A novel approach to calculate protein adsorption isotherms by molecular dynamics simulations

2020 ◽  
Vol 1620 ◽  
pp. 460940
Author(s):  
Sven Jakobtorweihen ◽  
Jonas Heuer ◽  
Thomas Waluga
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Adsorption ◽  
Adsorption Isotherms ◽  
Novel Approach ◽  
Dynamics Simulations

scholarly journals Combining enhanced sampling with experiment-directed simulation of the GYG peptide

2018 ◽  
Vol 17 (03) ◽  
pp. 1840007 ◽  
Author(s):  
Dilnoza B. Amirkulova ◽  
Andrew D. White
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Parallel Tempering ◽  
Collective Variables ◽  
Novel Approach ◽  
Sampling Problem ◽  
Combination Of Methods ◽  
Dynamics Simulations ◽  
Explicit Water

Experiment-directed simulation (EDS) is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics simulations of large systems. This work combines EDS with both the parallel-tempering or parallel-tempering well-tempered ensemble replica-exchange methods to enhance sampling. These methods are demonstrated on the GYG tripeptide in explicit water. The collective variables biased by EDS are chemical shifts, where the set-points are determined by NMR experiments. The results show that it is possible to enhance sampling with either parallel-tempering and parallel-tempering well-tempered ensemble in the EDS method. This combination of methods provides a novel approach for both accurately and exhaustively simulating biological systems.

Adsorption Patterns of Helium on Carbon and Cellulose Nanotubes: Molecular Dynamics Simulations

NANO ◽  
2017 ◽  
Vol 12 (03) ◽  
pp. 1750036
Author(s):  
Roya Majidi ◽  
Hamid Reza Taghiyari ◽  
Mahsa Ekhlasi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Adsorption Capacity ◽  
Adsorption Isotherms ◽  
Isosteric Heat ◽  
Gas Storage ◽  
Type I ◽  
Helium Adsorption ◽  
Different Temperatures ◽  
Dynamics Simulations

Molecular dynamics simulations were performed to study helium adsorption on carbon and cellulose nanotubes. Adsorption isotherms were analyzed at different temperatures and pressures. All adsorption isotherms for carbon and cellulose nanotubes were predicted to be of Langmuir shape type I. Helium adsorption was observed both inside and outside of open-ended tubes. Increasing temperatures caused lower helium adsorption on carbon and cellulose nanotubes. The calculated quantities confirmed that the adsorption capacity of the cellulose nanotube was greater than that of the carbon nanotube. The adsorption capacity, isosteric heat of adsorption and binding energy indicated that cellulose nanotubes as well as carbon nanotubes are proper materials for gas storage.

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