Monte Carlo Simulation of Electrodeposition of Copper:  A Multistep Free Energy Calculation

2008 ◽  
Vol 112 (13) ◽  
pp. 4036-4047 ◽  
Author(s):  
S. Harinipriya ◽  
Venkat R. Subramanian
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Free Energy ◽  
Free Energy Calculation ◽  
Energy Calculation

scholarly journals Reaction Pathway Sampling and Free Energy Analyses for Multimeric Protein Complex Disassembly with Employing Hybrid Configuration Bias Monte Carlo/Molecular Dynamics Simulation

2020 ◽  
Author(s):  
Ikuo Kurisaki ◽  
Shigenori Tanaka
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Free Energy ◽  
Ring Opening ◽  
Reaction Pathway ◽  
Dynamics Simulation ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Ring Opening Reaction ◽  
Hybrid Configuration

AbstractPhysicochemical characterization of multimeric biomacromolecule assembly and disassembly processes is a milestone to understand the mechanisms for biological phenomena at molecular level. Mass spectroscopy (MS) and structural bioinformatics (SB) approaches have become feasible to identify subcomplexes involved in assembly and disassembly, while they cannot provide atomic information sufficient for free energy calculation to characterize transition mechanism between two different sets of subcomplexes. To combine observations derived from MS and SB approaches with conventional free energy calculation protocols, we here designed a new reaction pathway sampling method with employing hybrid configuration bias Monte Carlo/Molecular Dynamics (hcbMC/MD) scheme and applied it to simulate disassembly process of serum amyloid P component (SAP) pentamer. The results we obtained are consistent with those of the earlier MS and SB studies with respect to SAP subcomplex species and the initial stage of SAP disassembly processes. Furthermore, we observed a novel dissociation event, ring-opening reaction of SAP pentamer. Employing free energy calculation combined with the hcbMC/MD reaction pathway trajectories, we moreover obtained experimentally testable observations on (1) reaction time of the ring-opening reaction and (2) importance of Asp42 and Lys117 for stable formation of SAP oligomer.

Free Energy Calculation Methods of Biomolecules

2011 ◽  
Vol 27 (5) ◽  
pp. 395-402 ◽  
Author(s):  
Changjun CHEN ◽  
Yanzhao HUANG ◽  
Yi XIAO
Keyword(s):  
Free Energy ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Calculation Methods

scholarly journals Predicting gas selectivity in organic ionic plastic crystals by free energy calculations

RSC Advances ◽  
2021 ◽  
Vol 11 (32) ◽  
pp. 19623-19629
Author(s):  
Vinay S. Kandagal ◽  
Jennifer M. Pringle ◽  
Maria Forsyth ◽  
Fangfang Chen
Keyword(s):  
Free Energy ◽  
Gas Separation ◽  
Free Energy Calculations ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Plastic Crystal ◽  
Plastic Crystals ◽  
New Type ◽  
Gas Molecules ◽  
Gas Selectivity

The free energy calculation shows the different free energy changes of the adsorption and absorption of gas molecules into an organic ionic plastic crystal, successfully predicting the gas selectivity of this new type of gas separation material.

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