3D Topology Research Articles

Artificially inserted strong promoter containing multiple G-quadruplexes induces long-range chromatin modification.

Although the role of G-quadruplex (G4) DNA structures has been suggested in chromosomal looping this was not tested directly. Here, to test causal function, an array of G4s, or control sequence that does not form G4s, were inserted within chromatin in cells. In vivo G4 formation of the inserted G4 sequence array, and not the control sequence, was confirmed using G4-selective antibody. Compared to the control insert, we observed a remarkable increase in the number of 3D chromatin looping interactions from the inserted G4 array. This was evident within the immediate topologically associated domain (TAD) and throughout the genome. Locally, recruitment of enhancer histone marks and the transcriptional coactivator p300/Acetylated-p300 increased in the G4-array, but not in the control insertion. Resulting promoter-enhancer interactions and gene activation were clear up to 5 Mb away from the insertion site. Together, these show the causal role of G4s in enhancer function and long-range chromatin interactions. Mechanisms of 3D topology are primarily based on DNA-bound architectural proteins that induce/stabilize long-range interactions. Involvement of the underlying intrinsic DNA sequence/structure in 3D looping shown here therefore throws new light on how long-range chromosomal interactions might be induced or maintained.

Artificially inserted strong promoter containing multiple G-quadruplexes induces long-range chromatin modification

Although the role of G-quadruplex (G4) DNA structures has been suggested in chromosomal looping this was not tested directly. Here, to test causal function, an array of G4s, or control sequence that does not form G4s, were inserted within chromatin in cells. In vivo G4 formation of the inserted G4 sequence array, and not the control sequence, was confirmed using G4-selective antibody. Compared to the control insert, we observed a remarkable increase in the number of 3D chromatin looping interactions from the inserted G4 array. This was evident within the immediate topologically associated domain (TAD) and throughout the genome. Locally, recruitment of enhancer histone marks and the transcriptional coactivator p300/Acetylated-p300 increased in the G4-array, but not in the control insertion. Resulting promoter-enhancer interactions and gene activation were clear up to 5 Mb away from the insertion site. Together, these show the causal role of G4s in enhancer function and long-range chromatin interactions. Mechanisms of 3D topology are primarily based on DNA-bound architectural proteins that induce/stabilize long-range interactions. Involvement of the underlying intrinsic DNA sequence/structure in 3D looping shown here therefore throws new light on how long-range chromosomal interactions might be induced or maintained.

Heat Shock Factor 1 forms nuclear condensates and restructures the yeast genome before activating target genes.

In insects and mammals, 3D genome topology has been linked to transcriptional states yet whether this link holds for other eukaryotes is unclear. Using both ligation proximity and fluorescence microscopy assays, we show that in Saccharomyces cerevisiae, Heat Shock Response (HSR) genes dispersed across multiple chromosomes and under the control of Heat Shock Factor (Hsf1) rapidly reposition in cells exposed to acute ethanol stress and engage in concerted, Hsf1-dependent intergenic interactions. Accompanying 3D genome reconfiguration is equally rapid formation of Hsf1-containing condensates. However, in contrast to the transience of Hsf1-driven intergenic interactions that peak within 10-20 min and dissipate within 1 h in the presence of 8.5% (v/v) ethanol, transcriptional condensates are stably maintained for hours. Moreover, under the same conditions, Pol II occupancy of HSR genes, chromatin remodeling, and RNA expression are detectable only later in the response and peak much later (>1 h). This contrasts with the coordinate response of HSR genes to thermal stress (39°C) where Pol II occupancy, transcription, histone eviction, intergenic interactions, and formation of Hsf1 condensates are all rapid yet transient (peak within 2.5-10 min and dissipate within 1 h). Therefore, Hsf1 forms condensates, restructures the genome and transcriptionally activates HSR genes in response to both forms of proteotoxic stress but does so with strikingly different kinetics. In cells subjected to ethanol stress, Hsf1 forms condensates and repositions target genes before transcriptionally activating them.

A new Zn(II)-based 3D MOF with PCU-like topology: Potent photocatalyst for nitrofurazone antibiotic degradation

Metal-organic frameworks (MOFs), a sub-class of coordination polymers, are versatile multidimensional materials that have the potential to serve as photocatalysts for the degradation of antibiotics found in wastewater. Herein, a new three dimensional (3D) Zn(II)-based MOF [Zn(TA)(bpyp)·3H2O] (1) (bypy = 2,5-bis(pyrid-4-yl)pyridine; H2TA = terephthalic acid) has been synthesized and characterized. The MOF 1 shows a 3D PCU-like topology and exhibits semiconducting properties with band gap of 3.34 eV and hence used as a photocatalyst for photodegradation of antibiotics viz. sulfasalazine (SLA), nitrofurazone (NFZ) and furazolidone (FZD) under simulated UV light irradiation. The photocatalytic results suggest that MOF 1 exhibits best photocatalytic activity for the photodegradation of nitrofurazone (NFZ) in 60 min time-span. The effects of initial concentration of NFZ, and photocatalyst dosage have been monitored for the photocatalytic performance of 1. The radical trapping experiments suggest that (holes) h+ and superoxide radical (O2·−) collectively catalyzes the photodecomposition of antibiotics. The possible mechanism for the antibiotic degradation by photocatalyst 1 have been proposed by integrating experiment with density of states (DOS) calculations and Hirshfeld surface analysis.

Patient-specific 3D-printed Splint for Mallet Finger Injury.

Despite the frequency of mallet finger injuries, treatment options can often be costly, time-consuming, and ill-fitted. Three-dimensional (3D) printing allows for the production of highly customized and inexpensive splints, which suggests potential efficacy in the prescription of casts for musculoskeletal injuries. This study explores how the use of engineering concepts such as 3D printing and topology optimization (TO) can improve outcomes for patients. 3D printing enables the direct fabrication of the patient-specific complex shapes while utilizing finite element analysis and TO in the design of the splint allowed for the most efficient distribution of material to achieve mechanical requirements while reducing the amount of material used. The reduction in used material leads to significant improvements in weight reduction and heat dissipation, which would improve breathability and less sweating for the patient, greatly increasing comfort for the duration of their recovery.

3D Topology Optimization and Mesh Dependency for Redesigning Locking Compression Plates Aiming to Reduce Stress Shielding.

Current fixation plates for bone fracture treatments are built with biocompatible metallic materials such as stainless steel, titanium, and its alloys (e.g., Ti6Al4V). The stiffness mismatch between the metallic material of the plate and the host bone leads to stress shielding phenomena, bone loss, and healing deficiency. This paper explores the use of three dimensional topology-optimization, based on compliance (i.e., strain energy) minimization, reshaping the design domain of three locking compression plates (four-screw holes, six-screw holes, and eight-screw holes), considering different volume reductions (25, 45, and 75%) and loading conditions (bending, compression, torsion, and combined loads). A finite-element study was also conducted to measure the stiffness of each optimized plate. Thirty-six designs were obtained. Results showed that for a critical value of volume reductions, which depend on the load condition and number of screws, it is possible to obtain designs with lower stiffness, thereby reducing the risk of stress shielding.

TOP2DFVT: An Efficient Matlab Implementation for Topology Optimization based on the Finite-Volume Theory

The finite-volume theory has shown to be numerically efficient and stable for topology optimization of continuum elastic structures. The significant features of this numerical technique are the local satisfaction of equilibrium equations and the employment of compatibility conditions along edges in a surface-averaged sense. These are essential properties to adequately mitigate some numerical instabilities in the gradient version of topology optimization algorithms, such as checkerboard, mesh dependence, and local minima issues. Several computational tools have been proposed for topology optimization employing analysis domains discretized with essential features for finite-element approaches. However, this is the first contribution to offer a platform to generate optimized topologies by employing a Matlab code based on the finite-volume theory for compliance minimization problems. The Top2DFVT provides a platform to perform 2D topology optimization of structures in Matlab, from domain initialization for structured meshes to data post-processing. This contribution represents a significant advancement over earlier publications on topology optimization based on the finite-volume theory, which needed more efficient computational tools. Moreover, the Top2DFVT algorithm incorporates SIMP and RAMP material interpolation schemes alongside sensitivity and density filtering techniques, culminating in a notably enhanced optimization tool. The application of this algorithm to various illustrative cases confirms its efficacy and underscores its potential for advancing the field of structural optimization.

Curvature programming of freestanding 3D mesostructures and flexible electronics based on bilayer ribbon networks

Three-dimensional (3D) buckling assembly of flexible electronics from strategically designed two-dimensional (2D) precursor structures has enabled important applications in a variety of areas, owing to its versatile applicability to a broad range of length scales and high-performance materials, as well as to a rich diversity of 3D topologies. Rational design methods that allow direct mapping of 3D mesostructures onto unknown 2D precursor structures and loading parameters are foundational to these assembly technologies, but face scientific challenges, such as the high nonlinearity of spatial deformations and tricky bifurcation behaviors. While a few inverse design methods based on the beam theory, topology optimization and machine learning algorithms have been reported, the shape programming of freestanding 3D mesostructures/electronics with highly complex curvature distributions remains elusive. In this work, we propose a curvature programming method based on bilayer ribbon networks, along with a mold-assisted assembly strategy, as a new route to customizable freestanding 3D mesostructures and electronics. Combined mechanics modeling, finite element analyses and experimental measurements allow a clear understanding of nonlinear bending-stretching coupled deformations of bilayer ribbon networks during the 2D-to-3D transformation. A parameter domain with one-to-one mapping of the dimensionless curvature and the bending stiffness ratio is identified, offering a theoretical basis of the curvature programming. By introducing a discretization strategy, a variety of regular (e.g., circles, ellipses, spirals and toroids) and biomimetic 3D curved ribbons and mesosurfaces (e.g., mimicking wavy vines, diatoms and arbitrarily curled leaves) were inversely designed and experimentally realized. A device demonstration capable of strain/temperature sensing and micro-LEDs indication suggests application opportunities in bioelectronics and microelectromechanical systems.

Three-Dimensional Measurements Of Deformable Oil Droplets In Turbulence

This work introduces an experimental facility designed to generate turbulence with a high energy dissipation rate of up to 0.3 m^2/s^3 , sufficient to induce deformation and fragmentation of oil droplets. The turbulence is produced by opposing arrays consisting of 24 jet streams in total, each with Reynolds numbers ranging from 12,000 to 50,000. Flow regimes are determined using 3D Particle Tracking Velocimetry (PTV) conducted in the center of the octagonal test section. The statistical analysis of the turbulence reveals a nearly homogeneous and isotropic nature. A 3D imaging system, equipped with six high-speed cameras, allows for the reconstruction of droplets using the multiple algebraic reconstruction technique algorithm, fostering both visualization and quantification of interface deformation. Additionally, the system enables the tracking of the breakup process. The presented setup is able to couple the measurements of the droplet shapes with surrounding turbulence in 3D dproplet topology reconstruction coupled with surrounding flow measurements. We demonstrate the capability of our imaging system and reconstruction methods for multiphase flow studies with an example of full 3D droplet topology reconstruction coupled with surrounding flow measurements.

Topology Optimization and 3D Printing of Steel Joints by SJ-BESO and FDM Method

Topology Optimization and 3D Printing of Steel Joints by SJ-BESO and FDM Method

Topological derivative based sensitivity analysis for three-dimensional discrete variable topology optimization

This study introduces a novel Topological Derivative-based Sensitivity Analysis (TDSA) methodology for three-dimensional (3D) discrete variable topology optimization. Recently, the authors pointed out that the discrete variable sensitivity can be related to the topological derivative, and thus can be rationally approximated by the specially customized topological derivative for plane stress problems. However, the 3D discrete variable sensitivity requires the 3D topological derivative with element-shaped (e.g., unit cube) domain perturbation, whose analytical solution is not available in the literature. This paper proposes a unified parameter fitting framework to calculate the 3D topological derivative with arbitrary shape 3D domain perturbation. The formula for spherical hole perturbation obtained through this parameter fitting framework is identical to the well-known analytical topological derivative formula. Further, the 3D discrete variable sensitivity can be easily obtained through element-shaped domain perturbation. With the recently proposed Sequential Approximate Integer Programming (SAIP), numerical examples demonstrate that TDSA is precise not only for the self-adjoint 3D minimum compliance problems but also for the non-adjoint 3D compliant mechanism design problems. In sum, numerical examples have been conducted by feeding the derived sensitivity to the SAIP optimization algorithms, and the correctness of the sensitivity information has been well demonstrated. This research further solidifies the foundation of rational discrete variable sensitivity analysis in 3D topology optimization.

Topological Spectra and Entropy of Chromatin Loop Networks

The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fiber is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors and RNA polymerases. This physical model leads to the natural emergence of clusters of proteins and binding sites, accompanied by the folding of chromatin into a set of topologies, each associated with a different network of loops. Here, we combine numerics and analytics to first classify these networks and then find their relative importance or statistical weight, when the properties of the underlying polymer are those relevant to chromatin. Unlike polymer networks previously studied, our chromatin networks have finite average distances between successive binding sites, and this leads to giant differences between the weights of topologies with the same number of edges and nodes but different wiring. These weights strongly favor rosettelike structures with a local cloud of loops with respect to more complicated nonlocal topologies. Our results suggest that genes should overwhelmingly fold into a small fraction of all possible 3D topologies, which can be robustly characterized by the framework we propose here. Published by the American Physical Society 2024

Multiscale topology optimization for the design of spatially-varying three-dimensional lattice structure

This paper introduces three dimensional (3D) topology optimization specifically tailored for designing spatially-varying primitive-cubic (CP) type lattice structures. The developed design process consists of three steps: pre-processing, main processing, and post-processing. In the pre-processing step, a surrogate model between lattice geometry variables and effective elasticity tensor is constructed using an artificial neural network. This surrogate model is essential because it enables the quick calculation of the effective elasticity tensor of lattice microstructure. In the subsequent main processing step, multiscale topology optimization is performed. During this step, lattice microstructure size and rotation design variables are optimized together with the macrostructure density design variables. Macrostructures are designed using a well-established three-field density scheme with a SIMP formulation. Formulations for spatially-varying 3D lattice microstructure are newly developed based on a unit quaternion rotation representation scheme. In the final post-processing step, a spatially-varying microstructure is restored using a de-homogenization scheme, newly developed particularly for the primitive-cubic (CP) type 3D lattice structures. The effectiveness and robustness of the proposed formulations are validated through three design examples for the compliance minimization problem. Moreover, a designed lattice structure is fabricated using an additive manufacturing machine.

One‐dimensional phenanthroline‐based covalent organic framework bearing single cobalt atoms for efficient photocatalytic CO2 reduction

AbstractMetalated covalent organic frameworks (COFs) for 2D and 3D topologies are continuously being developed, whereas metalated COFs with 1D topologies are still in their infancy. Here, a novel 1D phenanthroline‐based COF containing 4,4‐(1,10‐phenanthroline‐2,9‐diyl)bis[benzaldehyde] (PBA) is reported (PAD‐COF). Subsequently, a metalated 1D COF, Co SAS/PAD‐COF, is constructed using the bidentate ligand properties of PBA and anchoring the single Co atoms in PAD‐COF through a post‐synthetic modification strategy. This complex significantly improved the photocatalytic performance of PAD‐COF, and the CO yield of the optimized Co SAS/PAD‐COF was stable at 3091 µmol g−1 h−1 with a selectivity of 93%, which is approximately 43.7 times that of the original PAD‐COF. Experimental and theoretical results demonstrate the excellent CO2 photoreduction activity of Co SAS/PAD‐COF owing to the synergistic effect of single Co catalytic sites and PAD‐COF. Among them, PAD‐COF, as the host, adsorbs CO2 molecules and loads single Co atoms. Meanwhile, Co atoms function as catalytic sites and promote the adsorption and activation of CO2, while reducing the reaction energy barrier formed by the *COOH intermediates. Therefore, this unique metalated 1D COF provides a fresh approach to photocatalytic CO2 reduction.

3D model topology algorithm based on virtual reality visual features

This study proposes a virtual reconstruction method for fuzzy 3D images based on visual communication effects to improve recognition ability. This method includes constructing a grid distribution model for 3D images, recombining spatial information features using visual feature extraction, and detecting edges using contour feature extraction. A three-dimensional image visual communication model was established, and adaptive pixel reconstruction was achieved through fuzzy structure reconstruction method. Reconstruct the texture structure and grayscale histogram of 3D images to achieve high-quality virtual reconstruction. The simulation results verified the effectiveness of the method, and the designed simulation platform verified the accuracy and completeness of the method, demonstrating the improvement of existing systems and the potential for advancing the field of visual communication.

Geometric Complexity Control in Topology Optimization of 3D-Printed Fiber Composites for Performance Enhancement.

This paper investigates the impact of varying the part geometric complexity and 3D printing process setup on the resulting structural load bearing capacity of fiber composites. Three levels of geometric complexity are developed through 2.5D topology optimization, 3D topology optimization, and 3D topology optimization with directional material removal. The 3D topology optimization is performed with the SIMP method and accelerated by high-performance computing. The directional material removal is realized by incorporating the advection-diffusion partial differential equation-based filter to prevent interior void or undercut in certain directions. A set of 3D printing and mechanical performance tests are performed. It is interestingly found that, the printing direction affects significantly on the result performance and if subject to the uni direction, the load-bearing capacity increases from the 2.5D samples to the 3D samples with the increased complexity, but the load-bearing capacity further increases for the 3D simplified samples due to directional material removal. Hence, it is concluded that a restricted structural complexity is suitable for topology optimization of 3D-printed fiber composites, since large area cross-sections give more degrees of design freedom to the fiber path layout and also makes the inter-layer bond of the filaments firmer.

Benzenehexol‐Based 2D Conjugated Metal–Organic Frameworks with Kagome Lattice Exhibiting a Metallic State

Abstract2D conjugated metal–organic frameworks (2D c‐MOFs) are emerging as unique electroactive materials for electronics and spintronics. The structural design and discovery of Kagome‐type 2D c‐MOFs exhibiting a metallic state are of paramount significance, yet remain rarely explored. Here, the solution synthesis of benzenehexol‐based 2D c‐MOFs based is presented on the tetrahydroxy‐1,4‐quinone (THQ) ligand. This study shows that controlling the pH of the reaction system to ≈7.5 yields an energetically favorable nonporous Cu3(C6O6) with a Kagome lattice, while at a pH of ≈10, the known porous Cu3(C6O6)2 with a honeycomb lattice is obtained. The crystal structures of both Cu3(C6O6)2 and Cu3(C6O6) are resolved with near‐atomic precision (resolution, 1.8 Å) using an imaging technique. Unlike the p‐type semiconducting behavior of Cu3(C6O6)2, theoretical studies identify Cu3(C6O6) as a metal due to its unique structural topology. The metallic state of Cu3(C6O6) is experimentally validated by terahertz time‐domain spectroscopy (THz‐TDS), which shows an increase in conductivity upon cooling. Scattering‐type scanning near‐field optical microscopy (s‐SNOM) measurements further support these findings by revealing an increase in normalized reflectivity with decreasing temperature. This work provides a new avenue for tailoring the structural topology of 2D c‐MOFs to attain the Kagome lattice and metallic state.

Topology optimization and 3D printing of a unibody quadcopter airframe

The performance of any unmanned aerial vehicle largely depends upon its weight as this characteristic dictates its payload capacity and flight duration. This paper presents a multiphysics simulation method for designing a unibody quadcopter airframe with optimum weight in SolidWorks. By adopting the computer-aided topology optimization concept, the mass of the frame is decreased by 91% (from 1558.44 to 134.738 grams) after getting rid of the unwanted elements, while not compromising its structural rigidity. The efficacy of the model is assessed by finite element analysis and it is found that the stress would remain within the acceptable limit. The optimized structure shows an operating life of 1.6×105 cycles in the fatigue analysis and experiences significantly less drag force in the computational fluid dynamics test than the original airframe for several angles of attack, thus proving the superiority of the optimized frame over the initial model. Finally, additive manufacturing is performed to fabricate the optimized structure using PLA material. 3D printing through the fused deposition modeling technique is chosen since it is ideal for fabricating intricate engineering prototypes compared to orthodox manufacturing processes. While creating the frame, a 45° overhang angle is maintained to ensure the usage of less support material.

Crashworthiness of 3D Lattice Topologies under Dynamic Loading: A Comprehensive Study.

Periodic truss-based lattice materials, a particular subset of cellular solids that generally have superior specific properties as compared to monolithic materials, offer regularity and predictability that irregular foams do not. Significant advancements in alternative technologies-such as additive manufacturing-have allowed for the fabrication of these uniquely complex materials, thus boosting their research and development within industries and scientific communities. However, there have been limitations in the comparison of results for these materials between different studies reported in the literature due to differences in analysis approaches, parent materials, and boundary and initial conditions considered. Further hindering the comparison ability was that the literature generally only focused on one or a select few topologies. With a particular focus on the crashworthiness of lattice topologies, this paper presents a comprehensive study of the impact performance of 24 topologies under dynamic impact loading. Using steel alloy parent material (manufactured using Selective Laser Melting), a numerical study of the impact performance was conducted with 16 different impact energy-speed pairs. It was possible to observe the overarching trends in crashworthiness parameters, including plateau stress, densification strain, impact efficiency, and absorbed energy for a wide range of 3D lattice topologies at three relative densities. While there was no observed distinct division between the results of bending and stretching topologies, the presence of struts aligned in the impact direction did have a significant effect on the energy absorption efficiency of the lattice; topologies with struts aligned in that direction had lower efficiencies as compared to topologies without.

Comparison of in-plane compression of additively manufactured Ti6Al4V 2D auxetic structures: Lattice design, manufacturing speed, and failure mode

The metal-based 2D auxetic lattice structures hold the potential for multifunctional tasks in aerospace applications. However, the compression response of those manufactured by powder bed fusion process is underexplored. This study proposes a comprehensive comparison of in-plane quasi-static compression performance of 2D auxetic lattice structures, utilizing three designs (anti-tetrachiral (ATC), double arrow-headed (DAH), and tree-like re-entrant (TLR)), manufactured with stiff Ti6Al4V by the electron beam powder bed fusion process (PBF-EB) with various manufacturing speeds. The results revealed unique failure patterns and superior energy absorptions among 2D lattice structures in the literature. TLR design enhanced energy absorption by overcoming failures between DAH columns and exhibited the lowest standard deviations in specific energy absorption (SEA) values (9.75 %–12.62 %). Besides, Kernel average misorientation (KAM) values followed the order of DAH, TLR, and ATC, and inversely correlated with SEA values. ATC structures with the lowest KAM outperformed DAH and TLR by 47.5 % and 6.44 %, respectively. Scan speed variations affected SEA and porosity values differently for each lattice design while exhibiting similar microstructure characteristics. The findings in this study propose a significant contribution to the development of aerospace sandwich structures where harsh environments exist and employment of 2D topologies are required.