Computational modeling of biological systems is challenging because of the multitude of
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …

By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

Nanoscience and nanotechnology are recent revolutionary developments of science and
engineering that are evolving at a very fast pace. They are driven by the desire to fabricate …

We systematically parameterized a coarse-grained (CG) model for DNA that is compatible
with the Martini force field. The model maps each nucleotide into six to seven CG beads and …

We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-
grained model of DNA similar to that recently introduced in a study of DNA nanotweezers …

originally designed to reproduce the properties of DNA molecules with average sequences.
The new parametrization introduces sequence-dependent stacking and base-pairing …

Although the thermodynamics of DNA hybridization is generally well established, the
kinetics of this classic transition is less well understood. Providing such understanding has …

Recently, we saw a dramatic increase in the number of researches that rely on coarse-
grained (CG) simulations for large biomolecules. Here, first, we briefly describe recently …

To simulate long time and length scale processes involving DNA it is necessary to use a
coarse-grained description. Here we provide an overview of different approaches to such …

We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic
thermodynamics of short strands, duplex hybridization, single-stranded stacking, and hairpin …