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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 …
Physically Equivalent Intelligent Systems For Reasoning Under Uncertainty At Nanoscale, Santosh Khasanvis
Physically Equivalent Intelligent Systems For Reasoning Under Uncertainty At Nanoscale, Santosh Khasanvis
Doctoral Dissertations
Machines today lack the inherent ability to reason and make decisions, or operate in the presence of uncertainty. Machine-learning methods such as Bayesian Networks (BNs) are widely acknowledged for their ability to uncover relationships and generate causal models for complex interactions. However, their massive computational requirement, when implemented on conventional computers, hinders their usefulness in many critical problem areas e.g., genetic basis of diseases, macro finance, text classification, environment monitoring, etc. We propose a new non-von Neumann technology framework purposefully architected across all layers for solving these problems efficiently through physical equivalence, enabled by emerging nanotechnology. The architecture builds …