Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 16 of 16 for “"Potential of Mean Force (PMF)"”.
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Simulations of carbohydrate conformational dynamics and thermodynamics
… employed to establish the conformation freedom of selected carbohydrates. The focus is on the biologically important (1-4)-linked glucans, although the α(1-1) α and α(1-6) linkages are also investigated. Two principal types of potential of mean force (PMF) caltulation are used: free energy …
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Molecular modelling of the Streptococcus pneumoniae serogroup 6 capsular polysaccharide antigens
In this thesis, a systematic study of the structural characterization of the capsular polysaccharides of Streptococcus pneumoniae is conducted using Molecular Modelling methods. S.pneumoniae causes invasive pneumococcal disease (IPD), a leading cause of death in children under five. The serotypes …
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Validation of the charge equilibration lipid force field for simulations of phospholipid membranes with an application to the study of the free energetics of methyl guanidinium permeation across a DPPC bilayer
… group focused on the development and refinement of po-larizable charge equilibration (CHEQ) force fields for use in molecular dynamics (MD) simulations of phospholipid bilayers. We present results to further validate these force fields by extending to simulations of a model DPPC-water monolayer. …
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Electronic and solvent effects on monosaccharide conformations
The hydroxymethyl group rotational preferences of the monosaccharides glucose and galactose are different from each other and non-intuitive (from a steric point of view) in their preferences for gauche conformers. These molecules exhibit very different biological and thermodynamic properties in, …
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Electronic and solvent effects on monosaccharide conformations
The hydroxymethyl group rotational preferences of the monosaccharides glucose and galactose are different from each other and non-intuitive (from a steric point of view) in their preferences for gauche conformers. These molecules exhibit very different biological and thermodynamic properties in, …
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Molecular Dynamics of Interfacial Phenomena at Air/ice, Air/water, and Air/salt Water Interfaces
The purpose of this research is to investigate the adsorption of organic contaminants, namely polycyclic aromatic hydrocarbons (PAHs) and green leaf volatiles (GLVs), as well as their interactions with reactive oxygen species (ROSs) on atmospheric air/water and air/ice interfaces. In another series …
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Molecular Simulation Study of Oil Hydrocarbons, Dispersants and Other Organics in Atmospheric Air/Water Interfaces
The main objective of this dissertation is to study the interfacial properties of organic contaminants, in particular green leaf volatiles (GLVs), oil hydrocarbons [mainly intermediate-volatile organic compounds (IVOCs) and semi-volatile organic compounds (SVOCs)], as well as surfactant species …
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Surfactants at fluid interfaces: molecular modeling and deep learning
… models to predict the interfacial properties of sur factants. The first study investigates slippage modulation at brine–oil interfaces by surfactants, which is relevant to enhanced oil recovery operations. We identified a slip length of 1.2 nm at clean decane-brine interfaces. Introducing …
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How Atomic Level Interactions Drive Membrane Fusion: Insights From Molecular Dynamics Simulations
… project is focused on identifying the role of key players in the membrane fusion process at the atomic level with the use of molecular dynamics simulations. Membrane fusion of apposed bilayers is one of the most fundamental and frequently occurring biological phenomena in living organisms. …
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Carbon nanotubes and graphene in aqueous surfactant solutions : molecular simulations and theoretical modeling
… observations, on properties and applications of carbon nanotubes (CNTs) and graphene sheets dispersed in aqueous surfactant solutions. In particular, the role of the bile salt anionic surfactant, sodium cholate (SC), in dispersing single-walled carbon nanotubes (SWCNTs) and graphene sheets in …
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Multiscale Modeling of the Mechanical Behavior of Clay
The goal of this thesis is to develop a better understanding of the macroscopic engineering properties of clay through a bottom-up modeling approach, involving simulations at three length scales. At the nanoscale, molecular dynamics simulations were carried out to quantify the Potential of Mean …
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Molecular-thermodynamic and simulation-assisted modeling of interfacial energetics
… at material interfaces control the efficiency of chemical engineering processes as diverse as adsorption, emulsification, heat exchange, and froth flotation. In particular, the process of colloidal self-assembly harnesses the rich tapestry of interactions that operate at several length scales, …
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Ion Pairing in Aqueous Metal Sulfates and Platinum Group Metal Ammonium Solutions
The structure and dynamics of ions and ion pairs in solution play an integral part in several biological and chemical processes. Historically the calculation of ion pair association constants from computer simulations has been complicated due to the difficulty in validating metal ion force fields …
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On the dynamics and interparticle forces of electrostatically stabilized colloidal suspensions
In a broad spectrum of industrial and biomedical applications, the equilibrium and dynamic properties of colloidal suspensions play a pivotal role, with systems ranging from simple gold nanoparticles in electrolyte solutions to complex assemblies like micelles, vesicles, nanocapsules, and dendritic …
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Understanding and engineering molecular interactions and electronic transport at 2D materials interfaces
… with strong in-plane chemical bonds but weak out-of-plane, van der Waals (vdW) interactions. In order to realize potential applications of 2D materials in the areas of optoelectronics, surface modification, and complex materials, there are many engineering challenges associated with understanding …
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Molecular Dynamics study of defect evolution mechanisms in material of interests for quantum technologies [Studio di Dinamica Molecolare dei meccanismi di evoluzione dei difetti nei materiali di interesse per le tecnologie quantistiche]
Abbiamo studiato la formazione e l'evoluzione dei difetti nel 3C–SiC utilizzando simulazioni di dinamica molecolare classica con potenziali interatomici dipendenti dall'ambiente. Il benchmarking preliminare ha incluso parametri reticolari, energie di formazione dei difetti e calcoli del punto di …