Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow

2017 ◽  
Vol 15 (26) ◽  
pp. 5484-5502 ◽  
Author(s):  
Rachael A. Mansbach ◽  
Andrew L. Ferguson
Keyword(s):  
Self Assembly ◽  
Molecular Simulations ◽  
The Self ◽  
Coarse Grained ◽  
Hierarchical Assembly ◽  
Influence Of Ph

Coarse-grained molecular simulations reveal the influence of pH and flow on the self-assembly of DFAG-OPV3-GAFD optoelectronic peptides.

Coarse-grained simulation of the self-assembly of lipid vesicles concomitantly with novel block copolymers with multiple tails

Soft Matter ◽  
2021 ◽  
Author(s):  
Alexander Kantardjiev
Keyword(s):  
Molecular Dynamics ◽  
Block Copolymers ◽  
Self Assembly ◽  
Lipid Vesicles ◽  
The Self ◽  
Coarse Grained ◽  
Copolymer Concentration ◽  
Copolymer Structure ◽  
Coarse Grained Molecular Dynamics

We carried out a series of coarse-grained molecular dynamics liposome-copolymer simulations with varying extent of copolymer concentration in an attempt to understand the effect of copolymer structure and concentration on vesicle self-assembly and stability.

scholarly journals Variation of Interaction Zone Size For The Target Design of 2D Supramolecular Networks

2021 ◽  
Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Zone Size ◽  
Interaction Zone ◽  
Supramolecular Networks ◽  
Dynamics Simulations ◽  
Target Design

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...

The self-assembly mechanism of tetra-peptides from the motif of β-amyloid peptides: a combined coarse-grained and all-atom molecular dynamics simulation

RSC Advances ◽  
2016 ◽  
Vol 6 (102) ◽  
pp. 100072-100078 ◽  
Author(s):  
Lijun Liang ◽  
Li-Wei Wang ◽  
Jia-Wei Shen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Self Assembly ◽  
The Self ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Aβ Peptides ◽  
Amyloid Peptides ◽  
Assembly Mechanism ◽  
Β Amyloid

Understanding the self-assembly mechanisms of tetra-peptides from Aβ-peptides into different nanostructures.

Dissipative Particle Dynamics Studies on the Self-Assembling Dynamics of the Peptide Amphiphiles

2008 ◽  
Vol 1135 ◽  
Author(s):  
Taiga Seki ◽  
Noriyoshi Arai ◽  
Taku Ozawa ◽  
Tomoko Shimada ◽  
Kenji Yasuoka ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
The Self ◽  
Peptide Amphiphiles ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Self Assembling ◽  
Micro Structures ◽  
Good Agreement

ABSTRACTA coarse-grained model of peptide amphiphiles (PA) dissolved in aqueous solution was presented, where the effects of PA concentration, temperature and shear stress upon the self-assembly of PA were numerically studied by dissipative particle dynamics (DPD) simulation. We technically investigate the repulsion parameter aHW which indicates the repulsion force between the hydrophilic head of PA and water molecules, hence, at the same time, indicating the change in temperature. It was found that aHW played an important role in the self-assembly dynamics and in the resulting micro-structures of PA. By imposing shear strain on the simulation system, the formation of wormlike PA micelles was accelerated. The simulation results were in good agreement with our previous experimental results and the mechanism of shear-induced transition was proposed.

scholarly journals Identifying and Tracking Defects in Dynamic Supramolecular Polymers

2019 ◽  
Author(s):  
Piero Gasparotto ◽  
Davide Bochicchio ◽  
Michele Ceriotti ◽  
Giovanni M. Pavan
Keyword(s):  
Self Assembly ◽  
Noncovalent Interactions ◽  
Molecular Simulations ◽  
Machine Learning Techniques ◽  
Coarse Grained ◽  
Supramolecular Polymers ◽  
Structure Stability ◽  
Supramolecular Polymer ◽  
Soft Systems ◽  
Local Defects

A central paradigm of self-assembly is to create ordered structures starting from molecular<br>monomers that spontaneously recognize and interact with each other via noncovalent interactions.<br>In the recent years, great efforts have been directed toward reaching the perfection in the<br>design of a variety of supramolecular polymers and materials with different architectures. The<br>resulting structures are often thought of as ideally perfect, defect-free supramolecular fibers,<br>micelles, vesicles, etc., having an intrinsic dynamic character, which are typically studied at the<br>level of statistical ensembles to assess their average properties. However, molecular simulations<br>recently demonstrated that local defects that may be present or may form in these assemblies, and which are poorly captured by conventional approaches, are key to controlling their dynamic<br>behavior and properties. The study of these defects poses considerable challenges, as the<br>flexible/dynamic nature of these soft systems makes it difficult to identify what effectively constitutes<br>a defect, and to characterize its stability and evolution. Here, we demonstrate the power<br>of unsupervised machine learning techniques to systematically identify and compare defects in<br>supramolecular polymer variants in different conditions, using as a benchmark 5°A-resolution<br>coarse-grained molecular simulations of a family of supramolecular polymers. We shot that this<br>approach allows a complete data-driven characterization of the internal structure and dynamics<br>of these complex assemblies and of the dynamic pathways for defects formation and resorption.<br>This provides a useful, generally applicable approach to unambiguously identify defects in<br>these dynamic self-assembled materials and to classify them based on their structure, stability<br>and dynamics.<br>

scholarly journals Application of Mesoscale Simulation to Explore the pH Response of Eudragit S100 Used as the Novel Colon-Targeted Powder of Pulsatilla Saponin D

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Mingcheng Gong ◽  
Zhenhua Chen ◽  
Liangliang Zhou ◽  
Feng Gao ◽  
Jianxin Cheng ◽  
...  
Keyword(s):  
Self Assembly ◽  
Morphological Changes ◽  
Drug Carrier ◽  
Dissipative Particle Dynamics ◽  
Ph Sensitive ◽  
The Self ◽  
Coarse Grained ◽  
Release Mechanism ◽  
Eudragit S100 ◽  
Ph Conditions

As a pH-sensitive nanomaterial, Eudragit S100 has good colon targeting. However, little research has been carried out on its mesoscopic scale. In this paper, the self-assembly behavior of Pulsatilla saponins D (PSD) and Eudragit S100, as well as the loading and release mechanism of PSD, was investigated via computer simulations. The effects of the self-assembly characteristics of PSD and Eudragit S100 in the dry powder state on the drug-carrier ratio were explored by the coarse-grained molecular dynamics (CGMD) method. According to the pH-responsive feature of Eudragit S100, the drug protection under gastric pH conditions and release in colonic pH conditions were simulated through the dissipative particle dynamics (DPD) method, which has provided insights into the microscopic morphological changes in the pH-sensitive drug delivery systems.

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