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Full-Text Articles in Nanoscience and Nanotechnology
Molecular Dynamics Simulations Of Dna-Functionalized Nanoparticle Building Blocks On Gpus, Tyler Landon Fochtman
Molecular Dynamics Simulations Of Dna-Functionalized Nanoparticle Building Blocks On Gpus, Tyler Landon Fochtman
Graduate Theses and Dissertations
This thesis discusses massively parallel molecular dynamics simulations of nBLOCKs using graphical processing units. nBLOCKs are nanoscale building blocks composed of gold nanoparticles functionalized with single-stranded DNA molecules. To explore greater simulation time scales we implement our nBLOCK computational model as an extension to the coarse grain molecular simulator oxDNA. oxDNA is parameterized to match the thermodynamics of DNA strand hybridization as well as the mechanics of single stranded DNA and double stranded DNA. In addition to an in-depth review of our implementation details we also provide results of the model validation and performance tests. These validation and performance tests …
Directed Percolation And The Abstract Tile Assembly Model, Tyler Garrett Moore
Directed Percolation And The Abstract Tile Assembly Model, Tyler Garrett Moore
Graduate Theses and Dissertations
Self-assembly is a process by which simple components build complex structures through local interactions. Directed percolation is a statistical physical model for describing competitive spreading processes on lattices. The author describes an algorithm which can transform a tile assembly system in the abstract Tile Assembly Model into a directed percolation problem, and then shows simulations of the aTAM which support this algorithm. The author also investigates two new constructs designed for Erik Winfree's abstract Tile Assembly Model called the NULL tile and temperature 1.5. These constructs aid the translation between self-assembly and directed percolation and may assist self-assembly researchers in …