Insights into the effects of mutations on Cren7–DNA binding using molecular dynamics simulations and free energy calculations

2015 ◽  
Vol 17 (8) ◽  
pp. 5704-5711 ◽  
Author(s):  
Lin Chen ◽  
Qing-Chuan Zheng ◽  
Hong-Xing Zhang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Free Energy Calculations ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Dynamic Effects ◽  
Cellular Processes ◽  
Dynamics Simulations

Cren7 is involved in regulating essential cellular processes. We applied MD simulations and free energy calculation to explore the structural and dynamic effects of W26A, L28A, and K53A mutations.

scholarly journals Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

2014 ◽  
Vol 10 (7) ◽  
pp. 2677-2689 ◽  
Author(s):  
Yinglong Miao ◽  
William Sinko ◽  
Levi Pierce ◽  
Denis Bucher ◽  
Ross C. Walker ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Accelerated Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Disclosing crystal nucleation mechanism in lithium disilicate glass through molecular dynamics simulations and free-energy calculations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Federica Lodesani ◽  
Maria Cristina Menziani ◽  
Kei Maeda ◽  
Yoichi Takato ◽  
Shingo Urata ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Critical Radius ◽  
Lithium Disilicate ◽  
Free Energy Calculations ◽  
Nucleation Theory ◽  
Crystal Nucleation ◽  
Energy Calculation ◽  
Dynamics Simulations

Abstract Unraveling detailed mechanism of crystal nucleation from amorphous materials is challenging for both experimental and theoretical approaches. In this study, we have examined two methods to understand the initial stage of crystal precipitation from lithium disilicate glasses using molecular dynamics simulations. One of the methods is a modified exploring method to find structurally similar crystalline clusters in the glass models, enabling us to find three different embryos, such as Li2Si2O5 (LS2), Li2SiO3 (LS) and Li3PO4 (LP), in the 33Li2O·66SiO2·1P2O5 glass (LS2P1), in which P2O5 is added as a nucleating agent. Interestingly, LS2 and LP crystals were found inside the LS2P1 glass while LS crystal appeared on the glass surface, which agrees with experimental observations. The other method is free energy calculation using a subnano-scale spherical crystal embedded in the glass model. This method, which we called Free-Energy Seeding Method (FESM), allows us to evaluate free energy change as a function of crystal radius and to identify critical size of the crystal precipitation. The free energy profiles for LS and LS2 crystal nuclei in the LS2 glass models possess maximum energy at a critical radius as expected by classical nucleation theory. Furthermore, the critical radius and the energy barrier height agree well with recent experimental investigation, proving the applicability of this method to design glass–ceramics by atomistic modeling.

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