Atomistic Mechanism of Carbon Nanostructure Self-Assembly as Predicted by Nonequilibrium QM/MD Simulations

2012 ◽  
pp. 103-172 ◽  
Author(s):  
Stephan Irle ◽  
Alister J. Page ◽  
Biswajit Saha ◽  
Ying Wang ◽  
K. R. S. Chandrakumar ◽  
...  
Keyword(s):  
Self Assembly ◽  
Md Simulations ◽  
Carbon Nanostructure

scholarly journals All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields

2015 ◽  
Vol 51 (21) ◽  
pp. 4402-4405 ◽  
Author(s):  
Åge A. Skjevik ◽  
Benjamin D. Madej ◽  
Callum J. Dickson ◽  
Knut Teigen ◽  
Ross C. Walker ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayer ◽  
Self Assembly ◽  
Force Fields ◽  
Md Simulations ◽  
Bilayer Formation

In this work we report the first example of spontaneous lipid bilayer formation in unbiased all-atom molecular dynamics (MD) simulations.

scholarly journals Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly

Structure ◽  
2008 ◽  
Vol 16 (4) ◽  
pp. 621-630 ◽  
Author(s):  
Kathryn A. Scott ◽  
Peter J. Bond ◽  
Anthony Ivetac ◽  
Alan P. Chetwynd ◽  
Syma Khalid ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Self Assembly ◽  
Md Simulations ◽  
Coarse Grained

scholarly journals Simulation of lipid bilayer self-assembly using all-atom lipid force fields

2016 ◽  
Vol 18 (15) ◽  
pp. 10573-10584 ◽  
Author(s):  
Åge A. Skjevik ◽  
Benjamin D. Madej ◽  
Callum J. Dickson ◽  
Charles Lin ◽  
Knut Teigen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayer ◽  
Self Assembly ◽  
Force Fields ◽  
Md Simulations ◽  
Anionic Phospholipids

Spontaneous bilayer self-assembly of zwitterionic and anionic phospholipids probed by unbiased all-atom molecular dynamics (MD) simulations with three major lipid force fields.

scholarly journals Self-assembly in mixtures with competing interactions

Soft Matter ◽  
2021 ◽  
Author(s):  
Oksana Patsahan ◽  
Marek Litniewski ◽  
Alina Ciach
Keyword(s):  
Self Assembly ◽  
Md Simulations ◽  
Competing Interactions ◽  
Ordered Phases

Coexistence lines between gas and ordered phases in binary microsegregating mixtures are studied theoretically and by MD simulations.

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 A V(iii)-induced metallogel with solvent stimuli-responsive properties: structural proof-of-concept with MD simulations

RSC Advances ◽  
2021 ◽  
Vol 11 (58) ◽  
pp. 36801-36813
Author(s):  
Sima Sedghiniya ◽  
Janet Soleimannejad ◽  
Masumeh Foroutan ◽  
Mina Ebrahimi ◽  
Vahid Fadaei Naeini
Keyword(s):  
Self Assembly ◽  
Md Simulations ◽  
Proof Of Concept ◽  
Stimuli Responsive ◽  
Vanadium Ions

A new solvent stimuli-responsive metallogel (VGel) was synthesized through the introduction of vanadium ions into an adenine (Ade) and BTC organogel, and its supramolecular self-assembly was investigated from a computational viewpoint.

scholarly journals Structure and Dynamics of Curcumin Encapsulated Lecithin Micelles: A Molecular Dynamics Simulation Study

2021 ◽  
Vol 6 (3) ◽  
pp. 113-120
Author(s):  
Lukman Hakim ◽  
Diah Mardiana ◽  
Urnik Rokhiyah ◽  
Maria Lucia Ardhani Dwi Lestari ◽  
Zubaidah Ningsih
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Local Density ◽  
Center Of Mass ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Spherical Micelle ◽  
Natural Surfactant ◽  
Dynamics Response ◽  
Nano Emulsion

Curcumin is a natural product with potential pharmaceutical applications that can be augmented by drug delivery technology such as nano emulsion. Our study focuses on microscopic structural and dynamics response of curcumin encapsulation in micellar system with lecithin as a natural surfactant under variations of composition and temperature using molecular dynamics (MD) simulations. The results highlight the self-assembly of lecithin micelle, with curcumin encapsulated inside, from initial random configurations in the absence of external field. The variation of composition shows that lecithin can aggregate into spherical and rod-like micelle with the second critical micelle concentration lies between 0.17-0.22 mol dm−3. The radial local density centering at the micelle center of mass shows that the effective radius of micelle is indeed defined by the hydrophilic groups of lecithin molecule and theencapsulated curcumin molecules are positioned closer to these hydrophilic groups than the innermost part of the micelle. The spherical micelle is shown to be thermally stable within the temperature range of 277-310 K without a perceivable change in the spherical eccentricity. The dynamics of micelle are enhanced by the temperature, but it is shown to be insensitive to the variation of lecithin-curcumin composition within the studied range. Simulation results are in agreement with the pattern obtained from experimental results based on particle size, polydispersity index, and encapsulation efficiency.

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.

Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations

2012 ◽  
Vol 8 (5) ◽  
pp. 1556-1569 ◽  
Author(s):  
Johan F. Kraft ◽  
Mikkel Vestergaard ◽  
Birgit Schiøtt ◽  
Lea Thøgersen
Keyword(s):  
Self Assembly ◽  
Md Simulations ◽  
The Self ◽  
Atomic Resolution ◽  
Coarse Grained
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