Coarse-grained models for local density gradients.

Coarse-grained (CG) models provide superior computational efficiency for simulating soft materials. Unfortunately, CG models with conventional pair-additive potentials demonstrate limited transferability between bulk and interfacial environments. Recently, a growing number of CG models have supplemented these pair potentials with one-body potentials of the local density (LD) around each site.

Analysis of local density potentials.

Low resolution coarse-grained (CG) models are widely adopted for investigating phenomena that cannot be effectively simulated with all-atom (AA) models. Since the development of the many-body dissipative particle dynamics method, CG models have increasingly supplemented conventional pair potentials with one-body potentials of the local density (LD) around each site. These LD potentials appear to significantly extend the transferability of CG models, while also enabling more accurate descriptions of thermodynamic properties, interfacial phenomena, and many-body correlations.

BOCS: Bottom-up Open-source Coarse-graining Software.

We present the BOCS toolkit as a suite of open source software tools for parametrizing bottom-up coarse-grained (CG) models to accurately reproduce structural and thermodynamic properties of high-resolution models. The BOCS toolkit complements available software packages by providing robust implementations of both the multiscale coarse-graining (MS-CG) force-matching method and also the generalized-Yvon-Born-Green (g-YBG) method. The g-YBG method allows one to analyze and to calculate MS-CG potentials in terms of structural correlations.

Extending pressure-matching to inhomogeneous systems via local-density potentials.

Bottom-up coarse-grained models describe the intermolecular structure of all-atom (AA) models with desirable accuracy and efficiency. Unfortunately, structure-based models for liquids tend to dramatically overestimate the thermodynamic pressure and, consequently, tend to vaporize under ambient conditions. By employing a volume potential to introduce additional cohesion, self-consistent pressure-matching provides a simple and robust method for accurately reproducing the pressure equation of state (EoS) for homogeneous fluids, while still preserving an accurate description of intermolecular structure.

Trimethylamine -oxide stabilizes proteins via a distinct mechanism compared with betaine and glycine.

We report experimental and computational studies investigating the effects of three osmolytes, trimethylamine -oxide (TMAO), betaine, and glycine, on the hydrophobic collapse of an elastin-like polypeptide (ELP). All three osmolytes stabilize collapsed conformations of the ELP and reduce the lower critical solution temperature (LSCT) linearly with osmolyte concentration. As expected from conventional preferential solvation arguments, betaine and glycine both increase the surface tension at the air-water interface.