Sentence examples for by molecular dynamics using from inspiring English sources

Furthermore, Baudin et al. discussed the structural energies and surface properties over different orientations of the CeO2 by molecular dynamics using NPT ensemble [10, 11, 12].

Transport properties of PDMSM were successfully simulated by molecular dynamics using a very efficient united-atom force field.

Finally, both models were minimized (50,000 steps) and a trajectory of 1 ns was obtained by molecular dynamics using the CHARMM force field [ 70] in NAMD program [ 71].

The final set of distance and angle constraints was used to produce 500 structures in CYANA, and the 100 structures with the smallest constraint violations were refined by molecular dynamics using AMBER 9.

The α-helix of peptides 11438, 33207, 33208 and 33210 were built hydrated and minimized at 310°K by using QUANTA program; then the α-helix stability was studied by molecular dynamics using CHARMM, quantifying the mean number of hydrogen bonds that remains in the α-helix at 0.0, 0.5, 1.0, 1.5 and 2.0 ns during the molecular dynamics of the peptide in water at 310°K.

PEPstrMOD integrates Forcefield_NCAA and Forcefield_PTM force field libraries to handle 147 non-natural residues and 32 types of post-translational modifications respectively by performing molecular dynamics using AMBER.

Amber (Case et al. 2002) force field solution structures of I were generated by free molecular dynamics using the protocols described in the Material and methods.

Two MM2 energy minimizations were followed by an MM2 molecular dynamics using default parameters.

Given a query sequence, PEPstr extracts the secondary structure information using PSIPRED (16) and beta turn types information using BetaTurns (17) and integrates both types of information to obtain an initial structure, which is followed by energy minimization and molecular dynamics using AMBER 11 (11).

These three systems are studied using conductive atomic force microscopy experiments complemented by molecular dynamics simulations using the electrochemical dynamics with implicit degrees of freedom method.

We have studied protein ligand interactions by molecular dynamics simulations using software designed to exploit parallel computing architectures.