scholarly journals Probing the self-assembly dynamics and internal structure of amphiphilic hyaluronic acid conjugates by fluorescence spectroscopy and molecular dynamics simulations

Soft Matter ◽  
2018 ◽  
Vol 14 (23) ◽  
pp. 4762-4771 ◽  
Author(s):  
Denis Svechkarev ◽  
Alexander Kyrychenko ◽  
William M. Payne ◽  
Aaron M. Mohs
Keyword(s):  
Molecular Dynamics ◽  
Hyaluronic Acid ◽  
Fluorescence Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Internal Structure ◽  
Self Assembly ◽  
The Self ◽  
Dynamics Simulations

Side substituents on the hyaluronic acid backbone determine the morphology and hydration of the HA-derived nanoparticles hydrophobic domains.

scholarly journals The structure of clusters formed by Stockmayer supracolloidal magnetic polymers

2019 ◽  
Vol 42 (12) ◽  
Author(s):  
Ekaterina V. Novak ◽  
Elena S. Pyanzina ◽  
Pedro A. Sánchez ◽  
Sofia S. Kantorovich
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Critical Point ◽  
Internal Structure ◽  
Self Assembly ◽  
Hard Spheres ◽  
The Self ◽  
Liquid Transition ◽  
Soft Spheres ◽  
Dynamics Simulations

Abstract. Unlike Stockmayer fluids, that prove to undergo gas-liquid transition on cooling, the system of dipolar hard or soft spheres without any additional central attraction so far has not been shown to have a critical point. Instead, in the latter, one observes diverse self-assembly scenarios. Crosslinking dipolar soft spheres into supracolloidal magnetic polymer-like structures (SMPs) changes the self-assembly behaviour. Moreover, aggregation in systems of SMPs strongly depends on the constituent topology. For Y- and X-shaped SMPs, under the same conditions in which dipolar hard spheres would form chains, the formation of very large loose gel-like clusters was observed (E. Novak et al., J. Mol. Liq. 271, 631 (2018)). In this work, using molecular dynamics simulations, we investigate the self-assembly in suspensions of four topologically different SMPs --chains, rings, X and Y-- whose monomers interact via Stockmayer potential. As expected, compact drop-like clusters are formed by SMPs in all cases if the central isotropic attraction is introduced, however, their shape and internal structure turn out to depend on the SMPs topology. Graphical abstract

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...

Self-Assembly of Graphene Nanoribbons with Unsaturated Edges

2012 ◽  
Vol 1407 ◽  
Author(s):  
Andrew L. J. Pang ◽  
Viacheslav Sorkin ◽  
Yong-Wei Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Bond Order ◽  
Graphene Nanoribbons ◽  
The Self ◽  
Graphene Nanoscrolls ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Stable Structures

ABSTRACTWe studied the self-assembly mechanisms of Graphene Nanoribbon (GNR) with unsaturated edges and demonstrated the ability of GNR to self-assemble into novel stable structures. We proposed three mechanisms which dictate the self-assembly evolution of GNR with unsaturated edges. Using the Adaptive Intermolecular Reactive Empirical Bond-Order (AIREBO) potential, we performed molecular dynamics simulations on initially-planar GNRs with unsaturated edges. The simulation results showed that the self-assembly mechanisms and final conformations of the GNRs correlate well with the proposed GNR self-assembly mechanisms. Furthermore, the simulations also showed the ability of a narrow GNR to self-assemble into various nanostructures, such as tapered graphene nano-rings and graphene nanoscrolls with an embedded nanotube.

scholarly journals Thermodynamics of the self-assembly of non-ionic chromonic molecules using atomistic simulations. The case of TP6EO2M in aqueous solution

Soft Matter ◽  
2015 ◽  
Vol 11 (4) ◽  
pp. 680-691 ◽  
Author(s):  
Anna Akinshina ◽  
Martin Walker ◽  
Mark R. Wilson ◽  
Gordon J. T. Tiddy ◽  
Andrew J. Masters ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Liquid Crystal ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Atomistic Simulations ◽  
Aggregation Behaviour ◽  
Dynamics Simulations

Molecular dynamics simulations of non-ionic triphenylene-based chromonic liquid crystal molecules demonstrate self-assembly of the molecules into stacks and “quasi-isodesmic” aggregation behaviour.

scholarly journals Coarse-Grained Molecular Dynamics Simulations of the Self-Assembly of Amphiphilic Dendrimers as Gene Carriers

2015 ◽  
Vol 108 (2) ◽  
pp. 172a
Author(s):  
Valeria Marquez-Miranda ◽  
Iingrid Araya ◽  
Maria Belen Camarada ◽  
Lars Ratjen ◽  
Maria Carolina Otero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Gene Carriers ◽  
Amphiphilic Dendrimers ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

Understanding the self-assembly of amino ester-based benzene-1,3,5-tricarboxamides using molecular dynamics simulations

2017 ◽  
Vol 19 (1) ◽  
pp. 258-266 ◽  
Author(s):  
Karteek K. Bejagam ◽  
Richard C. Remsing ◽  
Michael L. Klein ◽  
Sundaram Balasubramanian
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Supramolecular Polymers ◽  
Amino Ester ◽  
Dynamics Simulations ◽  
Hydrogen Bonded

Amino ester-based benzene-1,3,5-tricarboxamides (BTAs) are widely studied experimentally for their facile self-assembly, which leads to strong three-fold hydrogen bonded supramolecular polymers.

scholarly journals Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

2018 ◽  
Vol 47 (10) ◽  
pp. 3470-3489 ◽  
Author(s):  
Pim W. J. M. Frederix ◽  
Ilias Patmanidis ◽  
Siewert J. Marrink
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Molecular Simulations ◽  
The Self ◽  
Supramolecular Polymers ◽  
Supramolecular Systems ◽  
Self Assembling ◽  
Dynamics Simulations

The self-assembly of bio-inspired supramolecular polymers can be unravelled using molecular dynamics simulations combined with experiments.

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