Simultaneous coherent structure coloring facilitates interpretable clustering of scientific data by amplifying dissimilarity

A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models

(2018) Brooke E. Husic et al.   Journal of Chemical Theory and Computation

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

MoleculeNet: a benchmark for molecular machine learning

(2018) Zhenqin Wu et al.   Chemical Science

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

(2018) Erol S. Kavvas et al.   Nature Communications

Rapid Water Transport by Long-Lasting Modon Eddy Pairs in the Southern Midlatitude Oceans

(2017) Chris W. Hughes et al.   GEOPHYSICAL RESEARCH LETTERS

Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations

(2017) Hao Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Ward Clustering Improves Cross-Validated Markov State Models of Protein Folding

(2017) Brooke E. Husic et al.   Journal of Chemical Theory and Computation

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

(2017) Lee-Ping Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Phytoplankton can actively diversify their migration strategy in response to turbulent cues

(2017) Anupam Sengupta et al.   NATURE

A coherent structure approach for parameter estimation in Lagrangian Data Assimilation

(2017) John Maclean et al.   PHYSICA D-NONLINEAR PHENOMENA

Coherent structure colouring: identification of coherent structures from sparse data using graph theory

(2016) Kristy L. Schlueter-Kuck et al.   JOURNAL OF FLUID MECHANICS

Pressure evolution in the shear layer of forming vortex rings

(2016) Kristy Schlueter-Kuck et al.   Physical Review Fluids

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Lagrangian based methods for coherent structure detection

(2015) Michael R. Allshouse et al.   CHAOS

A rough-and-ready cluster-based approach for extracting finite-time coherent sets from sparse and incomplete trajectory data

(2015) Gary Froyland et al.   CHAOS

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

(2015) Frank Noé et al.   Journal of Chemical Theory and Computation

A Data–Driven Approximation of the Koopman Operator: Extending Dynamic Mode Decomposition

(2015) Matthew O. Williams et al.   JOURNAL OF NONLINEAR SCIENCE

fastcluster: Fast Hierarchical, Agglomerative Clustering Routines forRandPython

(2015) Daniel Müllner   Journal of Statistical Software

Cluster-based reduced-order modelling of a mixing layer

(2014) Eurika Kaiser et al.   JOURNAL OF FLUID MECHANICS

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

(2013) Frank Noé et al.   MULTISCALE MODELING & SIMULATION

The impact of advective transport by the South Indian Ocean Countercurrent on the Madagascar plankton bloom

(2012) F. Huhn et al.   GEOPHYSICAL RESEARCH LETTERS

Simple few-state models reveal hidden complexity in protein folding

(2012) K. A. Beauchamp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Optimal Vortex Formation as a Unifying Principle in Biological Propulsion

(2008) John O. Dabiri   Annual Review of Fluid Mechanics