18 citations · 34 across the 4 of their papers we have counts for
4 papers
Optimal reaction coordinates and kinetic rates from the projected dynamics of transition paths
Line Mouaffac, Karen Palacio-Rodriguez, Fabio Pietrucci
Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algo…
Transition rates, survival probabilities, and quality of bias from time-dependent biased simulations
Karen Palacio-Rodriguez, Hadrien Vroylandt, Lukas S. Stelzl +3
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of…
Free Energy Landscapes, Diffusion Coefficients, and Kinetic Rates from Transition Paths
Karen Palacio-Rodriguez, Fabio Pietrucci
We address the problem of constructing accurate mathematical models of the dynamics of complex systems projected on a collective variable. To this aim we introduce a conceptually s…
A Bayesian approach for extracting free energy profiles from cryo-electron microscopy experiments using a path collective variable
Julian Giraldo-Barreto, Sebastian Ortiz, Erik H. Thiede +4
Cryo-electron microscopy (cryo-EM) extracts single-particle density projections of individual biomolecules. Although cryo-EM is widely used for 3D reconstruction, due to its single…