No description available.

This dissertation is dedicated to develop models and methods to bridge atomistic and continuum scales of deformation processes in asphalt-aggregate interfacial composite materials systems. The deformation and failure behaviors, e.g. nanoscale strength, deformation, stiffness, and adhesion/cohesion at asphalt-aggregate interfaces are all evaluated by means of atomistic simulations. The atomistic modeling approach is employed to simulate mechanical properties, which is connected by their common dependence on the nanoscale bonding and their sensitive dependences on mechanics and moisture sensitivity. Specifically, CVFF-aug forcefield is employed in the atomistic calculations to study the fundamental failure processes that appear at the interface as a result of a mechanical deformation. There are five primary aspects to this dissertation. First, the multiscale features of asphalt concrete materials are characterized by using nanoscale characterization & fabrication devices, e.g. High Resolution Optical Microscope (HROM), Environmental Scanning Electron Microscope (ESEM), Transmission Electron Microscope (TEM), Focused Ion Beam (FIB), and Atomistic Force Microscope (AFM). Second, based on the multiscale devices characterization of the interfaces, a 2-layer atomistic bitumen-rock interface structure is constructed. Interface structure evolution under uniaxial tension is performed with various deformation rates. Comparison is made between both theoretical and experimental characterizations of interface configuration. Molecular dynamics (MD) simulations are used to investigate potential relationships between interface structure and morphology. Influences of deformation rate and temperature factors are discussed in terms of interface region stress-strain relation and loading time duration. Third, molecular dynamics simulations are also performed to provide a characterization of atomic scale mechanical behaviors for a 3-layer confined shear structure which leads to interfacial shear failure. In addition, atomistic static simulation approach is employed to calculate a couple of mineral crystals' elastic constants. Furthermore, molecular dynamics simulations are also used to predict the static, thermodynamic, and mechanical properties of three asphalt molecular models. Fourth, the high performance parallel computing technology is extensively employed throughout this dissertation. In addition to use the large-scale MD program, LAMMPS, the author developed a high performance parallel distributive computing program, MPI_multistress, to implement the multiscale understanding/predicting of materials mechanical behaviors. Finally, this research also focuses on the evaluation of the susceptibility of aggregates and asphalts to moisture damage through understanding the nano-mechanisms that influence adhesive bond between aggregates and asphalt, as well as the cohesive strength and moisture susceptibility of the specific asphalt-aggregate interfaces. Surface energy theory and pull-out simulation are used to compute the adhesive bond strength between the aggregates and asphalt, as well as the cohesive bond strength within the binder. In general, this dissertation has focused on the development of nanoscale modeling methods to assess asphalt-aggregate interfacial atomistic deformation and failure behaviors, as well as moisture effects on asphalt mixture strength. Simulation results provide valuable insights into mechanistic details of nanoscale interactions, particularly under conditions of various deformation rates and different temperatures. The results obtained show that a reasonable agreement between the theoretical and pavement industry observations is satisfactory. We conclude that the theoretical calculations presented here are useful in asphalt concrete industry for predicting the mechanical properties of asphalt-aggregate interfaces, which are difficult to obtain experimentally because of their small size. / Ph. D.

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

No description available.

This thesis discusses Kaplan, a free conformer searching package, available at github.com/PeaWagon/Kaplan / Conformer searching algorithms find minima in the Potential Energy Surface (PES) of a molecule, usually by following a torsion-driven approach. The minima represent conformers, which are interchangeable via free rotation around bonds. Conformers can be used as input to computational analyses, such as drug design, that can convey molecular reactivity, structure, and function. With an increasing number of rotatable bonds, finding optima in the PES becomes more complicated, as the dimensionality explodes. Kaplan is a new, free and open-source software package written by the author that uses a ring-based Evolutionary Algorithm (EA) to find conformers. The ring, which contains population members (or pmems), is designed to allow initial PES exploration, followed by exploitation of individual energy wells, such that the most energetically-favourable structures are returned. The strengths and weaknesses of existing publicly available conformer searchers are discussed, including Balloon, RDKit, Openbabel, Confab, Frog2, and Kaplan. Since RDKit is usually considered to be the best free package for conformer searching, its conformers for the amino acids were optimised using the MMFF94 forcefield and compared to the conformers generated by Kaplan. Amino acid conformers are well characterised, and provide insight for protein substructure. Of the 20 molecules, Kaplan found a lower energy minima for 12 of the structures and tied for 5 of them. Kaplan allows the user to specify which dihedrals (by atom indices) to optimise and angles to use, a feature that is not offered by other programs. The results from Kaplan were compared to a known dataset of amino acid conformers. Kaplan identified all 57 conformers of methionine to within 1.2Å, and found identical conformers for the 5 lowest-energy structures (i.e. within 0.083Å), following forcefield optimisation. / Thesis / Master of Science (MSc) / A conformer search affords the low-energy arrangements of atoms that can be obtained via rotation around bonds. Conformers provide insight about the chemical reactivity and physical properties of a molecule. With increasing molecule size, the number of possible conformers increases exponentially. To search the space of possible conformers, this thesis presents Kaplan, which is a software package that implements a novel directed, stochastic, sampling technique based on an Evolutionary Algorithm (EA). Kaplan uses a special type of EA that stores sets of conformers in a ring-based structure. Unlike other conformer-specific packages, Kaplan provides the means to analyse and interact with found conformers. Known conformers of amino acids are used to verify Kaplan. Other tools for generating conformers are discussed, including a comparison of freely available software. Kaplan effectively finds the conformers of small molecules, but requires additional parametrisation to find the conformers of mid-sized molecules, such as Penta-Alanine.

The swelling properties of Bentonite are highly affected by clay content and the clay-water interactions that arise from the ion distribution in the diffuse double layer formed near the charged montmorillonite (or smectite) surfaces. Existing continuum models describing the electric double layers, such as classical Poisson-Boltzmann and DLVO theory, ignore the ion-ion correlations, which are especially important for multivalent ions at high surface charge and ionic strength. To better understand the clay-water interactions, atomistic models were developed using both density functional theory of fluids (DFT) as well as classical molecular dynamics (MD) methods. In order to increase our understanding of water-saturated, swelling smectite clays, a DFT, technique was initially developed that allowed more accurate predictions of important thermodynamic properties of the diffuse double layers. This DFT approach was then extended to handle systems with mixtures of different sizes and charges. The extended DFT model was verified against experiments and Monte-Carlo simulations. One practical application was to predict the ion exchange equilibria in Bentonite clays, which have wide practical usage in different areas. Nevertheless, in the DFT work it was realized that DFT demands that the particles, ions in this case, which are described as hard spheres, realistically cannot be described as such at low water loadings, when ion specific hydration forces govern the electric double layer properties. To study how the deformation of the hydration shells of Ca2+ influences the properties of compacted smectite clays, MD simulations using the CLAYFF forcefield were employed in order to account for the deformation of the hydration shells. Comparisons of DFT and MD modeling then allowed to demonstrate under which conditions DFT modeling becomes increasingly inaccurate and when it still can give accurate results. / Under senare år har mycket forskning ägnats åt att förstå egenskaperna hos svällande leror som används för att skydda mot läckage av föroreningar från kontaminerade områden och från framtida slutförvar av radionuklider. Den fria svällningen förorsakas av de starka osmotiska krafter som uppstår när vatten tränger in mellan de tunna elektriskt negativt laddade lermineralskikten och löser de laddningskompenserande jonerna i det diffusa dubbelskiktet. I flera arbeten användandes av sk. kontinuum-teori har vattenmolekylens form, specifika orientering och bindning till katjonerna i de nanometerstora utrymmen mellan lerpartiklarna ej beaktats samt ej heller hur de hydratiserade jonerna orienteras på de atomärt ojämna ytorna. Detta möjliggörs dock genom modellering av de enskilda atomernas och jonernas interaktioner med molekyldynamik simuleringar, MD. I detta arbete har programmet Gromacs använts tillsammans med kraftfältet CLAYFF för att studera dessa fenomen i montmorillonitleror med natrium- och kalciumjoner. Simuleringarna visar att natrium bildar transienta innersfärkomplex vilka orienterar sig i bi-triangulära fördjupningar på ytan, ungefär 3.8 Å från mitt-planet mellan lerytorna. Denna orientering observeras ända upp till att avståndet mellan ytorna ökat till större än motsvarande fem lager vattenmolekyler mellan lerpartiklarnas ytor. Detta sker inte med kalcium, oberoende av avståndet mellan ytorna. Natriumjoner koordineras med fyra vattenmolekyler och en syreatom på leran vid ett lager vatten mellan ytorna och med fem till sex vattenmolekyler, ortogonalt orienterade med ökande mängd vatten mellan ytorna, och med en hydratiserad jon-radie av 3.1 Å. Kalcium koordinerar till sju vattenmolekyler vid ett vattenlager mellan ytorna, men ökar till åtta ortogonalt orienterade vattenmolekyler med en jonradie på 3.3 Å vid större avstånd. Generellt visas att när avståndet mellan lerytorna är mindre än ca 10 Å, deformeras de annars symmetriskt hydratiserade jonerna. En jämförelse mellan MD simuleringar och med klassisk täthetsfunktionalteori, DFT, visar att den senare inte kan beskriva hur yttersfärkomplexen samverkar med laddningarna bundna närmast ytan, dvs i Stern-lagret. / <p>QC 20170403</p>