Resources

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Software

DNA Nanotechnology

CAD geometry → DNA origami sequences · 5 codes

ATHENAA GUI software that fully automates the sequence design of 2D and 3D wireframe DNA origami objects 2D · 3D

shape ↓ · edge →

DX edge double crossover

6HB edge 6-helix bundle

2Dplanar · free-form

PERDIX2D · DX edge

METIS2D · 6HB edge

3Dwireframe

DAEDALUS23D · DX edge

TALOS3D · 6HB edge

2D CAD · 3D PLY · GEO run the code scaffold · staple sequences experiment (wet lab)

DX edge = two helices (double crossover) 6HB edge = six-helix bundle 2D = planar mesh · 3D = polyhedral wireframe · dots = vertices

Computational Mechanics

2 codes · Fortran

2D SATURN An educational FEA package for linear static 2D plane stress...

3D MERCURY A FORTRAN-based FEA package for linear and nonlinear shell s...

DNA Nanotechnology

PERDIX Fortran

PERDIX automatically converts 2D CAD files into DNA sequences for free-form DNA origami design

Intel Fortran CompilerShapely 1.6.4, PyDistMesh 1.2MATLAB 2014-2018 (DistMesh)

Code Paper 1 Paper 2

ATHENA Python

A GUI software that fully automates the sequence design of 2D and 3D wireframe DNA origami objects

Python 3.7+ (numpy >= 1.16.2)PySide2 5.12.3 (Qt5 API, Qt3D, QML)Rendering: GLSL (OpenGL Shading)

Code Paper 1

METIS Fortran

Automates converting 2D CAD files to DNA sequences for 6HB-based DNA origami design

Fortran: Intel Fortran CompilerShapely 1.6.4, PyDistMesh 1.2MATLAB 2014-2018 (DistMesh)

Code Paper 1 Paper 2

TALOS Fortran

Automates converting 3D PLY files to DNA sequences for 6HB-based 3D DNA origami design

Intel Fortran Compiler (Fortran 90/95/2003/2008) via Intel Parallel Studio XE 2016-2018

Code Paper 1 Paper 2

DAEDALUS2 Fortran

Automates converting CAD files (GEO, PLY) to DNA sequences for DX-based wireframe design

Fortran: Intel Fortran Compiler (Fortran 90/95) via Intel Parallel Studio XE 2016-2018

Code Paper 1

Computational Mechanics

SATURN Fortran

An educational FEA package for linear static 2D plane stress analysis using 4-node elements

Intel Fortran Compiler (Fortran 90/95/2003/2008) via Intel Parallel Studio XE 2017+

Code

MERCURY Fortran

A FORTRAN-based FEA package for linear and nonlinear shell structural analysis using the MITC method

Intel Fortran Compiler (Fortran 90/95/2003/2008) via Intel Parallel Studio XE 2017+

Code Paper 1 Paper 2

Commercial Software

ANSYS Ansys 2023 R1 Academic Research

Structural Analysis & Design Optimization

Academic Research Structures
Academic Research Fluids

ansys.com

COMSOL COMSOL 2024 Academic Research

Multiphysics Modeling & Simulation

Multiphysics, Structural Mechanics, Nonlinear Structural Materials
CFD, Heat Transfer, Design

comsol.com

OriginLab OrginPro Origin Pro 2022b

Graphing for Science and Engineering

Node-Lock License
Node-Lock License w/Dongle

originlab.com

TecPlot Tecplot 360 Academic Network

CFD Visualization & Analysis

Tecplot 360, RS, Fieldview
Chorus, PyTecplot, SZL Server

tecplot.com