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.

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.

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 Dirichlet absorbing boundary conditions for classical and peridynamic diffusion-type models

2020 ◽  
Vol 66 (4) ◽  
pp. 773-793 ◽  
Author(s):  
Arman Shojaei ◽  
Alexander Hermann ◽  
Pablo Seleson ◽  
Christian J. Cyron
Keyword(s):  
Boundary Conditions ◽  
Materials Science ◽  
Unbounded Domains ◽  
Diffusion Models ◽  
Absorbing Boundary Conditions ◽  
The Finite Element Method ◽  
Absorbing Boundary ◽  
Diffusion Type ◽  
2D And 3D ◽  
Accuracy And Stability

Abstract Diffusion-type problems in (nearly) unbounded domains play important roles in various fields of fluid dynamics, biology, and materials science. The aim of this paper is to construct accurate absorbing boundary conditions (ABCs) suitable for classical (local) as well as nonlocal peridynamic (PD) diffusion models. The main focus of the present study is on the PD diffusion formulation. The majority of the PD diffusion models proposed so far are applied to bounded domains only. In this study, we propose an effective way to handle unbounded domains both with PD and classical diffusion models. For the former, we employ a meshfree discretization, whereas for the latter the finite element method (FEM) is employed. The proposed ABCs are time-dependent and Dirichlet-type, making the approach easy to implement in the available models. The performance of the approach, in terms of accuracy and stability, is illustrated by numerical examples in 1D, 2D, and 3D.

Nanotechnology and Their Applications in Science and Technology - Review

2021 ◽  
Vol 8 (1) ◽  
Keyword(s):  
Natural Science ◽  
Physical Science ◽  
Materials Science ◽  
Science And Technology ◽  
Nanometer Scale ◽  
Food Handling ◽  
Novel Materials ◽  
Food Applications ◽  
Nano Science ◽  
Technology Review

Nanotechnology is the investigation of tiny designs, having size of 0.1 to 100 nm. Nano medication is a generally new field of science and innovation. Brief clarification of different sorts of drug nano frameworks is given. Nanotechnology is serving to significantly improve, even alter, numerous innovation and industry areas: data innovation, energy, natural science, medication, country security, sanitation, and transportation, among numerous others. The present nanotechnology tackles current advancement in science, physical science, materials science, and biotechnology to make novel materials that have interesting properties on the grounds that their designs are resolved on the nanometer scale. Ongoing advances in Nano science and nanotechnology plan new and inventive applications in the food business. Nanotechnology presented to be a productive strategy in numerous fields, especially the food business and the space of utilitarian food varieties. However just like the condition with the development of any original food handling innovation, food bundling material, or food fixing, extra investigations are expected to exhibit the possible advantages of nanotechnologies and designed nanomaterial intended for use in food varieties without antagonistic wellbeing impacts. Nano emulsions show various benefits over customary emulsions because of the little beads size they contain: high optical lucidity, phenomenal actual consistency against gravitational parcel and drop aggregation, and further developed bio-availability of typified materials, which make them appropriate for food applications.

Time-Independent Finite Difference and Ghost Cell Method to Study Sloshing Liquid in 2D and 3D Tanks with Internal Structures

2013 ◽  
Vol 13 (3) ◽  
pp. 780-800 ◽  
Author(s):  
C. H. Wu ◽  
O. M. Faltinsen ◽  
B. F. Chen
Keyword(s):  
Finite Difference ◽  
Vertical Plate ◽  
Stokes Equations ◽  
Staggered Grid ◽  
Navier Stokes ◽  
Iteration Algorithm ◽  
Ghost Cell ◽  
Fluid Sloshing ◽  
Internal Structures ◽  
2D And 3D

AbstractA finite difference scheme with ghost cell technique is used to study viscous fluid sloshing in 2D and 3D tanks with internal structures. The Navier-Stokes equations in a moving coordinate system are derived and they are mapped onto a time-independent and stretched domain. The staggered grid is used and the revised SIMPLEC iteration algorithm is performed. The developed numerical model is rigorously validated by extensive comparisons with reported analytical, numerical and experimental results. The present numerical results were also validated through an experiment setup with a tank excited by an inclined horizontal excitation or a tank mounted by a vertical baffle. The method is then applied to a number of problems including sloshing fluid in a 2D tank with a bottom-mounted baffle and in a 3D tank with a vertical plate. The phenomena of diagonal sloshing waves affected by a vertical plate are investigated in detail in this work. The effects of internal structures on the resonant frequency of a tank with liquid are discussed and the present developed numerical method can successfully analyze the sloshing phenomenon in 2D or 3D tanks with internal structures.

scholarly journals An electrochemical biosensor exploiting binding-induced changes in electron transfer of electrode-attached DNA origami to detect hundred nanometer-scale targets

Nanoscale ◽  
2020 ◽  
Vol 12 (26) ◽  
pp. 13907-13911 ◽  
Author(s):  
Netzahualcóyotl Arroyo-Currás ◽  
Muaz Sadeia ◽  
Alexander K. Ng ◽  
Yekaterina Fyodorova ◽  
Natalie Williams ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Electrochemical Biosensor ◽  
Direct Detection ◽  
Dna Origami ◽  
Nanometer Scale ◽  
Recognition Element ◽  
Induced Changes

Using DNA origami as the recognition element in an electrochemical biosensor enables the selective and direct detection of “mesoscale” virus-sized analytes.

Programmed Nanopatterning of Organic/Inorganic Nanoparticles Using Nanometer-Scale Wells Embedded in a DNA Origami Scaffold

Small ◽  
2010 ◽  
Vol 6 (23) ◽  
pp. 2664-2667 ◽  
Author(s):  
Akinori Kuzuya ◽  
Naohiro Koshi ◽  
Mayumi Kimura ◽  
Kentaro Numajiri ◽  
Takahiro Yamazaki ◽  
...  
Keyword(s):  
Dna Origami ◽  
Inorganic Nanoparticles ◽  
Nanometer Scale

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.

Biochemical Processing of Materials: A Review

1994 ◽  
Vol 346 ◽  
Author(s):  
Larry L. Hench
Keyword(s):  
Molecular Orbital ◽  
Materials Science ◽  
Biological Systems ◽  
Nanometer Scale ◽  
List Type ◽  
Type Number ◽  
Hierarchical Processing ◽  
Stereochemical Control ◽  
Potential Applications ◽  
Potential Use

ABSTRACTMany biological systems have evolved means of controlling the architecture of inorganic-organic composites at a nanometer scale. The principles of biochemistry and materials science underlying the potential use of biochemical processing to develop new molecularly tailored materials are discussed, with emphasis on:methods of stereochemical control of the organic-inorganic interface,genetic and enzymic control of biosynthesis and biomineralization,molecular orbital modelling of bio organic-inorganic interfaces,barriers and limitations of biomimetic and hierarchical processing,examples of unique materials made with biochemical processing.needs and potential applications in human prostheses.

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