Molecular dynamic simulation with the Green Kubo method was employed to compute thermal conductivity of nanofluids in aggregated and non-aggregated states. Results show that the thermal conductivity enhancement of nanofluids in an aggregated state is higher than in a non-aggregated state, by up to ...
2.9.1 Molecular dynamic simulation Molecular dynamics (MD) simulation was carried out using GROMACS 2022.2. The following steps were utilized. 2.9.2 Preparation of enzyme The three-dimensional (3D) model of the ligand–protein complex was exported to.pdb format using Pymol. The dynamic behavior ...
Employing molecular dynamics simulations, we explored the dynamic processes of peptide-receptor interactions. We uncovered a crucial salt bridge between parent peptide and GLP-1R/GIPR at K20, a feature not discernible in cryo-electron microscopy structures. Building upon these insights, we developed ...
Virtual screening against Delta variant RBD, followed by molecular dynamics (MD) simulation and MM-GBSA binding energy calculations, to better estimate the binding affinity, has led to the identification of several lead candidates that possess potential therapeutic activity against Delta and may be ...
This paper investigates the dynamic behaviour of a hard needle-sphere binary system using a novel numerical technique called the Newton homotopy continuation (NHC) method. This mixture is representative of a polymer melt where both long chain molecules and monomers coexist. Since the intermolecular ...
functions; empirical parameterization of the force field; modifications in the force field for structure determination; internal dynamics and average structures; assessment of the simulation procedure; and effect of crystallographic atomic resolution on structural stability during molecular-dynamics simulation. ...
This situation was considered when the user already has Gromacs installed in his laboratory and only wants to facilitate the execution of the simulation commands sequence. But if the researcher chooses to execute the complete dynamic on the web server, just click on 'Execute' and the server will...
Initial simulations confirmed the role of ARG451 and TRP535 in the dynamic regulation of SMO. These data then were used as a reference for understanding the molecular dynamics of SMO-BST complex and thus predicted its mechanism of action.
Fig. 3: The molecular dynamics simulation results of GeTe and Li10GeP2S12using the proposed NVNMD. In panela, the phase transition processes of GeTe is reproduced, which contains initial crystalline phase (I), liquid phase (II), amorphous phase (III), and recrystallization (IV) shown in the...
However, within the reduced simulation of Tvfd a profound loop-cap transition into the redox center occurred within 6-ns of the start of the simulation and remained open throughout the rest of the 20-ns simulation. This large opening seen in the simulations supports the hypothesis that the ...