Nanoscale domains in ionic liquids: A statistical mechanics definition for molecular dynamics studies

Investigation of water-mediated intermolecular interactions with the adaptive resolution simulation technique

We use the adaptive resolution simulation (AdResS) technique to estimate the region in space where water-mediated effects in molecule-molecule interactions are relevant. AdResS is employed to identify the region around the solute (solvation shell) where the atomistic details of the hydrogen bonding network are relevant while outside water plays the role of a thermodynamic bath that can be described at simplified macroscopic level. The consequence is that for the interaction of two solutes the intermolecular distance at which water mediated effects start to be relevant is represented by the sum of the radii of the two respective solvation shells identified via AdResS. The hypothesis formulated above will be proven by calculating the solute-solute potential of mean force for different solutes. As test molecules we use amino acids derived from fragments of the FCHo2-F-BAR domain protein; this choice stems from the fact that the current results, beside proving the technical capability of AdResS in this context, may provide data for future actual coarse-grained models.

The transition from salt-in-water to water-in-salt nanostructures in water solutions of organic ionic liquids relevant for biological applications

Computer simulations show how nano-structural motifs in organic salts/water solutions change with salt content increasing from dilute to highly concentrated.

From adaptive resolution to molecular dynamics of open systems

ABSTRACT

We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on discussing its basic principles and presenting its current numerical and theoretical developments. Examples of applications to systems of interest to soft matter, chemical physics, and condensed matter illustrate the method's advantages and limitations in its practical use and thus settle the challenge for further future numerical and theoretical developments.

The physics of open systems for the simulation of complex molecular environments in soft matter

Molecular dynamics (MD) has become one of the most powerful tools of investigation in soft matter. Despite such success, simulations of large molecular environments are mostly run using the approximation of closed systems without the possibility of exchange of matter. Due to the molecular complexity of soft matter systems, an optimal simulation strategy would require the application of concurrent multiscale resolution approaches such that each part of a large system can be considered as an open subsystem at a high resolution embedded in a large coarser reservoir of energy and particles. This paper discusses the current capability and the future perspectives of multiscale adaptive resolution MD methods to satisfy the conceptual principles of open systems and to perform simulations of complex molecular environments in soft matter.