Persistent homology analysis of protein structure, flexibility, and folding

Molecular nonlinear dynamics and protein thermal uncertainty quantification

(2014) Kelin Xia et al.   CHAOS

Morse Theory for Filtrations and Efficient Computation of Persistent Homology

(2013) Konstantin Mischaikow et al.   DISCRETE & COMPUTATIONAL GEOMETRY

A fast alternating direction implicit algorithm for geometric flow equations in biomolecular surface generation

(2013) Wufeng Tian et al.   International Journal for Numerical Methods in Biomedical Engineering

Multiscale multiphysics and multidomain models—Flexibility and rigidity

(2013) Kelin Xia et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale geometric modeling of macromolecules II: Lagrangian representation

(2013) Xin Feng et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Multiscale geometric modeling of macromolecules I: Cartesian representation

(2013) Kelin Xia et al.   JOURNAL OF COMPUTATIONAL PHYSICS

MULTISCALE, MULTIPHYSICS AND MULTIDOMAIN MODELS I: BASIC THEORY

(2013) GUO-WEI WEI   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

Persistent Topology and Metastable State in Conformational Dynamics

(2013) Huang-Wei Chang et al.   PLoS One

Reeb Graphs: Approximation and Persistence

(2012) Tamal K. Dey et al.   DISCRETE & COMPUTATIONAL GEOMETRY

A fast algorithm for constructing topological structure in large data

(2012) Xu Liu et al.   Homology Homotopy and Applications

Persistent Brain Network Homology From the Perspective of Dendrogram

(2012) Hyekyoung Lee et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Multivariate Data Analysis Using Persistence-Based Filtering and Topological Signatures

(2012) B. Rieck et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Geometric modeling of subcellular structures, organelles, and multiprotein complexes

(2012) Xin Feng et al.   International Journal for Numerical Methods in Biomedical Engineering

Variational approach for nonpolar solvation analysis

(2012) Zhan Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Persistent Betti numbers for a noise tolerant shape-based approach to image retrieval

(2012) Patrizio Frosini et al.   PATTERN RECOGNITION LETTERS

Variational Multiscale Models for Charge Transport

(2012) Guo-Wei Wei et al.   SIAM REVIEW

A Topological Paradigm for Hippocampal Spatial Map Formation Using Persistent Homology

(2012) Y. Dabaghian et al.   PLoS Computational Biology

A Mayer–Vietoris Formula for Persistent Homology with an Application to Shape Recognition in the Presence of Occlusions

(2011) Barbara Di Fabio et al.   FOUNDATIONS OF COMPUTATIONAL MATHEMATICS

Topology-Based Kernels With Application to Inference Problems in Alzheimer's Disease

(2011) Deepti Pachauri et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Branching and Circular Features in High Dimensional Data

(2011) Bei Wang et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Semi-automatic surface and volume mesh generation for subject-specific biomedical geometries

(2011) Igor Sazonov et al.   International Journal for Numerical Methods in Biomedical Engineering

Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface

(2011) Duan Chen et al.   International Journal for Numerical Methods in Biomedical Engineering

Biomolecular surface construction by PDE transform

(2011) Qiong Zheng et al.   International Journal for Numerical Methods in Biomedical Engineering

Differential geometry based solvation model II: Lagrangian formulation

(2011) Zhan Chen et al.   JOURNAL OF MATHEMATICAL BIOLOGY

A Topological View of Unsupervised Learning from Noisy Data

(2011) P. Niyogi et al.   SIAM JOURNAL ON COMPUTING

Differential Geometry Based Multiscale Models

(2010) Guo-Wei Wei   BULLETIN OF MATHEMATICAL BIOLOGY

Computing Robustness and Persistence for Images

(2010) P Bendich et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Differential geometry based solvation model I: Eulerian formulation

(2010) Zhan Chen et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Multiscale molecular dynamics using the matched interface and boundary method

(2010) Weihua Geng et al.   JOURNAL OF COMPUTATIONAL PHYSICS

A microfluidic DNA computing processor for gene expression analysis and gene drug synthesis

(2009) Yu Zhang et al.   Biomicrofluidics

Topology and data

(2009) Gunnar Carlsson   BULLETIN OF THE AMERICAN MATHEMATICAL SOCIETY

Topological methods for exploring low-density states in biomolecular folding pathways

(2009) Yuan Yao et al.   JOURNAL OF CHEMICAL PHYSICS

Persistent homology of complex networks

(2009) Danijela Horak et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Protein elastic network models and the ranges of cooperativity

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Describing shapes by geometrical-topological properties of real functions

(2008) S. Biasotti et al.   ACM COMPUTING SURVEYS

Computing geometry-aware handle and tunnel loops in 3D models

(2008) Tamal K. Dey et al.   ACM TRANSACTIONS ON GRAPHICS

Localized homology

(2008) Afra Zomorodian et al.   COMPUTATIONAL GEOMETRY-THEORY AND APPLICATIONS

Geometric and potential driving formation and evolution of biomolecular surfaces

(2008) P. W. Bates et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Normal mode analysis for proteins

(2008) Lars Skjaerven et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

Topological analysis of population activity in visual cortex

(2008) G. Singh et al.   JOURNAL OF VISION