A theoretical and computational investigation of complex fluids and glasses

The present dissertation employs molecular simulation and statistical mechanical theories to investigate complex fluids and glasses. The goal is to gain a molecular-level understanding of some of the phenomena present in supercooled liquids, confined water, proteins, glasses, and chiral compounds.;The first study examines translational and rotational diffusion in a model of the fragile glass former ortho-terphenyl. The primary objectives are to identify evidence of spatially heterogeneous dynamics and compare how the rates of translation and rotation change relative to one another as the liquid is deeply supercooled. In addition, the breakdown of the Debye model of rotation is analyzed and an alternative formulation of rotational motion is presented.;The next study investigates the structure and mechanical properties of glassy water confined between silica-based surfaces with continuously tunable hydrophobicity and hydrophilicity, by computing and analyzing minimum energy and quenched configurations. The maximum sustainable transverse and normal stresses of thin water films are calculated and compared for various confining surfaces. In addition, the mode of mechanical failure is characterized as adhesive or cohesive depending on the strength of interactions between water and the confining surfaces.;The third study calculates atomic-level stresses on protein atoms after vitrification. Particular attention is paid to how these stresses change between an equilibrium state at ambient conditions and the quenched or glassy state. The possible effects on protein secondary structure are also analyzed to gauge the ability of theses stresses to disrupt the interactions that stabilize the secondary structure of proteins.;The final portion of the dissertation formulates a two-dimensional lattice model to study the equilibrium phase behavior of a ternary mixture composed of two enantiomeric forms of a chiral molecule and a non-chiral liquid solvent. The phase behavior of the model is qualitatively identical to that reported in a recent experimental study of solutions of amino acids, aimed at probing the liquid-phase control of asymmetric catalysis. The results suggest a possible thermodynamic scenario for the liquid-phase emergence of chiral imbalance in a prebiotic and presumably nearly racemic world.