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Equation-free multiscale computation: algorithms and applications

Annual review of physical chemistry, 2009-01, Vol.60 (1), p.321-344

2009

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From Discrete to Continuum Models of Three-Dimensional Deformations in Epithelial Sheets

Biophysical journal, 2015-07, Vol.109 (1), p.154-163

2015

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Shape Transformations of Epithelial Shells

Biophysical journal, 2016-04, Vol.110 (7), p.1670-1678

2016

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Learning emergent partial differential equations in a learned emergent space

Nature communications, 2022-06, Vol.13 (1), p.3318-3318, Article 3318

2022

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Dynamics of Inductive ERK Signaling in the Drosophila Embryo

Current biology, 2015-06, Vol.25 (13), p.1784-1790

2015

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Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps

Proceedings of the National Academy of Sciences - PNAS, 2009-09, Vol.106 (38), p.16090-16095

2009

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Systematic determination of order parameters for chain dynamics using diffusion maps

Proceedings of the National Academy of Sciences - PNAS, 2010-08, Vol.107 (31), p.13597-13602

2010

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Systematic characterization of protein folding pathways using diffusion maps: application to Trp-cage miniprotein

The Journal of chemical physics, 2015-02, Vol.142 (8), p.085101-085101

2015

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Inherent noise can facilitate coherence in collective swarm motion

Proceedings of the National Academy of Sciences - PNAS, 2009-04, Vol.106 (14), p.5464-5469

2009

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Limits of entrainment of circadian neuronal networks

Chaos (Woodbury, N.Y.), 2023-01, Vol.33 (1), p.013137

2023

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Bistability and oscillations in the Huang-Ferrell model of MAPK signaling

PLoS computational biology, 2007-09, Vol.3 (9), p.1819-1826

2007

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Dissipative particle dynamics simulations of polymer-protected nanoparticle self-assembly

The Journal of chemical physics, 2011-11, Vol.135 (18), p.184903-184903-10

2011

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Synthesizing developmental trajectories

PLoS computational biology, 2017-09, Vol.13 (9), p.e1005742-e1005742

2017

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Substrate-Dependent Control of ERK Phosphorylation Can Lead to Oscillations

Biophysical journal, 2011-12, Vol.101 (11), p.2572-2581

2011

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Coarse-grained analysis of stochasticity-induced switching between collective motion states

Proceedings of the National Academy of Sciences - PNAS, 2007-04, Vol.104 (14), p.5931-5935

2007

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Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

The Journal of chemical physics, 2014-09, Vol.141 (11), p.114102-114102

2014

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Optical imaging and control of genetically designated neurons in functioning circuits

Annual review of neuroscience, 2005-01, Vol.28 (1), p.533-563

2005

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Programmable heating and quenching for efficient thermochemical synthesis

Nature (London), 2022-05, Vol.605 (7910), p.470-476

2022

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Learning black- and gray-box chemotactic PDEs/closures from agent based Monte Carlo simulation data

Journal of mathematical biology, 2023-07, Vol.87 (1), p.15-15, Article 15

2023

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"Coarse" Stability and Bifurcation Analysis Using Time-Steppers: A Reaction-Diffusion Example

Proceedings of the National Academy of Sciences - PNAS, 2000-08, Vol.97 (18), p.9840-9843

2000

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Local conformal autoencoder for standardized data coordinates

Proceedings of the National Academy of Sciences - PNAS, 2020-12, Vol.117 (49), p.30918-30927

2020

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Kinetic Analysis of Nanostructures Formed by Enzyme-Instructed Intracellular Assemblies against Cancer Cells

ACS nano, 2018-04, Vol.12 (4), p.3804-3815

2018

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Coarse nonlinear dynamics and metastability of filling-emptying transitions : Water in carbon nanotubes

Physical review letters, 2005-09, Vol.95 (13), p.130603.1-130603.4, Article 130603

2005

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Chimeras in random non-complete networks of phase oscillators

Chaos (Woodbury, N.Y.), 2012-03, Vol.22 (1), p.013132-013132-9

2012

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Water Slug Formation and Motion in Gas Flow Channels: The Effects of Geometry, Surface Wettability, And Gravity

Langmuir, 2013-08, Vol.29 (31), p.9918-9934

2013

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Equation-free multiscale computation: algorithms and applications

From Discrete to Continuum Models of Three-Dimensional Deformations in Epithelial Sheets

Shape Transformations of Epithelial Shells

Learning emergent partial differential equations in a learned emergent space

Dynamics of Inductive ERK Signaling in the Drosophila Embryo

Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps

Systematic determination of order parameters for chain dynamics using diffusion maps

Systematic characterization of protein folding pathways using diffusion maps: application to Trp-cage miniprotein

Inherent noise can facilitate coherence in collective swarm motion

Limits of entrainment of circadian neuronal networks

Bistability and oscillations in the Huang-Ferrell model of MAPK signaling

Dissipative particle dynamics simulations of polymer-protected nanoparticle self-assembly

Synthesizing developmental trajectories

Substrate-Dependent Control of ERK Phosphorylation Can Lead to Oscillations

Coarse-grained analysis of stochasticity-induced switching between collective motion states

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

Optical imaging and control of genetically designated neurons in functioning circuits

Programmable heating and quenching for efficient thermochemical synthesis

Learning black- and gray-box chemotactic PDEs/closures from agent based Monte Carlo simulation data

"Coarse" Stability and Bifurcation Analysis Using Time-Steppers: A Reaction-Diffusion Example

Local conformal autoencoder for standardized data coordinates

Kinetic Analysis of Nanostructures Formed by Enzyme-Instructed Intracellular Assemblies against Cancer Cells

Coarse nonlinear dynamics and metastability of filling-emptying transitions : Water in carbon nanotubes

Chimeras in random non-complete networks of phase oscillators

Water Slug Formation and Motion in Gas Flow Channels: The Effects of Geometry, Surface Wettability, And Gravity

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