76 citations · 101 across the 8 of their papers we have counts for
8 papers
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…
Learning Neural Free-Energy Functionals with Pair-Correlation Matching
Jacobus Dijkman, Marjolein Dijkstra, René van Roij +3
The intrinsic Helmholtz free-energy functional, the centerpiece of classical density functional theory, is at best only known approximately for 3D systems. Here we introduce a meth…
Multi-objective optimization via equivariant deep hypervolume approximation
Jim Boelrijk, Bernd Ensing, Patrick Forré
Optimizing multiple competing objectives is a common problem across science and industry. The inherent inextricable trade-off between those objectives leads one to the task of expl…
Stochastic Optimal Control for Collective Variable Free Sampling of Molecular Transition Paths
Lars Holdijk, Yuanqi Du, Ferry Hooft +3
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a ch…
Simultaneous sampling of multiple transition channels using adaptive paths of collective variables
Alberto Pérez de Alba Ortíz, Bernd Ensing
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD)…
Double Helical Conformation and Extreme Rigidity in a Rodlike Polyelectrolyte
Ying Wang, Yadong He, Zhou Yu +11
The ubiquitous biomacromolecule DNA has an axial rigidity persistence length of ~50 nm, driven by its elegant double helical structure. While double and multiple helix structures a…