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.

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.

Phase Separated Morphology of P3HT:PCBM Bulk Heterojunction from Coarse-Grained Molecular Dynamics and Monte Carlo Simulation

2014 ◽  
Vol 1639 ◽  
Author(s):  
Tran Thinh To ◽  
Jing Han Yap ◽  
Rayavarapu Prasada Rao ◽  
Stefan Adams
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Active Layer ◽  
Bulk Heterojunction ◽  
Coarse Grained ◽  
Experimental Result ◽  
3 Dimensional ◽  
Coarse Grained Model ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

ABSTRACTMorphology of the active layer in bulk heterojunction P3HT:PCBM organic solar cell was studied using Monte Carlo (MC) and coarse-grained dynamics simulations. While coarse-grained molecular dynamics allow us to quickly estimate the P3HT:PCBM interfacial energy of bilayer structure as a function of underlying layer thickness, bridging the dimension and time gap between dynamics simulations and experiment is computationally expensive and therefore not viable. Using MC technique with input from dynamics simulations allowed us to speed up the calculation and obtain final morphological information based on energetics and entropy, and at the same time retained the physics fidelity in-built in our validated coarse-grained model. The final structure gives phase separated domains with dimension of approximately 12 nm, on par with reported experimental result. The method can be applied to other organic photovoltaics systems to predict active layer morphology relevant for device performance or 3-dimensional device modelling at continuum level.

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...

scholarly journals Molecular Dynamics Study of Ganglioside GM3/DPPC Membrane by Using Coarse-Grained Model

2016 ◽  
Vol 110 (3) ◽  
pp. 323a
Author(s):  
Kento Inoue ◽  
Eiji Ymamoto ◽  
Daisuke Takaiwa ◽  
Kenji Yasuoka ◽  
Masuhiro Mikami
Keyword(s):  
Molecular Dynamics ◽  
Coarse Grained ◽  
Ganglioside Gm3 ◽  
Coarse Grained Model
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