Self-Assembly of Peptide Scaffolds in Biosilica Formation:  Computer Simulations of a Coarse-Grained Model

2006 ◽  
Vol 128 (31) ◽  
pp. 10111-10117 ◽  
Author(s):  
Leonardo Lenoci ◽  
Philip J. Camp
Keyword(s):  
Computer Simulations ◽  
Self Assembly ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Peptide Scaffolds

scholarly journals Simulations of the 2D self-assembly of tripod-shaped building blocks

2020 ◽  
Vol 11 ◽  
pp. 884-890
Author(s):  
Łukasz Baran ◽  
Wojciech Rżysko ◽  
Edyta Słyk
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Diffraction Pattern ◽  
Triangular Lattice ◽  
Self Assembly ◽  
Building Blocks ◽  
Coarse Grained ◽  
Coarse Grained Model

We introduce a molecular dynamics (MD) coarse-grained model for the description of tripod building blocks. This model has been used by us already for linear, V-shape, and tetratopic molecules. We wanted to further extend its possibilities to trifunctional molecules to prove its versatility. For the chosen systems we have also compared the MD results with Monte Carlo results on a triangular lattice. We have shown that the constraints present in the latter method can enforce the formation of completely different structures, not reproducible with off-lattice simulations. In addition to that, we have characterized the obtained structures regarding various parameters such as theoretical diffraction pattern and average association number.

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 Self-assembly of small peptide amphiphiles, the structures formed and their applications. (A foods and home and personal care perspective)

2016 ◽  
Vol 374 (2072) ◽  
pp. 20150138 ◽  
Author(s):  
W. J. Frith
Keyword(s):  
Recent Work ◽  
Computer Simulations ◽  
Self Assembly ◽  
Coarse Grained ◽  
Gel Formation ◽  
Small Peptides ◽  
Huge Number ◽  
Small Peptide ◽  
Microscopic Scale ◽  
Future Developments

In this opinion piece, some specific challenges in the field of peptide self-assembly and gel formation are discussed. One major hurdle to finding functional small peptides is that there are a huge number of compounds to explore, which increases exponentially with the peptide size. This in itself creates a barrier to the discovery and application of materials, both through the difficulty of finding the peptides, and because protecting inventions also becomes more difficult. Recent work has shown that computer simulations may provide us a route to explore such a huge compound space; this is discussed along with the prospect for future developments. At the microscopic scale, many fibril-forming peptides form gels, apparently through a process of lateral association of primary self-assembled filaments, which leads to a relatively coarse-grained structure of rigid interconnects. However, recent data obtained on Fmoc-tyrosine gels appear to indicate that the gel microstructure is both more flexible and finer grained than previously believed. As such, it is clear that there is a considerable amount that is still not understood regarding this class of gel. This article is part of the themed issue ‘Soft interfacial materials: from fundamentals to formulation’.

Application of a coarse-grained model for the design of complex supramolecular networks

2020 ◽  
Vol 5 (2) ◽  
pp. 484-492 ◽  
Author(s):  
Ł. Baran ◽  
W. Rżysko
Keyword(s):  
Self Assembly ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Supramolecular Networks

Examples of self-assembly of molecules with different architectures.

scholarly journals Self-Assembly of Nanoparticles Decorated by Liquid Crystalline Groups: Computer Simulations

2020 ◽  
Author(s):  
Jaroslav Ilnytskyi
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulations ◽  
Self Assembly ◽  
Surface Density ◽  
Liquid Crystalline ◽  
Terminal Group ◽  
The Self ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Group Attachment

We present the results of the computer simulations for the self-assembly of decorated nanoparticles. The models are rather generic and comprise a central core and a shell of ligands containing terminal liquid crystalline group, including the case of the azobenzene chromophores. The simulations are performed using the coarse-grained molecular dynamics with the effective soft-core interparticle interaction potentials obtained from the atomistic simulations. The discussion is centred around the set of the self-assembled morphologies in a melt of 100–200 of such decorated nanoparticles obtained upon the change of the temperature, surface density of ligands, the type of the terminal group attachment, as well as the prediction of the possibility of photo-assisted self-assembly of the nanoparticles decorated by the azobenzene chromophores.

scholarly journals Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link

Soft Matter ◽  
2012 ◽  
Vol 8 (32) ◽  
pp. 8388 ◽  
Author(s):  
Cristiano De Michele ◽  
Lorenzo Rovigatti ◽  
Tommaso Bellini ◽  
Francesco Sciortino
Keyword(s):  
Self Assembly ◽  
Coarse Grained ◽  
Dna Duplexes ◽  
Coarse Grained Model
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