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Abstract This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with over 1 million nucleotides, create videos from simulation trajectories, and allow users to perform basic edits to DNA and RNA designs. We additionally introduce open-source software tools for extracting common structural parameters to characterize large DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in popularity in recent years and is frequently used to prototype new nucleic acid nanostructural designs, model biophysics of DNA/RNA processes, and rationalize experimental results. The newly introduced software tools facilitate the computational characterization of DNA/RNA designs by providing multiple analysis scripts, including mean structures and structure flexibility characterization, hydrogen bond fraying, and interduplex angles. The output of these tools can be loaded into oxView, allowing users to interact with the simulated structure in a 3D graphical environment and modify the structures to achieve the required properties. We demonstrate these newly developed tools by applying them to design and analysis of a range of DNA/RNA nanostructures.
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This content will become publicly available on September 9, 2025
SQuADDS: A validated design database and simulation workflow for superconducting qubit design
We present an open-source database of superconducting quantum device designs that may be used as the starting point for customized devices. Each design can be generated programmatically using the open-source Qiskit Metal package, and simulated using finite-element electromagnetic solvers. We present a robust workflow for achieving high accuracy on design simulations. Many designs in the database are experimentally validated, showing excellent agreement between simulated and measured parameters. Our database includes a front-end interface that allows users to generate "best-guess" designs based on desired circuit parameters. This project lowers the barrier to entry for research groups seeking to make a new class of devices by providing them a well-characterized starting point from which to refine their designs.
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- Award ID(s):
- 1936388
- PAR ID:
- 10565962
- Publisher / Repository:
- Quantum Journal
- Date Published:
- Journal Name:
- Quantum
- Volume:
- 8
- ISSN:
- 2521-327X
- Page Range / eLocation ID:
- 1465
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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