Temperature and Pressure Effects on Local Structure and Chain Packing incis-1,4-Polybutadiene from Detailed Molecular Dynamics Simulations

2006 ◽  
Vol 15 (5) ◽  
pp. 381-393 ◽  
Author(s):  
Georgia Tsolou ◽  
Vagelis A. Harmandaris ◽  
Vlasis G. Mavrantzas
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Local Structure ◽  
Pressure Effects ◽  
Chain Packing ◽  
Temperature And Pressure ◽  
Dynamics Simulations ◽  
Temperature And Pressure Effects

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.

scholarly journals Shear-rate dependence of thermodynamic properties of the Lennard-Jones truncated and shifted fluid by molecular dynamics simulations

2021 ◽  
Author(s):  
Martin P. Lautenschlaeger ◽  
Hans Hasse
Keyword(s):  
Molecular Dynamics ◽  
Shear Stress ◽  
Shear Rate ◽  
Molecular Dynamics Simulations ◽  
Local Structure ◽  
Rate Dependence ◽  
Lennard Jones ◽  
Fluid Properties ◽  
Dynamics Simulations ◽  
Shear Rate Dependence

It was shown recently that using the two-gradient method, thermal, caloric, and transport properties of fluids under quasi-equilibrium conditions can be determined simultaneously from nonequilibrium molecular dynamics simulations. It is shown here that the influence of shear stresses on these properties can also be studied using the same method. The studied fluid is described by the Lennard-Jones truncated and shifted potential with the cut-off radius r*c = 2.5σ. For a given temperature T and density ρ, the influence of the shear rate on the following fluid properties is determined: pressure p, internal energy u, enthalpy h, isobaric heat capacity cp, thermal expansion coefficient αp, shear viscosity η, and self-diffusion coefficient D. Data for 27 state points in the range of T ∈ [0.7, 8.0] and ρ ∈ [0.3, 1.0] are reported for five different shear rates (γ ̇ ∈ [0.1,1.0]). Correlations for all properties are provided and compared with literature data. An influence of the shear stress on the fluid properties was found only for states with low temperature and high density. The shear-rate dependence is caused by changes in the local structure of the fluid which were also investigated in the present work. A criterion for identifying the regions in which a given shear stress has an influence on the fluid properties was developed. It is based on information on the local structure of the fluid. For the self-diffusivity, shear-induced anisotropic effects were observed and are discussed.

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 Local structure of dilute aqueous DMSO solutions, as seen from molecular dynamics simulations

2017 ◽  
Vol 146 (23) ◽  
pp. 234507 ◽  
Author(s):  
Abdenacer Idrissi ◽  
Bogdan A. Marekha ◽  
Mohammed Barj ◽  
François Alexandre Miannay ◽  
Toshiyuki Takamuku ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Local Structure ◽  
Aqueous Dmso ◽  
Dynamics Simulations
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