Resources

This page contains links to resources generated for previously published papers.

Hocky Group Resources

Self-Assembly of Colloidal Diamond via the Depletion Interaction (2026)

Stepping up enhanced rate calculations with EATR-flooding (2026)

Light-controlled colloidal crystallization (2026)

Tutorial on quantifying and sampling biomolecular ensembles with ShapeGMM (2025)

Using Time Dependent Rate Analysis to Evaluate the Quality of Machine Learned Reaction Coordinates for Biasing and Computing Kinetics (2025)

Improved data-driven collective variables for biased sampling through iteration on biased data (2025)

A direct computational assessment of vinculin-actin unbinding kinetics reveals catch bonding behavior (2025)

Direct observation and control of non-classical crystallization pathways in binary colloidal systems (2025)

Beta-barrel proteins dictate the effect of core oligosaccharide composition on outer membrane mechanics (2025)

Enabling three-dimensional real space analysis of ionic colloidal crystallization (2024)

Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM (2024)

Computing equilibrium free energies through a nonequilibrium quench (2024)

Improved prediction of molecular response to pulling by combining force tempering with replica exchange methods (2024)

Molecular dynamics simulations support a multi-step Arp23 complex activation pathway (2023)

Reaction Coordinates for Conformational Transitions using Linear Discriminant Analysis on Positions (2023)

A Coarse-Grained Simulation Model for Colloidal Self-Assembly via Explicit Mobile Binders (2023)

Assessing models of force-dependent unbinding rates via infrequent metadynamics (2022)

Structural basis of fast- and slow-severing actin-cofilactin boundaries (2021)

Infinite Switch Simulated Tempering in Force (FISST) (2020)

Collaboration Resources

Large-Scale Multi-omic Biosequence Transformers for Modeling Protein-Nucleic Acid Interactions (2026)

Crystallization of non-convex colloids: the roles of particle shape and entropy (2025)

PLUMED Tutorials: a collaborative, community-driven learning ecosystem (2025)

Polysome collapse and RNA condensation fluidize the cytoplasm (2024)

Assessment of chemistry knowledge in large language models that generate code (2023)

Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories (2022)

Natural Language Processing Models That Automate Programming Will Transform Chemistry Research and Teaching (2022)

Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture (2021)

Residue-Level Allostery Propagates Through the Effective Coarse-Grained Hessian (2020)

Mechanical and kinetic factors drive sorting of F-actin crosslinkers on bundles (2019)

Promoting transparency and reproducibility in enhanced molecular simulations (2019)