Shear rate dependence of free energy barrier height for phenyl ring rotations in polystyrene based on non-equilibrium molecular dynamics simulations

2012 ◽  
Vol 38 (13) ◽  
pp. 1157-1168
Author(s):  
Wen-Yen Chang ◽  
Rong-Yeu Chang
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>


2021 ◽  
Author(s):  
Martin P. Lautenschlaeger ◽  
Hans Hasse

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.


2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>


Author(s):  
Kalil Bernardino ◽  
Mauro Ribeiro

The effect of shear rate on the viscosity and the structure of 1-ethyl-3-methylimidazolium based ionic liquids with three different anions (tetrafluoroborate, dicyanamide, and bis(trifluoromethylsulfonyl)imide) was studied by means of reverse...


Author(s):  
Zhiting Tian ◽  
Sang Kim ◽  
Ying Sun ◽  
Bruce White

The phonon wave packet technique is used in conjunction with the molecular dynamics simulations to directly observe phonon scattering at material interfaces. The phonon transmission coefficient of nanocomposites is examined as a function of the defect size, thin film thickness, orientation of interface to the heat flow direction. To generalize the results based on phonons in a narrow frequency range and at normal incidence, the effective thermal conductivity of the same nanocomposite structure is calculated using non-equilibrium molecular dynamics simulations for model nanocomposites formed by two mass-mismatched Ar-like solids and heterogeneous Si-SiCO2 systems. The results are compared with the modified effective medium formulation for nanocomposites.


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