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Advisors: Debenedetti, Pablo G.
Contributors: Chemical and Biological Engineering Department
Subjects: Chemical engineering
Issue Date: 2012
Publisher: Princeton, NJ : Princeton University
Abstract: In this dissertation, we use molecular simulation to investigate systems in which symmetry breaking, due to an interface or confining geometry, modifies the structural, dynamic and thermodynamic properties of water. We focus on two types of aqueous systems: confined and interfacial water films; and hydrophobic solvation. Throughout, the common denominator is the existence of a hydration layer, a three-dimensional (3D) region within which water's properties depart from those of the bulk liquid. The objective of this study is twofold: (i) to characterize water's structural and dynamic properties within this layer; (ii) to investigate the effect of water's hydration layer thermodynamics on conformational transitions of a hydrophobic, protein-like oligomer. In the first part of the dissertation, we use molecular dynamics (MD) simulations to investigate confined and interfacial water. The former category includes systems in which two solid surfaces confine a water film to a nanoscopic geometry; in the latter, an adsorbed film of water exists between solid-liquid and liquid-vapor interfaces. We first study the effect of surface polarity on confined water's translational and rotational dynamics. Our results show that water dynamic properties exhibit a non-monotonic dependence on surface polarity, a phenomenon explained by the different water structures observed on polar and apolar interfaces. Next, considering hydrophilic surfaces, we investigate the effect of confinement length scale (i.e., inter-surface separation, d) on confined water's molecular dynamics. We show that translational dynamics are surface-dominated (hence, slower than in the bulk) within ~1 nm from the nearest interface, while rotational dynamics exhibit slowing down within ~0.5 nm from the interface. We also find that, for d >= 1.0 nm, both the local in-plane diffusion coefficient and translational relaxation time collapse onto d-independent curves. Next, we investigate the properties of interfacial water on hydrophilic substrates. We evaluate the effect of water-surface (W-S) and water-water (W-W) interactions on film molecular structure, finding that W-S interactions determine film structure in 1-monolayer (ML) films. W-W interactions become equally important in thicker films, but without disrupting W-S interactions. Interface-induced modifications to the water structure propagate throughout films <= 4 ML in thickness. In the second part of the dissertation, we study oligomer conformational stability using a 3D lattice model in explicit water-like solvent, numerically solved with flat-histogram Monte Carlo simulation. The model incorporates the entropic penalty and enthalpic bonus that characterize water-water interactions in the hydrophobic hydration layer. We first focus on the effect of density and temperature on the stability of a flexible hydrophobic oligomer. We show that the model qualitatively reproduces features of protein systems, including cold, thermal and high-density unfolding (a phenomenon akin to pressure unfolding). Next, we exploit the 3D nature of the model to incorporate elements of secondary structure into the oligomer Hamiltonian. We show that a minimalist model incorporating meaningful inter-monomer energetics and the thermodynamics of hydrophobic solvation suffices to describe the thermal stability of helical oligomers.
Alternate format: The Mudd Manuscript Library retains one bound copy of each dissertation. Search for these copies in the library's main catalog
Type of Material: Academic dissertations (Ph.D.)
Language: en
Appears in Collections:Chemical and Biological Engineering

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