scholarly journals Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

2021 ◽  
Vol 49 (18) ◽  
pp. 10265-10274
Author(s):  
Hyungmin Jun ◽  
Xiao Wang ◽  
Molly F Parsons ◽  
William P Bricker ◽  
Torsten John ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Dna Origami ◽  
Coarse Grained ◽  
Top Down ◽  
Helix Bundle ◽  
Open Source Software Package ◽  
Algorithmic Approaches ◽  
High Degree ◽  
2D And 3D

Abstract Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

scholarly journals Rapid Prototyping of Wireframe Scaffolded DNA Origami using ATHENA

2020 ◽  
Author(s):  
Hyungmin Jun ◽  
Xiao Wang ◽  
William P. Bricker ◽  
Steve Jackson ◽  
Mark Bathe
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Materials Science ◽  
Dna Origami ◽  
Coarse Grained ◽  
Helix Bundle ◽  
Open Source Software Package ◽  
Algorithmic Approaches ◽  
High Degree ◽  
2D And 3D

ABSTRACTWireframe DNA origami assemblies can now be programmed automatically from the “top-down” using simple wireframe target geometries, or meshes, in 2D and 3D geometries using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (2HB or DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, stand-alone interface. Here, we present ATHENA, an open-source software package with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami in 2D or 3D using 2HB or 6HB edges. ATHENA enables external editing of sequences using the popular tool caDNAno, demonstrated here using asymmetric nanoscale positioning of gold nanoparticles, as well as atomic-level models for molecular dynamics, coarse-grained dynamics, or other computational chemistry simulation approaches. We anticipate ATHENA will significantly reduce the barrier for non-specialists to perform wireframe DNA origami sequence design and fabrication for custom applications in materials science, nanotechnology, therapeutics, and other areas.

scholarly journals Automated sequence design of 2D wireframe DNA origami with honeycomb edges

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Hyungmin Jun ◽  
Xiao Wang ◽  
William P. Bricker ◽  
Mark Bathe
Keyword(s):  
Design Procedure ◽  
Computational Approach ◽  
Dna Origami ◽  
Nanometer Scale ◽  
Top Down ◽  
Complex Objects ◽  
Sequence Design ◽  
Theoretical Support ◽  
Powerful Approach ◽  
2D And 3D

AbstractWireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale. Complex scaffold and staple routing needed to design wireframe DNA origami objects, however, render fully automated, geometry-based sequence design approaches essential for their synthesis. And wireframe DNA origami structural fidelity can be limited by wireframe edges that are composed only of one or two duplexes. Here we introduce a fully automated computational approach that programs 2D wireframe origami assemblies using honeycomb edges composed of six parallel duplexes. These wireframe assemblies show enhanced structural fidelity from electron microscopy-based measurement of programmed angles compared with identical geometries programmed using dual-duplex edges. Molecular dynamics provides additional theoretical support for the enhanced structural fidelity observed. Application of our top-down sequence design procedure to a variety of complex objects demonstrates its broad utility for programmable 2D nanoscale materials.

Graphical User Interface for Human Intervention in 2D-3D Registration of Medical Images

2013 ◽  
Author(s):  
Grant L. S. Marchelli ◽  
David R. Haynor ◽  
William R. Ledoux ◽  
Mark A. Ganter ◽  
Duane W. Storti
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
3D Imaging ◽  
Quality Measure ◽  
Reference Image ◽  
3D Registration ◽  
Data Set ◽  
Image Guided ◽  
2D And 3D

Image-guided medical therapies and image-guided biomechanical measurement systems often combine 2D and 3D imaging modalities. Determination of relations between the 2D and 3D imaging data is known as 2D-3D registration. Motivated by an ongoing project aimed at non-invasive, marker-free measurement of the kinematics of the bones in the foot during gait, we consider a registration approach that involves (1) computing projections of the 3D data set, (2) computing a quality measure to describe the agreement/discrepancy between the simulated projections and actual 2D images, and (3) optimization of the quality measure relative to the kinematic degrees of freedom to determine the optimal registration. For our particular project, the 3D imaging modality is CT scan, the 2D modality is bi-plane fluoroscopy, the computed projection is a digitally reconstructed radiograph (DRR), the quality measure is normalized cross-correlation (NCC) between a pair of DRRs and a pair of corresponding fluoroscope images, and the 2D imaging includes a sequence of several hundred stereo image pairs. We have recently released a software toolkit, DRRACC, that accelerates both the DRR and NCC computations via GPU-based parallel processing to enable more efficient automated determination of kinematic relations for optimal registration. While fully automated 2D-3D registration is desirable, there are situations (such as creating a reasonable starting configuration for optimization, re-starting after the optimizer fails to converge, and visual verification of registration relations) when it is desirable/necessary to have a human in the loop. In this paper, we present an OpenGL-based graphical user interface that employs the DRRACC toolkit to allow the user to manipulate the kinematics of individual objects (bones) segmented from the 3D imaging and to view the corresponding DRR and the associated correlation with a reference image in real time. We also present plots showing initial results for the dependence of the registration measure on pairs of kinematic parameters. The plots show well-defined peaks that support the hope for automated registration, but they also contain large relatively flat regions that may prove problematic for gradient-based optimizers and necessitate the sort of interface presented in this paper.

HOW TO USE CROP GROWTH MODEL WOFOST FOR FORECASTING GROWTH AND YIELD OF A CROP

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
LAL SINGH ◽  
PARMEET SINGH ◽  
RAIHANA HABIB KANTH ◽  
PURUSHOTAM SINGH ◽  
SABIA AKHTER ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Input Data ◽  
Growth And Yield ◽  
Weather Data ◽  
Data Sets ◽  
Crop Growth Model ◽  
Control Center ◽  
Field Crops ◽  
Crop Calendar

WOFOST version 7.1.3 is a computer model that simulates the growth and production of annual field crops. All the run options are operational through a graphical user interface named WOFOST Control Center version 1.8 (WCC). WCC facilitates selecting the production level, and input data sets on crop, soil, weather, crop calendar, hydrological field conditions, soil fertility parameters and the output options. The files with crop, soil and weather data are explained, as well as the run files and the output files. A general overview is given of the development and the applications of the model. Its underlying concepts are discussed briefly.

Sign in / Sign up

Export Citation Format

Share Document