6 papers
Sampling Free Energy Landscapes of Ionic Colloidal Crystal Systems using Machine-Learned Proxy Collective Variables
Michael S. Chen, Stefano Sacanna, Glen M. Hocky
Charged colloids coated with a polymer brush can be designed to preferentially self-assemble into different crystal structures by varying easy-to-tune experimental conditions. For…
PACSim: A Flexible Simulation Framework for Polymer-Attenuated Coulombic Self-Assembly
Philipp Höllmer, Nicole Smina, John P. Marquardt +4
Polymer-Attenuated Coulombic Self-Assembly (PACS) is a flexible experimental approach for generating crystals from simple colloidal building blocks. The central components are char…
Stepping up enhanced rate calculations with EATR-flooding
Nicodemo Mazzaferro, Willmor J Pena Ccoa, Pilar Cossio +1
Several recent methods have shown that it is possible to compute rate constants of very slow biomolecular processes using simulations where a time-dependent bias is added along one…
Large-Scale Multi-omic Biosequence Transformers for Modeling Protein-Nucleic Acid Interactions
Sully F. Chen, Robert J. Steele, Glen M. Hocky +3
The transformer architecture has revolutionized bioinformatics and driven progress in the understanding and prediction of the properties of biomolecules. To date, most biosequence…
Simulating dynamic bonding in soft materials
Tyla R. Holoman, B. P. Prajwal, Glen M. Hocky +1
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these ma…
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…