected only within a few nanometers from the wall surface, others are affected over long length scales, but the range is not clear. In this work, we have examined the dielectric response of confined water under the influence of external electric fields along with the dipolar fluctuations at equilibrium. The confinement induces a strong anisotropic effect which is evident up to 100 nm channel width, and may extend to macroscopic dimensions. The root-mean-square fluctuations of the total orientational dipole moment in the direction perpendicular to the surfaces is 1 order of magnitude smaller than the value attained in the parallel direction and is independent of the channel width. Consequently, the isotropic condition is unlikely to be recovered until the channel width reaches macroscopic dimensions. Consistent with dipole moment fluctuations, the effect of confinement on the dielectric response also persists up to channel widths considerably beyond 100 nm. When an electric field is applied in the perpendicular direction, the orientational relaxation is 3 orders of magnitude faster than the dipolar relaxation in the parallel direction and independent of temperature.

Mechanism for Asymmetric Nanoscale Electrowetting of an Ionic Liquid on Graphene

The electrowetting behavior of 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4]) confined between two oppositely charged graphene layers is investigated using molecular dynamics simulations. By introducing charges on the surface, counterions are attracted to the surface and co-ions are repelled from it, leading to the reduction of the solid-liquid interfacial free energy and consequently the contact angle. Recently, we have shown that changes in the contact angle upon charging the surface are asymmetric with respect to surface polarity and opposite to the changes in the solid-liquid interfacial free energy. In this work, the asymmetry of the solid-liquid interfacial free energy is shown to originate from differences in structural organization of the ions at the interface, with positively polarized surfaces inducing a more favorable electrostatic arrangement of the ions. Analysis of the liquid structure in the vicinity of the three phase contact line, however, shows that the ion size asymmetry, together with differences in orientational ordering of the cations on oppositely polarized surfaces, instead leads to enhanced spreading on the negatively polarized surfaces, resulting in a corresponding contact angle asymmetry.

Interfacial tension does not drive asymmetric nanoscale electrowetting on graphene

We report molecular dynamics simulations of the electrowetting behavior of liquids in confinement between two oppositely charged graphene sheets. We observe that changes in the static contact angles of water, salty (4 M NaCl) water, and 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4]) (a room temperature ionic liquid) exhibit an asymmetric dependence on electric field polarity. The solid-liquid interfacial tension, which is expected to drive these changes, has been calculated independently by integrating the reversible work performed upon introducing positive and negative surface charges. This quantity shows either no dependence on the polarity of the electric field (water) or a dependence exactly opposite to the one obtained by applying the Young-Lippmann equation to the observed contact angles ([bmim][BF4]). Our analysis indicates that the observed contact angle asymmetry finds its origin in the liquid structure in the vicinity of the three-phase contact line. In particular, it is suggested that the molecular orientation properties are crucial to determine the asymmetric wetting behavior of pure water; in addition, the contrast in the strength of the ion hydration shells has a decisive influence on the NaCl solution behavior.

Phase behavior of Langmuir monolayers with ionic molecular heads: Molecular simulations

We carried out Monte Carlo simulations in the N,Π,T ensemble of a Langmuir monolayer coarse-grained molecular model. Considering that the hydrophilic groups can be ionized by modulating acid-base interactions, here we study the phase behavior of a model that incorporates the short-range steric and long-range ionic interactions. The simulations were carried out in the reduced temperature range 0.1≤T*<4.0, where there is a competition of these interactions. Different order parameters were calculated and analyzed for several values of the reduced surface pressure in the interval, 1≤Π*≤40. For most of the surface pressures two directions of molecular tilt were found: (i) towards the nearest neighbor (NN) at low temperatures, T*<0.7, and most of the values of Π* and (ii) towards next-nearest neighbors (NNN) in the temperature interval 0.7≤T*<1.1 for Π*<25. We also found the coexistence of the NN and NNN at intermediate temperatures and Π*>25. A low-temperature reentrant disorder-order-disorder transition in the positions of the molecular heads and in the collective tilt of the tails was found for all the surface pressure values. It was also found that the molecular tails arranged forming "rotating patterns" in the temperature interval, 0.5<T*<1.5, at intermediate surface pressures. We estimated the monolayer's surface pressure versus temperature and the temperature versus area per molecule phase diagrams. It was found that the LE↔LC phase transition shifts to smaller temperatures when the molecular heads carry an ion in qualitative agreement with experimental observations of fatty acid monolayers with ionic head groups. Two surface pressure versus area per molecule isotherms were also calculated. At low temperatures near the LC-NN ↔ LC-NNN transitions and at higher temperatures close to the LE ↔ LC transitions. From these isotherms the monolayer's area compression modulus was obtained and its variation ranges in the LE and LC phases were found to be consistent with the experimental values.

The tunable hydrophobic effect on electrically doped graphene

Using molecular dynamics simulations, we study the hydrophobic effect on electrically doped single layer graphene. With doping levels measured in volts, large changes in contact angle occur for modest voltages applied to the sheet. The effect can be understood as a renormalization of the surface tension between graphene and water in the presence of an electric field generated by the dopant charge, an entirely collective effect termed electrowetting. Because the electronic density of states scales linearly in the vicinity of the Fermi energy, the cosine of the contact angle scales quartically with the applied voltage rather than quadratically, as it would for a two-dimensional metal or in multiple layer graphene. While electrowetting explains the phenomenon, it does not account for the slight asymmetry observed in the hydrophobic response between n- and p-doping.

Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge

Ewald summation, which has become the de facto standard for computing electrostatic interactions in biomolecular simulations, formally requires that the simulation box is neutral. For non-neutral systems, the Ewald algorithm implicitly introduces a uniform background charge distribution that effectively neutralizes the simulation box. Because a uniform distribution of counter charges typically deviates from the spatial distribution of counterions in real systems, artifacts may arise, in particular in systems with an inhomogeneous dielectric constant. Here, we derive an analytical expression for the effect of using an implicit background charge instead of explicit counterions, on the chemical potential of ions in heterogeneous systems, which (i) provides a quantitative criterium for deciding if the background charge offers an acceptable trade-off between artifacts arising from sampling problems and artifacts arising from the homogeneous background charge distribution, and (ii) can be used to correct this artifact in certain cases. Our model quantifies the artifact in terms of the difference in charge density between the non-neutral system with a uniform neutralizing background charge and the real neutral system with a physically correct distribution of explicit counterions. We show that for inhomogeneous systems, such as proteins and membranes in water, the artifact manifests itself by an overstabilization of ions inside the lower dielectric by tens to even hundreds kilojoules per mole. We have tested the accuracy of our model in molecular dynamics simulations and found that the error in the calculated free energy for moving a test charge from water into hexadecane, at different net charges of the system and different simulation box sizes, is correctly predicted by the model. The calculations further confirm that the incorrect distribution of counter charges in the simulation box is solely responsible for the errors in the PMFs.

Assessment of Common Simulation Protocols for Simulations of Nanopores, Membrane Proteins, and Channels

Molecular dynamics (MD) simulation has become a common technique to study biological systems. Transport of small molecules through carbon nanotubes and membrane proteins has been an intensely studied topic, and MD simulations have been able to provide valuable predictions, many of which have later been experimentally proven. Simulations of such systems pose challenges, and unexpected problems in commonly used protocols and methods have been found in the past few years. The two main reasons why some were not found before are that most of these newly discovered errors do not lead to unstable simulations. Furthermore, some of them manifest themselves only after relatively long simulation times. We assessed the reliability of the most common simulations protocols by MD and stochastic dynamics (SD) or Langevin dynamics, simulations of an alpha hemolysin nanochannel embedded in a palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer. Our findings are that (a) reaction field electrostatics should not be used in simulations of such systems, (b) local thermostats should be preferred over global ones since the latter may lead to an unphysical temperature distribution,