11 citations · 27 across the 10 of their papers we have counts for
6 papers · 1 filter
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…
Estimating the tails of the spectrum of the Hessian of the log-likelihood for \textit{ab-initio} single-particle reconstruction in electron cryomicroscopy
Aaditya V. Rangan, Wai-Shing Tang, Pilar Cossio +2
Electron cryomicroscopy (cryo-EM) is a technique in structural biology used to reconstruct accurate volumetric maps of molecules. One step of the cryo-EM pipeline involves solving…
Simulation-based inference of single-molecule experiments
Lars Dingeldein, Pilar Cossio, Roberto Covino
Single-molecule experiments are a unique tool to characterize the structural dynamics of biomolecules. However, reconstructing molecular details from noisy single-molecule data is…
CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM
Minkyu Jeon, Rishwanth Raghu, Miro Astore +6
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. Its unique ability to capture structural va…
Good rates from bad coordinates: the exponential average time-dependent rate approach
Nicodemo Mazzaferro, Subarna Sasmal, Pilar Cossio +1
Our ability to calculate rates of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in confo…
Active learning of Boltzmann samplers and potential energies with quantum mechanical accuracy
Ana Molina-Taborda, Pilar Cossio, Olga Lopez-Acevedo +1
Extracting consistent statistics between relevant free-energy minima of a molecular system is essential for physics, chemistry and biology. Molecular dynamics (MD) simulations can…