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The practical applications of surfactant solutions in confined geometries require a thorough understanding of the system properties. Coarse-grained simulation techniques are useful for studying the qualitative behaviour of these systems, whereas the atomistic molecular dynamics (MD) technique can be used to obtain a molecular-level description. In this work, canonical MD simulations were performed using GROMACS version 4.0 to investigate the self-assembling behaviour of sodium octanoate (SO) confined between two parallel walls. In particular, the effects of gap size, wall type, and surfactant concentrations on the morphology of the surfactant aggregates were studied to gain in-depth knowledge of the system. The simulation results reveal that the morphology of the micelles formed between two parallel walls are affected not only by the gap size and surfactant concentration, but also by the nature and characteristics of the confining walls. With the graphite walls, most octanoate molecules are adsorbed at lower concentrations, but they form micellar aggregates as the surfactant concentration increases. Spherical micelles were found in the larger gaps (4 nm and 5 nm) but not in the smaller gap (3 nm), and the micellar shape also changes with increasing surfactant concentration. SO forms bilayer structures instead of spherical micelles between two silica walls. Interestingly, in the hydrophilic silica confinement, the orientation of these bilayers changes with gap sizes, whereas in the hydrophobic silica confinement, these bilayers remain perpendicular to the wall in all cases. Potentials of mean force between different molecules and atomic groups were determined under different conditions in order to develop a better understanding of the simulation results. It reveals, the presence of the confinement can alter the intermolecular interactions among the surfactant molecules, which, in turn, directly affects the self-assembling process, particularly the size and shape of the aggregates. Indeed, the formation of bilayers in silica wall confinement, as opposed to spherical micelles in graphite confinement, is caused by the enhanced electrostatic interactions between the charged atoms in the solution. The results of this study are expected to provide further insight into the self-assembling behaviour of confined surfactant systems, and may ultimately lead to the development of novel nanomaterials.

No description available.

Ag nanoparticle (NP) paste was fabricated and used to bond Cu wire to Cu foil at low temperatures down to 433 K. The relatively low bonding temperature promotes this method to be used in polymer-based flexible electronics, which cannot withstand high bonding temperatures due the possible melting of the polymer substrate. Unlike low-temperature soldering techniquies, bonds formed by this method was proved to withstand temperatures higher than the bonding temperature, which also promotes it to be used in electronics that operate at high temperatures. The Ag NP paste was developed by increasing the concentration of 50 nm Ag NP sol from 0.001 vol.% to 0.1 vol.% by centrifugation. The 0.001 vol.% Ag NP sol was fabricated in water by reducing silver nitrate (AgNO3) using sodium citrate dihydrate (Na3C6H5O7.2H2O). The bond was formed by solid state sintering among the individual Ag NPs and solid state bonding of these Ag NPs onto both Cu wire and foil. Metallurgical bonds between Ag NPs and Cu were confirmed by transmission electron microscopy (TEM). The Ag NPs were coated with an organic shell to prevent sintering at room temperature. It was found that the organic shell decomposed at 433 K, defining the lowest temperature at which a bond could be formed. Shear tests showed that the joint strength increased as the bonding temperature increased due to enhanced sintering of Ag NPs at higher temperatures. For better understanding of the melting and the sintering kinetics of Ag NPs, a molecular dynamics (MD) simulation based on the embedded atom method (EAM) was conducted to different sizes of Ag NPs with diameters between 4 nm and 20 nm. Programmed heating of an equal rate was applied to all sizes of NPs to find the complete melting and surface premelting points and sintering kinetics of the Ag NPs. The initial structural configuration of the Ag NPs was FCC truncated octahedral, which found to be stable for this size range of NPs. As a first step toward drawing a phase map of stable solid phases of Ag NPs at different temperatures and sizes of Ag NPs, the stability of the FCC truncated octahedral was studied for Ag NPs in size range of 1 nm to 4 nm. The smallest Ag NPs at which this configuration is stable was determined as 1.8 nm. Unlike the previous theoretical models, this MD model predicted both complete melting and surface premelting points for a wider size range of NPs. Melting kinetics showed three different trends that are, respectively, associated with NPs in the size ranges of 4 nm to 7 nm, 8 nm to 10 nm, and 12 nm to 20 nm. Ag NPs in the first range melted at a single temperature without passing through a surface premelting stage. Melting of the second range started by forming a quasi-liquid layer that expanded to the core, followed by the formation of a liquid layer of 1.8 nm thickness that also subsequently expanded to the core with increasing temperature, completing the melting process. For particles in the third range, the 1.8 nm liquid layer was formed once the thickness of the quasi-liquid layer reached 5 nm. The liquid layer expanded to the core and formed thicker stable liquid layers as the temperature increased toward the complete melting point. The ratio of the quasi-liquid layer thickness to the NP radius showed a linear relationship with temperature. Sintering kinetics of two Ag NPs in the size range of 4 nm to 20 nm, and sintering of three and four Ag NPs of 4 nm diameter was also studied by MD simulation. The sintering process passed through three main stages. The first was the neck formation followed by a rapid increase of the neck radius to particle radius ratio at 50 K for 20 nm particles and at 10 K for smaller NPs. The second was characterized by a gradual linear increase of the neck radius to particle radius ratio as the temperature of the sintered structure was increased to the surface premelting point. A twin boundary was formed during the second stage that relaxed the sintered structure and decreased the average potential energy (PE) of all atoms. The third stage of sintering was a rapid shrinkage during surface premelting of the sintered structure. Based on pore geometry, densification occurred during the first stage for three 4 nm particles and during the second stage for four 4 nm particles. Sintering rates obtained here were higher than those obtained by theoretical models generally used for predicting sintering rates of micro-particles.

Two force fields, the GROMOS53A5/53A6 (united atom) and the AMBER95 (all atom) parameter sets, coupled with partial atomic charges derived from quantum mechanical calculations were evaluated for their ability to reproduce the known crystalline forms of the polyols mannitol and sorbitol. The force fields were evaluated using molecular dynamics simulations at 10 K (which is akin to potential energy minimization) with the simulation cell lengths and angles free to evolve. Both force fields performed relatively poorly, not being able to simultaneously reproduce all of the crystal structures within a 5% deviation level. The parameter sets were then systematically optimized using sensitivity analysis, and a revised AMBER95 set was found to reproduce the crystal structures with less than 5% deviation from experiment. The stability of the various crystalline forms for each of the parameter sets (original and revised) was then assessed in extended MD simulations at 298 K and 1 bar covering 1 ns simulation time. The AMBER95 parameter sets (original and revised) were found to be effective in reproducing the crystal structures in these more stringent tests. Remarkably, the performance of the original AMBER95 parameter set was found to be slightly better than that of the revised set in these simulations at 298 K. The results of this study suggest that, whenever feasible, one should include molecular simulations at elevated temperatures when optimizing parameters. / Dutch Top Institute Pharma

The dynamic properties of Palladium (Pd) and Aluminum (Al) metals and their alloys are investigated by means of Molecular Dynamics using the Quantum Sutton-Chen force field in five different concentrations. Calculations have been carried out for liquid structures. Although this study is done for liquid structures, basic solid state properties are also investigated to prove the validity of potential parameters. Results are compared with each other and with experimental, theoretical and simulated results. Liquid state transferability of Quantum Sutton-Chen parameters have been investigated and discussed. High temperature properties, which are not easy to work experimentally, are simulated and high temperature behavior of Pd-Al alloy is investigated.

In this thesis, issues pertaining to the dynamics of nanoscale liquid systems, such as nanojets and nanobridges, in vacuum as well as in ambient gaseous conditions, are explored using both extensive molecular dynamics simulations and theoretical analyses. The simulation results serve as ``theoretical experimental data' (together with laboratory experiments when available) for the formulation, implementation, and testing of modified hydrodynamic formulations, including stochastic hydrodynamics. These investigations aim at extending hydrodynamic formulations to the nanoscale regime. In particular, the instability, and breakup of liquid nanobridges and nanojets are addressed in details. As an application of the microscopic hydrodynamics, a heated-nozzle technique to generate and control nanojets is proposed. Both simulations and microscopic hydrodynamic modeling reveal the formation of a ``virtual convergent nozzle', which consists of a narrowing convergent liquid core within a growing evaporative sheath, by the nanojet itself inside the real nozzle. The diameter of the resulting ejected nanojet is much smaller than the diameter of the nozzle. By adjusting the temperature distribution of the real nozzle, the size and shape of the virtual nozzle are changed, which in turn changes the diameter and the direction of the ejected nanojet.

Computational tools play an important role in the description of biological systems. Scientists describe and study structure, conformational changes and interactions between molecules in silico, often as a cheaper and faster alternative for biosynthesis. The simulated dynamic behavior in time of a molecular system is a straight forward source of information about substrate-enzyme interactions at the atomic level, and a powerful tool for the identification of molecular properties important in enzymatic reactions. Our study is focused on the computational investigation of structure and substrate specificity of hydrolases important in biotransformation. The computational work was performed in close collaboration with biochemists-experimentalists from Charles University and the Microbiological Institute of the Academy of Sciences of the Czech Republic. Hydrolases have great a potential in the chemoenzymatic synthesis of modified carbohydrates with regulated properties. Carbohydrates, as substrates of hydrolases, are important in normal functionality of many organisms. They have a dual role in immune response regulation: some carbohydrates (like GlcNAc and ManNAc) participate in activation and some (like GalNAc) in suppressing immunity; glycosidase deficiency is associated with a number of lysosomal disorders. We used homology modeling, computational docking and molecular dynamics simulation (MD) methods for the complex study of fungal hydrolases: alpha-galactosidase/alpha-N-acetylgalactosaminidase from Aspergillus niger; beta-N-acetylhexosaminidases (HEX) (from Aspergillus oryzae and Penicillium oxalicum); nitrilase from Aspergillus niger. Our structural study unambigously demonstrates that the enzyme encoded by genes variant A (aglA) from A. niger is able to accept alpha-N-acetylgalactosamine as its substrate and explains structural features responsible for its specificity. Homology models of HEXs from P. oxalicum and A. oryzae were built and compared. Homology models were used to study the role of protein glycosylation, disulfide bonds, dimer formation and interaction with natural and modified substrates. Model of nitrilase from Aspergillus niger helped to analyze multimer formation.

abstract: A comprehensive and systematic investigation on the diffusion and phase behaviors of nanoparticles and macromolecules in two component liquid-liquid systems via Molecule Dynamic (MD) simulations is presented in this dissertation. The interface of biphasic liquid systems has attracted great attention because it offers a simple, flexible, and highly reproducible template for the assembly of a variety of nanoscale objects. However, certain important fundamental issues at the interface have not been fully explored, especially when the size of the object is comparable with the liquid molecules. In the first MD simulation system, the diffusion and self-assembly of nanoparticles with different size, shape and surface composition were studied in an oil/water system. It has been found that a highly symmetrical nanoparticle with uniform surface (e.g. buckyball) can lead to a better-defined solvation shell which makes the “effective radius” of the nanoparticle larger than its own radius, and thus, lead to slower transport (diffusion) of the nanoparticles across the oil-water interface. Poly(N-isopropylacrylamide) (PNIPAM) is a thermoresponsive polymer with a Lower Critical Solution Temperature (LCST) of 32°C in pure water. It is one of the most widely studied stimulus-responsive polymers which can be fabricated into various forms of smart materials. However, current understanding about the diffusive and phase behaviors of PNIPAM in ionic liquids/water system is very limited. Therefore, two biphasic water-ionic liquids (ILs) systems were created to investigate the interfacial behavior of PNIPAM in such unique liquid-liquid interface. It was found the phase preference of PNIPAM below/above its LCST is dependent on the nature of ionic liquids. This potentially allows us to manipulate the interfacial behavior of macromolecules by tuning the properties of ionic liquids and minimizing the need for expensive polymer functionalization. In addition, to seek a more comprehensive understanding of the effects of ionic liquids on the phase behavior of PNIPAM, PNIPAM was studied in two miscible ionic liquids/water systems. The thermodynamic origin causes the reduction of LCST of PNIPAM in imidazolium based ionic liquids/water system was found. Energy analysis, hydrogen boding calculation and detailed structural quantification were presented in this study to support the conclusions. / Dissertation/Thesis / Doctoral Dissertation Chemical Engineering 2017

Modéliser la déformation plastique des polycristaux est un objectif majeur de la science des matériaux. Tous les modèles actuels comportent une partie phénoménologique n´ecessitant un ajustement de paramètres sur des résultats expérimentaux. Cette thèse vise à mettre en place un nouveau modèle, justifié physiquement, sans paramètre ajustable et adapté à la modélisation du polycristal CFC en sollicitation monotone. Afin de mesurer les champs mécaniques à l’échelle du micromètre, des mesures de microdiffraction Laue ont été réalisées sur un tricristal de cuivre à une faible déformation plastique. Ces mesures nous renseignent sur les mécanismes plastiques intervenant très près des joints de grains et définissent des états de référence pour les simulations. On montre principalement que la déformation plastique s’accompagne d’un stockage de dislocations géométriquement nécessaires (GND) aux joints de grains, en relation avec l’apparition de contraintes internes à longue distance. Des simulations de Dynamique des Dislocations dans des bicristaux ont ´et´e réalisées afin de caractériser les phénomènes physiques mis en œuvre. Ces simulations confirment que l’interaction dislocations - joints de grains s’accompagne d’un stockage de GND sous la forme de microstructures tridimensionnelles très inhomogènes. Les propriétés mécaniques induites par ce phénomène complexe peuvent être quantifiées par des lois continues élaborées à partir de l’approximation théorique d’un empilement unidimensionnel. Les lois de comportement ainsi définies ont ensuite été incorporées dans une modélisation micromécanique de plasticité cristalline, jusqu’ici dédiée au monocristal CFC. Le modèle ainsi construit a maintenant la capacité de prédire les mesures réalisées sur le tricristal de cuivre. Nous avons ainsi mis en place un modèle physiquement justifié et adapté `a la modélisation du polycristal CFC en sollicitation monotone. / The modeling of strain hardening in polycrystals is a difficult and still standing task. Current existing models are partly phenomenological, as they always consider constitutive parameters adjusted on the experiment. The aim of the present study is to design a physically based model for the basic problem of monotonic deformation in the FCC polycrystal. Laue microdiffraction is used to measure the mechanical fields in the vicinity of grain boundaries in a copper tricrystal compress at 0.2%. These measurements aim to characterize the plastic phenomena involved and to provide experimental data as bench results for the simulations. Evidences of geometrically necessary dislocations (GND) storage close to the grain boundaries are given in relation with the apparition of longrange internal stresses. Dislocations Dynamics simulations are used to study the plastic strain close to a grain boundary in Cu bicrystals. We show that close to the boundaries plastic strain is associated to the storage of heterogeneous GNDs in complex 3D microstructures. The mechanical properties associate to such microstructure can be described with continuous laws based on a theoretical approximation assuming a 1D pile-up. The corresponding constitutive laws are then introduced in a crystal plasticity model initially devoted to FCC single crystal plasticity and solved with Finite Elements simulations. The new model we propose as now the capacity to reproduce or predict the experimental results we first obtained in the Cu tricrystal. In conclusion, a physically justified model is proposed to predict plastic deformation for the FCC polycrystal in monotonic deformation.