scholarly journals Variation in Properties of Pre-Nucleation Calcium Carbonate Clusters Induced by Aggregation: A Molecular Dynamics Study

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 102
Author(s):  
Bing-Bing Wang ◽  
Yi Xiao ◽  
Zhi-Ming Xu
Keyword(s):  
Molecular Dynamics ◽  
Calcium Carbonate ◽  
Molecular Dynamics Simulations ◽  
Hydration Number ◽  
Spontaneous Growth ◽  
Dynamics Simulations ◽  
The Relationship ◽  
Solubility Equilibrium ◽  
Supersaturated Solutions ◽  
Number Form

Numerous studies have speculated calcium carbonate (CaCO3) nucleation induced by pre-nucleation clusters (PNCs) aggregation. However, it is challenging for experiments to directly obtain the relationship between PNCs aggregation and nucleation. Herein, we employ molecular dynamics simulations to explore the variation during PNCs aggregation, which can describe the beginning stage of CaCO3 nucleation induced by PNCs aggregation in supersaturated solutions. The results reveal that the formation of CaCO3 nucleus consists of PNCs spontaneous growth, PNCs solubility equilibrium, and aggregation of PNCs inducing nucleation. The PNCs aggregation, accompanied by the variation in the configuration and stability of CaCO3 aggregate, breaks the solubility equilibrium of PNCs and creates conditions for the formation of the more stable nucleus. Besides, the CaCO3 nucleus with the higher coordination number and the lower hydration number form when decreasing the CaCO3 concentration or increasing the temperature. This work not only sheds light on the formation of the CaCO3 nucleus but also contributes to the explanation for CaCO3 polymorphism.

scholarly journals Probing the Relationship between Anti-Pneumocystis carinii Activity and DNA Binding of Bisamidines by Molecular Dynamics Simulations

Molecules ◽  
2015 ◽  
Vol 20 (4) ◽  
pp. 5942-5964 ◽  
Author(s):  
Teresa Żołek ◽  
Dorota Maciejewska ◽  
Jerzy Żabiński ◽  
Paweł Kaźmierczak ◽  
Mateusz Rezler
Keyword(s):  
Molecular Dynamics ◽  
Dna Binding ◽  
Molecular Dynamics Simulations ◽  
Pneumocystis Carinii ◽  
Dynamics Simulations ◽  
The Relationship

scholarly journals Interaction of stable aggregates drives the precipitation of calcium phosphate in supersaturated solutions

CrystEngComm ◽  
2019 ◽  
Vol 21 (42) ◽  
pp. 6354-6364 ◽  
Author(s):  
R. Innocenti Malini ◽  
C. L. Freeman ◽  
J. H. Harding
Keyword(s):  
Molecular Dynamics ◽  
Calcium Phosphate ◽  
Molecular Dynamics Simulations ◽  
Amorphous Calcium Phosphate ◽  
Calcium Phosphate Nanoparticles ◽  
Dynamics Simulations ◽  
First Time ◽  
Supersaturated Solutions

Using molecular dynamics simulations, we show for the first time that calcium phosphate nanoparticles of eight formula units are thermodynamically stable and could be key in the nucleation of amorphous calcium phosphate.

On the Relationship of the Relative Intensity I3 and a Cavity Number as Obtained from Computer Simulations

2012 ◽  
Vol 733 ◽  
pp. 183-189 ◽  
Author(s):  
Dušan Račko
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Free Volume ◽  
Computer Simulations ◽  
Relative Intensity ◽  
Complex Behavior ◽  
Volume Analysis ◽  
Dynamics Simulations ◽  
Relationship Of ◽  
The Relationship

In this contribution a generalized picture of the cavity number behavior is obtained by means of molecular dynamics simulations and consequent free volume analysis. The cavity number obtained for free volume cavities defined by different probe radii shows a complex behavior with the temperature. The number of cavities determined by small probes drops with the temperature. The number of cavities determined by large probes increases. This complex behavior of the cavity number can be discussed with the distinct behavior of the relative intensity, as observed in the experiment, and a support for the most basic of assumptions, that the cavity number relates to the relative intensity, is given.

Simulation of metal–organic framework self-assembly

2015 ◽  
Vol 17 (14) ◽  
pp. 8649-8652 ◽  
Author(s):  
Makoto Yoneya ◽  
Seiji Tsuzuki ◽  
Masaru Aoyagi
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Metal Organic Framework ◽  
Metal Organic Frameworks ◽  
Spontaneous Growth ◽  
Metal Organic ◽  
Initial Placement ◽  
Dynamics Simulations

Spontaneous growth of metal–organic frameworks (MOFs) composed of metal ions and 4,4′-bipyridine ligands was successfully demonstrated by molecular dynamics simulations, starting from a random initial placement of the metals and the ligands.

Molecular dynamics simulations of wild type and mutants of botulinum neurotoxin A complexed with synaptic vesicle protein 2C

2015 ◽  
Vol 11 (1) ◽  
pp. 223-231 ◽  
Author(s):  
Feng Wang ◽  
Hua Wan ◽  
Jian-ping Hu ◽  
Shan Chang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Synaptic Vesicle ◽  
Conformational Changes ◽  
Botulinum Neurotoxin ◽  
Wild Type ◽  
Botulinum Neurotoxin A ◽  
Synaptic Vesicle Protein ◽  
Dynamics Simulations ◽  
The Relationship

Using molecular dynamics simulations, we investigate the relationship between the conformational changes of BoNT/A-RBD:SV2C-LD and the interfacial interactions.

Homogeneous nucleation of NaCl in supersaturated solutions

2021 ◽  
Author(s):  
Cintia Pulido Lamas ◽  
Jorge R. Espinosa ◽  
María Martín Conde ◽  
Jorge Ramirez ◽  
Pablo Montero de Hijes ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Homogeneous Nucleation ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Approximate Approach ◽  
Seeding Method ◽  
Dynamics Simulations ◽  
Supersaturated Solutions

The Seeding method is an approximate approach to investigate nucleation that combines molecular dynamics simulations with classical nucleation theory. This technique has been successfully implemented in a broad range of...

scholarly journals Unveiling the mechanism of structure-dependent thermal transport behavior in self-folded graphene film: a multiscale study

Nanoscale ◽  
2020 ◽  
Vol 12 (47) ◽  
pp. 24138-24145
Author(s):  
Anran Wei ◽  
Han Ye ◽  
Yang Gao ◽  
Fenglin Guo
Keyword(s):  
Molecular Dynamics ◽  
Theoretical Model ◽  
Molecular Dynamics Simulations ◽  
Thermal Transport ◽  
Graphene Film ◽  
Transport Behavior ◽  
Dynamics Simulations ◽  
The Relationship

A theoretical model is developed to demonstrate the relationship between the fold length and thermal transport behavior in self-folded graphene film, validated by molecular dynamics simulations. The effect of tension is also revealed by this model.

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