Towards hybrid molecular simulations

In many biology, chemistry and physics applications molecular simulations can be used to study material and process properties. The level of detail needed in such simulations depends on the application. In some cases quantum mechanical simulations are indispensable. However, traditional ab-initio methods, usually employing plane waves or a linear combination of atomic orbitals as a basis, are extremely expensive in terms of computational as well as memory requirements. The well-known fact that electronic wave functions vary much more rapidly near the atomic nuclei than in inter-atomic regions calls for a multi-resolution approach, allowing one to use low resolution and to add extra resolution only in those regions where necessary, so limiting the costs. This is provided by an alternative basis formed of wavelets. Using such a wavelet basis, a method has been developed for solving electronic structure problems that has been applied successfully to 2D quantum dots and 3D molecular systems. In other cases, it suffices to use effective potentials to describe the atomic interaction instead of the use of the electronic structure, enabling the simulation of larger systems. Molecular dynamics simulations with such effective potentials have been used for a systematic study of surface wettability influence on particle and heat flow in nanochannels, showing that the effects at the solid-gas interface are crucial for the behavior of the whole nanochannel. Again in other cases even coarse grained models can be used where the average behavior of several atoms is combined into a single particle. Such a model, refraining from as much detail as possible while maintaining realistic behavior, has been developed for lipids and with this model the dynamics of membranes and vesicle formation have been studied in detail. A disadvantage of molecular dynamics simulations with effective potentials is that no reactions are possible. Therefore a new method has been developed, where molecular dynamics is coupled with stochastic reactions. Using this method, both unilamellar and multilamellar vesicle formation, and vesicle growth, bursting, and healing are shown. Still larger systems can be simulated using other methods, like the direct simulation Monte Carlo method. However, as shown for nanochannels, these methods are not always accurate enough. But, exploiting again that the finest level of detail is often only needed in part of the domain, a hybrid method has been developed coupling molecular dynamics, where needed for accuracy, and direct simulation Monte Carlo, where possible in order to speed up the calculation. Further development of such hybrid simulations will further increase molecular simulation’s scientific role

Reactivity of the Clay Mineral Montmorillonite: A First Principles Study

PhDThe recent development of clay-polymer nanocomposite materials has led to ail increased interest in the structure and properties of clay minerals. In this thesis the reactivity of the clay mineral montmorillonite is explored by means of density functional theory based calculations. In particular three aspects are considered: catalytic properties, cation migration and dehydroxylation. The origin of the catalytic properties of the clay mineral is investigated in the context of the synthesis of clay-polymer nanocomposite materials, by in sttu, intercalative polymerisation. It is found that catalysis is most likely to occur at the clay mineral lattice-edge where exposed aluminium atoms act as Lewis acid sites. Migration of lithium cations into the clay mineral lattice is explored by means of first principles molecular dynamics. Comparison of calculated hvdrox-vl stretching frequencies, with those from experiment indicates that cations migrate to vacant octahedral sites, as oppose to the ditrigonal cavities. Dehydroxylation of the clay mineral is examined by consideration of a cis-vacant pyrophyllite structure. It is shown that dehydroxylation leads to formation of a tyan8-vacant structure, with aluminium in trigonal bipyramidal coordination and a highly distorted tetrahedral layer. Differences in the dehydroxylation behaviour of cm and tran8-vacant pyrophyllite are shown to be due to the fact that in the former adjacent hydroxyl groups bridge different pairs of aluminium atoms, while in the latter they are both bonded to the same pair. Overall density functional theory based calculations are shown to be a powerful tool for the studly of the structure and reactivity of clay minerals.Queen Mary University of London W.R. Grace & Co

Time-Resolved Phase-Sensitive Second Harmonic Generation Spectroscopy of the Hydrated Electron at the Water/Air Interface

The hydrated electron attracts attention since its discovery over fifty years ago. Being one of the products of the ionization of water, hydrated electrons, which are free electrons in water, play significant roles in biological damage, atmospheric chemistry, nuclear chemistry, etc.. However, despite its importance and the large number of studies on the hydrated electron many aspects of it are still not resolved. One of these concern its existence and behaviour at the water surface, which is of great interest since many of the processes it is involved in take place at interfaces. In this work, a technique is developed, that is based on the second harmonic generation (SHG) and enables the study dynamics of the hydrated electron at the water/air interface. By introducing a local oscillator, which interferes with obtained SHG from the water surface, a signal directly proportional to the sample concentration is obtained, in contrast to the quadratic dependence from conventional SHG. Moreover, the technique allows phase information to be obtained, which enables the determination of the real and imaginary parts of the 2nd order non-linear susceptibility. In addition to this, the technique uses a lock-in measurement, removing large constant offset from the interference. The technique yields high quality data on adsorbates with low surface concentration and has been extended to the time domain which provides insight into the dynamics of hydrated electrons at the water/air interface. In this experiment, the electron was generated using the charge-transfer-to-solvent transition of iodide and probed primarily over the first few picoseconds. This probes the initial solvation of the electron at the interface. Our results suggest that the dynamics are similar to the dynamics observed in the bulk, although the added phase-sensitivity provides new information about early solvation dynamics

Aspects of structural and electronic disorder in network materials: approaches to simulation

Disorder in solids is one of the critical problems facing exponents of simulation-based studies in the mineral sciences. This thesis presents some novel techniques which can be used to probe the structure and dynamics of such systems under simulation. Two techniques are focussed upon. Firstly, the use of simulated charge as a probe to investigate the bonding and electrochromic properties of materials (particularly tungsten trioxide); secondly, derivation of a novel algorithm (Constrained Linear Maximization) for prediction of transition states by simulation, and its application to diffusion simulations in both crystalline network silicates and silica glass.EPSR