Soft and biological matter is characterized by physical properties that are determined by the interplay of disparate length and time scales. Multiscale simulation techniques that couple multiple models at different resolutions provide the most efficient way to span many orders of magnitude in the spatiotemporal scales involved in these systems.
AdResS: Adaptive Resolution Simulation
SWINGER: Dynamic Clustering Algorithm
STOCK: Structure Mapper and Online Coarse-Graining Kit for Molecular Simulations
Coupling Atomistic and Continuum Hydrodynamics
Open Boundary Molecular Dynamics
Open molecular systems exchange mass, momentum, and energy with their surroundings. Our OBMD methodology enables us to perform equilibrium molecular dynamics simulations in the grand-canonical ensemble as well as nonequilibrium fluid flow simulations. The flow is introduced via an external boundary condition while the equations of motion for the bulk remain unaltered.
We simulate fluid flows past and through nano-objects using computational fluid dynamics aiming to reproduce essential features of the fluid flows computed by molecular dynamics. Computational advantages of computational fluid dynamics allow for simulations well beyond the current reach of molecular dynamics.
Adaptive resolution simulation of an atomistic protein in MARTINI water
We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly.
Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.
Adaptive resolution simulation of a DNA molecule in salt solution
We present a multiscale simulation of a DNA molecule in 1 M NaCl salt solution environment, employing the adaptive resolution simulation approach that allows the solvent molecules, i.e., water and ions, to change their resolution from atomistic to coarse-grained and vice versa adaptively on-the-fly.
SWINGER is a dynamic clustering algorithm that can concurrently assemble, disassemble, and reassemble water bundles, consisting of several water molecules. Thus, it allows for a seamless coupling between standard atomistic and supramolecular water models in adaptive resolution simulations.
SWINGER paves the way for efficient multiscale simulations of biomolecular systems without compromising the accuracy of atomistic water models.
The core domain of the simulation box is solved using the all-atom resolution. The coarse-grained layer introduced by AdResS is located at the outer part of the open simulation box to enable the insertion of large molecules into the system.
In the explicit domain, the water molecules and ions are both overtly present in the system, whereas in the implicit water domain, only the ions are explicitly present and the water is described as a continuous dielectric medium. Water molecules are inserted and deleted into/from the system in the intermediate buffer domain that acts as a water reservoir to the explicit domain, with both water molecules and ions free to enter or leave the explicit domain.
Our approach is general and allows for efficient molecular simulations of biomolecules solvated in bathing salt solutions at any ionic strength condition.