1 citations · 2 across the 4 of their papers we have counts for
10 papers
ESPResSo++: A Fast and Extensible Molecular Simulation Package for Coarse-Grained Models
Zhen-Hao Xu, James Vance, Nikita Tretyakov +9
ESPResSo++ is an open-source software package for molecular dynamics (MD) simulations with a particular emphasis on coarse-grained (CG) models of soft matter systems. Written in C+…
Protein Dynamics Beyond Structure Prediction
Juliette Griffié, Sviatlana Shashkova, Antonio Ciarlo +41
The ability to predict protein three-dimensional structures from amino acid sequences is a landmark achievement in molecular biology, where recent deep learning approaches such as…
Split-Flows: Measure Transport and Information Loss Across Molecular Resolutions
Sander Hummerich, Tristan Bereau, Ullrich Köthe
By reducing resolution, coarse-grained models greatly accelerate molecular simulations, unlocking access to long-timescale phenomena, though at the expense of microscopic informati…
Data-Efficient Multidimensional Free Energy Estimation via Physics-Informed Score Learning
Daniel Nagel, Tristan Bereau
Many biological processes involve numerous coupled degrees of freedom, yet free-energy estimation is often restricted to one-dimensional profiles to mitigate the high computational…
Fokker-Planck Score Learning: Efficient Free-Energy Estimation under Periodic Boundary Conditions
Daniel Nagel, Tristan Bereau
Accurate free-energy estimation is essential in molecular simulation, yet the periodic boundary conditions (PBC) commonly used in computer simulations have rarely been explicitly e…
Navigating Chemical Space: Multi-Level Bayesian Optimization with Hierarchical Coarse-Graining
Luis J. Walter, Tristan Bereau
Molecular discovery within the vast chemical space remains a significant challenge due to the immense number of possible molecules and limited scalability of conventional screening…