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Full-Text Articles in Engineering
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 …
A Hybrid Partially Reconfigurable Overlay Supporting Just-In-Time Assembly Of Custom Accelerators On Fpgas, Zeyad Tariq Aklah
A Hybrid Partially Reconfigurable Overlay Supporting Just-In-Time Assembly Of Custom Accelerators On Fpgas, Zeyad Tariq Aklah
Graduate Theses and Dissertations
The state of the art in design and development flows for FPGAs are not sufficiently mature to allow programmers to implement their applications through traditional software development flows. The stipulation of synthesis as well as the requirement of background knowledge on the FPGAs' low-level physical hardware structure are major challenges that prevent programmers from using FPGAs. The reconfigurable computing community is seeking solutions to raise the level of design abstraction at which programmers must operate, and move the synthesis process out of the programmers' path through the use of overlays. A recent approach, Just-In-Time Assembly (JITA), was proposed that enables …