scholarly journals Stochastic Yield Catastrophes and Robustness in Self-Assembly

2019 ◽  
Author(s):  
Florian M. Gartner ◽  
Isabella R. Graf ◽  
Patrick Wilke ◽  
Philipp M. Geiger ◽  
Erwin Frey
Keyword(s):  
Self Assembly ◽  
Limiting Factor ◽  
Nucleation Process ◽  
Guiding Principle ◽  
Highly Sensitive ◽  
High Production ◽  
Demographic Fluctuations ◽  
Specific Implementation ◽  
Stochastic Yield ◽  
Different Characteristics

ABSTRACTA guiding principle in self-assembly is that, for high production yield, nucleation of structures must be significantly slower than their growth. However, details of the mechanism that impedes nucleation are broadly considered irrelevant. Here, we analyze self-assembly into finite-sized target structures employing mathematical modeling. We investigate two key scenarios to delay nucleation: (i) by introducing a slow activation step for the assembling constituents and, (ii) by decreasing the dimerization rate. These scenarios have widely different characteristics. While the dimerization scenario exhibits robust behavior, the activation scenario is highly sensitive to demographic fluctuations. These demographic fluctuations ultimately disfavor growth compared to nucleation and can suppress yield completely. The occurrence of this stochastic yield catastrophe does not depend on model details but is generic as soon as number fluctuations between constituents are taken into account. On a broader perspective, our results reveal that stochasticity is an important limiting factor for self-assembly and that the specific implementation of the nucleation process plays a significant role in determining the yield.

scholarly journals Stochastic yield catastrophes and robustness in self-assembly

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Florian M Gartner ◽  
Isabella R Graf ◽  
Patrick Wilke ◽  
Philipp M Geiger ◽  
Erwin Frey
Keyword(s):  
Self Assembly ◽  
Limiting Factor ◽  
Nucleation Process ◽  
Guiding Principle ◽  
Highly Sensitive ◽  
High Production ◽  
Demographic Fluctuations ◽  
Specific Implementation ◽  
Stochastic Yield ◽  
Different Characteristics

A guiding principle in self-assembly is that, for high production yield, nucleation of structures must be significantly slower than their growth. However, details of the mechanism that impedes nucleation are broadly considered irrelevant. Here, we analyze self-assembly into finite-sized target structures employing mathematical modeling. We investigate two key scenarios to delay nucleation: (i) by introducing a slow activation step for the assembling constituents and, (ii) by decreasing the dimerization rate. These scenarios have widely different characteristics. While the dimerization scenario exhibits robust behavior, the activation scenario is highly sensitive to demographic fluctuations. These demographic fluctuations ultimately disfavor growth compared to nucleation and can suppress yield completely. The occurrence of this stochastic yield catastrophe does not depend on model details but is generic as soon as number fluctuations between constituents are taken into account. On a broader perspective, our results reveal that stochasticity is an important limiting factor for self-assembly and that the specific implementation of the nucleation process plays a significant role in determining the yield.

Detection of Biothiols Using Some Novel Chemosensors: An Overview

2020 ◽  
Vol 17 ◽  
Author(s):  
Jiko Raut ◽  
Prithidipa Sahoo
Keyword(s):  
Redox Homeostasis ◽  
Logic Gates ◽  
Thiol Group ◽  
Cellular Growth ◽  
Detection Techniques ◽  
Guiding Principle ◽  
Highly Sensitive ◽  
Parkinson’S Diseases ◽  
Metal Cofactor ◽  
Atherosclerotic Cardiovascular Diseases

Abstract:: Thiol-containing amino acids and peptides play crucial roles in many physiological processses. For example, Cysteine (Cys) and Homocysteine (Hcy) are considered to be related to a number of health disorders such as renal failure, AIDS, Alzheimer’s and Parkinson’s diseases, atherosclerotic cardiovascular diseases, neutral tube defects, and coronary heart disease. Glutathione (GSH), an important tripeptide with a thiol group, performs vital biological functions that are in-volved in combating oxidative stress and maintaining redox homeostasis. Cysteine also plays important roles in our bodies as an antioxidant, a metal cofactor binder in enzymes, and a protein structure stabilizer by disulfide bond formation in the proteins. Hcy are involved in cellular growth and GSH in redox homeostasis. Hence, the rapid, sensitive, and selective de-tection of such biothiols is of considerable importance and significant interest. Different fluorescent chemosensors have been introduced to develop and improve the detection techniques and accuracy of these biothiols. In this review article we have presented some research works to show a guiding principle for the design of effective chemosensors which are highly sensitive and selective for the detection of particular a group of biothiols in aqueous medium. In line with these develop-ments, the researchers have developed novel chemosensors that signal binding events of these above mentioned biothiols through their optical properties. The binding mechanism and properties have also been established with different theoretical studies. Their applications in the form of colorimetric kit, logic gates, live cell imaging, and quantification from different bi-ological samples have also been developed.

Sensitive and selective determination of hydroxychloroquine in the presence of uric acid using a new nanostructure self-assembled monolayer modified electrode: optimization by multivariate data analysis

The Analyst ◽  
2014 ◽  
Vol 139 (16) ◽  
pp. 4064-4072 ◽  
Author(s):  
Asma Khoobi ◽  
Sayed Mehdi Ghoreishi ◽  
Mohsen Behpour
Keyword(s):  
Uric Acid ◽  
Self Assembly ◽  
Multivariate Data Analysis ◽  
Covalent Modification ◽  
Carbon Electrode ◽  
Self Assembled Monolayer ◽  
Selective Determination ◽  
Highly Sensitive ◽  
Electrochemical Nanosensor

A highly sensitive electrochemical nanosensor was developed using covalent modification of a glassy carbon electrode (GCE) by self-assembly of a novel Schiff base.

Lab in a tube: a fast-assembled colorimetric sensor for highly sensitive detection of oligonucleotides based on a hybridization chain reaction

RSC Advances ◽  
2015 ◽  
Vol 5 (55) ◽  
pp. 44714-44721 ◽  
Author(s):  
Siqi Zhang ◽  
Kun Wang ◽  
Zhenyu Li ◽  
Zhongmin Feng ◽  
Ting Sun
Keyword(s):  
Complex Formation ◽  
Dna Sequence ◽  
Self Assembly ◽  
The Self ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Highly Sensitive ◽  
G Quadruplex ◽  
Colored Product ◽  
Highly Sensitive Detection

Upon adding THBV, the self-assembly of THBV with H1 allows the rest of the DNA sequence of H1 to accelerate H1–H2 complex formation. The G-quadruplex at the end of the H1–H2 complex could catalyze TMB into a colored product.

Self-assembly of ultrathin gold nanowires and single walled carbon nanotubes as a highly sensitive substrate for surface enhanced Raman spectroscopy

2016 ◽  
Vol 40 (9) ◽  
pp. 7286-7289 ◽  
Author(s):  
Yuanchao Zhang ◽  
Jingquan Liu ◽  
Da Li ◽  
Fuhua Yan ◽  
Xin Wang ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Raman Spectroscopy ◽  
Self Assembly ◽  
Single Walled Carbon Nanotubes ◽  
Surface Enhanced Raman Spectroscopy ◽  
Gold Nanowires ◽  
Highly Sensitive ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Walled Carbon Nanotubes

Self-assembly of ultrathin gold nanowires and single-walled carbon nanotubes as highly sensitive substrates for surface enhanced Raman spectroscopy.

Fabrication of a Composite Coating by Laser, Nanoparticles Self-Assembly and Electrodeposition

2021 ◽  
Vol 1032 ◽  
pp. 84-90
Author(s):  
Ou Chuan Lin ◽  
Ying Luo Zhou ◽  
Jing Li ◽  
Virgil Bunyan
Keyword(s):  
Composite Coating ◽  
Self Assembly ◽  
Surface Coating ◽  
Laser Processing ◽  
Substrate Surface ◽  
Substrate Material ◽  
Processing Method ◽  
Coating Materials ◽  
Different Characteristics ◽  
Micro Morphology

In this paper, a composite micromachining process is introduced. By adjusting the surface microstructure, a composite coating with two kinds of materials with different characteristics was fabricated. Carbon steel is used as the substrate material, and laser processing is used to obtain the micro morphology on the substrate surface. nanoSiC particles were selected as one of the coating materials, and the SiC coating was added through the process of micropore induced nanoparticles self-assembly. Ni was selected as another coating material and added by electrodeposition. This processing method can be used to prepare multifunctional surface coating, combining the characteristics of different materials. This work can provide an idea to create more excellent multifunctional surfaces.

Dye encapsulated zinc-based metal-organic framework as a dual-emission sensor for highly sensitive detection of antibiotics

2021 ◽  
Author(s):  
Kang Wang ◽  
Yuhan Duan ◽  
Jiajing Chen ◽  
Haiying Wang ◽  
Hui-Yan Liu
Keyword(s):  
Self Assembly ◽  
Metal Organic Framework ◽  
Sensitive Detection ◽  
Dual Emission ◽  
Highly Sensitive ◽  
Metal Organic ◽  
Highly Sensitive Detection ◽  
Organic Framework

Self-assembly of two Zn-MOFs, [Zn2L(DMF)3]•H2O•5DMF (1) and [Zn2L(H2O)2]•4H2O•3DMF (2) were achieved with an amide-functionalized tetracarboxylate ligand under similar conditions. Incorporated amide groups make the tetratopic linkers exhibit different configurations, tetrahedron...

scholarly journals Graphene Templated DNA Arrays and Biotin-Streptavidin Sensitive Bio-Transistors Patterned by Dynamic Self-Assembly of Polymeric Films Confined within a Roll-on-Plate Geometry

Nanomaterials ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1468
Author(s):  
Sangheon Jeon ◽  
Jihye Lee ◽  
Rowoon Park ◽  
Jeonghwa Jeong ◽  
Min Chan Shin ◽  
...  
Keyword(s):  
Graphene Oxide ◽  
Self Assembly ◽  
Patterned Surfaces ◽  
Dna Arrays ◽  
Simple Strategy ◽  
Modified Dna ◽  
Highly Sensitive ◽  
Wide Range ◽  
Surface Chemistries ◽  
Plate Geometry

Patterning of surfaces with a simple strategy provides insights into the functional interfaces by suitable modification of the surface by novel techniques. Especially, highly ordered structural topographies and chemical features from the wide range of interfaces have been considered as important characteristics to understand the complex relationship between the surface chemistries and biological systems. Here, we report a simple fabrication method to create patterned surfaces over large areas using evaporative self-assembly that is designed to produce a sacrificial template and lithographic etch masks of polymeric stripe patterns, ranging from micrometer to nanoscale. By facilitating a roll-on-plate geometry, the periodically patterned surface structures formed by repetitive slip-stick motions were thoroughly examined to be used for the deposition of the Au nanoparticles decorated graphene oxide (i.e., AuNPs, ~21 nm) and the formation of conductive graphene channels. The fluorescently labeled thiol-modified DNA was applied on the patterned arrays of graphene oxide (GO)/AuNPs, and biotin-streptavidin sensitive devices built with graphene-based transistors (GFETs, effective mobility of ~320 cm2 V−1 s−1) were demonstrated as examples of the platform for the next-generation biosensors with the high sensing response up to ~1 nM of target analyte (i.e., streptavidin). Our strategy suggests that the stripe patterned arrays of polymer films as sacrificial templates can be a simple route to creating highly sensitive biointerfaces and highlighting the development of new chemically patterned surfaces composed of graphene-based nanomaterials.

A novel fluorescent peptidyl probe for highly sensitive and selective ratiometric detection of Cd(ii) in aqueous and bio-samplesviametal ion-mediated self-assembly

2018 ◽  
Vol 42 (22) ◽  
pp. 18143-18151 ◽  
Author(s):  
Kwan Ho Jung ◽  
Semin Oh ◽  
Joohee Park ◽  
Yu Jin Park ◽  
See-Hyoung Park ◽  
...  
Keyword(s):  
Self Assembly ◽  
Live Cells ◽  
Self Assembling ◽  
Highly Sensitive ◽  
Ratiometric Detection

A fluorescent peptidyl probe based on a Cd(ii)-triggered self-assembling process was proposed for ratiometric detection for Cd(ii) in urine and live cells.

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