Thermodynamics-based methods, including molecular dynamics (MD) simulations, enable our understanding of protein's conformational detail at the atomic level. Proteins are flexible molecules. MD simulation provides information about the dynamic perturbations that occur in a protein or protein–ligand complex...
Molecular Dynamics (MD) simulations of uniaxial tension at nanolevel have been carried out at a constant rate of loading (500ms−1) on some single-crystal cubic metals, both FCC (Al, Cu, and Ni) and BCC (Fe, Cr, and W) to investigate the nature of deformation and fracture. Failure ...
Molecular dynamics (MD) simulations of the dependence of C–C bond lengths and bond angles on the tensile strain in single-wall carbon nanotubes (SWCNT)Molecular dynamics (MD) simulations of the dependence of C–C bond lengths and bond angles on the tensile strain in single-wall carbon nanotub...
Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. The early view of proteins as relatively rigid structures has been replaced by a dynamic model in which the internal motions and resulting conformational change...
dynamic detachment behavior is studied using MD simulations. Simulation Methods The MD simulations have been performed using a modified version of the MDCASK code [4], implemented with the Finnis-Sinclair N-body potential to describe the atomic interactions in Mo [5]. The ...
3.3 Molecular dynamic simulations results In order to understand the conformational changes and evaluate the binding of THN_RD9 against Mtb ATP synthase (PDB ID: 7NK7), we have carried out MD simulation for a period of 100 ns for THN_RD9-Mtb ATP synthase complex. The simulation was evaluated...
In this study, a molecular dynamic (MD) simulation is employed to determine the thermodynamic properties of asphalt binder components, namely, asphaltene and resin, before and after oxidative aging. For oxidative aging of asphaltenes, the percentage of oxygen considered in MD simulations is 0.1, 1...
These membrane models exhibit the structural and dynamic features of membrane bilayer, which have been investigated and verified by MDS31,32. Cholesterol is one of the major components of eukaryotic cell membrane and also reported to have a large effect on the membrane permeability33. Generally ...
The difference between the structure factors of the dynamic and the harmonic Fibonacci chain lies in the temperature dependence of the phonon line width. If a bias is introduced in the well depth, dispersionless optic phonon bands split off. 展开 ...
The structure was kindly provided to us by Srirupa Chakraborty46 - see the paper for detailed information of structure and molecular dynamic flexible fitting to EM-cryo map. In our figures containing residue indexes on the axis, we also highlight key structural motifs of kinesin following the ...