Effective coarse-grained solid–fluid potentials and their application to model adsorption of fluids on heterogeneous surfaces

2014 ◽  
Vol 16 (36) ◽  
pp. 19165-19180 ◽  
Author(s):  
Esther Forte ◽  
Andrew J. Haslam ◽  
George Jackson ◽  
Erich A. Müller
Keyword(s):  
Free Energy ◽  
Temperature Dependence ◽  
Particle Surface ◽  
Surface Interaction ◽  
Coarse Grained ◽  
Heterogeneous Surfaces ◽  
Present Contribution ◽  
Surface Potentials ◽  
Fluid Surface

In the present contribution we emphasise the necessity of using an adequate averaging procedure to obtain effective fluid–surface potentials. A procedure to develop free-energy-averaged fluid–surface potentials retaining the important temperature dependence of the coarse-grained particle-surface interaction is described.

scholarly journals An investigation of free-energy-averaged (coarse-grained) potentials for fluid adsorption on heterogeneous solid surfaces

2019 ◽  
Vol 21 (46) ◽  
pp. 25558-25568 ◽  
Author(s):  
Srikanth Ravipati ◽  
Amparo Galindo ◽  
George Jackson ◽  
Andrew J. Haslam
Keyword(s):  
Free Energy ◽  
Solid Surface ◽  
Body Fluid ◽  
Solid Surfaces ◽  
Coarse Grained ◽  
Heterogeneous Surfaces ◽  
Mapping Procedure ◽  
Adsorption On Heterogeneous Surfaces ◽  
Heterogeneous Solid

A FEA mapping procedure for providing coarse-grained, two-body fluid–solid potentials (describing the interaction between a fluid molecule and a solid surface) is investigated, and adapted to allow study of adsorption on heterogeneous surfaces.

scholarly journals How proteins open fusion pores: insights from molecular simulations

2020 ◽  
Author(s):  
H. Jelger Risselada ◽  
Helmut Grubmüller
Keyword(s):  
Free Energy ◽  
Fusion Proteins ◽  
Graphics Processing Units ◽  
Fusion Reaction ◽  
Molecular Simulations ◽  
Minimum Free Energy ◽  
Free Energy Calculations ◽  
Coarse Grained ◽  
Fusion Pore ◽  
Graphics Processing

AbstractFusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.

Heat capacity of activation for the hydrolysis of methanesulfonyl chloride and benzenesulfonyl chloride in light and heavy water

1969 ◽  
Vol 47 (22) ◽  
pp. 4199-4206 ◽  
Author(s):  
R. E. Robertson ◽  
B. Rossall ◽  
S. E. Sugamori ◽  
L. Treindl
Keyword(s):  
Heat Capacity ◽  
Free Energy ◽  
Temperature Dependence ◽  
Heavy Water ◽  
Bond Formation ◽  
Sulfonyl Chlorides ◽  
Benzenesulfonyl Chloride ◽  
Methanesulfonyl Chloride ◽  
Hydrolysis Of ◽  
Parameter Temperature Dependence

Rates of solvolysis of methanesulfonyl chloride and benzenesulfonyl chloride have been determined in H2O and D2O. The free energy, enthalpy, entropy, and heat capacity of activation were calculated. The exceptional accuracy of the data permitted an estimation of dΔCp≠/dT from a four parameter temperature dependence of the kinetic rates.From these data we conclude that both sulfonyl chlorides hydrolyse by the same mechanism (Sn2) The change in R from CH3 to C6H5 in RSO2Cl did not alter ΔCp≠ but ΔS≠ (20°) was changed from −8.32 to −13.25 cal deg−1 mole−1, respectively. The significance of this difference is attributed to the probability of bond formation rather than to differences in solvent reorganization.

scholarly journals Distributions of experimental protein structures on coarse-grained free energy landscapes

2015 ◽  
Vol 143 (24) ◽  
pp. 243153 ◽  
Author(s):  
Kannan Sankar ◽  
Jie Liu ◽  
Yuan Wang ◽  
Robert L. Jernigan
Keyword(s):  
Free Energy ◽  
Protein Structures ◽  
Coarse Grained ◽  
Energy Landscapes ◽  
Free Energy Landscapes

scholarly journals Free-energy coarse-grained potential for C60

2015 ◽  
Vol 143 (16) ◽  
pp. 164509 ◽  
Author(s):  
D. M. Edmunds ◽  
P. Tangney ◽  
D. D. Vvedensky ◽  
W. M. C. Foulkes
Keyword(s):  
Free Energy ◽  
Coarse Grained
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