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 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 Two-Dimensional Ordering of Solute Nanoclusters at a Close-Packed Stacking Fault: Modeling and Experimental Analysis

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Hajime Kimizuka ◽  
Shu Kurokawa ◽  
Akihiro Yamaguchi ◽  
Akira Sakai ◽  
Shigenobu Ogata
Keyword(s):  
Materials Science ◽  
Orientational Order ◽  
Stacking Fault ◽  
Coarse Grained ◽  
Scanning Tunneling ◽  
Two Dimensional ◽  
Tunneling Microscopy ◽  
Solute Cluster ◽  
Entropic Effect ◽  
High Degree

Abstract Predicting the equilibrium ordered structures at internal interfaces, especially in the case of nanometer-scale chemical heterogeneities, is an ongoing challenge in materials science. In this study, we established an ab-initio coarse-grained modeling technique for describing the phase-like behavior of a close-packed stacking-fault-type interface containing solute nanoclusters, which undergo a two-dimensional disorder-order transition, depending on the temperature and composition. Notably, this approach can predict the two-dimensional medium-range ordering in the nanocluster arrays realized in Mg-based alloys, in a manner consistent with scanning tunneling microscopy-based measurements. We predicted that the repulsively interacting solute-cluster system undergoes a continuous evolution into a highly ordered densely packed morphology while maintaining a high degree of six-fold orientational order, which is attributable mainly to an entropic effect. The uncovered interaction-dependent ordering properties may be useful for the design of nanostructured materials utilizing the self-organization of two-dimensional nanocluster arrays in the close-packed interfaces.

scholarly journals Autonomously designed free-form 2D DNA origami

2019 ◽  
Vol 5 (1) ◽  
pp. eaav0655 ◽  
Author(s):  
Hyungmin Jun ◽  
Fei Zhang ◽  
Tyson Shepherd ◽  
Sakul Ratanalert ◽  
Xiaodong Qi ◽  
...  
Keyword(s):  
Materials Science ◽  
Dna Origami ◽  
Free Form ◽  
Nanometer Scale ◽  
Dna Duplexes ◽  
Sequence Design ◽  
Internal Structures ◽  
Design Paradigm ◽  
2D And 3D ◽  
Unique Ability

Scaffolded DNA origami offers the unique ability to organize molecules in nearly arbitrary spatial patterns at the nanometer scale, with wireframe designs further enabling complex 2D and 3D geometries with irregular boundaries and internal structures. The sequence design of the DNA staple strands needed to fold the long scaffold strand to the target geometry is typically performed manually, limiting the broad application of this materials design paradigm. Here, we present a fully autonomous procedure to design all DNA staple sequences needed to fold any free-form 2D scaffolded DNA origami wireframe object. Our algorithm uses wireframe edges consisting of two parallel DNA duplexes and enables the full autonomy of scaffold routing and staple sequence design with arbitrary network edge lengths and vertex angles. The application of our procedure to geometries with both regular and irregular external boundaries and variable internal structures demonstrates its broad utility for nanoscale materials science and nanotechnology.

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.

Remote On-Line Control of a High-Voltage in situ Transmission Electron Microscope with A Rational User Interface

1996 ◽  
Vol 54 ◽  
pp. 384-385
Author(s):  
M.A. O’Keefe ◽  
J. Taylor ◽  
D. Owen ◽  
B. Crowley ◽  
K.H. Westmacott ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
User Interface ◽  
Transmission Electron Microscope ◽  
High Voltage ◽  
Materials Science ◽  
Transmission Electron ◽  
On Line ◽  
Electron Microscopes

Remote on-line electron microscopy is rapidly becoming more available as improvements continue to be developed in the software and hardware of interfaces and networks. Scanning electron microscopes have been driven remotely across both wide and local area networks. Initial implementations with transmission electron microscopes have targeted unique facilities like an advanced analytical electron microscope, a biological 3-D IVEM and a HVEM capable of in situ materials science applications. As implementations of on-line transmission electron microscopy become more widespread, it is essential that suitable standards be developed and followed. Two such standards have been proposed for a high-level protocol language for on-line access, and we have proposed a rational graphical user interface. The user interface we present here is based on experience gained with a full-function materials science application providing users of the National Center for Electron Microscopy with remote on-line access to a 1.5MeV Kratos EM-1500 in situ high-voltage transmission electron microscope via existing wide area networks. We have developed and implemented, and are continuing to refine, a set of tools, protocols, and interfaces to run the Kratos EM-1500 on-line for collaborative research. Computer tools for capturing and manipulating real-time video signals are integrated into a standardized user interface that may be used for remote access to any transmission electron microscope equipped with a suitable control computer.

Investigation of Au SAMs Photoclick Derivatization by PM-IRRAS

2019 ◽  
Author(s):  
Mark Workentin ◽  
François Lagugné-Labarthet ◽  
Sidney Legge
Keyword(s):  
Cell Adhesion ◽  
Self Assembly ◽  
Materials Science ◽  
Fibroblast Cell ◽  
Fine Tuning ◽  
Chemical System ◽  
Infrared Reflection ◽  
Assembled Monolayers ◽  
One Step ◽  
High Degree

In this work we present a clean one-step process for modifying headgroups of self-assembled monolayers (SAMs) on gold using photo-enabled click chemistry. A thiolated, cyclopropenone-caged strained alkyne precursor was first functionalized onto a flat gold substrate through self-assembly. Exposure of the cyclopropenone SAM to UV-A light initiated the efficient photochemical decarbonylation of the cyclopropenone moiety, revealing the strained alkyne capable of undergoing the interfacial strain-promoted alkyne-azide cycloaddition (SPAAC). Irradiated SAMs were derivatized with a series of model azides with varied hydrophobicity to demonstrate the generality of this chemical system for the modification and fine-tuning of the surface chemistry on gold substrates. SAMs were characterized at each step with polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS) to confirm successful functionalization and reactivity. Furthermore, to showcase the compatibility of this approach with biochemical applications, cyclopropenone SAMs were irradiated and modified with azide-bearing cell adhesion peptides to promote human fibroblast cell adhesion, then imaged by live cell fluorescence microscopy. Thus, the “photoclick” methodology reported here represents an improved, versatile, catalyst-free protocol that allows for a high degree of control over the modification of material surfaces, with applicability in materials science as well as biochemistry.<br>

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