ATOMISTIC MODELING AND MECHANICS OF SELF-ASSEMBLED ORGANIC NANOTUBES

2011 ◽  
Vol 03 (04) ◽  
pp. 667-684 ◽  
Author(s):  
LUIS RUIZ ◽  
SINAN KETEN
Keyword(s):  
Hydrogen Bonds ◽  
Large Scale ◽  
Shear Failure ◽  
Cyclic Peptide ◽  
Building Blocks ◽  
Great Promise ◽  
Deformation And Failure ◽  
Self Assembling ◽  
Self Assembled ◽  
Organic Nanotubes

Organic building blocks inspired by biological systems are promising for fabricating nanostructured materials for a broad range of applications such as antimicrobials, biosensors, electronics, and biomaterials. Self-assembling cyclic peptide organic nanotubes have shown great promise for these applications due to their precise structural features, diverse chemical functionalization capabilities and exceptional stability arising from arrangement of hydrogen bonds into cooperative clusters. Mechanical behavior of organic nanotubes is important for various possible applications ranging from subnanoporous selective membranes to molecular templates for electronics. However, large-scale deformation mechanisms of organic nanotubes have not been studied thus far. Here we investigate the mechanisms involved in the large deformation and failure of self-assembled organic nanotubes, focusing on geometry effects characteristic of protein nanostructures. We carry out molecular dynamics simulations to assess the role of hydrogen bonds as weak interactions in the context of deformation and failure processes involving bending and shear loads. Mechanisms of failure are found to depend on the cross-sectional geometry and the deformation rate, where a transition to localized shear failure is observed at high-strain rates. Our results provide important physical insight into the mechanics of organic nanotubes central to emerging applications of self-assembling peptides in biomedicine and biotechnology.

Self-assembling organic nanotubes based on a cyclic peptide architecture

Nature ◽  
1993 ◽  
Vol 366 (6453) ◽  
pp. 324-327 ◽  
Author(s):  
M. Reza Ghadiri ◽  
Juan R. Granja ◽  
Ronald A. Milligan ◽  
Duncan E. McRee ◽  
Nina Khazanovich
Keyword(s):  
Cyclic Peptide ◽  
Self Assembling ◽  
Organic Nanotubes

scholarly journals Correction: Self-assembling organic nanotubes based on a cyclic peptide architecture

Nature ◽  
1994 ◽  
Vol 372 (6507) ◽  
pp. 709-709 ◽  
Author(s):  
M. Reza Ghadiri ◽  
Juan R. Granja ◽  
Ronald A. Milligan ◽  
Duncan E. McRee ◽  
Nina Khazanovich
Keyword(s):  
Cyclic Peptide ◽  
Self Assembling ◽  
Organic Nanotubes

Symmetrical Tris(4,6-diamino-5-methylene-2-pyrimidones): New Building Blocks for Self-Assembly of Hollow Spherical Supramolecules Locked by Hydrogen Bonds

1996 ◽  
Vol 61 (10) ◽  
pp. 1464-1472 ◽  
Author(s):  
Daniel Alexander ◽  
Petr Holý ◽  
Pavel Fiedler ◽  
Zdeněk Havlas ◽  
Jiří Závada
Keyword(s):  
Molecular Modeling ◽  
Hydrogen Bonds ◽  
Gas Phase ◽  
Self Assembly ◽  
Building Blocks ◽  
The Self ◽  
Circumstantial Evidence ◽  
Self Assembling ◽  
Molecular Modeling Study ◽  
Modeling Study

Concise synthesis of the tris(pyrimidones) 1a,b is described. Molecular modeling study demonstrated that both the prepared models 1a,b are capable of self-assembling under formation of spherical dimers locked by 18 hydrogen bonds. Extreme insolubility in all common solvents precluded investigation of the self-assembly in solution. Circumstantial evidence in favor of the self-assembly has been provided in the solid and gas phase.

Analysis on Causes of Deformation and Failure of Large Scale Underground Powerhouse

2011 ◽  
Vol 71-78 ◽  
pp. 644-650 ◽  
Author(s):  
Jin Yu Dong ◽  
Ji Hong Yang ◽  
Guo Xiang Yang ◽  
Fa Quan Wu
Keyword(s):  
Large Scale ◽  
Shear Failure ◽  
Surrounding Rock ◽  
Concrete Cracking ◽  
Underground Powerhouse ◽  
Deformation And Failure ◽  
Underground Caverns ◽  
Geological Conditions ◽  
The Right

Jinoping No.1 is a dominant reservoir cascade hydropower station which locates at the downstream of Yalong river. The underground powerhouse locates at the right bank of the dam, lithology is marble that belongs to the second member of Zagunao group. It is constructed at region with very complicated geological conditions and high geo-stress. Concrete cracking, spalling and steel buckling and bending occurred at the downstream crown after supporting. This paper analysed the causes of deformation and failure through geological analysis and numerical simulation, and concluded that deformation and failure mainly occurred at the region where the quality of surrounding rock belongs to Ⅲ1 and had nothing to do with the unstable block cut by cracks; stress field of surrounding rock varied continueously with the proceeding of successive excavation of underground powerhouse, so the compressive stress and shear stress concentration occurred which caused the compression and shear failure of downstream crown and made it bending to the free face. It is significant to the further enforcement of this project and to the research on other similar underground caverns theoretically and practically.

scholarly journals Self-assembly of Functional Nanostructures by Short Helical Peptide Building Blocks

2019 ◽  
Vol 26 (2) ◽  
pp. 88-97 ◽  
Author(s):  
Santu Bera ◽  
Ehud Gazit
Keyword(s):  
Self Assembly ◽  
Amyloid Fibrils ◽  
Building Blocks ◽  
Smart Devices ◽  
Helical Peptides ◽  
Functional Roles ◽  
Mesoscale Structures ◽  
Self Assembling ◽  
Wide Range ◽  
Self Assembled

The self-assembly of short peptide building blocks into well-ordered nanostructures is a key direction in bionanotechnology. The formation of β -sheet organizations by short peptides is well explored, leading to the development of a wide range of functional assemblies. Likewise, many natural proteinaceous materials, such as silk and amyloid fibrils, are based on β-sheet structures. In contrast, collagen, the most abundant protein in mammals, is based on helical arrangement. Similar to β-sheet structures, short helical peptides have been recently discovered to possess a diverse set of functionalities with the potential to fabricate artificial self-assembling materials. Here, we outline the functional roles of self-assembled nanostructures formed by short helical peptides and their potential as artificial materials. We focus on the association between self-assembled mesoscale structures and their material function and demonstrate the way by which this class of building blocks bears the potential for diverse applications, such as the future fabrication of smart devices.

Self-assembled fibrillar networks comprised of a naturally-occurring cyclic peptide—LOB3

RSC Advances ◽  
2016 ◽  
Vol 6 (47) ◽  
pp. 40765-40776 ◽  
Author(s):  
M. A. Rogers ◽  
Q. Feng ◽  
V. Ladizhansky ◽  
D. B. Good ◽  
A. K. Smith ◽  
...  
Keyword(s):  
Cyclic Peptide ◽  
Self Assembling ◽  
Naturally Occurring ◽  
Self Assembled

LOB3, a naturally-occurring orbitide, is capable of self-assembling into 1D nano-fibers and ultimately 3D molecular gel networks in acetonitrile.

Recent advances in the fabrication and bio-medical applications of self-assembled dipeptide nanostructures

Nanomedicine ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. 139-163
Author(s):  
Sonika Chibh ◽  
Jibanananda Mishra ◽  
Avneet Kour ◽  
Virander S Chauhan ◽  
Jiban J Panda
Keyword(s):  
Significant Role ◽  
Self Assembly ◽  
Biomedical Applications ◽  
Building Blocks ◽  
Natural Phenomenon ◽  
Medical Applications ◽  
Self Assembling ◽  
Recent Advances ◽  
Potential Applications ◽  
Self Assembled

Molecular self-assembly is a widespread natural phenomenon and has inspired several researchers to synthesize a compendium of nano/microstructures with widespread applications. Biomolecules like proteins, peptides and lipids are used as building blocks to fabricate various nanomaterials. Supramolecular peptide self-assembly continue to play a significant role in forming diverse nanostructures with numerous biomedical applications; however, dipeptides offer distinctive supremacy in their ability to self-assemble and produce a variety of nanostructures. Though several reviews have articulated the progress in the field of longer peptides or polymers and their self-assembling behavior, there is a paucity of reviews or literature covering the emerging field of dipeptide-based nanostructures. In this review, our goal is to present the recent advancements in dipeptide-based nanostructures with their potential applications.

scholarly journals Self-Assembling Lectin Nano-Block Oligomers Enhance Binding Avidity to Glycans

2022 ◽  
Vol 23 (2) ◽  
pp. 676
Author(s):  
Shin Irumagawa ◽  
Keiko Hiemori ◽  
Sayoko Saito ◽  
Hiroaki Tateno ◽  
Ryoichi Arai
Keyword(s):  
De Novo ◽  
Building Blocks ◽  
Cell Labeling ◽  
Carbohydrate Binding ◽  
Specific Cell ◽  
High Avidity ◽  
Functional Protein ◽  
Self Assembling ◽  
Self Assembled ◽  
Binding Avidity

Lectins, carbohydrate-binding proteins, are attractive biomolecules for medical and biotechnological applications. Many lectins have multiple carbohydrate recognition domains (CRDs) and strongly bind to specific glycans through multivalent binding effect. In our previous study, protein nano-building blocks (PN-blocks) were developed to construct self-assembling supramolecular nanostructures by linking two oligomeric proteins. A PN-block, WA20-foldon, constructed by fusing a dimeric four-helix bundle de novo protein WA20 to a trimeric foldon domain of T4 phage fibritin, self-assembled into several types of polyhedral nanoarchitectures in multiples of 6-mer. Another PN-block, the extender PN-block (ePN-block), constructed by tandemly joining two copies of WA20, self-assembled into cyclized and extended chain-type nanostructures. This study developed novel functional protein nano-building blocks (lectin nano-blocks) by fusing WA20 to a dimeric lectin, Agrocybe cylindracea galectin (ACG). The lectin nano-blocks self-assembled into various oligomers in multiples of 2-mer (dimer, tetramer, hexamer, octamer, etc.). The mass fractions of each oligomer were changed by the length of the linkers between WA20 and ACG. The binding avidity of the lectin nano-block oligomers to glycans was significantly increased through multivalent effects compared with that of the original ACG dimer. Lectin nano-blocks with high avidity will be useful for various applications, such as specific cell labeling.

scholarly journals Single-Step Organization of Plasmonic Gold Metamaterials with Self-Assembled DNA Nanostructures

Research ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Shaokang Ren ◽  
Jun Wang ◽  
Chunyuan Song ◽  
Qian Li ◽  
Yanjun Yang ◽  
...  
Keyword(s):  
Large Scale ◽  
Single Step ◽  
High Yield ◽  
Great Promise ◽  
Dna Nanostructures ◽  
One Pot ◽  
Dna Tiles ◽  
Surface Enhanced Raman ◽  
Self Assembled ◽  
The One

Self-assembled DNA nanostructures hold great promise as nanoscale templates for organizing nanoparticles (NPs) with near-atomistic resolution. However, large-scale organization of NPs with high yield is highly desirable for nanoelectronics and nanophotonic applications. Here, we design five-strand DNA tiles that can readily self-assemble into well-organized micrometer-scale DNA nanostructures. By organizing gold nanoparticles (AuNPs) on these self-assembled DNA nanostructures, we realize the fabrication of one- and two-dimensional Au nanostructures in single steps. We further demonstrate the one-pot synthesis of Au metamaterials for highly amplified surface-enhanced Raman Scattering (SERS). This single-step and high-yield strategy thus holds great potential for fabricating plasmonic metamaterials.

Combinatorial Peptide Libraries for Selecting Inorganic-Binding Proteins: A Step in Molecular Biomimetics

2003 ◽  
Vol 773 ◽  
Author(s):  
C. Tamerler ◽  
S. Dinçer ◽  
D. Heidel ◽  
N. Karagûler ◽  
M. Sarikaya
Keyword(s):  
Binding Proteins ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Inorganic Materials ◽  
Combinatorial Peptide Libraries ◽  
Self Assembling ◽  
Complex Functions ◽  
Recent Developments ◽  
Specific Proteins ◽  
Molecular Biomimetics

AbstractProteins, one of the building blocks in organisms, not only control the assembly in biological systems but also provide most of their complex functions. It may be possible to assemble materials for practical technological applications utilizing the unique advantages provided by proteins. Here we discuss molecular biomimetic pathways in the quest for imitating biology at the molecular scale via protein engineering. We use combinatorial biology protocols to select short polypeptides that have affinity to inorganic materials and use them in assembling novel hybrid materials. We give an overview of some of the recent developments of molecular engineering towards this goal. Inorganic surface specific proteins were identified by using cell surface and phage display technologies. Examples of metal and metal oxide specific polypeptides were represented with an emphasis on certain level of specificities. The recognition and self assembling characteristics of these inorganic-binding proteins would be employed in develeopment of hybrid multifunctional materials for novel bio- and nano-technological applications.

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