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.

Absorption of Mechanical Energy via Formation of Ice Nanotubes in Zeolite

2021 ◽  
Author(s):  
Kenji Mochizuki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Heterogeneous System ◽  
Mechanical Energy ◽  
Bulk Water ◽  
Pure Silica ◽  
Dynamics Simulations ◽  
First Time

Abstract Molecular dynamics simulations are carried out for a heterogeneous system composed of bulk water and pure-silica zeolites of the AFI type. Our simulations show, for the first time, the...

scholarly journals Detection of Posner's clusters during calcium phosphate nucleation: a molecular dynamics study

2017 ◽  
Vol 5 (35) ◽  
pp. 7274-7284 ◽  
Author(s):  
Giulia Mancardi ◽  
Carlos Ernesto Hernandez Tamargo ◽  
Devis Di Tommaso ◽  
Nora H. de Leeuw
Keyword(s):  
Molecular Dynamics ◽  
Calcium Phosphate ◽  
Molecular Dynamics Simulations ◽  
Aggregation Process ◽  
Phosphate Ions ◽  
Dynamics Simulations

Molecular dynamics simulations of calcium and phosphate ions in water show that Posner-like clusters originate during the aggregation process.

Molecular insight into the Mullins effect: irreversible disentanglement of polymer chains revealed by molecular dynamics simulations

2017 ◽  
Vol 19 (29) ◽  
pp. 19468-19477 ◽  
Author(s):  
Chi Ma ◽  
Tuo Ji ◽  
Christopher G. Robertson ◽  
R. Rajeshbabu ◽  
Jiahua Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Model ◽  
Polymer Chains ◽  
Mullins Effect ◽  
Key Characteristics ◽  
Dynamics Simulations ◽  
First Time ◽  
Insight Into

For the first time, the key characteristics associated with the Mullins effect are captured by a molecular model.

scholarly journals Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: Insights from accelerated molecular dynamics simulations

2019 ◽  
Author(s):  
Juan A. Bueren-Calabuig ◽  
Marcus Bage ◽  
Victoria H. Cowling ◽  
Andrei V. Pisliakov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Rna Polymerase Ii ◽  
Active Site ◽  
Allosteric Regulation ◽  
Dynamic Network ◽  
Binding Model ◽  
Accelerated Molecular Dynamics ◽  
Dynamics Simulations ◽  
First Time

ABSTRACTThe RNA guanine-7 methyltransferase (RNMT) in complex with RNMT-Activating Miniprotein (RAM) catalyses the formation of a N7-methylated guanosine cap structure on the 5’ end of nascent RNA polymerase II transcripts. The mRNA cap protects the transcript from exonucleases and recruits cap-binding complexes that mediate RNA processing, export and translation. By using microsecond standard and accelerated molecular dynamics simulations, we provide for the first time a detailed molecular mechanism of allosteric regulation of RNMT by RAM. We show that RAM selects the RNMT active site conformations that are optimal for binding of substrates (AdoMet and the cap), thus enhancing their affinity. Furthermore, our results strongly suggest the likely scenario in which the cap binding promotes the subsequent AdoMet binding, consistent with the previously suggested cooperative binding model. By employing the dynamic network and community analyses, we revealed the underlying long-range allosteric networks and paths that are crucial for allosteric regulation by RAM. Our findings complement and explain previous experimental data on RNMT activity. Moreover, this study provides the most complete description of the cap and AdoMet binding poses and interactions within the enzyme’s active site. This information is critical for the drug discovery efforts that consider RNMT as a promising anti-cancer target.

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.

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...

MOLECULAR DYNAMICS SIMULATIONS OF LIQUID CRYSTAL ANCHORING AT AN AMORPHOUS POLYMER SURFACE

1999 ◽  
Vol 10 (02n03) ◽  
pp. 415-429 ◽  
Author(s):  
T. P. DOERR ◽  
P. L. TAYLOR
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystal ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amorphous Polymer ◽  
Polymer Surface ◽  
The Other ◽  
Substantial Fraction ◽  
Dynamics Simulations ◽  
First Time

Atomistic molecular dynamics simulations have been used, apparently for the first time, to investigate the anchoring behavior of a liquid crystal at the interface with an amorphous polymer. The simulations studied a system consisting of the nematogen 5CB at the surface of amorphous polyethylene, and used the simple Dreiding II force field. The simulations indicate a preference for nonplanar anchoring. Two distinct microscopic paths have been identified by which the liquid crystal changes orientation at the surface. In one case, only one or a few of the 5CB molecules are rotating at any particular time. In the other case, a substantial fraction of the molecules rotate simultaneously.

Molecular dynamics simulations of the enhanced recovery of confined methane with carbon dioxide

2015 ◽  
Vol 17 (47) ◽  
pp. 31887-31893 ◽  
Author(s):  
Quanzi Yuan ◽  
Xueyan Zhu ◽  
Kui Lin ◽  
Ya-Pu Zhao
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Enhanced Recovery ◽  
Dynamics Simulations ◽  
First Time

For the first time, the enhanced recovery of confined methane (CH4) with carbon dioxide (CO2) is investigated through molecular dynamics simulations.

Chemical reactions of a CL-20 crystal under heat and shock determined by ReaxFF reactive molecular dynamics simulations

2020 ◽  
Vol 22 (40) ◽  
pp. 23323-23332
Author(s):  
Fuping Wang ◽  
Lang Chen ◽  
Deshen Geng ◽  
Jianying Lu ◽  
Junying Wu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Reactions ◽  
Reactive Molecular Dynamics ◽  
Dynamics Simulations ◽  
First Time

For the first time, different chemical reactions of CL-20 under heat and shock were studied using ReaxFF reactive molecular dynamics.

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