Beyond the Lennard-Jones model: a simple and accurate potential function probed by high resolution scattering data useful for molecular dynamics simulations

2008 ◽  
Vol 10 (36) ◽  
pp. 5489 ◽  
Author(s):  
Fernando Pirani ◽  
Simona Brizi ◽  
Luiz F. Roncaratti ◽  
Piergiorgio Casavecchia ◽  
David Cappelletti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Molecular Dynamics Simulations ◽  
Potential Function ◽  
Scattering Data ◽  
Lennard Jones ◽  
Jones Model ◽  
Dynamics Simulations

scholarly journals Studies of Conformational Changes of Tubulin Induced by Interaction with Kinesin Using Atomistic Molecular Dynamics Simulations

2021 ◽  
Vol 22 (13) ◽  
pp. 6709
Author(s):  
Xiao-Xuan Shi ◽  
Peng-Ye Wang ◽  
Hong Chen ◽  
Ping Xie
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Binding Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Weak Interactions ◽  
Molecular Motor ◽  
Structural Data ◽  
Calculated Binding Energy ◽  
Dynamics Simulations

The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin head and tubulin are studied on the basis of the available high-resolution structural data. We found that the strong interaction can induce rapid large conformational changes of the tubulin, whereas the weak interaction cannot. Furthermore, we found that the large conformational changes of the tubulin have a significant effect on the interaction of the tubulin with the head in the weak-microtubule-binding ADP state. The calculated binding energy of the ADP-bound head to the tubulin with the large conformational changes is only about half that of the tubulin without the conformational changes.

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.

scholarly journals Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

2020 ◽  
Vol 16 (4) ◽  
pp. e1007870 ◽  
Author(s):  
Andreas Haahr Larsen ◽  
Yong Wang ◽  
Sandro Bottaro ◽  
Sergei Grudinin ◽  
Lise Arleth ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Small Angle ◽  
Scattering Data ◽  
X Ray ◽  
Dynamics Simulations
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