Visual analysis for space–time aggregation of biomolecular simulations

Abstract

Conducting a current through a nanopore allows for the analysis of molecules inside the pore because a current modulation caused by the electrostatic properties of the passing molecules can be measured. This mechanism shows great potential for DNA sequencing, as the four different nucleotide bases induce different current modulations. We present a visualisation approach to investigate this phenomenon in our simulations of DNA within a nanopore by combining state-of-the-art molecular visualisation with vector field illustration. By spatial and temporal aggregation of the ions transported through the pore, we construct a velocity field which exhibits the induced current modulations caused by ion flux. In our interactive analysis using parametrisable three-dimensional visualisations, we encountered regions where the ion motion unexpectedly opposes the direction of the applied electric field.

Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures

“…The underlying algorithm abstracts the natural bumpiness of molecular surfaces, while preserving large-scale structural features. Ertl et al [19] combined isosurfaces of the ion density around molecules with streamlines that indicate ion direction and velocity to analyze the motion of ions around the DNA in a nanopore. In our case, the overall shape of the DNA structure and, consequently, of the double helix is of the highest importance.…”

sMolBoxes: Dataflow Model for Molecular Dynamics Exploration

“…These clusters are then annotated with arc-shaped arrows in 3D representation of the molecule. When the simulation contains many spatially-distributed trajectories of molecules, such as lipids, the overview representation often utilizes streamline-based representations, such as in MolPathFinder [1] or in the approach proposed by Ertl et al [9]. In the latter, the authors perform a spatial and temporal aggregation of ions transported through a porous structure, resulting in a velocity field visualization.…”

Visualization of Biomolecular Structures: State of the Art Revisited

“…A similar approach was used by Ertl et al . [EKK*14] to analyze the motion of ions around DNA in a nanopore. Due to the repetitive nature of the DNA and the periodic boundary conditions, they not only used temporal but also spatial aggregation of the ion densities and velocities.…”

“…Depending on the simulation, this might be given implicitly (e.g. [EKK*14]). Otherwise, a central molecule that moves freely during the simulation has to be aligned onto a reference frame.…”