The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago. Based on a building block principle, the model combines speed and versatility while maintaining chemical specificity. Here we review the current state of the model. We describe recent highlights as well as shortcomings, and our ideas on the further development of the model.

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Perspective on the Martini model.

Valorization of disposable COVID-19 mask through the thermo-chemical process

Initial reaction mechanisms of cellulose pyrolysis revealed by ReaxFF molecular dynamics

Initial reaction mechanisms of lignin pyrolysis were studied by large-scale ReaxFF molecular dynamics simulations (ReaxFF MD) facilitated by the first GPU-enabled code (GMD-Reax) and the unique reaction analysis tool (VARxMD). Simulations were performed over wide temperature ranges both for heat up at 300–2100 K and for NVT at 500–2100 K with a large lignin model, which contained 15920 atoms and was constructed based on Adler’s softwood lignin model. By utilizing the relatively continuous observation for pyrolysate evolution in slow heat up simulations, three stages for lignin pyrolysis are proposed by pyrolysate fractions. The underlying mechanisms for the three stages are revealed by analyzing the species structure evolution and the reactions of linkages, aryl units, propyl chains, and methoxy substituents. Stage I is characterized with the complete decomposition of source lignin molecules at low temperatures dominated by breaking of α-O-4 and β-O-4 linkages. The temperature in stage II is relatively hi...

Initial Mechanisms for an Overall Behavior of Lignin Pyrolysis through Large-Scale ReaxFF Molecular Dynamics Simulations

Phase separation of intrinsically disordered proteins is important for the formation of membraneless organelles or biomolecular condensates, which play key roles in the regulation of biochemical processes within cells. In this work, we investigated the phase separation of different sequences of a coarse-grained model for intrinsically disordered proteins and discovered a surprisingly rich phase behavior. We studied both the fraction of total hydrophobic parts and the distribution of hydrophobic parts. Not surprisingly, sequences with larger hydrophobic fractions showed conventional liquid-liquid phase separation. The location of the critical point was systematically influenced by the terminal beads of the sequence due to changes in interfacial composition and tension. For sequences with lower hydrophobicity, we observed not only conventional liquid-liquid phase separation but also re-entrant phase behavior in which the liquid phase density decreases at lower temperatures. For some sequences, we observed the formation of open phases consisting of aggregates, rather than a normal liquid. These aggregates had overall lower densities than the conventional liquid phases and exhibited complex geometries with large interconnected string-like or membrane-like clusters. Our findings suggest that minor alterations in the ordering of residues may lead to large changes in the phase behavior of the protein, a fact of significant potential relevance for biology.

Model for disordered proteins with strongly sequence-dependent liquid phase behavior

Study of high density polyethylene (HDPE) pyrolysis with reactive molecular dynamics

Large-scale coarse-grained molecular dynamics simulations have been performed to investigate the self-assemblies of dodecyltrimethylammonium bromide (DTAB) and gemini surfactants 12−S−12 (S = 6, 14, and 20). At the concentrations investigated, the surfactants experience fast aggregation of monomers into oligomers until the cluster numbers reach maxima. For DTAB, larger aggregates grow at the expense of monomers, but for gemini surfactants, the growth of clusters is accomplished via the merging of oligomers. In the final stage, spherical and worm-like micelles coexist in the systems of DTAB and 12−6−12, and in gemini systems with longer spacers, namely, 12−14−12 and 12−20−12, well-defined vesicles are formed through expansion and curving of bilayer-like structures. Through detailed analysis of the vesicle structures, many of the 12−20−12 surfactants are found to have their headgroups at different surfaces, with the spacers bridging the inner and outer surface of the vesicle.

Coarse-grained molecular dynamics simulation of ammonium surfactant self-assemblies: micelles and vesicles.

Molecular dynamics simulations have been performed on the monolayers of dodecyltrimethylammonium bromide and gemini surfactants 12−S−12 with S = 3, 6, and 12 at the n-heptane/water interfaces. The ...

Bin Kong

Papers

Study of high density polyethylene (HDPE) pyrolysis with reactive molecular dynamics

Coarse-grained molecular dynamics simulation of ammonium surfactant self-assemblies: micelles and vesicles.

Molecular Dynamics Simulations of Ammonium Surfactant Monolayers at the Heptane/ Water Interface

Conformational transition characterization of glass transition behavior of polymers

Studies on some factors influencing the interfacial tension measurement of polymers