The application of coarse-grained (CG) models in biology is essential to access large length and time scales required for the description of many biological processes. The ELNEDIN protein model is based on the well-known MARTINI CG force-field and incorporates additionally harmonic bonds of a certain spring constant within a defined cutoff distance between pairs of residues, in order to preserve the native structure of the protein. In this case, the use of unbreakable harmonic bonds hinders the study of unfolding and folding processes. To overcome this barrier we have replaced the harmonic bonds with Lennard-Jones interactions based on the contact map of the native protein structure as is done in Go̅-like models. This model exhibits very good agreement with all-atom simulations and the ELNEDIN. Moreover, it can capture the structural motion linked to particular catalytic activity in the Man5B protein, in agreement with all-atom simulations. In addition, our model is based on the van der Waals radii, instead of a cutoff distance, which results in a smaller contact map. In conclusion, we anticipate that our model will provide further possibilities for studying biological systems based on the MARTINI CG force-field by using advanced-sampling methods, such as parallel tempering and metadynamics.

By molecular dynamics simulation of a coarse-grained bead-spring-type model for a cylindrical molecular brush with a backbone chain of N(b) effective monomers to which with grafting density σ side chains with N effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side chain lengths are in the range 5 ≤ N ≤ 40, backbone chain lengths are in the range 50 ≤ N(b) ≤ 200, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer chains are accessible, N(b) ≤ 1027, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of the side chains and the backbone chain and discuss their N-dependence in terms of power laws and the associated effective exponents. We show that even at the theta point the side chains are considerably stretched, their linear dimension depending on the solvent quality only weakly. Effective persistence lengths are extracted both from the orientational correlations and from the backbone end-to-end distance; it is shown that different measures of the persistence length (which would all agree for Gaussian chains) are not mutually consistent with each other and depend distinctly both on N(b) and the solvent quality. A brief discussion of pertinent experiments is given.

Conformations of a bottle-brush polymer with two types (A,B) of grafted side chains are studied by molecular dynamics simulations, using a coarse-grained bead−spring model with side chains of up to N = 50 effective monomers. Varying the solvent quality and the grafting density, the crossover from the “pearl-necklace” structure to dense cylinders is studied. Whereas for small grafting density, A- and B-chains form separate collapsed chains, at intermediate grafting density, larger “pearls” containing several chains are observed, exhibiting microphase separation between A and B in “dumbbell”-type configurations. At still larger grafting density, short-range order of “Janus dumbbell”-type is observed. It is argued that because of the quasi-1D character of bottle-brush polymers with stiff backbones, all phase changes occur gradually, and no sharp-phase transitions like in bulk polymer mixtures or block copolymer melts can be observed.

The intriguing ability of certain surfactant molecules to drive the superspreading of liquids to complete wetting on hydrophobic substrates is central to numerous applications that range from coating flow technology to enhanced oil recovery. Despite significant experimental efforts, the precise mechanisms underlying superspreading remain unknown to date. Here, we isolate these mechanisms by analyzing coarse-grained molecular dynamics simulations of surfactant molecules of varying molecular architecture and substrate affinity. We observe that for superspreading to occur, two key conditions must be simultaneously satisfied: the adsorption of surfactants from the liquid-vapor surface onto the three-phase contact line augmented by local bilayer formation. Crucially, this must be coordinated with the rapid replenishment of liquid-vapor and solid-liquid interfaces with surfactants from the interior of the droplet. This article also highlights and explores the differences between superspreading and conventional surfactants, paving the way for the design of molecular architectures tailored specifically for applications that rely on the control of wetting.

The surfactant-driven superspreading of droplets on hydrophobic substrates is considered. A key element of the superspreading mechanism is the adsorption of surfactant molecules from the liquid-vapour interface onto the substrate through the contact line, which must be coordinated with the replenishment of interfaces with surfactant from the interior of the droplet. We use molecular dynamics simulations with coarse-grained force fields to provide a detailed structural description of the droplet shape and surfactant dynamics during the superspreading process. We also provide a simple method for accurate estimation of the contact angle subtended by the droplets at the contact line.

Molecular-dynamics simulations are used to study the structure of bottlebrush polymers with rigid backbones, for various grafting densities, side chain lengths, and varying solvent quality. While we confirm different states of the bottlebrush proposed by Sheiko et al. (Eur. Phys. J. E, 13 (2004) 125) we find that the transition between stretched and collapsed brushes occurs in a rather gradual manner. The pearl-necklace structure occurring at intermediate grafting densities and rather low temperatures has a pronounced medium-range order along the backbone.

A range of technologies require the directed motion of nanoscale droplets on solid substrates. A way of realizing this effect is durotaxis, whereby a stiffness gradient of a substrate can induce directional motion without requiring an energy source. Here, we report on the results of extensive molecular dynamics investigations of droplets on a surface with varying stiffness. We find that durotaxis is enhanced by increasing the stiffness gradient and, also, by increased wettability of the substrate, in particular, when droplet size decreases. We anticipate that our study will provide further insights into the mechanisms of nanoscale directional motion.

Bottle-brush polymers, where flexible side chains containing N=20 to 50 effective monomers are grafted to a rigid backbone, are studied by molecular dynamics simulations, varying the grafting density σ and the solvent quality. Whereas for poor solvents and large enough σ the molecular brush is a cylindrical object, homogeneous in axial direction, for intermediate values of σ an axially inhomogeneous structure of "pearl-necklace" type is formed. The "pearls," however, have a strongly nonspherical ellipsoidal shape, due to the fact that several side chains cluster together in one pearl, qualitatively consistent with predictions of Sheiko et al. [Eur. Phys. J. E 13, 125 (2004)] We analyze the structure of these pearls and study both the transition to the axially uniform cylinder at high σ and to the trivial pearl-necklace structure at small σ, where each pearl contains a single collapsed chain only.