Download or read book Molecular Dynamics Simulations to Study Molecular Interactions at Biologically and Mechanically Important Surfaces written by Dineli Thakshila Sarasavi Ranathunga and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this dissertation molecular dynamics computer simulations (MD) were used to explore molecular scale behavior in order to interpret experimental results and guide challenging experimental work. In Chapters 2, 3 and 4 MD simulations were utilized to study a new immunointeractive surface approach to induce titanium implant osseointegration, using the constructive inflammatory effects of high mobility group box 1 (HMGB1) protein. First, in Chapter 2 the protein, ion and water interactions with the rutile (110) TiO2 surface induced by surface hydroxylation were investigated. In an aqueous environment, we show the direct binding of HMGB1 to the TiO2 surface regardless of its hydroxylation state, which causes structural changes to the protein, thereby affecting its biological function. Hence, to find a compromise between stable adsorption and preservation of protein activity in Chapter 3 we study the advantages of dicationic imidazolium-based ionic liquids (IonLs) containing amino acid anions to serve as a vehicle for delivering proteins on the surface of TiO2 implants. A strongly bound well structured IonL coating formed on the TiO2 surface effectively blocking HMGB1 from direct adsorption on the implant. Additionally, the protein is immobilized due to IonL cations and anions which bind to oppositely charged amino acids on the protein surface. In order to account for the different biological roles of HMGB1, the different HMGB1 isoforms were studied in Chapter 4. Once the IonL/HMGB1 coating on the TiO2 surface comes into contact with water, the protein release mechanism and the integrity of its receptor binding sites were investigated. Imidazolium based IonLs are becoming increasingly popular not only in bioengineering but also in many other fields due to their promising properties. Because of the large number of cation and anion combinations available, it is not feasible to experimentally measure IonL properties over a wide range of composition and operating conditions. Therefore, fast and reliable methods such as molecular modeling tools are needed to acquire these properties. However, to validate and tune the molecular modeling approach some experimental data is required. Therefore, in Chapter 5 by combining experiments with molecular modeling we explore the properties of a series of IonLs. In Chapter 6, we used MD simulations to study vapor condensation which is an area with a wide range of industrial applications. We provide molecular insight into the condensation mechanism as a function of surface wettability using surfaces chemisorbed with alkanethiol self-assembled monolayers. By changing the alkanethiol head group chemistry, the surface wettability was tuned and the role of surface wettability on the rate of water condensation was studied. We show that decreasing surface hydrophobicity significantly increases the electrostatic forces between water molecules and the surface, thus increasing the water condensation rate. We also provide connections with other microscopic and macroscopic interfacial characterizations. In Chapter 7, we used MD simulations to link experimentally observed anion sensing, specifically towards nitrate, nitrite, iodide, and thiocyanate by polyvinylpyrrolidone (PVP) polymer, to anion interactions on the polymer surface and concomitant changes in the polymer aggregation state. Supporting the experimental observations, our results suggest that anions associating most strongly to the surface of PVP quench its fluorescence to the greatest extent.