Effective dynamics along given reaction coordinates, and reaction rate theory

Finding Transition Pathways on Manifolds

(2016) Tiejun Li et al.   MULTISCALE MODELING & SIMULATION

Ergodic theorem, ergodic theory, and statistical mechanics

(2015) Calvin C. Moore   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exact dynamical coarse-graining without time-scale separation

(2014) Jianfeng Lu et al.   JOURNAL OF CHEMICAL PHYSICS

Construction of dissipative particle dynamics models for complex fluids via the Mori–Zwanzig formulation

(2014) Zhen Li et al.   Soft Matter

Approximating selected non-dominant timescales by Markov state models

(2013) Marco Sarich et al.   Communications in Mathematical Sciences

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Microscopic derivation of particle-based coarse-grained dynamics

(2013) Sergei Izvekov   JOURNAL OF CHEMICAL PHYSICS

A decomposition of irreversible diffusion processes without detailed balance

(2013) Hong Qian   JOURNAL OF MATHEMATICAL PHYSICS

A Micro-Macro Parareal Algorithm: Application to Singularly Perturbed Ordinary Differential Equations

(2013) Frédéric Legoll et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Estimating the Eigenvalue Error of Markov State Models

(2012) Natasa Djurdjevac et al.   MULTISCALE MODELING & SIMULATION

Climate science in the tropics: waves, vortices and PDEs

(2012) Boualem Khouider et al.   NONLINEARITY

The heterogeneous multiscale method

(2012) Assyr Abdulle et al.   ACTA NUMERICA

Potential and flux decomposition for dynamical systems and non-equilibrium thermodynamics: Curvature, gauge field, and generalized fluctuation-dissipation theorem

(2011) Haidong Feng et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Ergodic and nonergodic processes coexist in the plasma membrane as observed by single-molecule tracking

(2011) A. V. Weigel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reduced models for binocular rivalry

(2010) Carlo R. Laing et al.   JOURNAL OF COMPUTATIONAL NEUROSCIENCE

On the Approximation Quality of Markov State Models

(2010) Marco Sarich et al.   MULTISCALE MODELING & SIMULATION

Effective dynamics using conditional expectations

(2010) Frédéric Legoll et al.   NONLINEARITY

Mori–Zwanzig formalism as a practical computational tool

(2009) Carmen Hijón et al.   FARADAY DISCUSSIONS

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Some recent techniques for free energy calculations

(2009) Eric Vanden-Eijnden   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computing generalized Langevin equations and generalized Fokker-Planck equations

(2009) E. Darve et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maximum likelihood drift estimation for multiscale diffusions

(2009) A. Papavasiliou et al.   STOCHASTIC PROCESSES AND THEIR APPLICATIONS

Equation-Free Multiscale Computation: Algorithms and Applications

(2008) Ioannis G. Kevrekidis et al.   Annual Review of Physical Chemistry

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

An applied mathematics perspective on stochastic modelling for climate

(2008) A. J Majda et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations

(2008) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA