Polyelectrolyte Adsorption on a Charged Surface. Free Energy Calculation from Monte Carlo Simulations Using Jarzynski Equality

2008 ◽  
Vol 41 (21) ◽  
pp. 8267-8274 ◽  
Author(s):  
Claudio F. Narambuena ◽  
Dante M. Beltramo ◽  
Ezequiel P. M. Leiva
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Monte Carlo Simulations ◽  
Surface Free Energy ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Charged Surface ◽  
Polyelectrolyte Adsorption ◽  
Jarzynski Equality

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

Polyelectrolyte Adsorption on a Charged Surface. A Study by Monte Carlo Simulations

2007 ◽  
Vol 40 (20) ◽  
pp. 7336-7342 ◽  
Author(s):  
Claudio F. Narambuena ◽  
Dante M. Beltramo ◽  
Ezequiel P. M. Leiva
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Charged Surface ◽  
Polyelectrolyte Adsorption

Comparison of Surface Free Energy Calculation Methods

2015 ◽  
Vol 791 ◽  
pp. 259-265 ◽  
Author(s):  
Jacek Domińczuk ◽  
Anna Krawczuk
Keyword(s):  
Free Energy ◽  
Surface Free Energy ◽  
Surface Preparation ◽  
Contact Angle Measurement ◽  
Angle Measurement ◽  
Free Energy Calculation ◽  
Boundary Phase ◽  
Polar Component ◽  
Energy Calculation ◽  
Liquid Boundary

The paper presents the main methods of surface free energy calculation of solids based on the contact angle measurement. The basic of splitting the surface free energy into components as well as interactions at the solid-liquid boundary phase considered while developing calculation models were presented. Basing on test results of surface free energy of 0H18N9T stainless steel, the relation between the method of surface preparation and the surface free energy were shown. The analysis focuses on change of the polar part. Differences between methods were indicated and it was pointed that skipping the polar component in analysis of adhesive joints strength results in deterioration of prediction model.

The solid surface free energy calculation

2004 ◽  
Vol 271 (2) ◽  
pp. 454-472 ◽  
Author(s):  
S. Siboni ◽  
C. Della Volpe ◽  
D. Maniglio ◽  
M. Brugnara
Keyword(s):  
Free Energy ◽  
Surface Free Energy ◽  
Solid Surface ◽  
Free Energy Calculation ◽  
Energy Calculation

The solid surface free energy calculation

2004 ◽  
Vol 271 (2) ◽  
pp. 434-453 ◽  
Author(s):  
C. Della Volpe ◽  
D. Maniglio ◽  
M. Brugnara ◽  
S. Siboni ◽  
M. Morra
Keyword(s):  
Free Energy ◽  
Surface Free Energy ◽  
Solid Surface ◽  
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.

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