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SAMSON 2021.png
The main user interface.
Stable release
SAMSON 2021 / 2021
Written inC++ (Qt)
Operating systemWindows, macOS, Linux
Platformx86, x86-64
Available inEnglish
TypeMolecular design

SAMSON (Software for Adaptive Modeling and Simulation Of Nanosystems) is a computer software platform for molecular design being developed by OneAngstrom and previously by the NANO-D group at the French Institute for Research in Computer Science and Automation (INRIA).[2]

SAMSON has a modular architecture that makes it suitable for different domains of nanoscience, including material science,[3] life science,[4] and drug design[5].[6][7][8][9][10][11]

SAMSON Elements

SAMSON Elements are modules for SAMSON, developed with the SAMSON software development kit (SDK). SAMSON Elements help users perform tasks in SAMSON, including building new models, performing calculations, running interactive or offline simulations, and visualizing and interpreting results.

SAMSON Elements may contain different class types, including for example:

SAMSON Elements expose their functions to SAMSON and other Elements through an introspection mechanism, and may thus be integrated and pipelined.

Modeling and simulation

SAMSON represents nanosystems using five categories of models:

Simulators (potentially interactive ones) are used to build physically-based models, and predict properties.

Data graph

All models and simulators are integrated into a hierarchical, layered structure that form the SAMSON data graph. SAMSON Elements interact with each other and with the data graph to perform modeling and simulation tasks. A signals and slots mechanism makes it possible for data graph nodes to send events when they are updated, which makes it possible to develop e.g., adaptive simulation algorithms.[12][13][14]

Node specification language

SAMSON has a node specification language (NSL) that users may employ to select data graph nodes based on their properties. Example NSL expressions include:


SAMSON is developed in C++ and implements many features to ease developing SAMSON Elements, including:

SAMSON Connect

SAMSON, SAMSON Elements and the SAMSON Software Development Kit are distributed via the SAMSON Connect website.[6] The site acts as a repository for the SAMSON Elements being uploaded by developers, and users of SAMSON choose and add Elements from SAMSON Connect.

See also


  1. ^ "Terms of use". SAMSON Connect. Retrieved 2020-05-30.
  2. ^ NANO-D - INRIA
  3. ^ Contreras, M. Leonor; Villarroel, Ignacio; Rozas, Roberto (2021). "Automated Generation of Zigzag Carbon Nanotube Models Containing Haeckelite Defects". Intelligent Computing. Lecture Notes in Networks and Systems. Vol. 284. pp. 371–377. doi:10.1007/978-3-030-80126-7_28. ISBN 978-3-030-80125-0. S2CID 238030853.
  4. ^ Mostafa, Amr A.; El-Rahman, Soheir N. Abd; Shehata, Said; Abdallah, Naglaa A.; Omar, Hanaa S. (2021). "Assessing the effects of a novel biostimulant to enhance leafminer resistance and plant growth on common bean". Scientific Reports. 11 (1): 20020. doi:10.1038/s41598-021-98902-z. PMC 8501134. PMID 34625596.
  5. ^ Barazorda-Ccahuana, Haruna Lux; Nedyalkova, Miroslava; Mas, Francesc; Madurga, Sergio (2021). "Unveiling the Effect of Low pH on the SARS-CoV-2 Main Protease by Molecular Dynamics Simulations". Polymers. 284 (21): 3823. doi:10.3390/polym13213823. PMID 34771379.
  6. ^ a b SAMSON Connect
  7. ^ SAMSON 0.7.0 is available - Macs in Chemistry
  8. ^ RDKit in SAMSON - Macs in Chemistry
  9. ^ Vaucher, Alain C.; Reiher, Markus (2016). "Molecular Propensity as a Driver for Explorative Reactivity Studies". Journal of Chemical Information and Modeling. 56 (8): 1470–1478. arXiv:1604.06748. doi:10.1021/acs.jcim.6b00264. PMID 27447367. S2CID 3549945.
  10. ^ Vaucher, Alain C.; Reiher, Markus (2017). "Steering Orbital Optimization out of Local Minima and Saddle Points Toward Lower Energy". Journal of Chemical Theory and Computation. 13 (3): 1219–1228. arXiv:1701.00128. doi:10.1021/acs.jctc.7b00011. PMID 28207264. S2CID 4406796.
  11. ^ Miao, Haichao; De Llano, Elisa; Sorger, Johannes; Ahmadi, Yasaman; Kekic, Tadija; Isenberg, Tobias; Gröller, M. Eduard; Barišić, Ivan; Viola, Ivan (2017). "Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures" (PDF). IEEE Transactions on Visualization and Computer Graphics. 24 (1): 1014–1024. doi:10.1109/TVCG.2017.2743981. PMID 28866510. S2CID 9479885.
  12. ^ Artemova, Svetlana; Redon, Stephane (2012). "Adaptively Restrained Particle Simulations". Physical Review Letters. 109 (19): 190201:1–5. Bibcode:2012PhRvL.109s0201A. doi:10.1103/PhysRevLett.109.190201. PMID 23215362.
  13. ^ Bosson, Mael; Grudinin, Sergei; Bouju, Xavier; Redon, Stephane (2012). "Interactive physically-based structural modeling of hydrocarbon systems". Journal of Computational Physics. 231 (6): 2581–2598. Bibcode:2012JCoPh.231.2581B. CiteSeerX doi:10.1016/
  14. ^ Bosson, Mael; Grudinin, Sergei; Redon, Stephane (2013). "Block-Adaptive Quantum Mechanics: An Adaptive Divide-and-Conquer Approach to Interactive Quantum Chemistry". Journal of Computational Chemistry. 34 (6): 492–504. doi:10.1002/jcc.23157. PMID 23108532. S2CID 2298570.