John J. Molina

A transferable ab initio based force field for aqueous ions.

We present a new polarizable force field for aqueous ions (Li(+), Na(+), K(+), Rb(+), Cs(+), Mg(2 +), Ca(2 +), Sr(2 +), and Cl(-)) derived from condensed phase ab initio calculations. We use maximally localized Wannier functions together with a generalized force and dipole-matching procedure to determine the whole set of parameters. Experimental data are then used only for validation purposes and a good agreement is obtained for structural, dynamic, and thermodynamic properties. The same procedure applied to crystalline phases allows to parametrize the interaction between cations and the chloride anion. Finally, we illustrate the good transferability of the force field to other thermodynamic conditions by investigating concentrated solutions.

Hydrodynamic interactions of self-propelled swimmers

The hydrodynamic interactions of a suspension of self-propelled particles are studied using a direct numerical simulation method which simultaneously solves for the host fluid and the swimming particles. A modified version of the “Smoothed Profile” (SP) method is developed to simulate microswimmers as squirmers, which are spherical particles with a specified surface-tangential slip velocity between the particles and the fluid. This simplified swimming model allows one to represent different types of propulsion (pullers and pushers) and is thus ideal to study the hydrodynamic interactions among swimmers. We use the SP method to study the diffusive behavior which arises due to the swimming motion of the particles, and show that there are two basic mechanisms responsible for this phenomena: the hydrodynamic interactions caused by the squirming motion of the particles, and the particle–particle collisions. This dual nature gives rise to two distinct time- and length-scales, and thus to two diffusion coefficients, which we obtain by a suitable analysis of the swimming motion. We show that the collisions between swimmers can be interpreted in terms of binary collisions, in which the effective collision radius is reduced due to the collision dynamics of swimming particles in viscous fluids. At short time-scales, the dynamics of the swimmer is analogous to that of an inert tracer particle in a swimming suspension, in which the diffusive motion is caused by fluid-particle collisions. Our results, along with the simulation method we have introduced, will allow us to gain a better understanding of the complex hydrodynamic interactions of self-propelled swimmers.

Primitive models of ions in solution from molecular descriptions: a perturbation approach.

The development of simple, primitive model descriptions for electrolyte solutions is usually carried out by fitting the system parameters to reproduce some experimental data. We propose an alternative method, that allows one to derive implicit solvent models of electrolyte solutions from all-atom descriptions. We obtain analytic expressions for the thermodynamic and structural properties of the ions, which are in good agreement with the underlying explicit solvent representation, provided that ion association is taken into account. Effective ion-ion potentials are derived from molecular dynamics simulations and are used within a first-order perturbation theory to derive the best possible description in terms of charged hard-spheres. We show that our model provides a valid description for a series of 1-1 electrolytes.

Models of electrolyte solutions from molecular descriptions: The example of NaCl solutions

We present a method to derive implicit solvent models of electrolyte solutions from all-atom descriptions; providing analytical expressions of the thermodynamic and structural properties of the ions consistent with the underlying explicit solvent representation. Effective potentials between ions in solution are calculated to perform perturbation theory calculations, in order to derive the best possible description in terms of charged hard spheres. Applying this method to NaCl solutions yields excellent agreement with the all-atom model, provided ion association is taken into account.

Atomistic Description of Binary Lanthanoid Salt Solutions: A Coarse-Graining Approach

The experimental difficulties inherent to the solution chemistry of actinoids and lanthanoids have led to the use of a wide variety of models, from the microscopic to the macroscopic scale, in an attempt to represent their solution properties. Molecular dynamics (MD) simulations, with explicit solvents, have been successfully used to describe the structural characteristics, but the limits on the accessible length and time scales do not allow for an equivalent description of the macroscopic properties. In this study, we propose a multiscale approach, based on MD simulation results, to study the thermodynamic and structural properties of a series of lanthanoid-chloride aqueous solutions. An inversion procedure, based on the approximate hypernetted chain (HNC) closure and the Stillinger-Lovett sum rules for ionic liquids, is used to obtain the effective ion-ion potentials from MD-generated radial distribution functions (RDF). Implicit solvent Monte Carlo (MC) simulations are then performed to compute the osmotic coefficients of the salt solutions. This coarse-grained strategy provides accurate effective pair potentials for the lanthanoid salts, derived from an atomic model. The method presented here is an attempt to bridge the gap between MD and the thermodynamic properties of solutions that are experimentally measured.

Purely hydrodynamic origin for swarming of swimming particles.

Three-dimensional simulations with fully resolved hydrodynamics are performed to study the collective motion of model swimmers in bulk and confinement. Calculating the dynamic structure factor, we clarified that the swarming in bulk systems can be understood as a pseudoacoustic mode. Under confinement between flat parallel walls, this pseudoacoustic mode leads to a traveling wavelike motion. This swarming behavior is due purely to the hydrodynamic interactions between the swimmers and depends strongly on the type and strength of swimming (i.e., pusher or puller).

Multi-scale modelling of uranyl chloride solutions

Classical molecular dynamics simulations with explicit polarization have been successfully used to determine the structural and thermodynamic properties of binary aqueous solutions of uranyl chloride (UO2Cl2). Concentrated aqueous solutions of uranyl chloride have been studied to determine the hydration properties and the ion-ion interactions. The bond distances and the coordination number of the hydrated uranyl are in good agreement with available experimental data. Two stable positions of chloride in the second hydration shell of uranyl have been identified. The UO2(2+)-Cl(-) association constants have also been calculated using a multi-scale approach. First, the ion-ion potential averaged over the solvent configurations at infinite dilution (McMillan-Mayer potential) was calculated to establish the dissociation/association processes of UO2 (2+)-Cl(-) ion pairs in aqueous solution. Then, the association constant was calculated from this potential. The value we obtained for the association constant is in good agreement with the experimental result (KUO2Cl(+) = 1.48 l mol(-1)), but the resulting activity coefficient appears to be too low at molar concentration.

Sedimentation of non-Brownian spheres at high volume fractions

We performed direct numerical simulations of non-Brownian sedimenting particles, using a smooth profile method over a wide range of volume fractions from 0.01 to 0.5. We found that hydrodynamic velocity fluctuations scale as ϕ1/2, both parallel and perpendicular to gravity at low volume fractions (ϕ ≤ 0.04) due to anisotropic microstructure and decay with further increase in ϕ because of many body hydrodynamic interactions. Unlike velocity fluctuations, vertical relaxation times scale as ϕ−1/2 for the full range of volume fractions, whereas horizontal relaxation times decrease as ϕ−1/2 at low volume fractions, remain unchanged and then decrease sharply at high volume fractions. Similarly, horizontal and vertical diffusion coefficients increase as ϕ1/2 at low volume fractions. Moreover, vertical diffusion decays with further increase in ϕ, whereas horizontal diffusion remains unchanged and then decreases. The microstructure analysis of the suspension showed that at low volume fractions the anisotropic microstructure determines the transport properties and at ϕ > 0.12 many body interactions govern the system properties, whereas a cross-over exists in between these two regimes.

Diffusion of colloidal particles in swimming suspensions

Previously, we have proposed to analyse the hydrodynamic interactions in a suspension of swimmers with respect to an effective hydrodynamic diffusion coefficient, which only considers the fluctuating motion caused by the stirring of the fluid. In this work, we study the diffusion of colloidal particles immersed in a bath of swimmers. To accurately resolve the many-body hydrodynamic interactions responsible for this diffusion, we use a direct numerical simulation scheme based on the smooth profile method. We consider a squirmer model for the self-propelled swimmers, as it accurately reproduces the flow field generated by real microorganisms, such as bacteria or spermatozoa. We show that the diffusion coefficients of the colloids are comparable with the effective diffusion coefficients of the swimmers, provided that the concentration of swimmers is high enough. At low concentrations, the difference in the way colloids and swimmers react to the flow leads to a reduction in the diffusion coefficient of the colloids. This is clearly seen in the appearance of a negative-correlation region for the velocity-correlation function of the colloids, which does not exist for the swimmers.

Direct numerical simulations of sedimenting spherical particles at non-zero Reynolds number

We performed direct numerical simulations, using a smoothed profile method to investigate the inertial effects on the static and dynamic properties of a sedimenting suspension over a wide range of volume fractions from 0.01 to 0.4. We found that at Reynolds number Re ≤ 0.5, static and dynamic properties show the typical non-Brownian, Stokes regime characteristics, due to insignificant inertial effects. The microstructure analysis at the high Re revealed that at Re = 1 inertial forces have significant effects and these create a deficiency of particles around a given particle, which is more pronounced in the direction of gravity than in the perpendicular direction. This deficiency decreased the velocity fluctuations and particle diffusion in the vertical direction, whereas both of these properties remain unchanged in the perpendicular direction. Moreover, at Re = 10, strong inertial forces generated a significant deficit of particles in both directions, which decreased velocity fluctuations and particle diffusion in both directions. We also observed that the range of volume fraction affected by inertial forces is increased with the increase of Re. At high volume fraction ϕ ≳ 0.15, intrinsic many-body interactions dominate the phenomena and govern the transport properties thereafter.