The hydrophobic effect: Molecular dynamics simulations of water confined between extended hydrophobic and hydrophilic surfaces

2004 ◽  
Vol 120 (20) ◽  
pp. 9729-9744 ◽  
Author(s):  
Morten Ø. Jensen ◽  
Ole G. Mouritsen ◽  
Günther H. Peters
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Effect ◽  
Hydrophilic Surfaces ◽  
Dynamics Simulations

scholarly journals Achilles: A Tool for Contact Angle Estimation from Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Sumith Yesudasan
Keyword(s):  
Molecular Dynamics ◽  
Contact Angle ◽  
Molecular Dynamics Simulations ◽  
Water Droplet ◽  
Dynamics Simulation ◽  
Hydrophilic Surfaces ◽  
Interfacial Physics ◽  
Droplet Liquid ◽  
Dynamics Simulations ◽  
Molecular Dynamics Results

In this work, a tool for estimating the contact angle from the molecular dynamics simulations is developed and presented. The tool (Achilles) can detect water droplet on hydrophobic and hydrophilic surfaces. The tool can reconstruct the droplets broken across the periodic boundaries. Further a neighbor density based accurate filter is used to find the droplet liquid vapor interface and a circle is fitted using it after removing the dense layers of water next to solid surface. This fitted circle is solved for contact angle and results are outputted in the form of graphical images and text. The entire content of the internal computations of the tool is broken down into 4 phases and users can monitor the outcomes at every phase through output images. The tool is tested using sample molecular dynamics results of water droplet on hydrophobic and hydrophilic surfaces. We believe this tool can be a good addition to the molecular dynamics simulation community who work on the interfacial physics, droplet evaporation, super hydrophobic surfaces, and wettability etc.

Molecular dynamics study of coil-to-globule transition in a thermo-responsive oligomer bound to various surfaces: hydrophilic surfaces stabilize the coil form

2018 ◽  
Vol 20 (47) ◽  
pp. 29754-29763 ◽  
Author(s):  
Giuseppe Consiglio ◽  
Giuseppe Forte
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrophilic Surfaces ◽  
Responsive Polymer ◽  
Different Temperatures ◽  
Dynamical Properties ◽  
Dynamics Simulations ◽  
Covalently Bound

The structural and dynamical properties of 40-mer of thermo-responsive polymer PNIPAM covalently bound to different surfaces have been studied, at different temperatures, by means of molecular dynamics simulations.

scholarly journals Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Krystel El Hage ◽  
Florent Hédin ◽  
Prashant K Gupta ◽  
Markus Meuwly ◽  
Martin Karplus
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Effect ◽  
Md Simulations ◽  
Water Molecules ◽  
Human Hemoglobin ◽  
Standard Size ◽  
Wide Range ◽  
Dynamics Simulations

Recent molecular dynamics (MD) simulations of human hemoglobin (Hb) give results in disagreement with experiment. Although it is known that the unliganded (T0) and liganded (R4) tetramers are stable in solution, the published MD simulations of T0 undergo a rapid quaternary transition to an R-like structure. We show that T0 is stable only when the periodic solvent box contains ten times more water molecules than the standard size for such simulations. The results suggest that such a large box is required for the hydrophobic effect, which stabilizes the T0 tetramer, to be manifested. Even in the largest box, T0 is not stable unless His146 is protonated, providing an atomistic validation of the Perutz model. The possibility that extra large boxes are required to obtain meaningful results will have to be considered in evaluating existing and future simulations of a wide range of systems.

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