Date of Graduation


Document Type


Degree Name

Master of Science in Computer Science (MS)

Degree Level



Computer Science & Computer Engineering


Matthew J. Patitz

Committee Member

Gordon Beavers

Second Committee Member

Jacob Hendricks

Third Committee Member

Jin-Woo Kim

Fourth Committee Member

Qinghua Li


Applied sciences, Dna nanotechnology, Graphical processing units, Molecular dynamics, Oxdna


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 are comprised of over a hundred separate simulations spanning in simulation length from one thousand to ten million times steps and with simulation sizes ranging from 16 to 27832 particles. Together these tests show the ability of our implementation to handle the full range of basic nBLOCK topologies in a diverse set of conditions. A selection of the utilities developed during the course of this thesis are also discussed. We provide descriptions of the scripting utilities which support nBLOCK assembly generation, simulation, and analysis.