Coupling between membrane undulations and lipid curvature leads to transient local enrichment of cardiolipin in mitochondrial membranes Lee et al., 2025 Submitted

Spatial Modeling Algorithms for Reactions and Transport in Biological Cells Francis et al., 2024 Nat. Comput. Sci.

Membrane mechanics dictate axonal morphology and function Griswold et al., 2024 Nat. Neurosci.

Setting the Curve: The Biophysical Properties of Lipids in Mitochondrial Form and Function Venkatraman et al., 2024 Journal of Lipid Research

Modeling the Mechanochemical Feedback for Membrane-Protein Interactions Using a Continuum Mesh Model Lee et al., 2024 Methods in Enzymology

Biophysical modeling of synaptic plasticity Lee et al., 2024 Annu. Rev. Biophys.

Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome Venkatraman et al., 2023 EMBO J.

SMART: Spatial Modeling Algorithms for Reaction and Transport Laughlin et al., 2023 JOSS

ActuAtor, a Listeria-inspired molecular tool for generating force in living cells: Controlled deformation of intracellular organizations Nakamura et al., 2023 Cell Reports

The ins and outs of membrane bending by intrinsically disordered proteins Yuan et al., 2023 Science Advances

Spatiotemporal Modelling Reveals Geometric Dependence of AMPAR Dynamics on Dendritic Spine Morphology Bell et al., 2022 The Journal of Physiology

Mem3DG: An open-source software framework for 3-D membrane mechanochemical dynamics using discrete differential geometry on triangulated meshes Zhu et al., 2022 Biophys. Reports

Role of the Triplet State and Protein Dynamics in the Formation and Stability of the Tryptophan Radical in an Apoazurin Mutant López-Peña et al., 2022 J. Phys. Chem. B

Dendritic Spine Morphology Regulates Calcium-Dependent Synaptic Weight Change Bell et al., 2022 J. Gen. Physiol.

Benchmarking Ensemble Docking Methods in D3R Grand Challenge 4 Gan et al., 2022 J. Comput. Aided. Mol. Des.

Morphological Principles of Neuronal Mitochondria Mendelsohn et al., 2021 J. Comp. Neurol.

Value of Models for Membrane Budding Lee et al., 2021 Curr. Opin. Cell Biol.

Independent Markov Decomposition: Towards modeling kinetics of biomolecular complexes Hempel et al., 2021 Proc. Natl. Acad. Sci.

Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations Vasan et al., 2021 Front. Phys.

3D Mesh Processing Using GAMer 2 to Enable Reaction-Diffusion Simulations in Realistic Cellular Geometries Lee et al., 2020 PLOS Comp. Biol.

An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries Lee et al., 2020 Biophys. J.

The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh Generation Lee et al., 2019 ACM Trans. Math. Softw.

Structural Basis for Ligand Modulation of the CCR2 Conformational Landscape Taylor et al., 2019 Proc. Natl. Acad. Sci.

Quantitative Ranking of β-cyclodextrin Ligand Binding Kinetics With SEEKR, a Hybrid MD/BD/Milestoning Approach Jagger et al., 2018 J. Phys. Chem. Lett.

Exascale Computing: A New Dawn for Computational Biology Lee et al., 2018 Comput. Sci. Eng.

Two Relations to Estimate Membrane Permeability Using Milestoning Votapka et al., 2016 J. Phys. Chem. B

Emerging Computational Methods for the Rational Discovery of Allosteric Drugs Wagner et al., 2016 Chem. Rev.

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds Lee et al., 2016 J. Chem. Inf. Model.

Known Structure, Unknown Function: An Inquiry-Based Undergraduate Biochemistry Laboratory Course Gray et al., 2015 Biochem. Mol. Biol. Educ.

Application of Molecular-Dynamics Based Markov State Models to Functional Proteins Malmstrom et al., 2014 J. Chem. Theory Comput.

Mem3DG - 3D computational model for lipid membranes

membrane-spectral-analysis - Compute fluctuation spectra of biological membranes

smart - Spatial Modeling Algorithms for Reactions and Transport

gamer - Geometry-preserving Adaptive Mesher

ActuAtorForceEstimation - Estimating forces on the membrane by ActuAtor

casc - Colored Abstract Simplicial Complex Library