4 papers
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…
Consistent Projection of Langevin Dynamics: Preserving Thermodynamics and Kinetics in Coarse-Grained Models
Vahid Nateghi, Lara Neureither, Selma Moqvist +3
Coarse graining (CG) is an important task for efficient modeling and simulation of complex multi-scale systems, such as the conformational dynamics of biomolecules. This work prese…
Marginal Girsanov Reweighting: Stable Variance Reduction for Long-Timescale Dynamics from Biased Simulation
Yan Wang, Hao Wu, Simon Olsson
Recovering unbiased kinetic and thermodynamic observables from the enhanced sampling simulations is a central challenge in rare-event sampling. Classical Girsanov Reweighting (GR)…
Thermodynamic Interpolation: A generative approach to molecular thermodynamics and kinetics
Selma Moqvist, Weilong Chen, Mathias Schreiner +2
Using normalizing flows and reweighting, Boltzmann Generators enable equilibrium sampling from a Boltzmann distribution, defined by an energy function and thermodynamic state. In t…