(For authors only) Acknowledgement formulations

For publications by people working on the project:

"This work has been partially funded by the EU Commission (contract INFSO-RI-261523) through collaboration with ScalaLife"

For publications that were facilitated through ScalaLife (e.g. help of experts, etc.)

"This work makes use of results produced by the ScalaLife project which is co-funded by the European Commission (under contract number INFSO-RI-261523). More information is available at http://www.scalalife.eu".

Scientific Publications

1. (Journal) Tim Meyer, Marco D’Abramo, Adam Hospital, Manuel Rueda, Carles Ferrer-Costa, Alberto Pérez, Oliver Carrillo, Jordi Camps, Carles Fenollosa, Dmitry Repchevsky, Josep Lluis Gelpí, and Modesto Orozco: MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories, 18/11, P. 1399-1409, (2010), (doi:10.1016/j.str.2010.07.013).
2. (Book chapter) Modesto Orozco, Laura Orellana, Adam Hospital, Athi N. Naganathan, Agustí Emperador, Oliver Carrillo and J.L.Gelpí: Coarse Grained Representation of Protein Flexibility. Foundations, Successes and Shortcomings,  In "Computational Chemistry Methods in Structural Biology". Advances in Protein Chemistry and Structural Biology, vol. 80. Ed. C. Christov. Elsevier (2010)
   Note: Articles (1) and (2) are directly related to the achivements in WP7-Interface Definitions & Data Exchange
3. (Journal) Z. Rinkevicius, N. A. Murugan, J. Kongsted, K. Aidas, A. H. Steindal, and H. Ågren, "Density Functional Theory/Molecular Mechanics Approach for Electronic g-Tensors of Solvated Molecules", J. Phys. Chem. B., http://pubs.acs.org/doi/abs/10.1021/jp1108653
   Note: Article (3) is directly related to the achivements in Dalton software
4. (Proceedings) Rossen Apostolov, Lilit Axner, Hans Agren, Eduard Ayugade, Mihai Duta, Jose Luis Gelpi, Judit Gimenez, Ramon Goni, Berk Hess, Ferdinand Jamitzky, Dieter Kranzmuller, Jesus Labarta, Erwin Laure, Erik Lindahl, Modesto Orozco, Magnus Peterson, Helmut Satzger, AnneTrefethen, "ScalaLife - Scalable Software Services for Life Science", in Proceedings of 9th HealthGrid conference (2011)
   Note: Article (4) is directly related to the ScalaLife Competence Center
5. (Proceedings) Xavier Aguilar, Michael Schliephake, Olav Vahtras, Judit Gimenez and Erwin Laure, "Scaling Dalton, a molecular electronic structure program" in 7th IEEE International Conference on eScience (eScience 2011)
6. (Journal) Z. Rinkevicius, N. A. Murugan, J. Kongsted, B. Frecuş, A. H. Steindal, and H. Ågren, "Density Functional Restricted–Unrestricted/Molecular Mechanics Theory for Hyperfine Coupling Constants of Molecules in Solution", J. Chem. Theory Comput., Articles ASAP,  2011. DOI: 10.1021/ct2003572
   Note: Articles (5) and (6) are directly related to the achivements in Dalton software
7. (Online) ScalaLife in Scientific Computer World: http://www.bsc.cat/about-bsc/press/bsc-in-the-media/visualising-future-medicine or http://www.scientific-computing.com/signIn.php?issue_id=22&pageStartFrom=42
8. (Journal) Joakim P. M. Jämbeck, Alexander P. Lyubartsev, "An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes", J. Chem. Theory Comput., DOI: 10.1021/ct300342n, June 26, 2012
9. (White paper) Simen Reine,Thomas Kjærgaard, Trygve Helgaker, Olav Vahtras, Zilvinas Rinkevicius, Bogdan Frecus, Thomas W. Keal, Andrew Sunderland, Paul Sherwood, Michael Schliephake, Xavier Aguilar, Lilit Axner, Maria Francesca Iozzi, Ole Widar Saastad, Judit Gimenez, "Petascaling and Performance Analysis of DALTON on Different Platforms", PRACE white paper: (http://www.prace-ri.eu/IMG/pdf/Petascaling_and_Performance_Analysis_of_D...)
10. (White paper) Fabio Affinito, Andrew Emerson, Leandar Litov, Peicho Petkov, Rossen Apostolov, Lilit Axner, Berk Hess, Erik Lindahl, Maria Francesca Iozzi, "Performance Analysis and Petascaling Enabling of GROMACS", PRACE white paper (http://www.prace-ri.eu/IMG/pdf/Performance_Analysis_and_Petascaling_Enab...)
11. (Journal) Joakim P.M. Jämbeck and Alexander P. Lyubartsev, "Another Piece of the Membrane Puzzle: Extending Slipids Further", J. Chem. Theory Comput., DOI: 10.1021/ct300777p
12. (Proceedings) Rossen Apostolov, Hans Agren, Lilit Axner, Eduard Ayguade, Mihai Duta, Jose Luis Gelpi, Judit Gimenez, Ramon Goni,
    Berk Hess, Ferdinand Jamitzky, Dieter Kranzmueller, Jesus Labarta, Erwin Laure, Erik Lindahl, Modesto Orozco, Magnus Peterson,
    Helmut Satzger, Albert Solernou, Anne Trefethen, "ScalaLife – Scalable Software Services for Life Sciences" in eChallenges e-2012 Conference Proceedings, (2012). View paper
13. (Journal) Pedro Sfriso, Agusti Emperador, Laura Orellana, Adam Hospital, Josep Lluis Gelpí, and Modesto Orozco, "Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations", J. Chem. Theory Comput., 2012, 8 (11), pp 4707–4718, DOI: 10.1021/ct300494q (August 23, 2012)
14. (Journal) X. Aguilar, M. Schliephake, O. Vahtras, J. Gimenez, and E. Laure, "Scalability analysis of Dalton, a molecular structure program", Future Generation Computer Systems, Elsevier, (to appear 2013).
15. (Journal) Jaime Axel Rosal Sandberg and Zilvinas Rinkevicius, "An algorithm for the efficient evaluation of two-electron repulsion integrals over contracted Gaussian-type basis functions", J. Chem. Phys. 137, 234105 (2012)
16. (Journal) Adam Hospital, Pau Andrio, Carles Fenollosa, Dmjan Cicin-Sain, Modesto Orozco and Josep Ll. Gelpí. "MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.Bioinformatics. ;28(9):1278-1279.  (2102) DOI: 10.1093/bioinformatics/bts139
    Note: Article (16) is directly related to the achivements in WP7-Interface Definitions & Data Exchange
17. (Journal) Raimondi, F.; Felline, A.; Portella, G.; Orozco, M and Fanelli, F. “Light on the structural communication in Ras GTPases”, J. Biomol. Struct. and Dyn. iFirst, 2012, 1-16
18. (Journal) Carrillo, O., Laughton, C. and Orozco, M. “Fast Atomistic Molecular Dynamics Simulations from Essential Dynamics Samplings”, J. Chem. Theor. Comput., 2012, 8, 792-799
19. (Journal) Fernanda Rodriguez, Sarah L. Rouse, Claudia E. Tait, Jeffrey Harmer, Antonio De Riso, Christiane R. Timmel, Mark S. P. Sansom, Ben C. Berks and Jason R. Schnell, "Structural model for the protein-translocating element of the twin-arginine transport system", March 7, 2013, doi: 10.1073/pnas.1219486110, PNAS March 19, 2013
20. (Journal) Agusti Emperador, Albert Solernou, Pedro Sfriso, Carles Pons, Josep Lluis Gelpi, Juan Fernandez-Recio and Modesto Orozco, "Efficient Relaxation of Protein–Protein Interfaces by Discrete Molecular Dynamics Simulations",
    
    J. Chem. Theory Comput., 2013, 9 (2), pp 1222–1229,DOI: 10.1021/ct301039e.
21. (Brochure) Satzger et. al, "Supercomputing at the Leading Edge", published by Gauss Centre for Supercompuing, for ISC2013 (2013)
22. (Proceedings) A. Solernou, J. Thiyagalingam, M. C. Duta, A. E. Trefethen, "The Effect of Topology-Aware Process and Thread Placement on Performance and Energy", Lect. Notes Comput. Sci., 7905., 2013
     

Poster presentations

1. Joakim P. M. Jämbeck, Alexander P. Lyubartsev, "Stockholm lipids: a refined all-atom force field for phospholipids", SeRC Third Annual Meeting 24 April 2012, Stockholm.  View poster.