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1. MENDEL: an automated design tool for DNA nanotechnology

   Guerrero, Jorge; Zadegan, Reza (September 2020, DNA26: 26th International Conference on DNA Computing and Molecular Programming)

   null (Ed.)

   Designing complex DNA nanostructures is a complicated process that requires efficient software to calculate and populate structural details. Most of the published software require manual manipulation and careful inspection of the models that increase the time cost and user error and decrease the flexibility of designing process. We created a python library that we coined MENDEL as a flexible and robust solution for automatic design of complex DNA nanostructures. MENDEL receives a set of sequential commands and creates the structures by following logical steps. Each step instructs the growth of the DNA nanostructure either by adding new nucleotides or repeating sections of arbitrary size and shape. User is able to monitor the design progress by executing the commands in Blender software’s scripting mode. Figure 1 shows an example of using MENDEL library to design a triple-layered origami that represents the word “MENDEL.” MENDEL generates the geometry preview, which helps to understand the design details. Moreover, for convenience, the exported file is compatible with caDNAno. Figure 2 shows the exported model when opened in caDNAno, and Figure 3 shows the modeling results obtained from CanDo for different number of layers. Future work include improving nucleotide twist and rise calculations, supporting honeycomb designs, detecting overlaps, inserting and skipping nucleotides, and generating molecular file formats such as Protein Data Bank (PDB). 

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2. scadnano: A browser-based, scriptable tool for designing DNA nanostructures.

   https://doi.org/10.4230/LIPIcs.DNA.2020.9  

   Doty, David; Lee, Benjamin L; Stérin, Tristan (September 2020, DNA 2020: Proceedings of the 26th International Conference on DNA Computing and Molecular Programming)

   null (Ed.)

   We introduce scadnano (short for "scriptable cadnano"), a computational tool for designing synthetic DNA structures. Its design is based heavily on cadnano [Douglas et al., 2009], the most widely-used software for designing DNA origami [Paul W. K. Rothemund, 2006], with three main differences: 1) scadnano runs entirely in the browser, with no software installation required. 2) scadnano designs, while they can be edited manually, can also be created and edited by a well-documented Python scripting library, to help automate tedious tasks. 3) The scadnano file format is easily human-readable. This goal is closely aligned with the scripting library, intended to be helpful when debugging scripts or interfacing with other software. The format is also somewhat more expressive than that of cadnano, able to describe a broader range of DNA structures than just DNA origami. 

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3. TMTDyn : A Matlab package for modeling and control of hybrid rigid–continuum robots based on discretized lumped systems and reduced-order models

   https://doi.org/10.1177/0278364919881685  

   Sadati, S.M. Hadi; Naghibi, S. Elnaz; Shiva, Ali; Michael, Brendan; Renson, Ludovic; Howard, Matthew; Rucker, Caleb D.; Althoefer, Kaspar; Nanayakkara, Thrishantha; Zschaler, Steffen; et al (January 2021, The International Journal of Robotics Research)

   null (Ed.)

   A reliable, accurate, and yet simple dynamic model is important to analyzing, designing, and controlling hybrid rigid–continuum robots. Such models should be fast, as simple as possible, and user-friendly to be widely accepted by the ever-growing robotics research community. In this study, we introduce two new modeling methods for continuum manipulators: a general reduced-order model (ROM) and a discretized model with absolute states and Euler–Bernoulli beam segments (EBA). In addition, a new formulation is presented for a recently introduced discretized model based on Euler–Bernoulli beam segments and relative states (EBR). We implement these models in a Matlab software package, named TMTDyn, to develop a modeling tool for hybrid rigid–continuum systems. The package features a new high-level language (HLL) text-based interface, a CAD-file import module, automatic formation of the system equation of motion (EOM) for different modeling and control tasks, implementing Matlab C-mex functionality for improved performance, and modules for static and linear modal analysis of a hybrid system. The underlying theory and software package are validated for modeling experimental results for (i) dynamics of a continuum appendage, and (ii) general deformation of a fabric sleeve worn by a rigid link pendulum. A comparison shows higher simulation accuracy (8–14% normalized error) and numerical robustness of the ROM model for a system with a small number of states, and computational efficiency of the EBA model with near real-time performances that makes it suitable for large systems. The challenges and necessary modules to further automate the design and analysis of hybrid systems with a large number of states are briefly discussed. 

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4. Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation

   https://doi.org/10.1093/nar/gkaa417  

   Poppleton, Erik; Bohlin, Joakim; Matthies, Michael; Sharma, Shuchi; Zhang, Fei; Šulc, Petr (May 2020, Nucleic Acids Research)

   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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5. Versatile computer-aided design of free-form DNA nanostructures and assemblies

   https://doi.org/10.1126/sciadv.adi0697  

   Pfeifer, Wolfgang G.; Huang, Chao-Min; Poirier, Michael G.; Arya, Gaurav; Castro, Carlos E. (July 2023, Science Advances)

   Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDNA, which enables design of complex 3D DNA assemblies with many components; however, the design of structures with free-form features like vertices or curvature still required iterative design guided by simulation feedback and user intuition. Here, we present an updated design tool, MagicDNA 2.0, that automates the design of free-form 3D geometries, leveraging design models informed by coarse-grained molecular dynamics simulations. Our GUI-based, stepwise design approach integrates a high level of automation with versatile control over assembly and subcomponent design parameters. We experimentally validated this approach by fabricating a range of DNA origami assemblies with complex free-form geometries, including a 3D Nozzle, G-clef, and Hilbert and Trifolium curves, confirming excellent agreement between design input, simulation, and structure formation. 

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