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Nonequilibrium statistical mechanics
TLDR
The paradoxes of irreversibility as mentioned in this paper is a well-known problem in nonlinear problems, and it has been studied extensively in the literature for a long time, e.g. in the context of projection operators.Abstract:
1. Brownian Motion and Langevin equations 2. Fokker-Planck equations 3. Master equations 4. Reaction rates 5. Kinetic models 6. Quantum dynamics 7. Linear response theory 8. Projection operators 9. Nonlinear problems 10. The paradoxes of irreversibility Appendicesread more
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TRANSITION PATH SAMPLING: Throwing Ropes Over Rough Mountain Passes, in the Dark
TL;DR: This article reviews the concepts and methods of transition path sampling, which allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states.
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PLUMED: a portable plugin for free-energy calculations with molecular dynamics
Massimiliano Bonomi,Davide Branduardi,Giovanni Bussi,Carlo Camilloni,Davide Provasi,Paolo Raiteri,Davide Donadio,Fabrizio Marinelli,Fabio Pietrucci,Ricardo A. Broglia,Ricardo A. Broglia,Michele Parrinello +11 more
TL;DR: A series of routines that can be interfaced with the most popular classical molecular dynamics codes through a simple patching procedure, which leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available.
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Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking.
TL;DR: This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion, and pays special attention to the ergodicity breaking parameters for the different anomalous stochastic processes.
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Summing up the noise in gene networks
Johan Paulsson,Johan Paulsson +1 more
TL;DR: Two studies show that negative feedback suppresses noise, and three others identify the sources of noise in gene expression, and a simple equation is presented that unifies and extends both the mathematical and biological perspectives.
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Nonequilibrium fluctuations, fluctuation theorems, and counting statistics in quantum systems
TL;DR: Fluctuation theorems (FTs) as discussed by the authors describe some universal properties of nonequilibrium fluctuations and are derived from a quantum perspective by introducing a two-point measurement on the system.