Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Design of Hierarchical Structures for Synchronized Deformations.

ABSTRACT: In this paper we propose a general method for creating a new type of hierarchical structures at any level in both 2D and 3D. A simple rule based on a rotate-and-mirror procedure is introduced to achieve multi-level hierarchies. These new hierarchical structures have remarkably few degrees of freedom compared to existing designs by other methods. More importantly, these structures exhibit synchronized motions during opening or closure, resulting in uniform and easily-controllable deformations. Furthermore, a simple analytical formula is found which can be used to avoid collision of units of the structure during the closing process. The novel design concept is verified by mathematical analyses, computational simulations and physical experiments.

SUBMITTER: Seifi H

PROVIDER: S-EPMC5259711 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Design of Hierarchical Structures for Synchronized Deformations.

Seifi Hamed H Javan Anooshe Rezaee AR Ghaedizadeh Arash A Shen Jianhu J Xu Shanqing S Xie Yi Min YM

Scientific reports 20170124

In this paper we propose a general method for creating a new type of hierarchical structures at any level in both 2D and 3D. A simple rule based on a rotate-and-mirror procedure is introduced to achieve multi-level hierarchies. These new hierarchical structures have remarkably few degrees of freedom compared to existing designs by other methods. More importantly, these structures exhibit synchronized motions during opening or closure, resulting in uniform and easily-controllable deformations. Fu ...[more]

PMID: 28117427

Similar Datasets

Crystal structures of human MGST2 reveal synchronized conformational changes regulating catalysis.

Project description:Microsomal glutathione S-transferase 2 (MGST2) produces leukotriene C4, key for intracrine signaling of endoplasmic reticulum (ER) stress, oxidative DNA damage and cell death. MGST2 trimer restricts catalysis to only one out of three active sites at a time, but the molecular basis is unknown. Here, we present crystal structures of human MGST2 combined with biochemical and computational evidence for a concerted mechanism, involving local unfolding coupled to global conformational changes that regulate catalysis. Furthermore, synchronized changes in the biconical central pore modulate the hydrophobicity and control solvent influx to optimize reaction conditions at the active site. These unique mechanistic insights pertain to other, structurally related, drug targets.

| S-EPMC7979937 | biostudies-literature

Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin structures

Project description:To investigate the mechanisms underlying the rearrangement patterns,we compared the rearrangement map with local chromatin structures and the three-dimensional genome architecture via assay for transposase-accessible chromatin using sequencing (ATAC-seq) and genome-wide chromosome conformation capture (Hi-C), respectively

2022-06-10 | GSE168182 | GEO

Hierarchical tensile structures with ultralow mechanical dissipation.

Project description:Structural hierarchy is found in myriad biological systems and has improved man-made structures ranging from the Eiffel tower to optical cavities. In mechanical resonators whose rigidity is provided by static tension, structural hierarchy can reduce the dissipation of the fundamental mode to ultralow levels due to an unconventional form of soft clamping. Here, we apply hierarchical design to silicon nitride nanomechanical resonators and realize binary tree-shaped resonators with room temperature quality factors as high as 7.8 × 108 at 107 kHz frequency (1.1 × 109 at T = 6 K). The resonators' thermal-noise-limited force sensitivities reach 740 zN/Hz1/2 at room temperature and 90 zN/Hz1/2 at 6 K, surpassing state-of-the-art cantilevers currently used for force microscopy. Moreover, we demonstrate hierarchically structured, ultralow dissipation membranes suitable for interferometric position measurements in Fabry-Pérot cavities. Hierarchical nanomechanical resonators open new avenues in force sensing, signal transduction and quantum optomechanics, where low dissipation is paramount and operation with the fundamental mode is often advantageous.

| S-EPMC9163184 | biostudies-literature

SWORD2: hierarchical analysis of protein 3D structures.

Project description:Understanding the functions and origins of proteins requires splitting these macromolecules into fragments that could be independent in terms of folding, activity, or evolution. For that purpose, structural domains are the typical level of analysis, but shorter segments, such as subdomains and supersecondary structures, are insightful as well. Here, we propose SWORD2, a web server for exploring how an input protein structure may be decomposed into 'Protein Units' that can be hierarchically assembled to delimit structural domains. For each partitioning solution, the relevance of the identified substructures is estimated through different measures. This multilevel analysis is achieved by integrating our previous work on domain delineation, 'protein peeling' and model quality assessment. We hope that SWORD2 will be useful to biologists searching for key regions in their proteins of interest and to bioinformaticians building datasets of protein structures. The web server is freely available online: https://www.dsimb.inserm.fr/SWORD2.

| S-EPMC9252838 | biostudies-literature

Hierarchical design of pseudosymmetric protein nanoparticles.

Project description:Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions1-3. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry4,5. Inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540, and 960 subunits. At 49, 71, and 96 nm diameter, these nanoparticles are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work represents an important step towards the accurate design of arbitrary self-assembling nanoscale protein objects.

| S-EPMC10371088 | biostudies-literature

Reversibly Switching Silver Hierarchical Structures via Reaction Kinetics.

Project description:Here we report a study on controllable synthesis of hierarchical silver structures via regulating reaction kinetics. Silver particles with various morphologies are synthesized by a solution-based reduction approach at the addition of amino acids. The amino acid is used to coordinate with silver ions to slow down the reduction of silver ions. With the increase of glycine concentration, the morphologies of silver particles switch from dendrites, to flowers and to compacted spheres, which is attributed to the decrease of reaction rate as a result of the coordination. Three more amino acids are examined and confirms the role of reaction kinetic in shaping silver particles. Furthermore, by increasing the concentration of the reductant, the silver morphologies change from compact spheres to loose flowers as a result of the increase of reaction rate. Therefore the silver hierarchical structure can be reversibly switched by reaction kinetics. The silver particles synthesized are tested for surface enhanced Raman scattering (SERS) property and the dendritic particles present a remarkable SERS activity. This study shows that reaction kinetics is a powerful tool to tune hierarchical structures of silver particles, which is expected to be transferable to other material systems.

| S-EPMC4595744 | biostudies-other

Facile fabrication of superhydrophobic surfaces with hierarchical structures.

Project description:Hierarchical structures were fabricated on the surfaces of SUS304 plates using a one-step process of direct microwave irradiation under a carbon dioxide atmosphere. The surface nanostructures were composed of chrome-doped hematite single crystals. Superhydrophobic surfaces with a water contact angle up to 169° were obtained by chemical modification of the hierarchical structures. The samples maintained superhydrophobicity under NaCl solution up to 2 weeks.

| S-EPMC5840334 | biostudies-literature

Superrepellency of underwater hierarchical structures on Salvinia leaf.

Project description:Biomimetic superhydrophobic surfaces display many excellent underwater functionalities, which attribute to the slippery air mattress trapped in the structures on the surface. However, the air mattress is easy to collapse due to various disturbances, leading to the fully wetted Wenzel state, while the water filling the microstructures is difficult to be repelled to completely recover the air mattress even on superhydrophobic surfaces like lotus leaves. Beyond superhydrophobicity, here we find that the floating fern, Salvinia molesta, has the superrepellent capability to efficiently replace the water in the microstructures with air and robustly recover the continuous air mattress. The hierarchical structures on the leaf surface are demonstrated to be crucial to the recovery. The interconnected wedge-shaped grooves between epidermal cells are key to the spontaneous spreading of air over the entire leaf governed by a gas wicking effect to form a thin air film, which provides a base for the later growth of the air mattress in thickness synchronously along the hairy structures. Inspired by nature, biomimetic artificial Salvinia surfaces are fabricated using 3D printing technology, which successfully achieves a complete recovery of a continuous air mattress to exactly imitate the superrepellent capability of Salvinia leaves. This finding will benefit the design principles of water-repellent materials and expand their underwater applications, especially in extreme environments.

| S-EPMC7007550 | biostudies-literature

Modeling and design by hierarchical natural moves.

Project description:We develop a unique algorithm implemented in the program MOSAICS (Methodologies for Optimization and Sampling in Computational Studies) that is capable of nanoscale modeling without compromising the resolution of interest. This is achieved by modeling with customizable hierarchical degrees of freedom, thereby circumventing major limitations of conventional molecular modeling. With the emergence of RNA-based nanotechnology, large RNAs in all-atom representation are used here to benchmark our algorithm. Our method locates all favorable structural states of a model RNA of significant complexity while improving sampling accuracy and increasing speed many fold over existing all-atom RNA modeling methods. We also modeled the effects of sequence mutations on the structural building blocks of tRNA-based nanotechnology. With its flexibility in choosing arbitrary degrees of freedom as well as in allowing different all-atom energy functions, MOSAICS is an ideal tool to model and design biomolecules of the nanoscale.

| S-EPMC3287004 | biostudies-literature

Facile solution-phase synthesis of gamma-Mn3O4 hierarchical structures.

Project description:BackgroundA lot of effort has been focused on the integration of nanorods/nanowire as building blocks into three-dimensional (3D) complex superstructures. But, the development of simple and effective methods for creating novel assemblies of self-supported patterns of hierarchical architectures to designed materials using a suitable chemical method is important to technology and remains an attractive, but elusive goal.ResultsThe hierarchical structure of Mn3O4 with radiated spherulitic nanorods was prepared via a simple solution-based coordinated route in the presence of macrocycle polyamine, hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-diene (CT) with the assistance of thiourea as an additive.ConclusionThis approach opens a new and facile route for the morphogenesis of Mn3O4 material and it might be extended as a novel synthetic method for the synthesis of other inorganic semiconducting nanomaterials such as metal chalcogenide semiconductors with novel morphology and complex form, since it has been shown that thiourea can be used as an effective additive and the number of such water-soluble macrocyclic polyamines also makes it possible to provide various kinds of ligands for different metals in homogeneous water system.

| S-EPMC1994067 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data