Publications

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Author Title [ Type(Asc)] Year
Journal
Y. Chen, Tascón, I., Neunuebel, R. M., Pallara, C., Brady, J., Kinch, L. N., Fernández-Recio, J., Rojas, A. L., Machner, M. P., and Hierro, A., Structural basis for Rab1 de-AMPylation by the Legionella pneumophila effector SidD., PLoS pathogens, vol. 9, no. 5. p. e1003382, 2013.
A. Rosell, Meury, M., Alvarez-Marimon, E., Costa, M., Pérez-Cano, L., Zorzano, A., Fernández-Recio, J., Palacín, M., and Fotiadis, D., Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc., Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 8. pp. 2966-71, 2014.
S. Ayuso-Tejedor, García-Fandiño, R., Orozco, M., Sancho, J., and Bernadó, P., Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering., Journal of molecular biology, vol. 406, no. 4. pp. 604-19, 2011.
A. Ramirez, Larriba-Pey, J. L., and Valero, M., A Stream Processor Front-end, IEEE Technical Committee on Computer Architecture Newsletter. pp. 10-13, 2000.
J. Oliver, Guitart, J., Ayguadé, E., Navarro, N., and Torres, J., Strategies for Efficient Exploitation of Loop-Level Parallelism in Java Concurrency and Computation, Concurrency and Computation: Practice and Experience, vol. 13, no. 8-9. pp. 663-680, 2001.
E. D. Babot, José, C., Cañellas, M., Sancho, F., Lucas, F., Guallar, V., Kalum, L., Lund, H., Gröbe, G., Scheibner, K., and , Steroid hydroxylation by basidiomycete peroxygenases: A combined experimental and computational study, Applied and environmental microbiology, vol. 81. American Society for Microbiology, pp. 4130–4142, 2015.
A. Hernández-Ortega, Ferreira, P., Merino, P., Medina, M., Guallar, V., and Martínez, A. T., Stereoselective Hydride Transfer by Aryl-Alcohol Oxidase, a Member of the GMC Superfamily., Chembiochem : a European journal of chemical biology. 2012.
J. L. Lérida, Solsona, F., Hernández, P., Giné, F., Hanzich, M., and Conde, J., State-based predictions with self-correction on Enterprise Desktop Grid environments, Journal of Parallel and Distributed Computing, vol. 73, no. 6. Elsevier, pp. 777-789, 2013.
J. - B. Girardo, Sharapov, S., Boom, J., Dumont, R., Eriksson, J., Fitzgerald, M., Garbet, X., Hawkes, N., Kiptily, V., Lupelli, I., Mantsinen, M., Sarazin, Y., Schneider, M., and , Stabilization of sawteeth with third harmonic deuterium ICRF-accelerated beam in JET plasmas, Physics of Plasmas (1994-present), vol. 23. AIP Publishing, p. 012505, 2016.
M. Perucho, Martí, J. M., Cela, J. M., Hanasz, M., de la Cruz, R., and Rubio, F., Stability of three-dimensional relativistic jets: implications for the FRI/FRII dichotomy, Astronomy & Astrophysics. 2009.
P. Villar, Spin bath interaction effects on the geometric phase, Physics Letters A, vol. 373. pp. 206 - 209, 2009.
A. Pajuelo, González, A., and Valero, M., Speculative Execution for Hiding Memory Latency. Computer Architecture News, 2005.
A. Queralt and Teniente, E., Specifying the Semantics of Operation Contracts in Conceptual Modeling, J. Data Semantics VII. pp. 33-56, 2006.
A. Aviñó, Portella, G., Ferreira, R., Gargallo, R., Mazzini, S., Gabelica, V., Orozco, M., and Eritja, R., Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures., The FEBS journal. 2013.
R. M. Badia, Gannon, D., and Lee, C., Special section: Selected papers from the 7th IEEE/ACM international conference on grid computing (Grid2006). Future Generation Computer Systems, 2008.
M. T. Pay, Jiménez-Guerrero, P., Jorba, O., Basart, S., Querol, X., Pandolfi, M., and Baldasano, J. M., Spatio-temporal variability of concentrations and speciation of particulate matter across spain in the caliope modeling system, Atmospheric Environment, vol. 46, no. January 2012. PERGAMON-ELSEVIER SCIENCE LTD, ENGLAND, pp. 376-396, 2012.
X. Rubio-Campillo, Cardona, F. X. H., and Gómez, M. Yubero, The Spatiotemporal Model of an 18th-Century City Siege, Social Science Computer Review. 2014.
M. Avila, Principe, J., and Codina, R., Spatial approximation of the radiation transport equation using a subgrid-scale finite element method, Computer Methods in Applied Mechanics and Engineering, vol. 200. pp. 425-438, 2011.
M. Viana, Pérez, C., Querol, X., Alastuey, A., and Baldasano, J. M., Spatial and temporal variability ofPM levels and composition in a complex summer atmospheric scenario in Barcelona (NE Spain), Atmospheric Environment, vol. 39, no. 29. PERGAMON-ELSEVIER SCIENCE LTD, ENGLAND , pp. 5343-5361, 2005.
A. Carrassi, Guemas, V., Doblas-Reyes, F. J., Volpi, D., and Asif, M., Sources of skill in near-term climate prediction. Part I: Generating initial conditions, Climate Dynamics. 2016.
R. Aubry, Houzeaux, G., Vázquez, M., and Cela, J. M., Some useful strategies for unstructured edge-based solvers on shared memory machines. Int. J. Numer. Engn., 2010.
A. Bidon-Chanal, Huertas, O., Orozco, M., and Luque, F. J., Solvation enthalpies of neutral solutes in water and octanol. Theor.Chem.Acc., 123, 11-20, 2009.
A. Ramirez, Larriba-Pey, J. L., Navarro, C., Valero, M., and Torrellas, J., Software Trace Cache for Commercial Applications, International Journal of Parallel Programming, vol. 30, no. 5. pp. 373-395, 2002.
A. Ramirez, Larriba-Pey, J. L., and Valero, M., Software Trace Cache, IEEE Transactions on Computers, vol. 54, no. 1. pp. 22-35, 2005.
J. Zalamea, Llosa, J., Ayguadé, E., and Valero, M., Software and Hardware Techniques to Optimize Register File Utilization in VLIW. International Journal of Parallel Programming, 2004.
A. Morari, Boneti, C., Cazorla, F., Gioiosa, R., Cher, C. - Y., Buyuktosunoglu, A., Bose, P., and Valero, M., SMT Malleability in IBM POWER5 and POWER6 Processors, IEEE Transactions on Computers, vol. 00. 2012.
E. M. Novoa, de Pouplana, L. R., and Orozco, M., Small Molecule Docking from Theoretical Structural Models, Computational Modeling of Biological Systems Biological and Medical Physics, Biomedical Engineering. pp. 75-95 , 2012.
M. Macías and Guitart, J., SLA Negotiation and Enforcement Policies for Revenue Maximization and Client Classification in Cloud Providers, Future Generation Computer Systems, vol. 41. pp. 19–31, 2014.
I. H. Moal and Fernández-Recio, J., SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models., Bioinformatics (Oxford, England), vol. 28, no. 20. pp. 2600-7, 2012.
F. M. Lucas and Guallar, V., Single vs. multiple ligand pathways in globins: A computational view., Biochimica et biophysica acta. 2013.
F. M. Lucas and Guallar, V., Single vs. multiple ligand pathways in globins: A computational view., Biochimica et biophysica acta. 2013.
E. Fadrná, Spacková, N., Sarzyñska, J., Koca, J., Orozco, M., Cheatham, T. E., and Sponer, J., Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields. J. Chem. Theory Comput., 2009, 5 (9), pp 2514?2530, 2009.
S. Marras, Moragues, M., Vázquez, M., Jorba, O., and Houzeaux, G., Simulations of moist convection by a variational multiscale stabilized finite element method, Journal of Computational Physics, vol. 252. pp. 195-218, 2013.
S. Marras, Moragues, M., Vázquez, M., Jorba, O., and Houzeaux, G., Simulations of moist convection by a variational multiscale stabilized finite element method, Journal of Computational Physics, vol. 252. ACADEMIC PRESS INC ELSEVIER SCIENCE, UNITED STATES, pp. 195 - 218, 2013.
A. Rico, Cabarcas, F., Villavieja, C., Pavlovic, M., Vega, A., Etsion, Y., Ramirez, A., and Valero, M., On the Simulation of Large-scale Architectures Using Multiple Application Abstraction Levels, ACM Transactions on Architecture and Code Optimization, vol. 8. p. 36, 2012.
J. González, Giménez, J., Casas, M., Moretó, M., Ramirez, A., Labarta, J., and Valero, M., Simulating Whole Supercomputer Applications, IEEE Micro, vol. 31. IEEE, pp. 32-45, 2011.
X. Rubio-Campillo, Cela, J. M., and Hernández, F. X., Simulating archaeologists? Using agent-based modelling to improve battlefield excavations, Journal of Archaeological Science, no. 39. pp. 347-356, 2012.
B. Hernandez, Perez, H., Isaac, R., Ruiz, S., DeGyves, O., and Toledo, L., Simulating and Visualizing Real-Time Crowds on GPU Clusters, Computación y Sistemas, vol. 18. pp. 651–664, 2014.
J. R. Amores and Houzeaux, G., Simulación numérica de flujo sanguineo: una herramienta útil en cirugía vascular. Angiología, 2003.
J. Prat, Antonijuan, J., Folch, A., Sala, A., Lucchetti, A., Sardà, F., and Manuel, A., A simplified model of the interaction of the trawl warps, the otterboards and netting drag, Fisheries Research, vol. 94, no. 1. ELSEVIER SCIENCE BV, NETHERLANDS, pp. 109-117, 2008.
A. Arbona, Artigues, A., Bona-Casas, C., Massó, J., Miñano, B., Rigo, A., Trias, M., and Bona, C., Simflowny: A general-purpose platform for the management of physical models and simulation problems, Computer Physics Communications, vol. 184, no. 10. Elsevier, pp. 2321–2331, 2013.
A. Roca, HernáNdez, C., Flich, J., Silla, F., and Duato, J., Silicon-aware Distributed Switch Architecture for On-chip Networks, J. Syst. Archit., vol. 59. Elsevier North-Holland, Inc., New York, NY, USA, pp. 505–515, 2013.
L. Lin, Huhs, G., Garcia, A., and Yang, C., SIESTA-PEXSI: Massively parallel method for efficient and accurate ab initio materials simulation, Bulletin of the American Physical Society, vol. 59. APS, 2014.
L. Lin, Garcia, A., Huhs, G., and Yang, C., SIESTA-PEXSI: massively parallel method for efficient and accurate ab initio materials simulation without matrix diagonalization, Journal of Physics: Condensed Matter, vol. 26. IOP Publishing, p. 305503, 2014.
P. Nithiarasu, Zienkiewicz, O. C., Satya Sai, B. V. K., Morgan, K., Codina, R., and Vázquez, M., Shock capturing viscosities for the general fluid mechanics algorithm. Int. J. Num. Meth. Fluids, 1998.
A. Gambaruto, Janela, J., Moura, A., and Sequeira, A., Shear-thinning effects of hemodynamics in patient-specific cerebral aneurysms, MBE, vol. 10. American Institute of Mathematical Sciences (AIMS), pp. 649–665, 2013.
A. Costa, Chiodini, G., Granieri, D., Folch, A., Hankin, R., Caliro, S., Avino, R., and Cardellini, C., A shallow-layer model for heavy gas dispersion from natural sources: Application and hazard assessment at Caldara di Manziana, Italy, Geochemistry Geophysics Geosystems, vol. 9, no. Q03002. AMER GEOPHYSICAL UNION , UNITED STATES, pp. 1-13, 2008.
M. Habibian, Martínez-Montero, S., Portella, G., Chua, Z., D Bohle, S., Orozco, M., and Damha, M. J., Seven-Membered Ring Nucleoside Analogues: Stereoselective Synthesis and Studies on Their Conformational Properties., Org Lett, vol. 17, no. 21. pp. 5416-5419, 2015.
F. Lordan, Tejedor, E., Ejarque, J., Rafanell, R., Álvarez, J., Marozzo, F., Lezzi, D., Sirvent, R., Talia, D., and Badia, R. M., ServiceSs: an interoperable programming framework for the Cloud, Journal of Grid Computing, vol. 12. Springer Netherlands, pp. 67-91, 2014.
J. Ejarque, Álvarez, J., Sirvent, R., and Badia, R. M., Service Orchestration on a Heterogeneous Cloud Federation, Computing and Informatics, vol. 31. pp. 45–60, 2012.

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