A. James Clark School of Engineering
Permanent URI for this communityhttp://hdl.handle.net/1903/1654
The collections in this community comprise faculty research works, as well as graduate theses and dissertations.
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Item WATER, ION, AND GRAPHENE: AN ODYSSEY THROUGH THE MOLECULAR SIMULATIONS(2019) Wang, Yanbin; Das, Siddhartha; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Water is known as the most common and complicated liquid on earth. Meanwhile, graphene, defined as single/few layer graphite, is the first member in the 2-dimensional materials family and has emerged as a magic material. Interactions between water and graphene generate many interesting phenomena and applications. This thesis focuses on applying molecular dynamics (MD), a powerful computational tool, for investigating the graphene-water interactions associated with various energetic and environmental applications, ranging from the wettability modification, species adsorption, and nanofluidic transport to seawater desalination. A key component of one domain of applications involves a third component, namely salt ions. This thesis attempts that and discovers a fundamentally new way in which the behavior of ions with the air-water interfaces should be probed. In Chapter 1, we introduce the motivation and methods and the overall structure of this thesis. Chapter 2 focuses on how MD simulations connect the statistical mechanics theory with the experimental observations. Chapter 3 discusses the simulation results revealing that the spreading of a droplet on a nanopillared graphene surface is driven by a pinned contact line and bending liquid-surface dynamics. Chapter 4 probes the interactions between a water drop and a holey graphene membrane, which is prepared by removing carbon atoms in a circular shape and which can serve as catalyst carriers. Accordingly, chapter 5 studies the effects of various terminations on water-holey graphene interactions, showing that water flows faster and more thoroughly through the membrane with hydrophobic terminations, compared to that with hydrophilic terminations. In chapter 6, simulations describe the generation of enhanced water-graphene surface area during the water-holey-graphene interactions in presence of an applied time-varying force on the water drop. In chapter 7, we focus on the ion-water interaction at the water-air interface to fully understand the fluidic dynamics during any seawater desalination. Our research revisits the energetic change while ion approaches water-air interface and shows that the presence of ion at the interface enhances capillary-wave fluctuation. Finally, in chapter 8 we summarize the main findings of the thesis and provide the scope of future research.Item Examining the role of water and hydrophobicity in folding, aggregation, and allostery(2018) Custer, Gregory Scott; Matysiak, Silvina; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Solvation and hydrophobicity drive many critical processes in nature, playing an important role in the folding of proteins, aggregation of surfactants into micelles, and in the disorder to order transitions that occur in some allosteric proteins upon ligand binding. Understanding how solvation and hydrophobicity affect these processes at a molecular level is important to finding new ways to use these processes, but it can be difficult to characterize these molecular details using experimental methods. Molecular dynamics (MD) simulations have proven useful in exploring details and thermodynamic conditions inaccessible in experiment, as MD captures the time evolution of the system at a molecular level. The phenomena which can be studied with an MD simulation depend on the mathematical model employed. Atomistic models provide the most detail for a simulation, but due to the computational costs required are not typically used to study phenomena which require large systems and time scales greater than several μs. Coarse-grained (CG) models reduce the complexity of the system being studied, enabling the exploration of phenomena that occur at longer time scales. We have developed CG models to study protein folding and surfactant aggregation. Our CG surfactant model uses a three-body potential to account for hydrogen bonding without an explicit electrostatic potential, reducing the computational cost of the model. With our surfactant model we studied the stability of non-ionic micelles at extremes of temperature, capturing a window of thermal stability with destabilization of the micelles at both high and low temperatures. We observed changes in structure and solvation of the micelle at low temperatures, with a shift in enthalpy of solvation water providing the driving force for destabilization. Solvation and hydrophobicity are also critical in the folding and stability of proteins. With a modified version of our surfactant model we characterized the folding landscape of a designed sequence which folds to a helical bundle in water. We found two competing folded states which differ by rotation of a helix and trade between hydrophobic packing and solvation of protein's core. Changes in hydrophobic packing can also be involved in the disorder to order transitions that occur upon liganding binding in an allosteric protein, such as the E. Coli biotin ligase/repressor (BirA), in which ligand binding promotes dimerization. We have used atomistic simulations of BirA mutants in collaboration with an experimental group to identify structural changes, accompanied by changes in solvation, at both the dimer interface and ligand binding regions for distal mutations which impact the functionality of BirA.Item Model-based Analysis of Atomic Layer Deposition Growth Kinetics and Multiscale Process Dynamics(2014) Travis, Curtisha Denise; Adomaitis, Raymond A.; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)A first principles model describing the reaction kinetics and surface species dynamics for the trimethylaluminum (TMA) and water half-reactions of alumina atomic layer deposition (ALD) is coupled with a dynamic film growth model and reactor-scale species transport model. The reaction kinetics model is based on reported enthalpies and transition state structures from published quantum-chemical computational studies; these data are used to determine kinetic parameters using statistical thermodynamics and absolute reaction rate theory. Several TMA half-reactions were modeled to account for TMA adsorption and subsequent reaction on a range of growth surfaces spanning bare to fully hydroxylated states. Several water reactions were also considered. By coupling the reaction rate models with surface species conservation equations, a dynamic model is created which is useful for examining the relative rates of competing surface reactions. To describe the continuous cyclic operation of the deposition reaction system, a numerical procedure to discretize limit-cycle solutions is developed and used to distinguish saturating growth per cycle from non-saturating conditions. The transition between the two regimes is studied as a function of precursor partial pressure, exposure times, and temperature. Finally, a cross-flow tubular ALD reactor system model is derived with components describing the precursor thermophysical properties, precursor delivery system, reactor-scale gas-phase dynamics, and surface reaction kinetics derived from absolute reaction rate theory. These model components are integrated to simulate the complete multiscale ALD process. Limit-cycle solutions defining continuous cyclic ALD reactor operation are computed with a fixed point algorithm based on temporal and spatial discretization within the reactor, resulting in an unambiguous definition of film growth per cycle. The use of the simulator for assisting in process design decisions and optimization frameworks is presented.