4 citations · 6 across the 6 of their papers we have counts for
6 papers
Optimal control of ribosome population for gene expression under periodic nutrient intake
Clément Soubrier, Eric Foxall, Luca Ciandrini +1
Translation of proteins is a fundamental part of gene expression that is mediated by ribosomes. As ribosomes significantly contribute to both cellular mass and energy consumption,…
ViDa: Visualizing DNA hybridization trajectories with biophysics-informed deep graph embeddings
Chenwei Zhang, Jordan Lovrod, Boyan Beronov +2
Visualization tools can help synthetic biologists and molecular programmers understand the complex reactive pathways of nucleic acid reactions, which can be designed for many poten…
Visualizing DNA reaction trajectories with deep graph embedding approaches
Chenwei Zhang, Khanh Dao Duc, Anne Condon
Synthetic biologists and molecular programmers design novel nucleic acid reactions, with many potential applications. Good visualization tools are needed to help domain experts mak…
EMPOT: partial alignment of density maps and rigid body fitting using unbalanced Gromov-Wasserstein divergence
Aryan Tajmir Riahi, Chenwei Zhang, James Chen +2
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…
Defining an action of SO(d)-rotations on images generated by projections of d-dimensional objects: Applications to pose inference with Geometric VAEs
Nicolas Legendre, Khanh Dao Duc, Nina Miolane
Recent advances in variational autoencoders (VAEs) have enabled learning latent manifolds as compact Lie groups, such as . Since this approach assumes that data lies on a su…
Oscillatory Survival Probability: Analytical, Numerical Study for oscillatory narrow escape and applications to neural network dynamics
K. Dao Duc, Z. Schuss, D. Holcman
We study the escape of Brownian motion from the domain of attraction of a stable focus with a strong drift. The boundary of is an unstable limit cycle of the d…