Atomistic simulations of confined species in 2D nanosructures: clays and C-S-H gel

246 p.In this thesis, atomistic simulations have been used to study and predict the properties of molecules and materials. The information provided by the molecular dynamics simulations complements and supports the experiments, helping in the interpretations of the results and serving as a guide for the design of new materials. First, the intercalation of two organic dyes, LDS-722 and pyronin Y, with two smectite clays, Laponite and saponite, has been studied. The simulation of these dye/clay systems has enable the understanding of their photophysical behavior, the dye aggregation and its diffusivity. The mechanical properties of these hybrid materials has also been characterized. Second, the retention of radiocesium in calcium silicate hydrates (C-S-H gel) has been evaluated, considering the impact of Cs concentration, Ca/Si ratio, counterions and Al incorporation in the silicate chains to form C-A-S-H. Third, the strengthening mechanisms in C-S-H gel that incorporates organic additives, APTES and PEG, has also been explored by molecular dynamics simulations. The bulk and Young¿s moduli have been determined by applying a hydrostatic and uniaxial pressures to the simulated systems, considering the effects of the hydrostatic pressure on the silicate chains and hydrogen bond network. The results presented in this thesis contribute to a better understanding of the guest-host interactions at atomic scale in the studied systems and may help in the design of new materials

Atomistic simulations of confined species in 2D nanosructures: clays and C-S-H gel

246 p.In this thesis, atomistic simulations have been used to study and predict the properties of molecules and materials. The information provided by the molecular dynamics simulations complements and supports the experiments, helping in the interpretations of the results and serving as a guide for the design of new materials. First, the intercalation of two organic dyes, LDS-722 and pyronin Y, with two smectite clays, Laponite and saponite, has been studied. The simulation of these dye/clay systems has enable the understanding of their photophysical behavior, the dye aggregation and its diffusivity. The mechanical properties of these hybrid materials has also been characterized. Second, the retention of radiocesium in calcium silicate hydrates (C-S-H gel) has been evaluated, considering the impact of Cs concentration, Ca/Si ratio, counterions and Al incorporation in the silicate chains to form C-A-S-H. Third, the strengthening mechanisms in C-S-H gel that incorporates organic additives, APTES and PEG, has also been explored by molecular dynamics simulations. The bulk and Young¿s moduli have been determined by applying a hydrostatic and uniaxial pressures to the simulated systems, considering the effects of the hydrostatic pressure on the silicate chains and hydrogen bond network. The results presented in this thesis contribute to a better understanding of the guest-host interactions at atomic scale in the studied systems and may help in the design of new materials

Nanoscale shear cohesion between cement hydrates: The role of water diffusivity under structural and electrostatic confinement

[EN] The calcium silicate hydrate (C-S-H) controls most of the final properties of the cement paste, including its mechanical performance. It is agreed that the nanometer-sized building blocks that compose the C-S-H are the origin of the mechanical properties. In this work, we employ atomistic simulations to investigate the relaxation process of C-S-H nanoparticles subjected to shear stress. In particular, we study the stress relaxation by rearrangement of these nanoparticles via sliding adjacent C-S-H layers separated by a variable interfacial distance. The simulations show that the shear strength has its maximum at the bulk interlayer space, called perfect contact interface, and decreases sharply to low values for very short interfacial distances, coinciding with the transition from 2 to 3 water layers and beginning of the water flow. The evolution of the shear strength as a function of the temperature and ionic confinement confirms that the water diffusion controls the shear strength.We gratefully acknowledge the financial support by "Departamento de Educacion, Politica Linguistica y Cultura del Gobierno Vasco" (IT912-16, IT1639-22). E.D.-R. acknowledges the postdoctoral fellowship from "Programa Posdoctoral de Perfeccionamiento de Personal Investigador Doctor" of the Basque Government. The authors thank for technical and human support provided by i2basque and SGIker (UPV/EHU/ERDF, EU), for the allocation of computational resources provided by the Scientific Computing Service

A comprehensive review of C-S-H empirical and computational models, their applications, and practical aspects

[EN] The C-S-H gel is an elusive material. Its variable composition and disordered nature complicate a complete characterization of its atomic structure, and the elaboration of models is key to understanding it. This work aims to review those proposed models, dividing them into empirical and computational models. After a brief description of related crystalline calcium silicate hydrates, empirical C-S-H models based on interpretation of experimental data are presented. Then, we focus on the historic development of atomistic models to study the C-S-H, until the current state of the art. We describe current computational C-S-H models built from the empirical models and computer simulations. We review common applications of these computational models: the aluminum incorporation, the elastic and mechanical properties, the diffusion of water and ions in nanopores, and C-S-H/organic composites. Finally, we discuss some practical aspects of the computational models and their interpretation, as well as possible future directions.The authors would like to acknowledge funding from “Departamento de Educación, Política Lingüística y Cultura del Gobierno Vasco” (Grant No. IT912-16 and IT1639-22) and the technical and human support provided by the Scientific Computing Service of SGIker (UPV/EHU/ ERDF, EU). E.D.-R. also acknowledges the postdoctoral fellowship from “Programa Posdoctoral de Perfeccionamiento de Personal Investigador Doctor” of the Basque Government

Adsorption and migration of Cs and Na ions in geopolymers and zeolites

Geopolymers may provide a more sustainable alternative to Portland Cement for various possible applications. Geopolymers have attracted particular interest for the immobilization of pollutants, owing to their high adsorption capacity, high thermal and chemical resistance, and low leachability. However, practical implementation is currently hindered by a limited understanding of how adsorption processes occur in geopolymers, and how they can be engineered to optimize the incorporation of pollutants and avoid their release. In this work, Molecular Dynamics simulations provide insights into these processes at the atomic scale, studying the role of host material composition and structure in the immobilization of Na and Cs ions. The simulations reveal that the most stable configurations for these ions are near the center of 6- and 8-membered aluminosilicate rings, where the coordination with the geopolymer is maximum. Higher contents of Al and degrees of crystallinity are found to yield more stable configurations for Cs ions, with more favorable adsorption enthalpies and lower diffusion coefficients. The comparison of different crystalline zeolite structures reveals that the framework of sodalite, used as the baseline to develop model geopolymer structures, is the most suitable for the immobilization of Cs since there are no channels and it is formed by small 4- and 6-member, all preventing Cs ions from escaping the cavities

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Atomistic simulations of confined species in 2D nanosructures: clays and C-S-H gel

246 p.In this thesis, atomistic simulations have been used to study and predict the properties of molecules and materials. The information provided by the molecular dynamics simulations complements and supports the experiments, helping in the interpretations of the results and serving as a guide for the design of new materials. First, the intercalation of two organic dyes, LDS-722 and pyronin Y, with two smectite clays, Laponite and saponite, has been studied. The simulation of these dye/clay systems has enable the understanding of their photophysical behavior, the dye aggregation and its diffusivity. The mechanical properties of these hybrid materials has also been characterized. Second, the retention of radiocesium in calcium silicate hydrates (C-S-H gel) has been evaluated, considering the impact of Cs concentration, Ca/Si ratio, counterions and Al incorporation in the silicate chains to form C-A-S-H. Third, the strengthening mechanisms in C-S-H gel that incorporates organic additives, APTES and PEG, has also been explored by molecular dynamics simulations. The bulk and Young¿s moduli have been determined by applying a hydrostatic and uniaxial pressures to the simulated systems, considering the effects of the hydrostatic pressure on the silicate chains and hydrogen bond network. The results presented in this thesis contribute to a better understanding of the guest-host interactions at atomic scale in the studied systems and may help in the design of new materials

Distinctive Diffusion Regimes of Organic Molecules in Clays: (De)coupled Motion with Water

The combination of organic and inorganic components enables the development of new generation of materials with innovative applications in many fields. Clays are commonly used to confine different ions and molecules since they act as an engineering barrier, avoiding the release of the entrapped species. In this work, we have employed molecular dynamics simulations to study the diffusivity of a variety of organic molecules enclosed in the interlaminar space of clays. We have found that the diffusivity of the organic molecules follows a universal trend, exhibiting low diffusion coefficients at low water contents, which are radically increased at a certain water content. This onset of diffusion is due to the rearrangement of the water molecules from monolayer to bilayer. At that point, the motion of the water/guest molecule cluster is decoupled, leading to the sharp increase of the diffusion coefficients.</div

Adsorption and Diffusion of Na+, Cs+ and Ca+2 Ions in C-S-H and C-a-S-H Nanopores

Cementitious materials act as a diffusion barrier, immobilizing liquid and solidradioactive waste and preventing their release into the biosphere. The retention capability of hydratedcement paste and its main hydration product, C-S-H gel, has been extensively explored experimentallyfor many alkali and alkaline earth cations. Nevertheless, the retention mechanisms of these cations atthe molecular scale are still unclear. In this paper, we have employed molecular dynamics simulationsto study the capacity of C-S-H to retain Cs, Ca and Na, analyzing the number of high-affinity sites onthe surface, the type of sorption for each cation and the diffusivity of these ions. We have also exploredthe impact of aluminum incorporation in C-S-H at a constant concentration of the ions in the gel pore.We found strong competition for surface sorption sites, with notable differences in the retention of thecations under study and a remarkable enhance of the adsorption in C-A-S-H with respect to C-S-H

Cs Retention and Diffusion in C-S-H at Different Ca/Si Ratios

Cement and concrete have been widely used as a barrier to isolate many types of contaminants, including radioactive waste, in repository sites. Nevertheless, the intrusion of groundwater in those nuclear repositories may release those contaminants by leaching mechanisms. Because of this, the retention and diffusion processes in cement matrix require to be analyzed in depth. The adsorption in cement and C‐S-H gel, its main hydration product, is influenced by factors as the pH, the composition or the alkali and alkaline earth content. In this work, molecular dynamics simulations were employed to study the role of Ca/Si ratio of the C‐S‐H in the capacity to retain Cs and diffusivity of these ions in gel pores. For that purpose, we built four different C‐S‐H models with Ca/Si ratios from 1.1 to 2.0. The results indicate better cationic retention at low Ca/Si ratios due to the interaction of the cations with the bridging silicate tetrahedrons. However, the average diffusion coefficients of the cations decrease at higher Ca/Si ratios because the high ionic constraint in the nanopore that induces a longrange ordering of the water molecules.</div