Marcello Sega

The generalized identification of truly interfacial molecules (ITIM) algorithm for nonplanar interfaces

We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used in ITIM and the circumsphere criterion used in the α-shapes approach, and can be regarded either as a reference-frame independent version of the former, or as an extended version of the latter that includes the atomic excluded volume. The new algorithm is applied to compute the intrinsic orientational order parameters of water around a dodecylphosphocholine and a cholic acid micelle in aqueous environment, and to the identification of solvent-reachable sites in four model structures for soot. The additional algorithm introduced for the calculation of intrinsic density profiles in arbitrary geometries proved to be extremely useful also for planar interfaces, as it allows to solve the paradox of smeared intrinsic profiles far from the interface.

Efficient Handling of Gaussian Charge Distributions: An Application to Polarizable Molecular Models.

We present a mesh-based Ewald summation method that is suitable for the calculation of the electrostatic interaction between Gaussian charge distributions, instead of point charges. As an application, we implemented the method in the Gromacs simulation package and tested it with a polarizable water model, showing that the interaction between Gaussian charge distributions can be computed with a small (10%) additional computational cost with respect to the point charge case. In addition, since the performance of polarizable models is strongly influenced by the number of iterations required for the self-consistent field solution, we tested also the Always Stable Predictor-Corrector (ASPC) method of Kolafa (Kolafa, J. J. Comp. Chem. 2003, 25, 335) as an alternative to the steepest descent (SD) based algorithm with predictor implemented in the Gromacs, and found that it speeds up the integration of the equations of motion by a factor of 1.6-2.0, depending on the target model.

Calculation of the intrinsic solvation free energy profile of an ionic penetrant across a liquid-liquid interface with computer simulations

We introduce the novel concept of an intrinsic free energy profile, allowing one to remove the artificial smearing caused by thermal capillary waves, which renders difficulties for the calculation of free energy profiles across fluid interfaces in computer simulations. We apply this concept to the problem of a chloride ion crossing the interface between water and 1,2-dichloroethane and show that the present approach is able to reveal several important features of the free energy profile which are not detected with the usual, nonintrinsic calculations. Thus, in contrast to the nonintrinsic profile, a free energy barrier is found at the aqueous side of the (intrinsic) interface, which is attributed to the formation of a water “finger” the ion pulls with itself upon approaching the organic phase. Further, by the presence of a nonsampled region, the intrinsic free energy profile clearly indicates the coextraction of the first hydration shell water molecules of the ion when entering the organic phase.

Regularization of the slip length divergence in water nanoflows by inhomogeneities at the Angstrom scale

We performed non-equilibrium Molecular Dynamics simulations of water flow in nano-channels with the aim of discriminating static from dynamic contributions of the solid surface to the slip length of the molecular flow. We show that the regularization of the slip length divergence at high shear rates, formerly attributed to the wall dynamics, is controlled instead by its static properties. Surprisingly, we find that atomic displacements at the Angstrom scale are sufficient to remove the divergence of the slip length and realize the no-slip condition. Since surface thermal fluctuations at room temperature are enough to generate these displacements, we argue that the no-slip condition for water can be achieved also for ideal surfaces, which do not present any surface roughness.

Kinetic dielectric decrement revisited: phenomenology of finite ion concentrations

With the help of a recently developed non-equilibrium approach, we investigate the ionic strength dependence of the Hubbard-Onsager dielectric decrement. We compute the depolarization of water molecules caused by the motion of ions in sodium chloride solutions from the dilute regime (0.035 M) up close to the saturation concentration (4.24 M), and find that the kinetic decrement displays a strong non-monotonic behavior, in contrast to the prediction of available models. We introduce a phenomenological modification of the Hubbard-Onsager continuum theory, which takes into account the screening due to the ionic cloud at the mean-field level and, which is able to describe the kinetic decrement at high concentrations including the presence of a pronounced minimum.

Two-dimensional percolation at the free water surface and its relation with the surface tension anomaly of water.

The percolation temperature of the lateral hydrogen bonding network of the molecules at the free water surface is determined by means of molecular dynamics computer simulation and identification of the truly interfacial molecules analysis for six different water models, including three, four, and five site ones. The results reveal that the lateral percolation temperature coincides with the point where the temperature derivative of the surface tension has a minimum. Hence, the anomalous temperature dependence of the water surface tension is explained by this percolation transition. It is also found that the hydrogen bonding structure of the water surface is largely model-independent at the percolation threshold; the molecules have, on average, 1.90 ± 0.07 hydrogen bonded surface neighbors. The distribution of the molecules according to the number of their hydrogen bonded neighbors at the percolation threshold also agrees very well for all the water models considered. Hydrogen bonding at the water surface can be well described in terms of the random bond percolation model, namely, by the assumptions that (i) every surface water molecule can form up to 3 hydrogen bonds with its lateral neighbors and (ii) the formation of these hydrogen bonds occurs independently from each other.

Pressure Profile Calculation with Mesh Ewald Methods

The importance of calculating pressure profiles across liquid interfaces is increasingly gaining recognition, and efficient methods for the calculation of long-range contributions are fundamental in addressing systems with a large number of charges. Here, we show how to compute the local pressure contribution for mesh-based Ewald methods, retaining the typical N log N scaling as a function of the lattice nodes N. This is a considerable improvement on existing methods, which include approximating the electrostatic contribution using a large cutoff and the, much slower, Ewald calculation. As an application, we calculate the contribution to the pressure profile across the water/vapor interface, coming from different molecular layers, both including and removing the effect of thermal capillary waves. We compare the total pressure profile with the one obtained using the cutoff approximation for the calculation of the stresses, showing that the stress distributions obtained using the Harasima and Irving-Kirkwood path are quite similar and shifted with respect to each other at most 0.05 nm.

The importance of chemical potential in the determination of water slip in nanochannels

Abstract.We investigate the slip properties of water confined in graphite-like nanochannels by non-equilibrium molecular dynamics simulations, with the aim of identifying and analyze separately the influence of different physical quantities on the slip length. In a system under confinement but connected to a reservoir of fluid, the chemical potential is the natural control parameter: we show that two nanochannels characterized by the same macroscopic contact angle --but a different microscopic surface potential-- do not exhibit the same slip length unless the chemical potential of water in the two channels is matched. Some methodological issues related to the preparation of samples for the comparative analysis in confined geometries are also discussed.Graphical abstract

Nonzero Ideal Gas Contribution to the Surface Tension of Water

Surface tension, the tendency of fluid interfaces to behave elastically and minimize their surface, is routinely calculated as the difference between the lateral and normal components of the pressure or, invoking isotropy in momentum space, of the virial tensor. Here we show that the anisotropy of the kinetic energy tensor close to a liquid-vapor interface can be responsible for a large part of its surface tension (about 15% for water, independent from temperature).

A simple approximation for the distribution of ions between charged plates in the weak coupling regime

Abstract The solution of the Poisson–Boltzmann equation for counterions confined between two charged plates is known analytically up to a constant, namely, the ion density in the middle of the channel. This quantity is relevant also because it gives access, through the contact theorem, to the osmotic pressure of the system. Here we compare the values of the ion density obtained by numerical and simulation approaches, and report a useful analytic approximation for the weak coupling regime in the absence of added salt, which predicts the value of the ion density in the worst case within 5%. The inclusion of higher order terms in a Laurent expansion can further improve the accuracy, at the expense of simplicity.