We report a Monte Carlo and molecular dynamics simulations study of carbon dioxide in hydrated sodium montmorillonite, including thermodynamical, structural and dynamical properties. In order to simulate the behaviour of a clay caprock in contact with a CO 2 reservoir, we consider clays in equilibrium with H 2 O−CO 2 mixtures under conditions close to relevant ones for geological storage, namely a temperature T =348 K, and pressures P=25 and 125 bar, and under which two bulk phases coexist: H 2 O-rich liquid on the one hand and CO 2-rich gas (P=25 bar) or supercritical fluid (P=125 bar) on the other hand. We first use grand-canonical MC simulations to determine the number of stable states in clay, their composition and the corresponding equilibrium interlayer distances. The vertical, horizontal and radial distribution functions of the confined mixture, subsequently obtained using molecular dynamics, reveal some structural feature induced by the presence of CO 2. Finally, the simulations indicate that carbon dioxide considerably influences the diffusion of mobile species in clays. We discuss these results by comparing them with those obtained for the bulk mixtures, as well as for Namontmorillonite in equilibrium with a pure water reservoir water at the same temperature and pressure.

Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C–H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P–N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files () has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.

We report a molecular simulation study of hydrodynamics in clay nanopores, with pore widths ranging from 3 to 10 nm. Understanding mass transfer through clay nanopores is necessary in many contexts such as groundwater hydrology, petroleum and gas reservoir engineering, as well as carbon dioxide sequestration or geological disposal of radioactive waste.Grand-canonical Monte-Carlo simulations first allow to determine the water content in the pores. We then analyze the structure and diffusion of confined water using equilibrium Molecular Dynamics. Finally, Non-Equilibrium MD allow to analyze the hydrodynamic behaviour of the confined fluid and assess the relevance of continuum hydrodynamics to describe the flow under a pressure gradient. The Navier-Stokes equation, using the density and viscosity of the bulk fluid, provides a reasonable description of the flow provided that the pore width is larger than 4 nm and that a slip boundary condition is used. We determine a slip length of 2.

We report the diffusion coefficient and viscosity of popular rigid water models: Two nonpolarizable ones (SPC/E with 3 sites, and TIP4P/2005 with 4 sites) and a polarizable one (DangChang, 4 sites). We exploit the dependence of the diffusion coefficient on the system size [Yeh and Hummer, J. Phys. Chem. B 108, 15873 (2004)] to obtain the size-independent value. This also provides an estimate of the viscosity of all water models, which we compare to the Green-Kubo result. In all cases, a good agreement is found. The TIP4P/2005 model is in better agreement with the experimental data for both diffusion and viscosity. The SPC/E and Dang-Chang water overestimate the diffusion coefficient and underestimate the viscosity.

The transport of fluids through the Earth's crust controls the redistribution of elements to form mineral and hydrocarbon deposits, the release and sequestration of greenhouse gases, and facilitates metamorphic reactions that influence lithospheric rheology. In permeable systems with a well-connected porosity, fluid transport is largely driven by fluid pressure gradients. In less permeable rocks, deformation may induce permeability by creating interconnected heterogeneities, but without these perturbations, mass transport is limited along grain boundaries or relies on transformation processes that self-generate transient fluid pathways. The latter can facilitate large-scale fluid and mass transport in nominally impermeable rocks without large-scale fluid transport pathways. Here, we show that pervasive, fluid-driven metamorphism of crustal igneous rocks is directly coupled to the production of nanoscale porosity. Using multi-dimensional nano-imaging and molecular dynamics simulations, we demonstrate that in feldspar, the most abundant mineral family in the Earth's crust, electrokinetic transport through reaction-induced nanopores (10-100 nm) can potentially be significant. This suggests that metamorphic fluid flow and fluid-mediated mineral transformation reactions can be considerably influenced by nanofluidic transport phenomena.

We report on a molecular simulation study of the origin of non-slip or slip hydrodynamic boundary conditions in clay nanopores, focussing on the role of electrostatics. We simulate hydrodynamic and electro-osmotic flows and consider both charged (montmorillonite) and uncharged (pyrophyllite) clays. We further use two commonly used force fields to analyze the effect of local interactions, in particular the effect of the polarity of the surface, in addition to the mere effect of the presence or absence of a net charge and counter-ions. For the 6 nm pore investigated here, the molecular velocity profile can be well described by continuum hydrodynamics only if (a) proper boundary conditions, with a slip or stagnation length determined from molecular simulation, are taken into account and (b) the ionic density profiles from MD simulations are used in the case of electro-osmotic flow, since the Poisson-Boltzmann equation fails to reproduce the ionic profiles, hence the force acting on the fluid. Among the considered force fields only CLAYFF predicts a hydrophobic pyrophyllite and hydrophilic montmorillonite, as expected from experimental behaviour. The non-slip or slip boundary conditions at clay surfaces strongly depend on electrostatic interactions of water molecules with the surface. The presence of a net charge results in an average electric field experienced by surface water molecules between the charged surface and the condensed layer counter-ions, which influences their orientation. The charge distribution inside the clay layer determines the polarity of the surface and hence the strength of hydrogen bonds donated by water molecules to surface oxygen atoms.

The active site in ethene oligomerization catalyzed by Ni-zeolites is proposed to be a mobile Ni(II) complex, based on density functional theory-based molecular dynamics (DFT-MD) simulations corroborated by continuous-flow experiments on Ni-SSZ-24 zeolite. The results of the simulations at operating conditions show that ethene molecules reversibly mobilize the active site as they exchange with the zeolite as ligands on Ni during reaction. Microkinetic modeling was conducted on the basis of free-energy profiles derived with DFT-MD for oligomerization on these mobile [(ethene)2-Ni-alkyl]+ species. The model reproduces the experimentally observed high selectivity to dimerization and indicates that the mechanism is consistent with the observed second-order rate dependence on ethene pressure.

We develop a model of transport in multiscale porous media which accounts for adsorption in the different porosity scales. This model employs statistical mechanics to upscale molecular simulation and describe adsorption and transport at larger time and length scales. Using atom-scale simulations, which capture the changes in adsorption and transport with temperature, pressure, pore size, etc., this approach does not assume any adsorption or flow type. Moreover, by relating the local chemical potential μ(r) and density ρ(r), the present model accounts for adsorption effects and possible changes in the confined fluid state upon transport. This model constitutes a bottom-up framework of adsorption and transport in multiscale materials as it (1) describes the adsorptiontransport interplay, (2) accounts for the hydrodynamics breakdown at the nm scale, and (3) is multiscale.