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physics.comp-ph1999
A Minimal Model of B-DNA
Alexey K. Mazur
Recently it has been found that stable and accurate molecular dynamics (MD) of B-DNA duplexes can be obtained in relatively inexpensive computational conditions with the bulk solve…
physics.comp-ph1998
A Rational Approach to Ring Flexibility in Internal Coordinate Dynamics
Alexey K. Mazur
Internal coordinate molecular dynamics (ICMD) is an efficient method for studying biopolymers, but it is readily applicable only to molecules with tree topologies, that is with no…
physics.comp-ph1998
The Hierarchy of Fast Motions in Protein Dynamics
Alexey K. Mazur
For many biological applications of molecular dynamics (MD) the importance of good sampling in conformational space makes it necessary to eliminate the fastest motions from the sys…