scholarly journals Tapered elasticæ as a route for axisymmetric morphing structures

Soft Matter ◽  
2020 ◽  
Vol 16 (33) ◽  
pp. 7739-7750
Author(s):  
Mingchao Liu ◽  
Lucie Domino ◽  
Dominic Vella
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Two Dimensional ◽  
3D Structures

Transforming flat two-dimensional (2D) sheets into three-dimensional (3D) structures by a combination of careful cutting and applied loads is an emerging manufacturing paradigm; we study how to design the cut pattern to obtain a desired 3D structure.

The effect of the coordination orientation of N atoms on polymeric structures: synthesis and characterization of one- and two-dimensional CuII coordination polymers based on 4-amino-3-(pyridin-2-yl)-5-[(pyridin-3-ylmethyl)sulfanyl]-1,2,4-triazole

2019 ◽  
Vol 75 (4) ◽  
pp. 443-450
Author(s):  
Guiying Zhu ◽  
Yang Lu ◽  
Guoxia Jin ◽  
Xuan Ji ◽  
Jianping Ma
Keyword(s):  
Hydrogen Bonding ◽  
Coordination Polymers ◽  
3D Structure ◽  
Three Dimensional ◽  
Great Influence ◽  
Two Dimensional ◽  
3D Network ◽  
Solvent Molecules ◽  
Bonding Systems ◽  
Polymeric Structures

Three new one- (1D) and two-dimensional (2D) CuII coordination polymers, namely poly[[bis{μ2-4-amino-3-(pyridin-2-yl)-5-[(pyridin-3-ylmethyl)sulfanyl]-1,2,4-triazole}copper(II)] bis(methanesulfonate) tetrahydrate], {[Cu(C13H12N5S)2](CH3SO3)2·4H2O} n (1), catena-poly[[copper(II)-bis{μ2-4-amino-3-(pyridin-2-yl)-5-[(pyridin-4-ylmethyl)sulfanyl]-1,2,4-triazole}] dinitrate methanol disolvate], {[Cu(C13H12N5S)2](NO3)2·2CH3OH} n (2), and catena-poly[[copper(II)-bis{μ2-4-amino-3-(pyridin-2-yl)-5-[(pyridin-4-ylmethyl)sulfanyl]-1,2,4-triazole}] bis(perchlorate) monohydrate], {[Cu(C13H12N5S)2](ClO4)2·H2O} n (3), were obtained from 4-amino-3-(pyridin-2-yl)-5-[(pyridin-3-ylmethyl)sulfanyl]-1,2,4-triazole with pyridin-3-yl terminal groups and from 4-amino-3-(pyridin-2-yl)-5-[(pyridin-4-ylmethyl)sulfanyl]-1,2,4-triazole with pyridin-4-yl terminal groups. Compound 1 displays a 2D net-like structure. The 2D layers are further linked through hydrogen bonds between methanesulfonate anions and amino groups on the framework and guest H2O molecules in the lattice to form a three-dimensional (3D) structure. Compound 2 and 3 exhibit 1D chain structures, in which the complicated hydrogen-bonding interactions play an important role in the formation of the 3D network. These experimental results indicate that the coordination orientation of the heteroatoms on the ligands has a great influence on the polymeric structures. Moreover, the selection of different counter-anions, together with the inclusion of different guest solvent molecules, would also have a great effect on the hydrogen-bonding systems in the crystal structures.

scholarly journals Computational Design and Analysis of a Magic Snake

2020 ◽  
Vol 12 (5) ◽  
Author(s):  
Zilong Li ◽  
Songming Hou ◽  
Thomas C. Bishop
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Computational Design ◽  
Space Curve ◽  
One Dimensional ◽  
3D Structures ◽  
Multi Scale ◽  
3D Space ◽  
Slender Bodies ◽  
Self Similar

Abstract The Magic Snake (Rubik’s Snake) is a toy that was invented decades ago. It draws much less attention than Rubik’s Cube, which was invented by the same professor, Erno Rubik. The number of configurations of a Magic Snake, determined by the number of discrete rotations about the elementary wedges in a typical snake, is far less than the possible configurations of a typical cube. However, a cube has only a single three-dimensional (3D) structure while the number of sterically allowed 3D conformations of the snake is unknown. Here, we demonstrate how to represent a Magic Snake as a one-dimensional (1D) sequence that can be converted into a 3D structure. We then provide two strategies for designing Magic Snakes to have specified 3D structures. The first enables the folding of a Magic Snake onto any 3D space curve. The second introduces the idea of “embedding” to expand an existing Magic Snake into a longer, more complex, self-similar Magic Snake. Collectively, these ideas allow us to rapidly list and then compute all possible 3D conformations of a Magic Snake. They also form the basis for multidimensional, multi-scale representations of chain-like structures and other slender bodies including certain types of robots, polymers, proteins, and DNA.

3D structure–2D plate interaction model

2019 ◽  
Vol 24 (10) ◽  
pp. 3354-3377 ◽  
Author(s):  
Matko Ljulj ◽  
Josip Tambača
Keyword(s):  
Elastic Layer ◽  
3D Structure ◽  
Three Dimensional ◽  
Interaction Model ◽  
Two Dimensional ◽  
Dimensional Problem ◽  
Dimensional Model ◽  
Limit Model ◽  
Two Dimensional Model ◽  
Thin Elastic Layer

In this paper, we derive models for the interaction of a linearized three-dimensional elastic structure with a thin elastic layer of possibly different material attached to it. Rigorous derivation is performed by considering a thin three-dimensional layer and the asymptotics of the solution of the full remaining three-dimensional problem when the thickness [Formula: see text] of the thin layer tends to zero. Furthermore, the attached thin material is assumed to have the elasticity coefficients which are of order [Formula: see text], for [Formula: see text] with respect to the coefficients of the three-dimensional body. In the limit, five different models are obtained with respect to different choices of p, namely [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text]. Furthermore a three-dimensional–two-dimensional model is proposed that has the same asymptotics as the original three-dimensional problem. This is convenient for applications because one does not have to decide in advance which limit model to use.

scholarly journals Quantum confinement and dielectric profiles of colloidal nanoplatelets of halide inorganic and hybrid organic–inorganic perovskites

Nanoscale ◽  
2016 ◽  
Vol 8 (12) ◽  
pp. 6369-6378 ◽  
Author(s):  
Daniel Sapori ◽  
Mikaël Kepenekian ◽  
Laurent Pedesseau ◽  
Claudine Katan ◽  
Jacky Even
Keyword(s):  
High Frequency ◽  
Quantum Confinement ◽  
Three Dimensional ◽  
Two Dimensional ◽  
3D Structures

Quantum confinement as well as high frequencyε∞and staticεsdielectric profiles are described for nanoplatelets of halide inorganic perovskites CsPbX3(X = I, Br, Cl) and hybrid organic–inorganic perovskites (HOP) in two-dimensional (2D) and three-dimensional (3D) structures.

scholarly journals Metastability relationship between two- and three-dimensional crystal structures: a case study of the Cu-based compounds

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shota Ono
Keyword(s):  
Crystal Structures ◽  
Three Dimensional ◽  
Building Blocks ◽  
Two Dimensional ◽  
3D Structures ◽  
Metallic Element ◽  
Computational Materials ◽  
Dynamics Simulations ◽  
Dimensional Crystal

AbstractSome of the three-dimensional (3D) crystal structures are constructed by stacking two-dimensional (2D) layers. To study whether this geometric concept, i.e., using 2D layers as building blocks for 3D structures, can be applied to computational materials design, we theoretically investigate the dynamical stability of copper-based compounds CuX (a metallic element X) in the B$$_h$$ h and L1$$_1$$ 1 structures constructed from the buckled honeycomb (BHC) structure and in the B2 and L1$$_0$$ 0 structures constructed from the buckled square (BSQ) structure. We demonstrate that (i) if CuX in the BHC structure is dynamically stable, those in the B$$_h$$ h and L1$$_1$$ 1 structures are also stable. Using molecular dynamics simulations, we particularly show that CuAu in the B$$_h$$ h and L1$$_1$$ 1 structures withstand temperatures as high as 1000 K. Although the interrelationship of the metastability between the BSQ and the 3D structures (B2 and L1$$_0$$ 0 ) is not clear, we find that (ii) if CuX in the B2 (L1$$_0$$ 0 ) structure is dynamically stable, that in the L1$$_0$$ 0 (B2) is unstable. This is rationalized by the tetragonal Bain path calculations.

scholarly journals Contrastive learning on protein embeddings enlightens midnight zone at lightning speed

2021 ◽  
Author(s):  
Michael Heinzinger ◽  
Maria Littmann ◽  
Ian Sillitoe ◽  
Nicola Bordin ◽  
Christine Orengo ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Sequence Similarity ◽  
3D Structure ◽  
Three Dimensional ◽  
Hierarchical Classification ◽  
Language Models ◽  
Sequence Alignments ◽  
Sequence Comparisons ◽  
Multiple Sequence ◽  
3D Structures

Thanks to the recent advances in protein three-dimensional (3D) structure prediction, in particular through AlphaFold 2 and RoseTTAFold, the abundance of protein 3D information will explode over the next year(s). Expert resources based on 3D structures such as SCOP and CATH have been organizing the complex sequence-structure-function relations into a hierarchical classification schema. Experimental structures are leveraged through multiple sequence alignments, or more generally through homology-based inference (HBI) transferring annotations from a protein with experimentally known annotation to a query without annotation. Here, we presented a novel approach that expands the concept of HBI from a low-dimensional sequence-distance lookup to the level of a high-dimensional embedding-based annotation transfer (EAT). Secondly, we introduced a novel solution using single protein sequence representations from protein Language Models (pLMs), so called embeddings (Prose, ESM-1b, ProtBERT, and ProtT5), as input to contrastive learning, by which a new set of embeddings was created that optimized constraints captured by hierarchical classifications of protein 3D structures. These new embeddings (dubbed ProtTucker) clearly improved what was historically referred to as threading or fold recognition. Thereby, the new embeddings enabled the intrusion into the midnight zone of protein comparisons, i.e., the region in which the level of pairwise sequence similarity is akin of random relations and therefore is hard to navigate by HBI methods. Cautious benchmarking showed that ProtTucker reached much further than advanced sequence comparisons without the need to compute alignments allowing it to be orders of magnitude faster. Code is available at https://github.com/Rostlab/EAT .

ASSESSING THE QUALITY OF THE HOMOLOGY-MODELED 3D STRUCTURES FROM ELECTROSTATIC STANDPOINT: TEST ON BACTERIAL NUCLEOSIDE MONOPHOSPHATE KINASE FAMILIES

2007 ◽  
Vol 05 (03) ◽  
pp. 693-715 ◽  
Author(s):  
PETRAS KUNDROTAS ◽  
PAULINA GEORGIEVA ◽  
ALEXANDRA SHOSHEVA ◽  
PETYA CHRISTOVA ◽  
EMIL ALEXOV
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
3D Models ◽  
Structural Defects ◽  
Large Protein ◽  
Homologous Proteins ◽  
X Ray ◽  
3D Structures ◽  
Large Sets

In this study, we address the issue of performing meaningful pKa calculations using homology modeled three-dimensional (3D) structures and analyze the possibility of using the calculated pKa values to detect structural defects in the models. For this purpose, the 3D structure of each member of five large protein families of a bacterial nucleoside monophosphate kinases (NMPK) have been modeled by means of homology-based approach. Further, we performed pKa calculations for the each model and for the template X-ray structures. Each bacterial NMPK family used in the study comprised on average 100 members providing a pool of sequences and 3D models large enough for reliable statistical analysis. It was shown that pKa values of titratable groups, which are highly conserved within a family, tend to be conserved among the models too. We demonstrated that homology modeled structures with sequence identity larger than 35% and gap percentile smaller than 10% can be used for meaningful pKa calculations. In addition, it was found that some highly conserved titratable groups either exhibit large pKa fluctuations among the models or have pKa values shifted by several pH units with respect to the pKa calculated for the X-ray structure. We demonstrated that such case usually indicates structural errors associated with the model. Thus, we argue that pKa calculations can be used for assessing the quality of the 3D models by monitoring fluctuations of the pKa values for highly conserved titratable residues within large sets of homologous proteins.

Quasi-static 3D structure of graphene ripple measured using aberration-corrected TEM

Nanoscale ◽  
2021 ◽  
Author(s):  
Yuhiro Segawa ◽  
Kenji Yamazaki ◽  
Jun Yamasaki ◽  
Kazutoshi Gohara
Keyword(s):  
Physicochemical Properties ◽  
Theoretical Calculations ◽  
3D Structure ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Free Standing ◽  
Aberration Corrected

Free-standing graphene has a three-dimensional (3D) structure, called a ripple, rather than a perfect two-dimensional (2D) crystal. Since theoretical calculations suggest that a ripple strongly influences various fundamental physicochemical properties...

scholarly journals RNA 3D Structure Prediction Using Coarse-Grained Models

2021 ◽  
Vol 8 ◽  
Author(s):  
Jun Li ◽  
Shi-Jie Chen
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Biological Functions ◽  
3D Structures ◽  
Rna Molecules ◽  
Atomic Structures ◽  
Long Time

The three-dimensional (3D) structures of Ribonucleic acid (RNA) molecules are essential to understanding their various and important biological functions. However, experimental determination of the atomic structures is laborious and technically difficult. The large gap between the number of sequences and the experimentally determined structures enables the thriving development of computational approaches to modeling RNAs. However, computational methods based on all-atom simulations are intractable for large RNA systems, which demand long time simulations. Facing such a challenge, many coarse-grained (CG) models have been developed. Here, we provide a review of CG models for modeling RNA 3D structures, compare the performance of the different models, and offer insights into potential future developments.

Origami-Based Self-Folding Structure Design and Fabrication Using Projection Based Stereolithography

2015 ◽  
Vol 137 (2) ◽  
Author(s):  
Dongping Deng ◽  
Yong Chen
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Experimental Tests ◽  
Middle Layer ◽  
Structure Design ◽  
The Self ◽  
Two Dimensional ◽  
Polystyrene Film ◽  
Folding Structure ◽  
Unique Capability

Self-folding structures have unique capability such as reconfiguration during their usage. Such capability can be beneficial for a wide variety of applications including biomedical and electronics products. In this paper, a novel fabrication approach based on a three-dimensional (3D) printing process is presented for fabricating self-folding structures that can be actuated in a heating environment. The thermo-actuating structures that are designed and fabricated by our method are two-dimensional (2D) origami sheets, which have multiple printed layers. The middle layer of an origami sheet is a prestrained polystyrene film with large shrinkage ratios when heated. Both its top and bottom surfaces are covered with cured resin that is printed in designed shapes. A foldable hinge is achieved by constraining the shrinkage of the film on one side while allowing the shrinkage of the film on another side when the origami sheet is exposed to a heating environment. Heuristic models of hinge's folding angles are developed based on the related folding mechanism. A 2D origami sheet design and fabrication method is presented for a given 3D structure. Various experimental tests are performed to verify the self-folding performance of the designed and fabricated origami sheets. Techniques on improving folding angle control are also discussed with possible applications.

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