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Molecular dynamics simulations of xDNA
Biopolymers, 2009AbstractxDNA is a modified DNA, which contains natural as well as expanded bases. Expanded bases are generated by the addition of a benzene spacer to the natural bases. A set of AMBER force‐field parameters were derived for the expanded bases and the structural dynamics of the xDNA decamer (xT5′ G xT A xC xG C xA xG T3′) · (xA5′ C T xG C G xT A xC A3′)
Mathew K, Varghese +3 more
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Molecular Dynamics Simulation of Nanoindentation
2004Molecular dynamics simulations are used to investigate the nucleation and dynamics of dislocations during nanoindentation of a (111) FCC plane. The core structure around the dislocation is visualized by coloring the atoms with deviating coordination number and its Burgers vector is automatically determined.
Michielsen, K +3 more
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This is a course document for introducing molecular dynamics originally developed as part of the Master in Bioinformatics curriculum at the Higher Institute of Biotechnology of Sidi Thabet, under the auspices of the University of Manouba, Tunisia, but could serve any person interested in structural bioinformatics and molecular modeling.
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2005
Abstract So far most of our discussion of energy storage and energy transport has been built on the reciprocal space: the dispersion relations between wavevectors and frequencies. We discarded the history of the motion of individual particles (electrons and atoms) and focused on their collective modal behavior.
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Abstract So far most of our discussion of energy storage and energy transport has been built on the reciprocal space: the dispersion relations between wavevectors and frequencies. We discarded the history of the motion of individual particles (electrons and atoms) and focused on their collective modal behavior.
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