Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

Roughness Volumes: An Improved RoughMob Concept for Predicting the Increase of Molecular Mobility upon Coarse-Graining

The reduced number of degrees of freedom in a coarse-grained molecular model compared to its parent atomistic model not only makes it possible to simulate larger systems for longer time scales but also results in an artificial mobility increase. The RoughMob method [Meinel, M. K. and Müller-Plathe, F. J. Chem. Theory Comput. 2020, 16, 1411.] linked the acceleration factor of the dynamics to the loss of geometric information upon coarse-graining. Our hypothesis is that coarse-graining a multiatom molecule or group into a single spherical bead smooths the molecular surface and, thus, leads to reduced intermolecular friction. A key parameter is the molecular roughness difference, which is calculated via a numerical comparison of the molecular surfaces of both the atomistic and coarse-grained models. Augmenting the RoughMob method, we add the concept of the region where the roughness acts. This information is contained in four so-called roughness volumes. For 17 systems of homogeneous hydrocarbon fluids, simple one-bead coarse-grained models are derived by the structure-based iterative Boltzmann inversion. They include 13 different homogeneous aliphatic and aromatic molecules and two different mapping schemes. We present a simple way to correlate the roughness volumes to the acceleration factor. The resulting relation is able to a priori predict the acceleration factors for an extended size and shape range of hydrocarbon molecules, with different mapping schemes and different densities.

Force probe simulations using an adaptive resolution scheme

Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In force probe molecular dynamics (FPMD) simulations, one pulls one end of the molecule with a constant velocity in order to induce the relevant conformational transitions. Since the extended configuration of the system has to fit into the simulation box together with the solvent such simulations are very time consuming. Here, we apply a hybrid scheme in which the solute is treated with atomistic resolution and the solvent molecules far away from the solute are described in a coarse-grained manner. We use the adaptive resolution scheme (AdResS) that has very successfully been applied to various examples of equilibrium simulations. We perform FPMD simulations using AdResS on a well studied system, a dimer formed from mechanically interlocked calixarene capsules. The results of the multiscale simulations are compared to all-atom simulations of the identical system and we observe that the size of the region in which atomistic resolution is required depends on the pulling velocity, i.e. the particular non-equilibrium situation. For large pulling velocities a larger all atom region is required. Our results show that multiscale simulations can be applied also in the strong non-equilibrium situations that the system experiences in FPMD simulations.

Coarse-Grained Models of RNA Nanotubes for Large Time Scale Studies in Biomedical Applications

In order to describe the physical properties of large time scale biological systems, coarse-grained models play an increasingly important role. In this paper we develop Coarse-Grained (CG) models for RNA nanotubes and then, by using Molecular Dynamics (MD) simulation, we study their physical properties. Our exemplifications include RNA nanotubes of 40 nm long, equivalent to 10 RNA nanorings connected in series. The developed methodology is based on a coarse-grained representation of RNA nanotubes, where each coarse bead represents a group of atoms. By decreasing computation cost, this allows us to make computations feasible for realistic structures of interest. In particular, for the developed coarse-grained models with three bead approximations, we calculate the histograms for the bond angles and the dihedral angles. From the dihedral angle histograms, we analyze the characteristics of the links used to build the nanotubes. Furthermore, we also calculate the bead distances along the chains of RNA strands in the nanoclusters. The variations in these features with the size of the nanotube are discussed in detail. Finally, we present the results on the calculation of the root mean square deviations for a developed RNA nanotube to demonstrate the equilibration of the systems for drug delivery and other biomedical applications such as medical imaging and tissue engineering.