The following videos and screenshots demonstrate how SAMSON can be used to model, simulate and render complex nanosystems.
ARPS: Adaptively Restrained Particle Simulations
SAMSON integrates ARPS - Adaptively Restrained Particle Simulations. This general, theoretically-grounded method is designed to speed up particle simulations by adaptively switching on and off positional degrees of freedom, while letting momenta evolve. In the following examples we demonstrate the benefits of this approach.
The first video illustrates an example where a particle is launched towards a initially static 2D system, and the collision cascade is simulated, first with a traditional particle simulation approach, then with adaptively restrained (AR) particles simulations at different precision thresholds. AR simulations make it possible to smoothly trade between precision and cost, reaching a 10 times speed-up while preserving the major features of the shock.
The second video illustrates an example where the goal is to compute the hydrodynamic radius of the solvated polymer. For any target precision, restraining solvent particles makes it possible to determine the hydrodynamic radius about four times faster than traditional simulations.
The following videos are captures of interactive editing sessions in SAMSON.
Modeling with a reactive force-field
SAMSON integrates incremental, adaptive algorithms to update the potential energy and interatomic forces. In the following examples, the Brenner potential is used to interactively model hydrocarbon systems.
The first video is a simple example showing the possibility to form and break bonds while the system is being minimized.
The second video shows how SAMSON may be used to interactively close a carbon nanotube. Physically-based modeling (simulation during modeling) helps the user build realistic models.
The third video shows a user bringing a buckyball in contact with a carbon nanotube.
The fourth video shows a user dragging a carbon nanotube to indent sheets of graphene.
Interactive modeling of symmetrical systems
SAMSON integrates algorithms which allow the user to model symmetrical systems [Grudinin and Redon, Journal of Computational Chemistry, 2010]. Only the main, asymmetric unit is stored in memory, but interactions between the asymmetric unit and its replicas are computed. Any set of transforms may be handled, and the approach may be used to model virus capsids, periodic boundary conditions, etc.
The first video explains the basic idea on a simple example.
The second video shows a user editing an apoferritin structure.
By loading electron density maps or cryo-EM maps into SAMSON, the user may interactively fit molecular structures to experimental data.
The following examples show how SAMSON may be used to interactively dock and undock molecules, using adaptive torsion-angle algorithms [Rossi et al, Bioinformatics, 2007].
The first example shows a typical molecular docking situation.
The second example shows a user of SAMSON open the loops of the HIV protease, and undock the ligands.
Adaptive torsion-angle quasi-statics
This video explains the basic idea behind the adaptive torsion-angle quasi-statics algorithms in SAMSON.