Temperature and pressure effects on GFP mutants: explaining spectral changes by molecular dynamics simulations and TD-DFT calculations

2016 ◽  
Vol 18 (18) ◽  
pp. 12828-12838 ◽  
Author(s):  
Emanuela Jacchetti ◽  
Edi Gabellieri ◽  
Patrizia Cioni ◽  
Ranieri Bizzarri ◽  
Riccardo Nifosì
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Function ◽  
Pressure Effects ◽  
Spectral Changes ◽  
Td Dft ◽  
Structural Perturbations ◽  
Temperature And Pressure ◽  
Dynamics Simulations ◽  
Temperature And Pressure Effects

By combining spectroscopic measurements under high pressure with molecular dynamics simulations and quantum mechanics calculations we investigate how sub-angstrom structural perturbations are able to tune protein function.

scholarly journals A NOVEL DESIGN OF PERISTALTIC CARBON NANO PUMP AND AN ANALYSIS OF HELIUM FLOW

2021 ◽  
Vol 55 (6) ◽  
Author(s):  
M. Gokhan Günay ◽  
Ubade Kemerli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Pump Design ◽  
Helium Atoms ◽  
Multi Walled Carbon Nanotubes ◽  
Temperature And Pressure ◽  
Dynamics Simulations ◽  
Walled Carbon Nanotubes ◽  
Novel Design ◽  
Main Carbon

A novel nano-scale pump that can transport atoms or small molecules with a peristaltic motion is designed. It is proven by molecular-dynamics simulations that the introduced nano-pump design works properly. The designed nano-pump consists of one main carbon nanotube named the flow tube and two rotors where multi-walled carbon nanotubes are attached. The pumping of helium atoms by the designed peristaltic carbon nano-pump is investigated by molecular-dynamics simulations. For varying rotor speeds and blade counts, time-averaged velocity, temperature, and pressure results of pumped helium atoms are calculated, and relationships between them are modeled as polynomial surfaces. The results showed that rotor frequency increases the velocity of helium linearly and the temperature and pressure of helium non-linearly. Furthermore, the blade count of the proposed mechanism does not substantially affect the velocity as per the previous studies in the literature.

Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure

2013 ◽  
Vol 139 (16) ◽  
pp. 164106 ◽  
Author(s):  
Ross A. Lippert ◽  
Cristian Predescu ◽  
Douglas J. Ierardi ◽  
Kenneth M. Mackenzie ◽  
Michael P. Eastwood ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Constant Temperature ◽  
Efficient Integration ◽  
Temperature And Pressure ◽  
Dynamics Simulations

scholarly journals Towards Protein Function Prediction Based on Molecular Dynamics Simulations

2021 ◽  
Vol 120 (3) ◽  
pp. 80a
Author(s):  
Nicolai Kozlowski ◽  
Malte Schäffner ◽  
Andreas Volkhardt ◽  
Helmut Grubmuller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Function ◽  
Protein Function Prediction ◽  
Function Prediction ◽  
Dynamics Simulations
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