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Full-Text Articles in Nanoscience and Nanotechnology
A Versatile Python Package For Simulating Dna Nanostructures With Oxdna, Kira Threlfall
A Versatile Python Package For Simulating Dna Nanostructures With Oxdna, Kira Threlfall
Computer Science and Computer Engineering Undergraduate Honors Theses
The ability to synthesize custom DNA molecules has led to the feasibility of DNA nanotechnology. Synthesis is time-consuming and expensive, so simulations of proposed DNA designs are necessary. Open-source simulators, such as oxDNA, are available but often difficult to configure and interface with. Packages such as oxdna-tile-binding pro- vide an interface for oxDNA which allows for the ability to create scripts that automate the configuration process. This project works to improve the scripts in oxdna-tile-binding to improve integration with job scheduling systems commonly used in high-performance computing environments, improve ease-of-use and consistency within the scripts compos- ing oxdna-tile-binding, and move …
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 …
Acceleration Of Ddscat Computation By Parallelization On A Supercomputer, Manoj V. Seeram
Acceleration Of Ddscat Computation By Parallelization On A Supercomputer, Manoj V. Seeram
Chemical Engineering Undergraduate Honors Theses
The DDSCAT software is enabled for use of MPI or OpenMP to distribute calculation of different particle orientations amongst multiple processors on a high performance system. Run times for these simulations have been tested to take hours or days however and simulating varying orientations is not always necessary. If a simulation with only one particle orientation is submitted, DDSCAT could still potentially parallelize the simulation by wavelength calculations but it is unknown if this is the case. In this paper, we will be (i) quantifying the reduction in computation time that MPI provides relative to an equivalent MPI disabled simulation …
Nanoscale Frictional Properties Of Nickel With One-Dimensional And Two-Dimensional Materials, Timothy K. Schlenger
Nanoscale Frictional Properties Of Nickel With One-Dimensional And Two-Dimensional Materials, Timothy K. Schlenger
Mechanical Engineering Undergraduate Honors Theses
When looking at the nanoscale, material interface interactions have been observed to exhibit particularly interesting properties. Our research looks into various combinations of carbyne and graphene atop a nickel block to look into the interface friction properties between them. Both the carbyne and graphene are tested using steered molecular dynamics (SMD) in sheering and peeling directions along the surface of the nickel block. These tests are then analyzed by comparing the magnitude of the acting force versus the displacement of the carbon allotrope sample across the nickel block. It is found that as the width of a carbon allotrope sample …
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 …