Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …

Highlights•Coarse-grained models are reduced representations of all-atom models that aim
to retain the essential molecular aspects for the system of interest.•Coarse-grained …

Coarse-grained models have long been considered indispensable tools in the investigation
of biomolecular dynamics and assembly. However, the process of simulating such models is …

ATP-hydrolysis-coupled actin polymerization is a fundamental mechanism of cellular force
generation,–. In turn, force, and actin filament (F-actin) nucleotide state regulate actin …

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent
of the COVID-19 pandemic. Computer simulations of complete viral particles can provide …

The “bottom-up” approach to coarse-graining, for building accurate and efficient
computational models to simulate large-scale and complex phenomena and processes, is …

In biology, self-assembly of proteins and energy-consuming reaction cycles are intricately
coupled. For example, tubulin is activated and deactivated for assembly by a guanosine …

Despite the high fidelity of bottom-up coarse-grained (CG) approaches to recapitulate the
structural correlations in atomistic simulations, the general use of bottom-up CG methods is …

Actin filaments elongate and shorten much faster at their barbed end than their pointed end,
but the molecular basis of this difference has not been understood. We use all-atom …

Coarse-grained (CG) molecular dynamics (MD) has become a method of choice for
simulating various large scale biomolecular processes; therefore, the systematic definition of …