arXiv:2606. 14737v1 Announce Type: cross Abstract: Molecular dynamics (MD) simulations generate trajectories in a high-dimensional configuration space whose analysis critically depends on molecular descriptors, typically handcrafted observables or learned kinetic embeddings.
By Dominik Geng, Florian Graf, Martin Uray, Roland Kwitt
arXiv:2410.20317v2 Announce Type: replace
Abstract: Molecular dynamics (MD) simulations are a principled but computationally expensive approach for studying protein conformational variability, making...
By Siddharth Viswanath, Xingzhi Sun, Lucas Lee, Danqi Liao, Hiren Madhu, David R. Johnson, Jo\~ao Felipe Rocha, Egbert Castro, Jackson D. Grady, Michael Perlmutter, Dhananjay Bhaskar, Smita Krishnaswamy
arXiv:2606. 17668v1 Announce Type: cross Abstract: Molecular dynamics (MD) simulation is computationally demanding, particularly for large-scale systems requiring long-term analysis.
By Kexin Wu, Luonan Chen, Renxiao Wang
arXiv:2605. 01625v3 Announce Type: replace Abstract: Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology.
By Viet Thanh Duy Nguyen, John K. Johnstone, Truong-Son Hy
arXiv:2606. 08375v1 Announce Type: new Abstract: All-atom generative modeling of 3D biomolecular complexes has emerged as the dominant paradigm for predicting the structure of proteins and protein-ligand systems.
By Gianluca Scarpellini, Ron Shprints, Peter Holderrieth, Juno Nam, Pranav Murugan, Rafael G\'omez-Bombarelli, Tommi Jaakola, Maruan Al-Shedivat, Nicholas Matthew Boffi, Avishek Joey Bose
arXiv:2510.07589v2 Announce Type: replace-cross
Abstract: Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conve...
By Juan Viguera Diez, Mathias Schreiner, Simon Olsson