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Statistical Mechanics: Theory and Molecular Simulation
1. Introduction 2. Classical Mechanics 3. Theoretical Foundations of Classical Statistical Mechanics 4. The Microcanonical Ensemble and Introduction to Molecular Dynamics 5. The Canonical Ensemble 6.Expand
Reversible multiple time scale molecular dynamics
TLDR
It is shown how the new RESPA methods are related to predictor–corrector integrators and how these methods can be used to accelerate the integration of the equations of motion of systems with Nose thermostats. Expand
Nosé-Hoover chains : the canonical ensemble via continuous dynamics
Nose has derived a set of dynamical equations that can be shown to give canonically distributed positions and momenta provided the phase space average can be taken into the trajectory average, i.e.,Expand
The nature of the hydrated excess proton in water
Explanations for the anomalously high mobility of protons in liquid water began with Grotthuss's idea, of ‘structural diffusion’ nearly two centuries ago. Subsequent explanations have refined thisExpand
Explicit reversible integrators for extended systems dynamics
Explicit reversible integrators, suitable for use in large-scale computer simulations, are derived for extended systems generating the canonical and isothermal-isobaric ensembles. The new methods areExpand
Aqueous basic solutions: hydroxide solvation, structural diffusion, and comparison to the hydrated proton.
TLDR
Many hydrogen-bonded liquids, molecular solids, and lowdimensional systems support anomalous diffusion mechanisms of topological charge defects created by the addition or removal of protons, including the “classic” cases of aqueous acidic and basic solutions. Expand
Non-Hamiltonian molecular dynamics: Generalizing Hamiltonian phase space principles to non-Hamiltonian systems
The use of non-Hamiltonian dynamical systems to perform molecular dynamics simulation studies is becoming standard. However, the lack of a sound statistical mechanical foundation for non-HamiltonianExpand
On the classical statistical mechanics of non-Hamiltonian systems
A consistent classical statistical mechanical theory of non-Hamiltonian dynamical systems is presented. It is shown that compressible phase space flows generate coordinate transformations with aExpand
Enol tautomers of Watson-Crick base pair models are metastable because of nuclear quantum effects.
TLDR
By accounting for nuclear quantum effects explicitly through Car-Parrinello path integral molecular dynamics calculations, this work finds the tautomeric enol form to be dynamically metastable, with lifetimes too insignificant to be implicated in DNA damage. Expand
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