As a first step in developing better molecular scale understanding of the effects of organic additives on the adsorption and mobility of radionuclides in cement under conditions of geological nuclear waste repositories, two complementary approaches, wet chemistry experiments and molecular dynamics (MD) computer simulations, were applied to study the sorption behaviour of two simple model systems: gluconate and uranyl on calcium silicate hydrate phases (C-S-H) - the principal mineral component of hardened cement paste (HCP). Experimental data on sorption and desorption kinetics and isotherms of adsorption for gluconate/C-S-H and U(VI)/C-S-H binary systems were collected and quantitatively analysed for C-S-H samples synthesised with various Ca/Si ratios (0.83, 1.0, 1.4) corresponding to various stages of HCP aging and degradation. Gluconate labelled with 14C isotope was used in order to improve the sensitivity of analytical detection technique (LSC) at particularly low concentrations (10(-8) -10(-5) Â mol/L). There is a noticeable effect of Ca/Si ratio on the gluconate sorption on C-S-H, with stronger sorption at higher Ca/Si ratios. Sorption of organic anions on C-S-H is mediated by the presence of Ca(2+) at the interface and strongly depends on the surface charge and Ca(2+) concentration. In parallel, classical MD simulations of the same model systems were performed in order to identify specific surface sorption sites most actively involved in the sorption of gluconate and uranyl on C-S-H and to clarify molecular mechanisms of adsorption.
This paper reviews atomistic force field parameterizations for molecular simulations of cementitious minerals, such as tricalcium silicate (C3S), portlandite (CH), tobermorites (model C-S-H). Computational techniques applied to these materials include classical molecular simulations, density functional theory and energy minimization. Such simulations hold promise to capture the nanoscale mechanisms operating in cementitious materials and guide in performance optimization. Many force fields have been developed, such as Born–Mayer–Huggins, InterfaceFF (IFF), ClayFF, CSH-FF, CementFF, GULP, ReaxFF, and UFF. The benefits and limitations of these approaches are discussed and a database is introduced, accessible via a web-link (http://cemff.epfl.ch). The database provides information on the different force fields, energy expressions, and model validations using systematic comparisons of computed data with benchmarks from experiment and from ab-initio calculations. The cemff database aims at helping researchers to evaluate and choose suitable potentials for specific systems. New force fields can be added to the database.
Экспериментально исследованы плазменно-пылевые структуры в тлеющем разряде гелия в диапазоне температур 5–300 К. Описана экспериментальная установка, предоставляющая возможность непрерыв- ного изменения температурного режима. Представлена методика обработки экспериментальных дан- ных. Проведено измерение межчастичных расстояний в диапазоне температур 9–295 К и их сравнение с величиной радиуса Дебая. Указаны диапазоны параметров эксперимента, при которых формируются плазменно-пылевые структуры и проявляются различные формы их поведения (вращение, колебания структур, образование вертикальных линейных цепочек и т. д.). Обсуждается применимость потенциала Юкавы к описанию структурных свойств пылевой плазмы в условиях эксперимента
The Callovo-Oxfordian clay formation (COx) is the potential host rock for long term nuclear waste repository in France. The clayey component of COx consists mostly of illite, smectite and interstratified illite/smectite (I/S) clay minerals. We performed a series of molecular dynamics (MD) computer simulations in order to quantify the molecular scale mechanisms responsible for the adsorption and transport of ions at the hydrated surfaces of illite, smectite, and I/S clays. New structural models of illite, smectite, and I/S allowed us to identify several structurally different adsorption sites at the basal surfaces of all three clay substrates. Adsorption free energy profiles above each individual adsorption site on each clay surface for a wide range of metal cations were then calculated and the metal sorption properties for the three clay surfaces are compared in terms of the preferable sorption sites and their surface distributions, most stable adsorption distances, and free energies of adsorption. The resulting equilibrium constants for surface adsorption and ion exchange were calculated and found in general agreement with available literature data. The observed discrepancies between the exchange energies obtained in the current MD simulations and the values obtained through the interpretation of recent X-ray reflectivity measurements can be attributed to the differences in the description of the exchange reaction equilibria between the experimental conditions and the simplified conditions of our simulations.
Grand Canonical Molecular Dynamics (GCMD) simulations were performed to investigate the intercalation of CO2 and H2O molecules in the interlayers of the smectite clay, Na-hectorite, at temperatures and pressures relevant to petroleum reservoir and geological carbon sequestration conditions and in equilibrium with H2O-saturated CO2. The computed adsorption isotherms indicate that CO2 molecules enter the interlayer space of Na-hectorite only when it is hydrated with approximately three H2O molecules per unit cell. The computed immersion energies show that the bilayer hydrate structure (2WL) contains less CO2 than the monolayer structure (1WL) but that the 2WL hydrate is the most thermodynamically stable state, consistent with experimental results for a similar Na-montmorillonite smectite. Under all T and P conditions examined (323–368 K and 90–150 bar), the CO2 molecules are adsorbed at the midplane of clay interlayers for the 1WL structure and closer to one of the basal surfaces for the 2WL structure. Interlayer CO2 molecules are dynamically less restricted in the 2WL structures. The CO2 molecules are preferentially located near basal surface oxygen atoms and H2O molecules rather than in coordination with Na+ ions. Accounting for the orientation and flexibility of the structural −OH groups of the clay layer has a significant effect on the details of the computed structure and dynamics of H2O and CO2 molecules but does not affect the overall trends with changing basal spacing or the principal structural and dynamical conclusions. Temperature and pressure in the ranges examined have little effect on the principal structural and energetic conclusions, but the rates of dynamical processes increase with increasing temperature, as expected.
Helical segments are common structural elements of membrane proteins. Dimerization and oligomerization of transmembrane (TM) α-helices provides the framework for spatial structure formation and protein-protein interactions. The membrane itself also takes part in the protein functioning. There are some examples of the mutual influence of the lipid bilayer properties and embedded membrane proteins. This work aims at the detail investigation of protein-lipid interactions using model systems: TM peptides corresponding to native protein segments. Three peptides were considered corresponding to TM domains of human glycophorin A (GpA), epidermal growth factor receptor (EGFR) and proposed TM-segment of human neuraminidase-1 (Neu1). A computational analysis of structural and dynamical properties was performed using molecular dynamics method. Monomers of peptides were considered incorporated into hydrated lipid bilayers. It was confirmed, that all these TM peptides have stable helical conformation in lipid environment, and the mutual adaptation of peptides and membrane was observed. It was shown that incorporation of the peptide into membrane results in the modulation of local and mean structural properties of the bilayer. Each peptide interacts with lipid acyl chains having special binding sites on the surface of central part of α-helix that exist for at least 200 ns. However, lipid acyl chains substitute each other faster occupying the same site. The formation of a special pattern of protein-lipid interactions may modulate the association of TM domains of membrane proteins, so membrane environment should be considered when proposing new substances targeting cell receptors.