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Articles 1 - 8 of 8
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 Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang
Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang
Dissertations, Theses, and Capstone Projects
Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …
Thermoelectric Transport In Disordered Organic And Inorganic Semiconductors, Meenakshi Upadhyaya
Thermoelectric Transport In Disordered Organic And Inorganic Semiconductors, Meenakshi Upadhyaya
Doctoral Dissertations
The need for alternative energy sources has led to extensive research on optimizing the conversion efficiency of thermoelectric (TE) materials. TE efficiency is governed by figure-of-merit (ZT) and it has been an enormously challenging task to increase ZT > 1 despite decades of research due to the interdependence of material properties. Most doped inorganic semiconductors have a high electrical conductivity and moderate Seebeck coefficient, but ZT is still limited by their high lattice thermal conductivity. One approach to address this problem is to decrease thermal conductivity by means of alloying and nanostructuring, another is to consider materials with an inherently low …
Parallel Algorithms For Time Dependent Density Functional Theory In Real-Space And Real-Time, James Kestyn
Parallel Algorithms For Time Dependent Density Functional Theory In Real-Space And Real-Time, James Kestyn
Doctoral Dissertations
Density functional theory (DFT) and time dependent density functional theory (TDDFT) have had great success solving for ground state and excited states properties of molecules, solids and nanostructures. However, these problems are particularly hard to scale. Both the size of the discrete system and the number of needed eigenstates increase with the number of electrons. A complete parallel framework for DFT and TDDFT calculations applied to molecules and nanostructures is presented in this dissertation. This includes the development of custom numerical algorithms for eigenvalue problems and linear systems. New functionality in the FEAST eigenvalue solver presents an additional level of …
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 …