scholarly journals A protein self-assembly model guided by electrostatic and hydrophobic dipole moments

PLoS ONE ◽  
2019 ◽  
Vol 14 (4) ◽  
pp. e0216253
Author(s):  
Angel Mozo-Villarías ◽  
Enrique Querol
Keyword(s):  
Self Assembly ◽  
Dipole Moments ◽  
Assembly Model

Capillary flows and self-assembly of porous hydrate structures

2012 ◽  
Vol 9 (1) ◽  
pp. 22-25
Author(s):  
S.V. Amel’kin ◽  
D.Ye. Igoshin
Keyword(s):  
Experimental Data ◽  
Aqueous Solution ◽  
Self Assembly ◽  
Capillary Flow ◽  
Secondary Crystallization ◽  
Assembly Model ◽  
Physical Processes ◽  
Good Correspondence ◽  
Solution Formation ◽  
Capillary Flows

A self-assembly model for porous hydrate structures is proposed, which takes into account the sequence of basic physical processes: hydrate growth on the surface of the aqueous solution, formation of islet structure, capillary flow, separation and transfer of secondary crystallization nuclei to the meniscus. The model was studied within the cellular automata method. A good correspondence between the results of the simulation and the experimental data is obtained.

scholarly journals A Self-assembly Model of Time-Dependent Glue Strength

2006 ◽  
pp. 290-304 ◽  
Author(s):  
Sudheer Sahu ◽  
Peng Yin ◽  
John H. Reif
Keyword(s):  
Self Assembly ◽  
Time Dependent ◽  
Assembly Model

scholarly journals Hierarchical self assembly of patterns from the Robinson tilings: DNA tile design in an enhanced Tile Assembly Model

2011 ◽  
Vol 11 (2) ◽  
pp. 323-338 ◽  
Author(s):  
Jennifer E. Padilla ◽  
Wenyan Liu ◽  
Nadrian C. Seeman
Keyword(s):  
Self Assembly ◽  
Assembly Model ◽  
Tile Assembly Model ◽  
Tile Assembly

scholarly journals Stacks of Azobenzene Stars: Self-Assembly Scenario and Stabilising Forces Quantified in Computer Modelling

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4387 ◽  
Author(s):  
Vladyslav Savchenko ◽  
Markus Koch ◽  
Aleksander S. Pavlov ◽  
Marina Saphiannikova ◽  
Olga Guskova
Keyword(s):  
Self Assembly ◽  
Density Functional ◽  
Computer Modelling ◽  
Light Stimulus ◽  
Dipole Moments ◽  
Intermolecular Forces ◽  
Binding Energies ◽  
The Self ◽  
Assembly Mechanism ◽  
Lateral Displacements

In this paper, the columnar supramolecular aggregates of photosensitive star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core and azobenzene arms are analyzed theoretically by applying a combination of computer simulation techniques. Without a light stimulus, the azobenzene arms adopt the trans-state and build one-dimensional columns of stacked molecules during the first stage of the noncovalent association. These columnar aggregates represent the structural elements of more complex experimentally observed morphologies—fibers, spheres, gels, and others. Here, we determine the most favorable mutual orientations of the trans-stars in the stack in terms of (i) the π – π distance between the cores lengthwise the aggregate, (ii) the lateral displacements due to slippage and (iii) the rotation promoting the helical twist and chirality of the aggregate. To this end, we calculate the binding energy diagrams using density functional theory. The model predictions are further compared with available experimental data. The intermolecular forces responsible for the stability of the stacks in crystals are quantified using Hirshfeld surface analysis. Finally, to characterize the self-assembly mechanism of the stars in solution, we calculate the hydrogen bond lengths, the normalized dipole moments and the binding energies as functions of the columnar length. For this, molecular dynamics trajectories are analyzed. Finally, we conclude about the cooperative nature of the self-assembly of star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core in aqueous solution.

The Maximum Matching Problem Based on Self-Assembly Model of Molecular Beacon

2018 ◽  
Vol 10 (2) ◽  
pp. 213-218 ◽  
Author(s):  
Jing Yang ◽  
Zhixiang Yin ◽  
Kaifeng Huang ◽  
Jianzhong Cui
Keyword(s):  
Self Assembly ◽  
Molecular Beacon ◽  
Maximum Matching ◽  
Assembly Model ◽  
Matching Problem
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