Software

The NANO-D group develops SAMSON, a software platform for modeling and simulation of nanosystems (SAMSON stands for “Software for Adaptive Modeling and Simulation Of Nanosystems”). SAMSON integrates all the algorithms developed in the group.

 

 

Features

Below are a few of the most important SAMSON features. You can also check out the gallery, which contains screenshots and videos demonstrating SAMSON.

 

Interactive structure edition

SAMSON core modeling and simulation algorithms rely on powerful adaptive methods which automatically refine computations where necessary. The user arbitrarily chooses the desired precision, and the adaptive algorithms automatically determine the most relevant degrees of freedom at each time step based on the user actions and the underlying force field. This approach allows for intuitive modeling of complex systems on low-end desktop computers.

In the example below, a user of SAMSON starts from a closed HIV protease model (a), and interactively deforms it to create an open structure in a few clicks (b) (see also the gallery). Adaptive computations and an underlying force field (in this example, the CHARMm19 force field) allow the user to rapidly create realistic, physically-based models with no atom clashes, correct bond lengths and angles, etc.

HIV Protease

 

The adaptive and multilevel algorithms rely on a hierarchical representation of molecular systems. The image below shows the assembly tree of a tetra-alanin, which describes the sequence of assembly operations.

Assembly tree


Minimization

SAMSON features adaptive algorithms for steepest descent and conjugate gradient minimization.


Experimental maps

SAMSON can load density maps obtained from crystallography or cryo-EM experiments. The user can interactively deform the molecular models and align them with the maps. Interactive alignment may be performed using any edition mode (adaptive, multilevel, etc.). Additionally, a force field derived from the density map may be automatically applied to the molecular system to facilitate alignment.

Interactive fitting

Interactive fitting

 

Symmetry and periodicity

SAMSON allows for interactive edition of molecular systems with arbitrary symmetry and periodicity. In the examples below, only one asymmetric unit is loaded in memory, but the simulation algorithms compute the interactions between this unit and all its replicas, so that the user may model complex systems (e.g. virus shells, fibers, etc.) on a desktop computer.

Foot And Mouth Disease VirusMicrotubule


Fast computation of interaction forces

SAMSON features generalized, adaptive multipole methods to compute the electrostatics of molecular systems. Adaptivity enables fast update of electrostatic terms when low precision is required.


Open architecture

Following modern design principles of modeling and simulation applications, SAMSON will have an open architecture, and  most functions are implemented as plug-ins. This will allow everyone to adapt SAMSON to their needs by quickly developing specialized plug-ins or scripts for parsing, modeling, editing, simulating, and visualizing nanosystems.