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 11 of 11 for “"Coarse-grained simulation"”.
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Development of Atomistic Potentials for Silicate Materials and Coarse-Grained Simulation of Self-Assembly at Surfaces
… isobaric-isothermal ensemble molecular dynamics simulations. The second is a study of thermodynamics and self-assembly in a particular class of athermal two-dimensional lattice models. The effects of shape on self-assembly and thermodynamics for polyominoes and tetrominoes were examined. Many …
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Diffusion, sub-diffusion, and escape: A study of over-damped Brownian motion
… depends upon the shape of the energy barriers. A coarse-grained simulation scheme, where particles are moved between lattice sites located at the potential minima, is proposed. Good agreement with Brownian dynamics simulations is observed. Motion in one-dimensional rough potentials is studied, and …
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Atomistic and mesoscale modeling of dislocation mobility
… its dynamics. This Thesis presents theories and simulations of dislocations in Si and BCC transition metals, with emphasis on the atomistic-mesoscale coupling. Contributions are made in both methods development and mechanistic understanding of dislocation mobility. For atomistic studies of …
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Multi-Level Coarse-Grained Modelling on DNA Functionalised Building Blocks
… strategy to demonstrate new horizons of coarse-grained simulation systems. From the detailed oxDNA molecular dynamics simulation of mimicking the most detailed behaviours of an individual DNA nanoparticle, to a second-level coarse-grained system with thousands of repeated units of …
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Interactions between nucleoid associated proteins and DNA in the presence of mechanical and chemical forces
… function. It has been shown in experiment and simulation that NAPs can adopt multiple binding states (i.e., the protein can be partially associated with its DNA substrate), which leads to complex binding and unbinding kinetics. For a simple binary system, where a protein can either be bound or …
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Preparation and stability of organic nanocrystals. Experimental and molecular simulation studies.
… of both experiments and molecular modelling and simulation, not only to determine the optimum parameters but also to gain mechanistic insight. The experimental studies utilised three rather distinct, relatively insoluble drugs, the hypoglycaemic glibenclamide, the anti-inflammatory ibuprofen, and …
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Simulation informed design of stimuli responsive structures and higher-order assemblies in DNA nanotechnology
… novel applications of DNA nanotechnology, where coarse-grained molecular simulation was used either for in silico prototyping, or experimental rationalisation. While each individual project has a relevant application, the underlying goal is to validate and identify the limits of modelling for …
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Mesoscale simulation of block copolymer phase separation and directed self-assembly processes: Applications for semiconductor manufacturing
A molecular dynamics coarse-grained block copolymer (BCP) model was developed and used to studied directed self-assembly (DSA), especially in regards to applications for semiconductor manufacturing. Most of the thesis is spent investigating the effect that guiding layer properties and block …
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Deriving Structural Insights About Mesoscale Chromatin Folding Using Coarse-Grained Oligonucleosome Modeling
… (~1kb). I developed an experimentally-validated coarse-grained polymer model and applied it 1) to show how chromatin fiber parameters, such as nucleosome spacing and breathing, impact chromatin organization on this scale–the mesoscale 2) to interpret mesoscale sequencing assay data and 3) to …
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Modeling and simulation of intrinsically disordered biomolecular systems
Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-05-01
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Accelerator-based look-up table for coarse-grained molecular dynamics computations
Molecular Dynamics (MD) is a simulation technique widely used by computational chemists and biologists to simulate and observe the physical properties of a system of particles or molecules. The method provides invaluable three-dimensional structural and transport property data for macromolecules …