Bulk viscosity of the Lennard‐Jones fluid for a wide range of states computed by equilibrium molecular dynamics

1987 ◽  
Vol 87 (12) ◽  
pp. 7195-7198 ◽  
Author(s):  
C. Hoheisel ◽  
R. Vogelsang ◽  
M. Schoen
Keyword(s):  
Molecular Dynamics ◽  
Bulk Viscosity ◽  
Lennard Jones ◽  
Wide Range

Transport coefficients of the Lennard–Jones fluid by molecular dynamics

1986 ◽  
Vol 64 (7) ◽  
pp. 773-781 ◽  
Author(s):  
D. M. Heyes
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Bulk Viscosity ◽  
Shear Viscosity ◽  
Diffusion Coefficients ◽  
Transport Coefficients ◽  
The Self ◽  
Nonequilibrium Molecular Dynamics ◽  
Self Diffusion ◽  
Lennard Jones

New nonequilibrium molecular dynamics (MD) calculations of the shear viscosity, bulk viscosity, and thermal conductivity are presented. Together with the self-diffusion coefficients obtained from equilibrium MD, the success of the Dymond–Batchinski expressions for the density and temperature dependence of these transport coefficients is demonstrated.The shear viscosity and self-diffusion coefficients are very good probes for the approach point of the solid-to-liquid phase change. The bulk viscosity and thermal conductivity are less useful in this respect.

scholarly journals Transport Properties of the Lennard-Jones Truncated and Shifted Fluid from Non-equilibrium Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Martin P. Lautenschläger ◽  
Hans Hasse
Keyword(s):  
Molecular Dynamics ◽  
Simulation Method ◽  
Self Diffusion ◽  
Lennard Jones ◽  
Wide Range ◽  
Data Correlations ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations ◽  
Good Agreement ◽  
Non Equilibrium

The thermal conductivity λ, shear viscosity η, and self-diffusion coefficient D of the Lennard-Jones fluid truncated and shifted at the cut-off radius rc=2.5σ (LJTS fluid) are determined for a wide range of liquid and supercritical states (T*=[0.6,10.0] and ρ*=[0.2,1.2]). The simulations are carried out using a non-equilibrium molecular dynamics (NEMD) method that was introduced recently and in which two gradients are applied simultaneously. It is shown that the two-gradient method is well-suited for studies of liquid and supercritical states. Data for λ, η, and D for about 350 state points are reported. Two variants of the simulation method, which differ in the accuracy and efficiency, are explored and found to yield consistent data. Correlations for λ, η, and Dρ of the LJTS fluid are provided. The data and the correlations are compared to literature data of Lennard-Jones (LJ) type fluids and good agreement is observed. The truncation of the LJ potential causes a slight increase in D, while it has no significant effect on λ and η.

Modeling the establishment of a saturated state of argon by molecular dynamics

2011 ◽  
Vol 8 (1) ◽  
pp. 172-181
Author(s):  
V.L. Malyshev ◽  
C.I. Mikhaylenko ◽  
E.F. Moiseeva
Keyword(s):  
Mathematical Modeling ◽  
Experimental Data ◽  
Molecular Dynamics ◽  
Equation Of State ◽  
Saturation State ◽  
Small Deviations ◽  
Lennard Jones ◽  
Wide Range ◽  
Molecular Dynamics Methods ◽  
Range Equation

Mathematical modeling of evaporation of liquid and condensation of gaseous argon is performed for small deviations from the saturation state. The simulation is performed using molecular dynamics methods, using the Lennard-Jones interaction potential. The thermodynamic parameters are calculated from the wide-range equation of state. The results of the calculations are compared with known experimental data.

Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump

2017 ◽  
Author(s):  
Jana Shen ◽  
Zhi Yue ◽  
Helen Zgurskaya ◽  
Wei Chen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Transmembrane Domain ◽  
Conformational Transition ◽  
Conformational Dynamics ◽  
Proton Release ◽  
Intrinsic Resistance ◽  
Constant Ph ◽  
Wide Range ◽  
Constant Ph Molecular Dynamics

AcrB is the inner-membrane transporter of E. coli AcrAB-TolC tripartite efflux complex, which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB pumps a wide range of toxic substrates by utilizing the proton gradient between periplasm and cytoplasm. Crystal structures of AcrB revealed three distinct conformational states of the transport cycle, substrate access, binding and extrusion, or loose (L), tight (T) and open (O) states. However, the specific residue(s) responsible for proton binding/release and the mechanism of proton-coupled conformational cycling remain controversial. Here we use the newly developed membrane hybrid-solvent continuous constant pH molecular dynamics technique to explore the protonation states and conformational dynamics of the transmembrane domain of AcrB. Simulations show that both Asp407 and Asp408 are deprotonated in the L/T states, while only Asp408 is protonated in the O state. Remarkably, release of a proton from Asp408 in the O state results in large conformational changes, such as the lateral and vertical movement of transmembrane helices as well as the salt-bridge formation between Asp408 and Lys940 and other sidechain rearrangements among essential residues.Consistent with the crystallographic differences between the O and L protomers, simulations offer dynamic details of how proton release drives the O-to-L transition in AcrB and address the controversy regarding the proton/drug stoichiometry. This work offers a significant step towards characterizing the complete cycle of proton-coupled drug transport in AcrB and further validates the membrane hybrid-solvent CpHMD technique for studies of proton-coupled transmembrane proteins which are currently poorly understood. <p><br></p>

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

scholarly journals Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

2021 ◽  
pp. 1-12
Author(s):  
Haiyan Li ◽  
Zanxia Cao ◽  
Guodong Hu ◽  
Liling Zhao ◽  
Chunling Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Binding Protein ◽  
Network Models ◽  
Md Simulations ◽  
Protein Domain ◽  
Opening Angle ◽  
Conformation Changes ◽  
Wide Range ◽  
Ribose Binding Protein

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

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