Date on Master's Thesis/Doctoral Dissertation

8-2024

Document Type

Doctoral Dissertation

Degree Name

Ph. D.

Department

Chemical Engineering

Degree Program

Chemical Engineering, PhD

Committee Chair

Jaeger, Vance

Committee Co-Chair (if applicable)

Gupta, Gautam

Committee Member

Gupta, Gautam

Committee Member

Sathitsuksanoh, Noppadon

Committee Member

Narayanan, Badri

Committee Member

Willing, Gerold

Author's Keywords

Molecular dynamics; simulation; constant pH; methods

Abstract

This dissertation explores the application of novel molecular dynamics simulation methods to better understand complex systems, with a particular focus on silica materials and protein interactions. Silica materials, known for their versatile surface and solution chemistries, play critical roles in catalysis, chromatography, and wastewater treatment. Despite their widespread use, the molecular-level interactions between silica surfaces and their environments remain poorly understood. To address this knowledge gap, we employed λ-dynamics enabled constant pH molecular dynamics to dynamically model protonation and deprotonation events on silica surfaces. Traditional experimental techniques such as x-ray crystallography, NMR, and cryo-EM are inadequate for probing structures in aqueous silica gels, and common spectroscopic methods often lack the resolution to study interfacial behaviors. Our approach leverages λ-dynamics to simulate titratable inorganic and organic sites, providing a detailed understanding of pH-driven processes involved in surface structuring and molecular adsorption. Additionally, this dissertation investigates the thermodynamics of protein interactions through alchemical free energy simulations. We applied alchemical mutations to the irsS2168 pinholin protein to study the impact of mutations on its activation process. This method allowed us to bypass prohibitive timescales in traditional MD, offering insights into the folding free energy changes upon mutation. The innovative use of alchemical mutations provided a deeper understanding of the molecular driving forces behind pinholin activity and its structural transitions, complementing existing experimental data. Our findings reveal significant insights into the cooperative effects of ions and adsorbates with the titration states of silica surfaces. The results highlight how ion concentration and species influence surface charge and adsorption processes. Furthermore, we discuss potential applications of the λ-dynamics CpHMD method beyond silica, suggesting its utility in studying a wide range of titratable inorganic and organic interfaces. By applying these new simulation methods to novel systems, this research advances the field of molecular dynamics simulations. The methodologies and insights gained have significant implications for the design and optimization of materials in catalysis, environmental remediation, and biotechnological applications. This work not only enhances our understanding of silica surface chemistry and protein interactions but also sets the stage for future explorations into complex interfacial phenomena across various scientific domains.

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