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Mathematical Methods of Classical Mechanics

Vladimir I. Arnold
TLDR
In this paper, Newtonian mechanics: experimental facts investigation of the equations of motion, variational principles Lagrangian mechanics on manifolds oscillations rigid bodies, differential forms symplectic manifolds canonical formalism introduction to pertubation theory.
Abstract: 
Part 1 Newtonian mechanics: experimental facts investigation of the equations of motion. Part 2 Lagrangian mechanics: variational principles Lagrangian mechanics on manifolds oscillations rigid bodies. Part 3 Hamiltonian mechanics: differential forms symplectic manifolds canonical formalism introduction to pertubation theory.

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Scalable molecular dynamics with NAMD

James C. Phillips, +9 more
- 01 Dec 2005 - 
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
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Scalable Molecular Dynamics with NAMD

James C. Phillips, +5 more
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Constant pressure molecular dynamics algorithms

Glenn J. Martyna, +2 more
- 01 Sep 1994 - 
TL;DR: In this paper, a modularly invariant equations of motion are derived that generate the isothermal-isobaric ensemble as their phase space averages, and the resulting methods are tested on two problems, a particle in a one-dimensional periodic potential and a spherical model of C60 in the solid/fluid phase.
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Nosé-Hoover chains : the canonical ensemble via continuous dynamics

Glenn J. Martyna, +2 more
- 15 Aug 1992 - 
TL;DR: In this paper, a modification of the Nose-Hoover dynamics is proposed which includes not a single thermostat variable but a chain of variables, Nose chains, which gives the canonical distribution where the simple formalism fails.
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Berry phase effects on electronic properties

Di Xiao, +2 more
- 06 Jul 2010 - 
TL;DR: In this paper, a detailed review of the role of the Berry phase effect in various solid state applications is presented. And a requantization method that converts a semiclassical theory to an effective quantum theory is demonstrated.