Lista de obras - Eric Vanden-Eijnden - Dominio Público Uruguay

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.

artículo científico publicado en 2013

A statistical mechanics framework captures the packing of monodisperse particles

Asymptotic Theory for the Probability Density Functions in Burgers Turbulence

artículo científico publicado en 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

artículo científico

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

artículo científico publicado en 2014

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

artículo científico publicado en 2009

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

artículo científico publicado en 2010

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

artículo científico publicado en 2016

Dynamic density functional theory with hydrodynamic interactions and fluctuations ⬇️

artículo científico publicado en 2014

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

artículo científico publicado en 2019

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

artículo científico publicado en 2018

Exact dynamical coarse-graining without time-scale separation ⬇️

artículo científico publicado en 2014

Exact rate calculations by trajectory parallelization and tilting

artículo científico publicado en 2009

Finite temperature string method for the study of rare events

artículo científico publicado en 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 ⬇️

artículo científico publicado el 20 de noviembre de 2012

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

artículo científico publicado en 2009

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

artículo científico publicado el 28 de febrero de 2011

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

artículo científico publicado en 2015

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

artículo científico publicado en 2017

Illustration of transition path theory on a collection of simple examples

artículo científico publicado en 2006

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

artículo científico publicado el 28 de febrero de 2013

Infinite switch simulated tempering in force (FISST)

artículo científico publicado en 2020

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

artículo científico publicado en 2016

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

artículo científico publicado en 2010

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

article

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

artículo científico publicado en 2019

Mapping the network of pathways of CO diffusion in myoglobin

artículo científico publicado en 2010

Markov state models based on milestoning

artículo científico publicado en 2011

Markovian milestoning with Voronoi tessellations

artículo científico publicado en 2009

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

Mori-Zwanzig formalism as a practical computational tool

artículo científico publicado en 2010

Multiscale implementation of infinite-swap replica exchange molecular dynamics

artículo científico publicado en 2016

Multiscale temporal integrators for fluctuating hydrodynamics. ⬇️

artículo científico publicado en 2014

Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates

artículo científico publicado en 2005

New methods: general discussion.

artículo científico publicado en 2016

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

artículo científico publicado en 2007

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

artículo científico publicado en 2008

Non-meanfield deterministic limits in chemical reaction kinetics

artículo científico publicado en 2006

Numerical computation of rare events via large deviation theory

scientific article published on 01 June 2019

On the assumptions underlying milestoning

artículo científico publicado en 2008

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

artículo científico publicado el 1 de septiembre de 2012

Optimal partition and effective dynamics of complex networks

scholarly article

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

artículo científico publicado en 2020

Optimized Markov state models for metastable systems ⬇️

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2008

Regularity and synchrony in motor proteins

artículo científico publicado en 2007

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

artículo científico publicado en 2009

Rogue waves and large deviations in deep sea.

artículo científico publicado en 2018

Self-guided Langevin dynamics via generalized Langevin equation

artículo científico publicado en 2015

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

artículo científico publicado en 2007

Single-sweep methods for free energy calculations

artículo científico publicado en 2008

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

artículo científico publicado en 2007

Some recent techniques for free energy calculations

artículo científico publicado en 2009

Spatiotemporal Self-Organization of Fluctuating Bacterial Colonies

artículo científico publicado en 2017

String method for the study of rare events

artículo científico publicado en 2002

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

artículo científico publicado en 2006

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

artículo científico publicado en 2009

The geometric minimum action method for computing minimum energy paths

artículo científico publicado en 2008

The heterogeneous multiscale method

artículo científico publicado en 2012

Transition path theory

artículo científico publicado en 2014

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

artículo científico publicado en 2005

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

artículo científico publicado en 2005

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

artículo científico publicado en 2010

Two distinct mechanisms of coherence in randomly perturbed dynamical systems

artículo científico publicado en 2005

Lista de obras de 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