Computational Investigation of Stellar Cooling, Noble Gas Nucleation, and Organic Molecular Spectra

Since the advent and optimization of the Hartree-Fock method, quantum chemistry has been utilized to investigate systems operating on timeframes and environments traditionally unavailable to bench-top chemistry. As computational methods have grown more robust and less time consuming, quantum chemistry has been utilized to investigate a range of fields, including the steadily growing discipline of computational astrochemistry. Through the lens of computational astrochemistry, chemistry that occurred billions of years ago can be explored with equal clarity to that which is currently happening in the cosmos. The work presented throughout this thesis is a series of investigations into different timeframes of the universe: 1) a study on novel cooling mechanisms of the earliest stars to ever form following the calamity of the big bang; 2) a look into the solvation of a ubiquitous molecule in noble gas atoms; and 3) an investigation of the anharmonic vibrational frequencies of a molecule that has promise to be a fundamental building block of amino acids in the ISM

NOVEL CARBON-BASED MATERIALS MIXING DIFFERENT HYBRIDIZATION KINDS

In the last twenty years, carbon-based materials and nanostructures have gained more and more popularity. Driven by the breakthrough-discovery and the synthesis of fullerenes, nanotubes, graphene and carbynes, also the search for new exotic carbon allotropes attracted increasing attention in the scientific community, also in view of applications. This thesis focuses on the construction and the investigation of three novel crystalline allotropes of carbon, all mixing different orbital hybridizations. We have employed state-of-the-art numerical simulations to investigate structural, electronic, and mechanical properties of the three structures. Two of these allotropes, novamene and protomene, combine sp2 and sp3 hybridizations and exhibit a semiconductor character in their lowest-energy Peierls-dimerized configuration. Both structures show transitions towards a metallic state at a relatively small energy cost. The third allotrope, zayedene, mixes sp, in the form of a linear chain, and sp3 providing an enclosing cage. This structure exhibits a clear metallic character due to the dangling bonds inside the cavity. We predict characteristic high-frequency vibrations associated with sp chain stretching modes. We also investigate the thermodynamic stability of zayedene at standard conditions. Finally we suggest how hundreds of different allotropes can be built from the simple ones investigated

Investigation of Optical and Structural Properties of GeSn Heterostructures

Silicon (Si)-based optoelectronics have gained traction due to its primed versatility at developing light-based technologies. Si, however, features indirect bandgap characteristics and suffers relegated optical properties compared to its III-V counterparts. III-Vs have also been hybridized to Si platforms but the resulting technologies are expensive and incompatible with standard complementary-metal-oxide-semiconductor processes. Germanium (Ge), on the other hand, have been engineered to behave like direct bandgap material through tensile strain interventions but are well short of attaining extensive wavelength coverage. To create a competitive material that evades these challenges, transitional amounts of Sn can be incorporated into Ge matrix to form direct bandgap GeSn alloys that have led to the increasing possibility of engineering a suite of low-cost, light emission sources that applies to a wide range of infrared photonics and optoelectronics systems. Hence, the importance of studying the structural and optical properties of these GeSn heterostructures cannot be overemphasized. The first part of this dissertation investigates the structural and optical properties of SiGeSn/GeSn/SiGeSn quantum wells (QWs) where the photoluminescence (PL) behaviors of thick (22 nm in well) and thin (9 nm in well) GeSn QW samples are compared. Using PL results from two excitation lasers (532 nm and 1550 nm lasers) as well as studying their respective optical transitions, the result reveals that the thicker well sample shows i) a more direct bandgap outcome in addition to a much lower ground energy Г valley; ii) a higher carrier density within the well, and iii) an increased barrier height coupled with improved carrier confinement. All of these resulted in a significantly enhanced emission that allows for the first-ever estimation of GeSn QWs quantum efficiency (QE) while also suggesting a path towards efficient mid-infrared devices. To further improve the carrier confinement while also reducing the carrier leakage in the thicker well design, a SiGeSn/GeSn/GeSn/SiGeSn separate confinement heterostructure (SCH) is introduced. The sample is characterized and the optical properties are compared with the previously reported 9 nm and 22 nm well non-SCH samples. Based on the optical transition analysis, the SCH QW also shows significantly higher carrier confinement compared to reference samples. In addition to these studies, an attempt is made to investigate advanced quantum well structures through an all-inclusive structural and optical study of SiGeSn/GeSn/SiGeSn multi-quantum wells (MQWs). The resulting analysis shows evidence of intermixing diffusion during growth. The second part of this work provides insights into the behavior of annealed GeSn bulk samples near the indirect-to-direct transition point. The study attempts to provide connections between the strain, composition, and defect densities before and after annealing. The result reveals the impact of annealing on a sample may either i) lower the strain giving rise to an increased PL while reducing the energy separation or ii) introduce misfit dislocation/ surface roughness leading to an affected or decreased PL. Finally, this work also explores the low-temperature capability of our in-house plasma-enhanced ultra-high vacuum chemical vapor deposition system through the growth of Si-on-Ge epitaxy and pressure-dependent growth of GeSn bulk heterostructures

Structural Elucidation of Membrane Proteins Involved in Photosynthesis

abstract: Over the last century, X-ray crystallography has been established as the most successful technique for unravelling the structure-function relationship in molecules. For integral membrane proteins, growing well-ordered large crystals is a challenge and hence, there is room for improving current methods of macromolecular crystallography and for exploring complimentary techniques. Since protein function is deeply associated with its structural dynamics, static position of atoms in a macromolecule are insufficient to unlock the mechanism. The availability of X-ray free electron lasers presents an opportunity to study micron-sized crystals that could be triggered (using light, small molecules or physical conditions) to capture macromolecules in action. This method of ‘Time-resolved serial crystallography’ answers key biological questions by capturing snapshots of conformational changes associated with multi-step reactions. This dissertation describes approaches for studying structures of large membrane protein complexes. Both macro and micro-seeding techniques have been implemented for improving crystal quality and obtaining high-resolution structures. Well-diffracting 15-20 micron crystals of active Photosystem II were used to perform time-resolved studies with fixed-target Roadrunner sample delivery system. By employing continuous diffraction obtained up to 2 A, significant progress can be made towards understanding the process of water oxidation. Structure of Photosystem I was solved to 2.3 A by X-ray crystallography and to medium resolution of 4.8 A using Cryogenic electron microscopy. Using complimentary techniques to study macromolecules provides an insight into differences among methods in structural biology. This helps in overcoming limitations of one specific technique and contributes in greater knowledge of the molecule under study.Dissertation/ThesisDoctoral Dissertation Biochemistry 201

Applying simulation techniques to train railway traction drivers

The writer analyses the introduction of a simulator enabled approach to railway traction driver training and assesses whether the transition from a conventional training delivery process has been effective. The evaluation of effectiveness is based on a study of Iarnród Éireann’s simulator system. Evidence is contained within four supporting strands, i.e., the change in relevant operational risk that has been calculated using ex ante and ex post runs of Iarnród Éireann’s risk model, the internal rate of return on the financial investment necessary to effect the change, the results of an operator attitudinal study and the findings of an independent expert audit. The study establishes that simulation is an effective training medium. The attributes of the system and the use cases that resulted in this finding are described. The writer also presents additional value-adding training objectives that could increase the project’s internal rate of return or IRR. The study affirms that the required verisimilitude of a simulator system is a function of the training goals and the nature of the skills under development. Design features and use strategies can mitigate for potential negative effects of simulator operation. The findings have industry-wide relevance for those tasked with providing effective training to the 133,000 train drivers within the European Union

Molecular Dynamics Simulations using Advanced Sampling and Polarizable Force Fields

Molecular dynamics (MD) simulations were carried out for aqueous dipeptides, water over self-assembled monolayer (SAM) surfaces, and the nicotinic acetylcholine receptor (nAChR) ion channel. The main goal is to use advanced methods to increase the accuracy of molecular dynamics simulations while seeking solutions to problems relevant to chemistry, biophysics and materials science. In addition, activation energies of several cyclodimerization reactions were studied quantum mechanically. The simulations of the aqueous dipeptides and SAM surfaces involve modeling and detailed analysis of interfacial water, which is of interest to a range of fields from biology to materials science. For example, water has a central role in biology and medicine since biomolecules cannot function without water. Both sets of simulations were performed using both polarizable and nonpolarizable force fields. These systems were used as a test ground to assess the effects of explicit incorporation of polarizability and also to determine whether the models can adequately reproduce the experimental data, in particular, the aggregation data of aqueous dipeptides and contact angles of water over SAMs of different chemical character. Since the systems are well-characterized and relatively simple, they provide excellent models to test polarizable force fields to increase the accuracy of molecular dynamics simulations. Polarizable water was depolarized around dipeptide solutes and also at the interface with different SAM surfaces, reflecting its ability to adapt to heterogeneous electrostatic environments. Although the water shows more realistic structure and dynamics in the polarizable simulations, the peptide aggregation behavior agrees less well with the experiment. In this case, neither model successfully reproduces the experimental degree of aggregation. In the case of SAM surfaces, both sets of simulations produce fairly similar results. More studies are suggested to further test and improve the polarizable force fields. The third system studied is the modeling of wild-type and mutant nAChR ion channel proteins. Adaptive biasing force method was used to achieve improved sampling, and subsequently increase the efficiency and accuracy of MD simulations. The nAChR channels are involved in a number of cognitive and brain functions including learning and memory. Dysfunction in these receptors are associated in a variety of neuronal diseases including epilepsy, schizophrenia and Alzheimer\u27s Disease. The present study models the wild-type and two physiologically-relevant mutant structures to assess the effects of mutations on ion translocation energetics and the geometry of the channel. Open channel (conducting, active) structures were obtained from the available closed channel structure. One of the mutants was found to increase the energetic barrier for ion translocation, while the other one decreased the barrier. The ion channel structures were analyzed in detail to understand the structural changes that took place during the channel opening. The channel opening was found to be mediated by large-scale helix motions rather than small-scale side chain motions. Aside from the MD simulations, the final project involves quantum mechanical simulations, which are often needed in parametrization of molecular dynamics force fields. Density functional theory (DFT) calculations were employed to calculate the activation energies of three cyclodimerization reactions of trifluorovinyl ether monomers. The results agree with and further explain the experimentally observed reactivity in these types of reactions

Laboratory-directed research and development: FY 1996 progress report

This report summarizes the FY 1996 goals and accomplishments of Laboratory-Directed Research and Development (LDRD) projects. It gives an overview of the LDRD program, summarizes work done on individual research projects, and provides an index to the projects` principal investigators. Projects are grouped by their LDRD component: Individual Projects, Competency Development, and Program Development. Within each component, they are further divided into nine technical disciplines: (1) materials science, (2) engineering and base technologies, (3) plasmas, fluids, and particle beams, (4) chemistry, (5) mathematics and computational sciences, (6) atomic and molecular physics, (7) geoscience, space science, and astrophysics, (8) nuclear and particle physics, and (9) biosciences

Cornerstones in Contemporary Inorganic Chemistry

A collection of essential research articles and scientific reviews covering some of the most pertinent and topical areas of study that currently constitute Inorganic Chemistry in the early 21st century

Dynamics of sliding mechanisms in nanoscale friction

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2002.Includes bibliographical references.Nanotribology is the study of friction and wear at the nanoscale, with relevance to such applications as micromechanical systems (MEMS) and thin, hard coatings. For these systems, classical laws of friction are inappropriate due to the small dimensions of the sliding elements and the lack of excessive plastic deformation. This thesis presents a theoretical investigation of friction at the sliding interface by Molecular Dynamics (MD) simulations of ideal Lennard-Jones solids. The effect of the interfacial structure on the frictional behavior is investigated by simulating a variety of interface configurations: commensurate, noncommensurate (or grain boundary), and amorphous. The effect of adhesion on the frictional behavior is also explored through a parametric study. For the commensurate interface, the degree of adhesion determines whether sliding occurs in the frictional or "frictionless" regime; the former is distinguishable by the presence of jump phenomena, the principal mechanism of friction in the MD model. The Sigma-5 [100](310) symmetric tilt grain boundary exhibits three distinct sliding regimes which are, in the order of increasing adhesion, frictionless sliding, frictional sliding, and sliding coupled with grain boundary migration. Twist grain boundaries of the (111) plane exhibit frictionless sliding for all degrees of adhesion. Among the structures simulated, the grain boundary systems have the lowest friction due to the intrinsic misorientation at the sliding interface. In the amorphous system, sliding occurs by a series of random local slips due to the individual atomic motion associated with the disordered structure.(cont.) Increasing the adhesion leads to the initiation of a shear-induced crystallization process followed by an extremely rapid growth of the crystalline cluster. Friction in the amorphous system increases with adhesion only up to a certain limit due to the onset of bulk deformation. Similar trends have been observed in AFM measurements of the friction of thin, hard coatings.by Shon W. Yim.Ph.D