scholarly journals DNA Self-Assembly and Computation Studied with a Coarse-Grained Dynamic Bonded Model

2012 ◽  
pp. 123-134 ◽  
Author(s):  
Carsten Svaneborg ◽  
Harold Fellermann ◽  
Steen Rasmussen
Keyword(s):  
Self Assembly ◽  
Coarse Grained

Simulation studies of the interactions between membrane proteins and detergents

2005 ◽  
Vol 33 (5) ◽  
pp. 910-912 ◽  
Author(s):  
P.J. Bond ◽  
J. Cuthbertson ◽  
M.S.P. Sansom
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Self Assembly ◽  
Kinetic Mechanism ◽  
Coarse Grained ◽  
Simulation Studies ◽  
High Resolution Data ◽  
Biologically Relevant ◽  
Structure And Dynamics ◽  
Detergent Interactions

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.

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...

Drying-Mediated Hierarchical Self-Assembly of Nanoparticles:  A Dynamical Coarse-Grained Approach

2008 ◽  
Vol 112 (12) ◽  
pp. 4498-4506 ◽  
Author(s):  
Orly Kletenik-Edelman ◽  
Elina Ploshnik ◽  
Asaf Salant ◽  
Roy Shenhar ◽  
Uri Banin ◽  
...  
Keyword(s):  
Self Assembly ◽  
Coarse Grained

scholarly journals Controlling the length of porphyrin supramolecular polymers via coupled equilibria and dilution-induced supramolecular polymerization

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Elisabeth Weyandt ◽  
Luigi Leanza ◽  
Riccardo Capelli ◽  
Giovanni M. Pavan ◽  
Ghislaine Vantomme ◽  
...  
Keyword(s):  
Complex Systems ◽  
Self Assembly ◽  
Chiral Discrimination ◽  
Coarse Grained ◽  
Supramolecular Polymers ◽  
Supramolecular System ◽  
Precise Control ◽  
Aggregate Morphology ◽  
The Individual ◽  
Supramolecular Polymerization

AbstractMulti-component systems often display convoluted behavior, pathway complexity and coupled equilibria. In recent years, several ways to control complex systems by manipulating the subtle balances of interaction energies between the individual components have been explored and thereby shifting the equilibrium between different aggregate states. Here we show the enantioselective chain-capping and dilution-induced supramolecular polymerization with a Zn2+-porphyrin-based supramolecular system when going from long, highly cooperative supramolecular polymers to short, disordered aggregates by adding a monotopic Mn3+-porphyrin monomer. When mixing the zinc and manganese centered monomers, the Mn3+-porphyrins act as chain-cappers for Zn2+-porphyrin supramolecular polymers, effectively hindering growth of the copolymer and reducing the length. Upon dilution, the interaction between chain-capper and monomers weakens as the equilibria shift and long supramolecular polymers form again. This dynamic modulation of aggregate morphology and length is achieved through enantioselectivity in the aggregation pathways and concentration-sensitive equilibria. All-atom and coarse-grained molecular simulations provide further insights into the mixing of the species and their exchange dynamics. Our combined experimental and theoretical approach allows for precise control of molecular self-assembly and chiral discrimination in complex systems.

scholarly journals Self Assembly of Model Polymers into Biological Random Networks

2020 ◽  
Author(s):  
Matthew Bailey ◽  
Mark Wilson
Keyword(s):  
Network Structure ◽  
Biological Networks ◽  
Self Assembly ◽  
Short Range ◽  
External Pressure ◽  
Coarse Grained ◽  
Random Networks ◽  
Network Structures ◽  
Polymer Model ◽  
Microscope Images

<div>The properties of biological networks, such as those found in the ocular lens capsule, are difficult to study without simplified models.</div><div>Model polymers are developed, inspired by "worm-like'' curve models, that are shown to spontaneously self assemble</div><div>to form networks similar to those observed experimentally in biological systems.</div><div>These highly simplified coarse-grained models allow the self assembly process to be studied on near-realistic time-scales.</div><div>Metrics are developed (using a polygon-based framework)</div><div>which are useful for describing simulated networks and can also be applied to images of real networks.</div><div>These metrics are used to show the range of control that the computational polymer model has over the networks, including the polygon structure and short range order.</div><div>The structure of the simulated networks are compared to previous simulation work and microscope images of real networks. </div><div>The network structure is shown to be a function of the interaction strengths, cooling rates and external pressure. </div><div>In addition, "pre-tangled'' network structures are introduced and shown to significantly influence the subsequent network structure.</div><div>The network structures obtained fit into a region of the network landscape effectively inaccessible to random</div><div>(entropically-driven) networks but which are occupied by experimentally-derived configurations.</div>

Self-assembly of coarse-grained ionic surfactants accelerated by graphics processing units

Soft Matter ◽  
2012 ◽  
Vol 8 (8) ◽  
pp. 2385-2397 ◽  
Author(s):  
David N. LeBard ◽  
Benjamin G. Levine ◽  
Philipp Mertmann ◽  
Stephen A. Barr ◽  
Arben Jusufi ◽  
...  
Keyword(s):  
Self Assembly ◽  
Graphics Processing Units ◽  
Coarse Grained ◽  
Ionic Surfactants ◽  
Graphics Processing

scholarly journals Coarse-grained simulations of the solution-phase self-assembly of poly(3-hexylthiophene) nanostructures

Nanoscale ◽  
2013 ◽  
Vol 5 (5) ◽  
pp. 2017 ◽  
Author(s):  
Kyra N. Schwarz ◽  
Tak W. Kee ◽  
David M. Huang
Keyword(s):  
Self Assembly ◽  
Solution Phase ◽  
Coarse Grained ◽  
Coarse Grained Simulations

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.

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