With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.

For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an interpretation in terms of an effective generalized grand canonical approach. The method is applied to liquid water at ambient conditions.

Simulation schemes for liquids or strongly fluctuating systems that allow to change the molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surroundings introduce conceptual problems of thermodynamic consistency. In this work we present a general scheme based on thermodynamic arguments which ensures a thermodynamic equilibrium among molecules of different representations. The robustness of the algorithm is tested for two examples, namely, an adaptive resolution simulation, atomistic/coarse grained, for a liquid of tetrahedral molecules, and an adaptive resolution simulation of a binary mixture of tetrahedral molecules and spherical solutes.

We investigate the hydrodynamic properties of a spherical colloid model, which is composed of a shell of point particles by hybrid mesoscale simulations, which combine molecular dynamics simulations for the sphere with the multiparticle collision dynamics approach for the fluid. Results are presented for the center-of-mass and angular velocity correlation functions. The simulation results are compared with theoretical results for a rigid colloid obtained as a solution of the Stokes equation with no-slip boundary conditions. Similarly, analytical results of a point-particle model are presented, which account for the finite size of the simulated system. The simulation results agree well with both approaches on appropriative time scales; specifically, the long-time correlations are quantitatively reproduced. Moreover, a procedure is proposed to obtain the infinite-system-size diffusion coefficient based on a combination of simulation results and analytical predictions. In addition, we present the velocity field in the vicinity of the colloid and demonstrate its close agreement with the theoretical prediction. Our studies show that a point-particle model of a sphere is very well suited to describe the hydrodynamic properties of spherical colloids, with a significantly reduced numerical effort.

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