Visualizing DNA reaction trajectories with deep graph embedding approaches

1 code implementation • 6 Nov 2023 • Chenwei Zhang, Khanh Dao Duc, Anne Condon

Synthetic biologists and molecular programmers design novel nucleic acid reactions, with many potential applications.

Dimensionality Reduction Graph Embedding

ViDa: Visualizing DNA hybridization trajectories with biophysics-informed deep graph embeddings

1 code implementation • 6 Nov 2023 • Chenwei Zhang, Jordan Lovrod, Boyan Beronov, Khanh Dao Duc, Anne Condon

Visualization tools can help synthetic biologists and molecular programmers understand the complex reactive pathways of nucleic acid reactions, which can be designed for many potential applications and can be modelled using a continuous-time Markov chain (CTMC).

Dimensionality Reduction

EMPOT: partial alignment of density maps and rigid body fitting using unbalanced Gromov-Wasserstein divergence

1 code implementation • 1 Nov 2023 • Aryan Tajmir Riahi, Chenwei Zhang, James Chen, Anne Condon, Khanh Dao Duc

Aligning EM density maps and fitting atomic models are essential steps in single particle cryogenic electron microscopy (cryo-EM), with recent methods leveraging various algorithms and machine learning tools.

Benchmarking Cryogenic Electron Microscopy (cryo-EM)

The pathway elaboration method for mean first passage time estimation in large continuous-time Markov chains with applications to nucleic acid kinetics

no code implementations • 11 Jan 2021 • Sedigheh Zolaktaf, Frits Dannenberg, Mark Schmidt, Anne Condon, Erik Winfree

We then compare the performance of pathway elaboration with the stochastic simulation algorithm (SSA) for MFPT estimation on 237 of the reactions for which SSA is feasible.