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

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.

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 Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile

2021 ◽  
Vol 11 (5) ◽  
pp. 2357
Author(s):  
Ruixin Li ◽  
Haorong Chen ◽  
Hyeongwoon Lee ◽  
Jong Hyun Choi
Keyword(s):  
Self Assembly ◽  
Mechanical Energy ◽  
Single Layer ◽  
Md Simulations ◽  
Dna Origami ◽  
Coarse Grained ◽  
Initial Curvature ◽  
Coarse Grained Model ◽  
Reconfigurable Structures ◽  
Computational Platform

DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn, which is slightly different from that of native B-form DNA (~10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.

scholarly journals Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile

2021 ◽  
Author(s):  
Ruixin Li ◽  
Haorong Chen ◽  
Hyeongwoon Lee ◽  
Jong Hyun Choi
Keyword(s):  
Self Assembly ◽  
Mechanical Energy ◽  
Single Layer ◽  
Md Simulations ◽  
Dna Origami ◽  
Coarse Grained ◽  
Initial Curvature ◽  
Coarse Grained Model ◽  
Reconfigurable Structures ◽  
Computational Platform

ABSTRACTDNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn which is slightly different from that of native B-form DNA (10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.

Developing Coarse-Grained Force Fields of Poly (methylmethacrylate-b-2-vinylpyridine) from Atomistic Simulation

2012 ◽  
Vol 562-564 ◽  
pp. 123-128 ◽  
Author(s):  
Bo Du ◽  
Zi Lu Wang ◽  
Xue Hao He
Keyword(s):  
Mechanical Properties ◽  
Force Field ◽  
Self Assembly ◽  
Atomistic Simulation ◽  
Polymer Melts ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Inversion Method ◽  
Coarse Grained Model ◽  
Vinyl Pyridine

A coarse-grained force field for poly (methylmethacrylate-b-2-vinyl pyridine) is developed based on the Iterative Boltzmann Inversion method. The proposed coarse-grained model, successfully reproduced the properties of the polymer melts obtained from atomistic simulations, may provide an efficient way to study their mechanical properties and self-assembly behaviors.

The energy landscape as a unifying theme in molecular science

2004 ◽  
Vol 363 (1827) ◽  
pp. 357-377 ◽  
Author(s):  
David J. Wales
Keyword(s):  
Potential Energy ◽  
Self Assembly ◽  
Energy Surface ◽  
Energy Landscape ◽  
Magic Number ◽  
Building Blocks ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
The Right ◽  
Molecular Science

The potential energy surface (PES) underlies most calculations of structure, dynamics and thermodynamics in molecular science. In this contribution connections between the topology of the PES and observable properties are developed for a coarse–grained model of virus capsid self–assembly. The model predicts that a thermodynamically stable, kinetically accessible icosahedral shell exists for pentameric building blocks of the right shape: not too flat and not too spiky. The structure of the corresponding PES is probably common to other systems where directed searches avoid Levinthal's paradox, such as ‘magic number’ clusters, protein folding and crystallization.

scholarly journals Coarse-grained model of tropoelastin self-assembly into nascent fibrils

2019 ◽  
Vol 3 ◽  
pp. 100016 ◽  
Author(s):  
A. Tarakanova ◽  
J. Ozsvar ◽  
A.S. Weiss ◽  
M.J. Buehler
Keyword(s):  
Self Assembly ◽  
Coarse Grained ◽  
Coarse Grained Model
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