Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

Molecular dynamics simulation is a powerful computational technique to study biomolecular
systems, which complements experiments by providing insights into the structural dynamics …

Dynamic processes involving macromolecular complexes are essential to cell function.
These processes take place over a wide variety of length scales from nanometers to …

Abstract We introduce Springs, Sites, and Langevin Dynamics (SpringSaLaD), a
comprehensive software platform for spatial, stochastic, particle-based modeling of …

Growing computing capacity and algorithmic advances have facilitated the study of
increasingly large biomolecular systems at longer timescales. However, with these larger …

Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently
could provide reliable answers to questions pertaining to the structure-function relationship …

Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

In the last years, we have been observing remarkable improvements in the field of protein
dynamics. Indeed, we can now study protein dynamics in atomistic details over several …

Molecular dynamics simulations capture the behavior of biological macromolecules in full
atomic detail, but their computational demands, combined with the challenge of …

Molecular dynamics simulations have evolved into a mature technique that can be used
effectively to understand macromolecular structure-to-function relationships. Present …