Wireframe Structures Research Articles

Dynamic 4D facial capture pipeline with appearance driven progressive retopology based on optical flow

This paper presents a production-oriented 4D facial reconstruction pipeline designed to produce high-fidelity facial mesh sequences with a consistently structured topology, while preserving the wireframe structure specified by artists. We have designed and developed a compact, efficient, and fast optical capture system based on synchronized camera arrays for high-precision dynamic 3D facial imaging. Unlike prevailing methods that primarily concentrate on single-frame reconstruction, often reliant on labor-intensive manual annotation, our framework exploits the constraint of appearance consistency to autonomously establish feature correspondence and uphold temporal coherence within the mesh. Consequently, our approach eliminates mesh drifting and jitter, enabling full parallelization for dynamic facial expression capture. The proposed pipeline decouples the non-linear deformation of facial expressions from the rigid movements of the skull through a stable external device. Leveraging progressive retopology, our methodology employs artist-guided templates as priors, ensuring the preservation of wireframe structures across the result sequence. Progressive retopology is achieved by constraining different fine-grained features of 3D landmarks, scan surface shapes, and appearance textures. The results of our study showcase facial mesh sequences with production-quality topology, adept at faithfully reproducing character expressions from photographs while achieving artist-friendly stable facial movements.

Three-dimensional magnetic nanotextures with high-order vorticity in soft magnetic wireframes

Additive nanotechnology enable curvilinear and three-dimensional (3D) magnetic architectures with tunable topology and functionalities surpassing their planar counterparts. Here, we experimentally reveal that 3D soft magnetic wireframe structures resemble compact manifolds and accommodate magnetic textures of high order vorticity determined by the Euler characteristic, χ. We demonstrate that self-standing magnetic tetrapods (homeomorphic to a sphere; χ = + 2) support six surface topological solitons, namely four vortices and two antivortices, with a total vorticity of + 2 equal to its Euler characteristic. Alternatively, wireframe structures with one loop (homeomorphic to a torus; χ = 0) possess equal number of vortices and antivortices, which is relevant for spin-wave splitters and 3D magnonics. Subsequent introduction of n holes into the wireframe geometry (homeomorphic to an n-torus; χ < 0) enables the accommodation of a virtually unlimited number of antivortices, which suggests their usefulness for non-conventional (e.g., reservoir) computation. Furthermore, complex stray-field topologies around these objects are of interest for superconducting electronics, particle trapping and biomedical applications.

Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges.

In recent years, interest in wireframe DNA origami has increased, with different designs, software, and applications emerging at a fast pace. It is now possible to design a wide variety of shapes by starting with a 2D or 3D mesh and using different scaffold routing strategies. The design choices of the edges in wireframe structures can be important in some applications and have already been shown to influence the interactions between nanostructures and cells. In this work, we increase the alternatives for the design of A-trail routed wireframe DNA structures by using four-helix bundles (4HB). Our approach is based on the incorporation of additional helices to the edges of the wireframe structure to create a 4HB on a square lattice. We first developed the software for the design of these structures, followed by a demonstration of the successful design and folding of a library of structures, and then, finally, we investigated the higher mechanical rigidity of the reinforced structures. In addition, the routing of the scaffold allows us to easily incorporate these reinforced edges together with more flexible, single helix edges, thereby allowing the user to customize the desired stiffness of the structure. We demonstrated the successful folding of this type of hybrid structure and the different stiffnesses of the different parts of the nanostructures using a combination of computational and experimental techniques.

Predicting the Free-Form Shape of Structured DNA Assemblies from Their Lattice-Based Design Blueprint.

Structured DNA assemblies have been designed primarily on a three-dimensional lattice because it is easy to arrange and cross-link the helices there. However, when we design free-form structures including wireframes and topologically closed circular objects on a lattice, artificially stretched bonds connecting bases are inevitably and arbitrarily formed. They often lead to nonconvergence or convergence to a wrong configuration in computational analysis to predict the equilibrium shape of the structure when started from its lattice-based configuration, which hinders the design process of free-form structures. Here, we present a computational procedure enabling the shape prediction of free-form structures from their lattice-based design blueprint without any convergence issue. It automatically partitions the structure into substructures and relocates them into a new configuration. When the analysis for calculating the equilibrium shape begins from this configuration, no convergence issue occurs because substructures and stretched bonds connecting them do not overlap and intertwine each other during analysis. Using the proposed approach, we could obtain the free-form shape of a comprehensive set of wireframe and circular structures accurately and quickly. We further demonstrated that it also facilitated a design of wireframe structures with nonstraight edges.

Hybrid Wireframe DNA Nanostructures with Scaffolded and Scaffold‐Free Modules

AbstractThe scaffolded DNA origami approach and the scaffold‐free LEGO approach both demonstrate an extraordinary self‐assembly capability for constructing all kinds of complex DNA nanostructures. Combining the construction elements of the two approaches, we introduce a hybrid framework to build wireframe structures in this study. A collection of two‐dimensional (2D) and three‐dimensional (3D) wireframe structures are presented to showcase the simple and versatile design. Our development reveals more of the ever‐expanding design space of structural DNA nanotechnology.

Hybrid Wireframe DNA Nanostructures with Scaffolded and Scaffold‐Free Modules

The scaffolded DNA origami approach and the scaffold-free LEGO approach both demonstrate an extraordinary self-assembly capability for constructing all kinds of complex DNA nanostructures. Combining the construction elements of the two approaches, we introduce a hybrid framework to build wireframe structures in this study. A collection of two-dimensional (2D) and three-dimensional (3D) wireframe structures are presented to showcase the simple and versatile design. Our development reveals more of the ever-expanding design space of structural DNA nanotechnology.

Complex wireframe DNA nanostructures from simple building blocks

DNA nanostructures with increasing complexity have showcased the power of programmable self-assembly from DNA strands. At the nascent stage of the field, a variety of small branched objects consisting of a few DNA strands were created. Since then, a quantum leap of complexity has been achieved by a scaffolded ‘origami’ approach and a scaffold-free approach using single-stranded tiles/bricks—creating fully addressable two-dimensional and three-dimensional DNA nanostructures designed on densely packed lattices. Recently, wireframe architectures have been applied to the DNA origami method to construct complex structures. Here, revisiting the original wireframe framework entirely made of short synthetic strands, we demonstrate a design paradigm that circumvents the sophisticated routing and size limitations intrinsic to the scaffold strand in DNA origami. Under this highly versatile self-assembly framework, we produce a myriad of wireframe structures, including 2D arrays, tubes, polyhedra, and multi-layer 3D arrays.

Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles.

The field of structural DNA nanotechnology offers a wide range of design strategies with which to build structures with a desired aspect ratio, size, and shape. Compared with traditional close-packed DNA structures, triangulated wireframe structures require less material per surface or volume unit and improve the stability in biologically relevant conditions due to the reduced electrostatic repulsion. Herein, we expand the design space of the DNA single-stranded tile method to cover a range of anisotropic, finite, triangulated wireframe structures as well as a number of one-dimensional crystalline assemblies. These structures are composed of six-arm junctions with a single double helix as connecting edges that assemble in physiologically relevant salinities. For a reliable folding of the structures, single-stranded spacers 2-4 nucleotides long have to be introduced in the junction connecting neighboring arms. Coarse-grained molecular dynamics simulations using the oxDNA model suggests that the spacers prevent the stacking of DNA helices, thereby facilitating the assembly of planar geometries.

Structural Transformation of Wireframe DNA Origami via DNA Polymerase Assisted Gap-Filling.

The programmability of DNA enables constructing nanostructures with almost any arbitrary shape, which can be decorated with many functional materials. Moreover, dynamic structures can be realized such as molecular motors and walkers. In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer. For this purpose, four different wireframe DNA origami structures were designed to have single-stranded gap regions. This reduced the number of staple strands needed to determine the shape and size of the final structure after gap filling. For this, several DNA polymerases and single-stranded binding (SSB) proteins were tested, with T4 DNA polymerase being the best fit. The structures could be folded in as little as 6 min, and the subsequent optimized gap-filling reaction was completed in less than 3 min. The introduction of flexible gap regions results in fully collapsed or partially bent structures due to entropic spring effects. Finally, we demonstrated structural transformations of such deformed wireframe DNA origami structures with DNA polymerases including the expansion of collapsed structures and the straightening of curved tubes. We anticipate that this approach will become a powerful tool to build DNA wireframe structures more material-efficiently, and to quickly prototype and test new wireframe designs that can be expanded, rigidified, or mechanically switched. Mechanical force generation and structural transitions will enable applications in structural DNA nanotechnology, plasmonics, or single-molecule biophysics.

Modelos de brotes arbustivos o algas en arquitectura. O cómo replicar un vegetal mediante la Agregación Limitada por Difusión (DLA)

En el presente artículo se expone el desarrollo de un método de diseño de estructuras ramificadas del tipo algas marinas o formas arbustivas que se basa en la agregación limitada por difusión (DLA) para definir su geometría. Se ha usado la DLA para reproducir unas reglas de crecimiento convincentes o verosímiles a partir de lo aprendido de visores programables como el NetLogo (Wilensky 1999). En concreto, las herramientas que reproducen la simulación aprendida de NetLogo son el software Grasshopper para generar las geometrías, el plug-in Exoskeleton para obtener superficies envolventes a dichas estructuras alámbricas, y el plug-in Weaverbird para suavizar transiciones entre caras de malla. Ésta última herramienta permite suavizar la malla mediante iteraciones que aumentan o no el número de caras, lo que permite entender algunas teorías sobre transiciones suaves en bifurcaciones de estructuras naturales (Mattheck 1990).Este artículo sirve además para reflexionar acerca de cómo modelos físico cinéticos basados en mecanismos inspirados en la Inteligencia Artificial ayudan a compartir métodos de análisis con otras disciplinas como la cibernética o la dinámica de fluidos o las ciencias sociales y del medioambiente. ¿Por qué puede ocurrir esto? Por el rigor en el lenguaje que todo el rato pretende referirse a poblaciones de individuos, a ciclos de vida, a sistemas multivariables, a reglas de reciprocidad o a pactos con partículas próximas.

Construction of a Polyhedral DNA 12-Arm Junction for Self-Assembly of Wireframe DNA Lattices.

A variety of different tiles for the construction of DNA lattices have been developed since the structural DNA nanotechnology field was born. The majority of these are designed for the realization of close-packed structures, where DNA helices are arranged in parallel and tiles are connected through sticky ends. Assembly of such structures requires the use of cation-rich buffers to minimize repulsion between parallel helices, which poses limits to the application of DNA nanostructures. Wireframe structures, on the other hand, are less susceptible to salt concentration, but the assembly of wireframe lattices is limited by the availability of tiles and motifs. Herein, we report the construction of a polyhedral 12-arm junction for the self-assembly of wireframe DNA lattices. Our approach differs from traditional assembly of DNA tiles through hybridization of sticky ends. Instead, the assembly approach presented here uses small polyhedral shapes as connecting points and branch points of wires in a lattice structure. Using this design principle and characterization techniques, such as transmission electron microscopy, single-particle reconstruction, patterning of gold nanoparticles, dynamic light scattering, UV melting analyses, and small-angle X-ray scattering among others, we demonstrated formation of finite 12-way junction structures, as well as 1D and 2D short assemblies, demonstrating an alternative way of designing polyhedral structures and lattices.

Simplifying DNA origami design

DNA Nanotechnology Many intricate nanostructures have been made with DNA origami. This process occurs when a long DNA scaffold develops a particular shape after hybridization with short staple strands. Most designs, however, require a difficult iterative procedure of refining the base pairing. Veneziano et al. now report algorithms that automate the design of arbitrary DNA wireframe structures. Synthesizing and structurally characterizing a variety of nanostructures allowed for verification of the algorithms' accuracy. Science , this issue p. [1534][1] [1]: http://www.sciencemag.org/content/352/6293/1534

Designer nanoscale DNA assemblies programmed from the top down.

Scaffolded DNA origami is a versatile means of synthesizing complex molecular architectures. However, the approach is limited by the need to forward-design specific Watson-Crick base pairing manually for any given target structure. Here, we report a general, top-down strategy to design nearly arbitrary DNA architectures autonomously based only on target shape. Objects are represented as closed surfaces rendered as polyhedral networks of parallel DNA duplexes, which enables complete DNA scaffold routing with a spanning tree algorithm. The asymmetric polymerase chain reaction is applied to produce stable, monodisperse assemblies with custom scaffold length and sequence that are verified structurally in three dimensions to be high fidelity by single-particle cryo-electron microscopy. Their long-term stability in serum and low-salt buffer confirms their utility for biological as well as nonbiological applications.

Staple-Free DNA Self-Assembly

Scaffolded DNA origami uses a single-stranded DNA scaffold that spans all duplexes in a target nanostructure to hybridize with shorter helper staple strands using anti-parallel (DX) crossovers to stabilize the target geometry. While this design approach is powerful for achieving high-yield folding for diverse target structures, it is limited to contain crossovers that are spaced a minimum of ten base pairs apart and requires the use of numerous staple strands that limits both the minimum size of structural motifs and control over single-strand stoichiometry to achieve proper folding. In contrast, parallel (PX) crossovers have been used to achieve higher crossover density with 5-6 base pair spacing, eliminating the need for numerous helper strands and enabling higher rigidity nanostructures. Here, we explore application of a top-down computational approach to generate sequence designs for thermodynamically stable 3D wireframe structures that exhibit kinetically favorable folding properties, verified using experimental characterization.

Complex wireframe DNA origami nanostructures with multi-arm junction vertices.

Structural DNA nanotechnology and the DNA origami technique, in particular, have provided a range of spatially addressable two- and three-dimensional nanostructures. These structures are, however, typically formed of tightly packed parallel helices. The development of wireframe structures should allow the creation of novel designs with unique functionalities, but engineering complex wireframe architectures with arbitrarily designed connections between selected vertices in three-dimensional space remains a challenge. Here, we report a design strategy for fabricating finite-size wireframe DNA nanostructures with high complexity and programmability. In our approach, the vertices are represented by n × 4 multi-arm junctions (n = 2-10) with controlled angles, and the lines are represented by antiparallel DNA crossover tiles of variable lengths. Scaffold strands are used to integrate the vertices and lines into fully assembled structures displaying intricate architectures. To demonstrate the versatility of the technique, a series of two-dimensional designs including quasi-crystalline patterns and curvilinear arrays or variable curvatures, and three-dimensional designs including a complex snub cube and a reconfigurable Archimedean solid were constructed.

Effect of Concentration-dependent Disjoining Pressure on Vertical Draining Flow

We construct a mathematical model to describe the flow in a vertical soap film that is draining under gravity, assuming that the film is supported by two wire frame structures at both the top and bottom. A two-term surfactant concentration-dependent disjoining pressure is included in the model allowing the development of thin, stable and rigid film. The modeling results in three coupled partial differential equations including the film thickness, the surfactant concentration, and the slip or surface velocity by lubrication theory, which are solved numerically by using FREEFEM program. The evolution processes of the thin film are investigated numerically under effect of concentration-dependent disjoining pressure as well as concentration-independent disjoining pressure for compared. More over, the effect of two factors, namely the attraction strength coefficient α1 and repulsion strength coefficient α2 in the concentration-dependent disjoining pressure function are investigated thoroughly. Results show that the evolution time varies with α1 and α2. Reducing α1 promotes the draining process of flow, while decreasing α2 impedes the evolution process.

Wireframe and Tensegrity DNA Nanostructures

CONSPECTUS: Not only can triangulated wireframe network and tensegrity design be found in architecture, but it is also essential for the stability and organization of biological matter. Whether the scaffolding material is metal as in Buckminster Fuller's geodesic domes and Kenneth Snelson's floating compression sculptures or proteins like actin or spectrin making up the cytoskeleton of biological cells, wireframe and tensegrity construction can provide great stability while minimizing the material required. Given the mechanical properties of single- and double-stranded DNA, it is not surprising to find many variants of wireframe and tensegrity constructions in the emerging field of DNA nanotechnology, in which structures of almost arbitrary shape can be built with nanometer precision. The success of DNA self-assembly relies on the well-controlled hybridization of complementary DNA strands. Consequently, understanding the fundamental physical properties of these molecules is essential. Many experiments have shown that double-stranded DNA (in its most commonly occurring helical form, the B-form) behaves in a first approximation like a relatively stiff cylindrical beam with a persistence length of many times the length of its building blocks, the base pairs. However, it is harder to assign a persistence length to single-stranded DNA. Here, normally the Kuhn length is given, a measure that describes the length of individual rigid segments in a freely jointed chain. This length is on the order of a few nucleotides. Two immediate and important consequences arise from this high flexibility: single-stranded DNA is almost always present in a coiled conformation, and it behaves, just like all flexible polymers in solution, as an entropic spring. In this Account, we review the relation between the mechanical properties of DNA and design considerations for wireframe and tensegrity structures built from DNA. We illustrate various aspects of the successful evolution of DNA nanotechnology starting with the construction of four-way junctions and then allude to simple geometric objects such as the wireframe cube presented by Nadrian Seeman along with a variety of triangulated wireframe constructions. We examine DNA tensegrity triangles that self-assemble into crystals with sizes of several hundred micrometers as well as prestressed DNA origami tensegrity architecture, which uses single-stranded DNA with its entropic spring behavior as tension bearing components to organize stiff multihelix bundles in three dimensions. Finally, we discuss emerging applications of the aforementioned design principles in diverse fields such as diagnostics, drug delivery, or crystallography. Despite great advances in related research fields like protein and RNA engineering, DNA self-assembly is currently the most accessible technique to organize matter on the nanoscale, and we expect many more exciting applications to emerge.

The experimental analysis of the double joint type change effect on the joint destruction process in uniaxial shearing test

This paper analyzes the shearing strength analysis of double joints made of various joining techniques. The capabilities of S350 GD sheet metal joining using the ClinchRivet technique were presented. The joint strength researches based on the uniaxial shearing test of the overlay joints for steel sheet of 1mm thickness, which is used in the light gauge steel profiles in the wireframe structures of residential and commercial buildings.The results achieved for joints arranged in parallel and perpendicular to the load for specified joint spacing were discussed. The assessment of joint effectiveness were performed for both homogenous double joints and for various combinations of these joints.

Drainage of particle-stabilised aluminium composites through single films and Plateau borders

Liquid metallic alloys with and without stabilizing particles such as TiB2 or SiC were processed to single films or artificial single Plateau borders to clarify the stabilization mechanisms of metallic foams based on the same melts. First, isolated single films were pulled out of a liquid metal by using circular wire frames of various sizes. Modified wire frame structures comprising double or quadruple parallel frames were then used to create artificial metallic Plateau borders. Drainage in single metallic films between two Plateau borders was studied by cutting films vertically and analysing their cross sections. Particle movement in liquid films was observed in-situ via synchrotron X-ray radioscopy. It was found that Mg-free liquid metallic alloys containing stabilising particles are less stable and rupture immediately because of unhindered drainage. In contrast, films made of AlSi9Mg0.6 alloy containing TiB2 or SiC are stable for long holding times. Our study shows that the complexity of drainage and evolution of Plateau borders in true metal foams can be studied by using a simple model system based on a single metallic film between two artificial Plateau borders.

Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures

DNA nanotechnology enables the programmed synthesis of intricate nanometer-scale structures for diverse applications in materials and biological science. Precise control over the 3D solution shape and mechanical flexibility of target designs is important to achieve desired functionality. Because experimental validation of designed nanostructures is time-consuming and cost-intensive, predictive physical models of nanostructure shape and flexibility have the capacity to enhance dramatically the design process. Here, we significantly extend and experimentally validate a computational modeling framework for DNA origami previously presented as CanDo [Castro,C.E., Kilchherr,F., Kim,D.-N., Shiao,E.L., Wauer,T., Wortmann,P., Bathe,M., Dietz,H. (2011) A primer to scaffolded DNA origami. Nat. Meth., 8, 221–229.]. 3D solution shape and flexibility are predicted from basepair connectivity maps now accounting for nicks in the DNA double helix, entropic elasticity of single-stranded DNA, and distant crossovers required to model wireframe structures, in addition to previous modeling (Castro,C.E., et al.) that accounted only for the canonical twist, bend and stretch stiffness of double-helical DNA domains. Systematic experimental validation of nanostructure flexibility mediated by internal crossover density probed using a 32-helix DNA bundle demonstrates for the first time that our model not only predicts the 3D solution shape of complex DNA nanostructures but also their mechanical flexibility. Thus, our model represents an important advance in the quantitative understanding of DNA-based nanostructure shape and flexibility, and we anticipate that this model will increase significantly the number and variety of synthetic nanostructures designed using nucleic acids.