scholarly journals How does an amorphous surface influence molecular binding? – ovocleidin-17 and amorphous calcium carbonate

2015 ◽  
Vol 17 (26) ◽  
pp. 17494-17500 ◽  
Author(s):  
Colin L. Freeman ◽  
John H. Harding ◽  
David Quigley ◽  
P. Mark Rodger
Keyword(s):  
Molecular Dynamics ◽  
Calcium Carbonate ◽  
Molecular Dynamics Simulations ◽  
Amorphous Calcium Carbonate ◽  
Molecular Binding ◽  
Dynamics Simulations ◽  
Amorphous Surface

Molecular dynamics simulations of the protein ovocleidin-17 binding to the surface of amorphous calcium carbonate highlighting the residues contacting the surface.

scholarly journals Role of Internal Stress in the Early-Stage Nucleation of Amorphous Calcium Carbonate Gels

2020 ◽  
Vol 10 (12) ◽  
pp. 4359 ◽  
Author(s):  
Qi Zhou ◽  
Tao Du ◽  
Lijie Guo ◽  
Gaurav Sant ◽  
Mathieu Bauchy
Keyword(s):  
Molecular Dynamics ◽  
Calcium Carbonate ◽  
Driving Force ◽  
Early Stage ◽  
Local Stress ◽  
Amorphous Calcium Carbonate ◽  
Local Coordination ◽  
Dynamics Simulations ◽  
Over Time

Although calcium carbonate (CaCO3) precipitation plays an important role in nature, its mechanism remains only partially understood. Further understanding the atomic driving force behind the CaCO3 precipitation could be key to facilitate the capture, immobilization, and utilization of CO2 by mineralization. Here, based on molecular dynamics simulations, we investigate the mechanism of the early-stage nucleation of an amorphous calcium carbonate gel. We show that the gelation reaction manifests itself by the formation of some calcium carbonate clusters that grow over time. Interestingly, we demonstrate that the gelation reaction is driven by the existence of some competing local molecular stresses within the Ca and C precursors, which progressively get released upon gelation. This internal molecular stress is found to originate from the significantly different local coordination environments exhibited by Ca and C atoms. These results highlight the key role played by the local stress acting within the atomic network in governing gelation reactions.

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.

Influence of compatible solute ectoine on distinct DNA structures: thermodynamic insights into molecular binding mechanisms and destabilization effects

2018 ◽  
Vol 20 (40) ◽  
pp. 25861-25874 ◽  
Author(s):  
Ewa Anna Oprzeska-Zingrebe ◽  
Susann Meyer ◽  
Alexander Roloff ◽  
Hans-Jörg Kunte ◽  
Jens Smiatek
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Compatible Solute ◽  
Dna Hairpins ◽  
Dna Structures ◽  
Molecular Binding ◽  
Theoretical Approaches ◽  
Dynamics Simulations ◽  
Binding Mechanisms

We study ectoine-induced destabilization effects on DNA hairpins by a combination of atomistic molecular dynamics simulations, experiments, and theoretical approaches.

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