List of works - Eric Vanden-Eijnden

A Dynamical Central Limit Theorem for Shallow Neural Networks ⬇️

article by Zhengdao Chen et al published November 2020 in Advances in Neural Information Processing Systems 33

A climbing string method for saddle point search.

scientific article published in April 2013

A statistical mechanics framework captures the packing of monodisperse particles

Asymptotic Theory for the Probability Density Functions in Burgers Turbulence

scientific article published on 27 September 1999

Averaged equation for energy diffusion on a graph reveals bifurcation diagram and thermally assisted reversal times in spin-torque driven nanomagnets

Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics

scientific article published on September 2005

Comparison between Mean Forces and Swarms-of-Trajectories String Methods.

scientific article published in February 2014

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

scientific article

DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator

scientific article

Direct generation of loop-erased transition paths in non-equilibrium reactions

scientific article published on 10 October 2016

Dynamic density functional theory with hydrodynamic interactions and fluctuations ⬇️

scientific article published in June 2014

Dynamical Computation of the Density of States and Bayes Factors Using Nonequilibrium Importance Sampling

scientific article published on 01 April 2019

Emulsion patterns in the wake of a liquid-liquid phase separation front

scientific article published on 21 March 2018

Exact dynamical coarse-graining without time-scale separation ⬇️

scientific article published in July 2014

Exact rate calculations by trajectory parallelization and tilting

scientific article published in July 2009

Finite temperature string method for the study of rare events

scientific article published in April 2005

Fluctuations in the heterogeneous multiscale methods for fast–slow systems

Force-Clamp Analysis Techniques Give Highest Rank to Stretched Exponential Unfolding Kinetics in Ubiquitin ⬇️

scientific article published on November 20, 2012

Free energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials

scientific article

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI ⬇️

scientific article published on February 28, 2011

Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations ⬇️

scientific article

Geometric approach to optimal nonequilibrium control: Minimizing dissipation in nanomagnetic spin systems ⬇️

scientific article published on 25 January 2017

Illustration of transition path theory on a collection of simple examples

scientific article published in August 2006

Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials

scientific article published in February 2013

Infinite switch simulated tempering in force (FISST)

scientific article published on 01 June 2020

Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics

scientific article

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

scientific article

Low-Order Stochastic Mode Reduction for a Realistic Barotropic Model Climate

article

Mapping saddles and minima on free energy surfaces using multiple climbing strings

scientific article published on 01 September 2019

Mapping the network of pathways of CO diffusion in myoglobin

scientific article published in January 2010

Markov state models based on milestoning

scientific article published in May 2011

Markovian milestoning with Voronoi tessellations

scientific article

Metastability of the Nonlinear Wave Equation: Insights from Transition State Theory ⬇️

Mori-Zwanzig formalism as a practical computational tool

scientific article published in January 2010

Multiscale implementation of infinite-swap replica exchange molecular dynamics

scientific article published on 03 October 2016

Multiscale temporal integrators for fluctuating hydrodynamics. ⬇️

scientific article published on 18 December 2014

Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates

scientific article published in November 2005

New methods: general discussion.

scientific article published on 8 December 2016

Noise can play an organizing role for the recurrent dynamics in excitable media

scientific article

Noise-induced mixed-mode oscillations in a relaxation oscillator near the onset of a limit cycle

scientific article published in March 2008

Non-meanfield deterministic limits in chemical reaction kinetics

scientific article published in June 2006

Numerical computation of rare events via large deviation theory

scientific article published on 01 June 2019

On the assumptions underlying milestoning

scientific article published in November 2008

On-the-fly free energy parameterization via temperature accelerated molecular dynamics ⬇️

scientific article published on September 1, 2012

Optimal partition and effective dynamics of complex networks

scholarly article

Optimization and Generalization of Shallow Neural Networks with Quadratic Activation Functions ⬇️

scientific article published in November 2020

Optimized Markov state models for metastable systems ⬇️

scientific article published in July 2016

Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions

scientific article

Parameters as interacting particles: long time convergence and asymptotic error scaling of neural networks ⬇️

Pathways of maximum likelihood for rare events in nonequilibrium systems: application to nucleation in the presence of shear

scientific article published on 9 April 2008

Polymorphism at 129 dictates metastable conformations of the human prion protein N-terminal β-sheet.

scientific article published on 30 September 2016

Regular gaits and optimal velocities for motor proteins

scientific article published on 13 June 2008

Regularity and synchrony in motor proteins

scientific article published in November 2007

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

scientific article published in May 2009

Rogue waves and large deviations in deep sea.

scientific article published on 16 January 2018

Self-guided Langevin dynamics via generalized Langevin equation

scientific article

Simplified and improved string method for computing the minimum energy paths in barrier-crossing events

scientific article published in April 2007

Single-sweep methods for free energy calculations

scientific article published in May 2008

Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain

scholarly article

Some recent techniques for free energy calculations

scientific article published on 01 August 2009

Spatiotemporal Self-Organization of Fluctuating Bacterial Colonies

scientific article published on 3 November 2017

String method for the study of rare events

scientific article published on 12 August, 2002

String method in collective variables: minimum free energy paths and isocommittor surfaces

scientific article published in July 2006

The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models

scientific article published in January 2009

The geometric minimum action method for computing minimum energy paths

scientific article published in February 2008

The heterogeneous multiscale method

scientific article published on 19 April 2012

Transition path theory

scientific article published on January 2014

Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide

scientific article

Transition state theory: variational formulation, dynamical corrections, and error estimates.

scientific article published in November 2005

Transition-path theory and path-finding algorithms for the study of rare events

scientific article published on January 2010

Two distinct mechanisms of coherence in randomly perturbed dynamical systems

scientific article published on 14 September 2005

List of works by Eric Vanden-Eijnden

A Dynamical Central Limit Theorem for Shallow Neural Networks ⬇️

A climbing string method for saddle point search.

A statistical mechanics framework captures the packing of monodisperse particles

Asymptotic Theory for the Probability Density Functions in Burgers Turbulence

Averaged equation for energy diffusion on a graph reveals bifurcation diagram and thermally assisted reversal times in spin-torque driven nanomagnets

Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics

Comparison between Mean Forces and Swarms-of-Trajectories String Methods.

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator

Direct generation of loop-erased transition paths in non-equilibrium reactions

Dynamic density functional theory with hydrodynamic interactions and fluctuations ⬇️

Dynamical Computation of the Density of States and Bayes Factors Using Nonequilibrium Importance Sampling

Emulsion patterns in the wake of a liquid-liquid phase separation front

Exact dynamical coarse-graining without time-scale separation ⬇️

Exact rate calculations by trajectory parallelization and tilting

Finite temperature string method for the study of rare events

Fluctuations in the heterogeneous multiscale methods for fast–slow systems

Force-Clamp Analysis Techniques Give Highest Rank to Stretched Exponential Unfolding Kinetics in Ubiquitin ⬇️

Free energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI ⬇️

Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations ⬇️

Geometric approach to optimal nonequilibrium control: Minimizing dissipation in nanomagnetic spin systems ⬇️

Illustration of transition path theory on a collection of simple examples

Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials

Infinite switch simulated tempering in force (FISST)

Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

Low-Order Stochastic Mode Reduction for a Realistic Barotropic Model Climate

Mapping saddles and minima on free energy surfaces using multiple climbing strings

Mapping the network of pathways of CO diffusion in myoglobin

Markov state models based on milestoning

Markovian milestoning with Voronoi tessellations

Metastability of the Nonlinear Wave Equation: Insights from Transition State Theory ⬇️

Mori-Zwanzig formalism as a practical computational tool

Multiscale implementation of infinite-swap replica exchange molecular dynamics

Multiscale temporal integrators for fluctuating hydrodynamics. ⬇️

Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates

New methods: general discussion.

Noise can play an organizing role for the recurrent dynamics in excitable media

Noise-induced mixed-mode oscillations in a relaxation oscillator near the onset of a limit cycle

Non-meanfield deterministic limits in chemical reaction kinetics

Numerical computation of rare events via large deviation theory

On the assumptions underlying milestoning

On-the-fly free energy parameterization via temperature accelerated molecular dynamics ⬇️

Optimal partition and effective dynamics of complex networks

Optimization and Generalization of Shallow Neural Networks with Quadratic Activation Functions ⬇️

Optimized Markov state models for metastable systems ⬇️

Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions

Parameters as interacting particles: long time convergence and asymptotic error scaling of neural networks ⬇️

Pathways of maximum likelihood for rare events in nonequilibrium systems: application to nucleation in the presence of shear

Polymorphism at 129 dictates metastable conformations of the human prion protein N-terminal β-sheet.

Regular gaits and optimal velocities for motor proteins

Regularity and synchrony in motor proteins

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

Rogue waves and large deviations in deep sea.

Self-guided Langevin dynamics via generalized Langevin equation

Simplified and improved string method for computing the minimum energy paths in barrier-crossing events

Single-sweep methods for free energy calculations

Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain

Some recent techniques for free energy calculations

Spatiotemporal Self-Organization of Fluctuating Bacterial Colonies

String method for the study of rare events

String method in collective variables: minimum free energy paths and isocommittor surfaces

The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models

The geometric minimum action method for computing minimum energy paths

The heterogeneous multiscale method

Transition path theory

Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide

Transition state theory: variational formulation, dynamical corrections, and error estimates.

Transition-path theory and path-finding algorithms for the study of rare events

Two distinct mechanisms of coherence in randomly perturbed dynamical systems