Publications

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J. Fernández-Recio, Computational structural analysis and energetics of protein interactions: identifying disease-associated residues, XXXVIII Congreso SEBBM. Valencia. 2015.
F. C. Lombardo, Mazzitelli, F. D., Vázquez, M., and Villar, P., Computing the Casimir energy using the point-matching method, Phys. Rev. D, vol. 80. American Physical Society, p. 065018, 2009.
P. Benedicte, Kosmidis, L., Quiñones, E., Abella, J., and Cazorla, F., A Confidence Assessment of WCET Estimates for Software Time Randomized Caches, 14th International Conference on Industrial Informatics (INDIN). IEEE, 2016.
B. Islam, Sgobba, M., Laughton, C., Orozco, M., Sponer, J., Neidle, S., and Haider, S., Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale., Nucleic acids research, vol. 41, no. 4. pp. 2723-35, 2013.
C. Pallara and Fernández-Recio, J., Conformational heterogeneity enhances protein-protein recognition, XXXVIII Congreso SEBBM. Valencia. 2015.
A. N. Naganathan and Orozco, M., The conformational landscape of an intrinsically disordered DNA-binding domain of a transcription regulator., The journal of physical chemistry. B, vol. 117, no. 44. pp. 13842-50, 2013.
G. Andreotti, de Vaca, I. Cabeza, Poziello, A., Monti, M. Chiara, Guallar, V., and Cubellis, M. Vittoria, Conformational Response to Ligand Binding in Phosphomannomutase2 INSIGHTS INTO INBORN GLYCOSYLATION DISORDER, Journal of Biological Chemistry, vol. 289. American Society for Biochemistry and Molecular Biology, pp. 34900–34910, 2014.
C. Pallara, Rueda, M., and Fernández-Recio, J., Conformational selection mechanism in protein-protein association: insights from docking, II Jornada de Bioinformàtica i Biologia Computacional (Barcelona). 2014.
L. Pérez-Cano, Eliahoo, E., Lasker, K., Wolfson, H. J., Glaser, F., Manor, H., Bernadó, P., and Fernández-Recio, J., Conformational transitions in human translin enable nucleic acid binding., Nucleic acids research, vol. 41, no. 21. pp. 9956-66, 2013.
H. Saneyoshi, Mazzini, S., Aviñó, A., Portella, G., González, C., Orozco, M., Marquez, V. E., and Eritja, R., Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer. Nucleic Acids Res. 2009 September; 37(17): 5589?5601, 2009.
S. Signorelli, Dans, P. D., E Coitiño, L., Borsani, O., and Monza, J., Connecting proline and γ-aminobutyric acid in stressed plants through non-enzymatic reactions, PLoS One, vol. 10, no. 3. p. e0115349, 2015.
M. Rueda, Ferrer, C., Meyer, T., Pérez, A., Camps, J., Hospital, A., Gelpí, J. L., and Orozco, M., A consensous view to Protein Dynamics. Proc. Natl. Acad. Sci. USA, 2007.
M. Jamroz, Orozco, M., Kolinski, A., and Kmiecik, S., Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field. JCT, 2013.
L. Kosmidis, Abella, J., Quiñones, E., Wartel, F., Farrall, G., and Cazorla, F., Containing Timing-Related Certification Cost in Automotive Systems Deploying Complex Hardware, 51th Design Automation Conference (DAC) 2014. San Francisco, United States, pp. 1–6, 2014.
R. González, Content Aware Architectures, Universitat Politècnica de Catalunya (UPC), 2009.
R. González, Cristal, A., Ortega, D., Veidenbaum, A., and Valero, M., A Content Aware Integer Register File Organization, International Symposium on Computer Architecture (ISCA 2004). IEEE/ACM Press, München, Germany, pp. 314–324, 2004.
R. González, Cristal, A., Ortega, D., and Valero, M., Content Aware Register File Organisation. Computer Architecture Department, Universitat Politècnica de Catalunya (UPC), 2003.
G. Fernandez, Abella, J., Quiñones, E., Rochange, C., Vardanega, T., and Cazorla, F., Contention in Multicore Hardware Shared Resources: Understanding of the State of the Art, 14th International Workshop on Worst-Case Execution Time Analysis. OASIcs, Madrid, Spain, pp. 31–42, 2014.
A. Jokanovic, Minkenberg, C., Sancho, J. C., Beivide, R., Rodriguez, G., and Labarta, J., Contention-aware Node Allocation Policy for High-performance Capacity Systems, Proceedings of the 2012 Interconnection Network Architecture: On-Chip, Multi-Chip Workshop. ACM, New York, NY, USA, pp. 5–8, 2012.
J. Jalle, Fernández, M., Abella, J., Andersson, J., Patte, M., Fossati, L., Zulianello, M., and Cazorla, F., Contention-Aware Performance Monitoring Counter Support for Real-Time MPSoCs, 11th IEEE International Symposium on Industrial Embedded Systems (SIES). 2016.
P. Fuentes, Vallejo, E., Garcia, M., Rodríguez, G., Minkenberg, C., and Valero, M., Contention-based Nonminimal Adaptive Routing in High-radix Networks, 29th IEEE International Parallel & Distributed Processing Symposium. pp. 103-112, 2015.
M. Orozco, Marchán, I., and Soteras, I., Continuum analysis of conformational sampling in solution, Continuum Solvation Models in Chemical Physics: Theory and Application, 2007.
M. Gonçalves, Jiménez-Guerrero, P., and Baldasano, J. M., Contribution of atmospheric processes affecting the dynamics of air pollution in South-Western Europe during a typical summertime photochemical episode, Atmospheric Chemistry and Physics, vol. 9, no. 3. COPERNICUS GESELLSCHAFT MBH , GERMANY, pp. 849-864, 2009.
M. Gonçalves, Jiménez-Guerrero, P., and Baldasano, J. M., Contribution of Atmospheric Processes Affecting the Dynamics of Air Pollution in Coastal Urban Areas of the Southwestern Mediterranean: Case of Barcelona. Harbours, Air Quality and Climate Change-HAQCC2008, Rotterdam (The Netherlands), 2008.
M. Gonçalves, Jiménez-Guerrero, P., and Baldasano, J. M., Contribution of atmospheric processes to photochemical pollution by using a process analysis tool in the north-eastern and central Iberian Peninsula. ACCENT/GLOREAM Workshop, Berlin (Germany), 2008.
P. Jiménez-Guerrero, Pérez, C., Jorba, O., and Baldasano, J. M., Contribution of Saharan dust in an integrated air quality system and its on-line assessment, Geophysical Research Letters, vol. 35, no. L03814. AMER GEOPHYSICAL UNION, UNITED STATES, pp. 1-6, 2008.
A. Folch, Costa, A., and Macedonio, G., Contributions from the FIRB Project: the APOLLO procedure and the FALL3D ash dispersal model. 1st SAVAA Users Workshop, Rome, 2009.
P. Jiménez-Guerrero, Parra, R., and Baldasano, J. M., Control of Ozone precursors in a very complex industrial terrain by using multiscale mested air quality models with fine spatial resolution (1km2)., Journal of the Air&Waste Management Association, vol. 55, no. August. AIR & WASTE MANAGEMENT ASSOC, UNITED STATES, pp. 1085-1099, 2005.
A. Pajuelo, González, A., and Valero, M., Control-Flow Independence Reuse via Dynamic Vectorization. IPDPS05, IEEE-ACM 19th International Parallel and Distributed Processing Symposium, 2005.
S. Girbal, Moretó, M., Grasset, A., Abella, J., Quiñones, E., Cazorla, F., and Yehia, S., On the Convergence of Mainstream and Mission Critical Markets, 50th Annual Design Automation Conference (DAC). ACM, Austin (Texas), United States, pp. 1–10, 2013.
G. D'Amico, Pappalardo, G., Wiegner, M., Trickl, T., Rizi, V., Sicard, M., Gerding, M., Papayannis, A., Amiridis, V., Mona, L., Mamouri, R. E., Balis, D., Bösenberg, J., Chaikovski, F., De Tomasi, F., Grigorov, I., Mattis, I., Mitev, V., Müller, D., Nickovic, S., Pérez, C., Pietruczuk, A., Pisani, G., Ravetta, F., and Rizi, V., Coordinated lidar observations of Saharan dust over Europe in the frame of EARLINET-ASOS project during CALIPSO overpasses: a case study analysis with modeling support. 3rd International Workshop on Mineral Dust. Leipzig, Germany, 2008.
C. Acosta, Cazorla, F., Ramirez, A., and Valero, M., Core to Memory Interconnection Implications for Forthcoming On-Chip Multiprocessors, 1st Workshop on Chip Multiprocessor Memory Systems and Interconnects (CMP-MSI 2007). 2007.
Y. Etsion, Ramirez, A., Badia, R. M., and Labarta, J., Cores as Functional Units: A Task-Based, Out-of-Order, Dataflow Pipeline, Advanced Computer Architecture and Compilation for Embedded Systems (ACACES). 2009.
S. Esteban-Martín, Fenwick, R. Bryn, AAdén, J. \, Cossins, B., Bertoncini, C. W., Guallar, V., Wolf-Watz, M., and Salvatella, X., Correlated Inter-Domain Motions in Adenylate Kinase, PLoS computational biology, vol. 10. Public Library of Science, p. e1003721, 2014.
B. R Fenwick, Orellana, L., Esteban-Martín, S., Orozco, M., and Salvatella, X., Correlated motions are a fundamental property of β-sheets., Nat Commun, vol. 5. p. 4070, 2014.
E. Onate, Codina, R., and Vázquez, M., Cost-efficiency analysis of finite element solutions for high speed Euler flows. Stuttgart (Germany), 1994.
R. Bertran, González, M., Martorell, X., Navarro, N., and Ayguadé, E., Counter-Based Power Modeling Methods: Top-Down vs. Bottom-Up, Computer Journal, vol. 56. pp. 198–213, 2013.
R. Bertran, González, M., Martorell, X., Navarro, N., and Ayguadé, E., Counter-Based Power Modeling Methods: Top-Down vs. Bottom-Up, The Computer Journal. 2012.
T. Nakashima, Tsubokura, M., Vázquez, M., Owen, H., and Doi, Y., Coupled analysis of unsteady aerodynamics and vehicle motion of a road vehicle in windy conditions, Computers & Fluids, vol. 80. pp. 1 - 9, 2013.
P. Lafortune, Aris, R., Vázquez, M., and Houzeaux, G., Coupled electromechanical model of the heart, Int. J. Numer. Meth. Bio. Engn., vol. 28. pp. 72-86, 2012.
P. Lafortune, Aris, R., Vázquez, M., and Houzeaux, G., Coupled Electromechanical Model of the Heart: Parallel Finite Element formulation, International Journal for Numerical Methods in Biomedical Engineering. John Wiley & Sons, 2012.
D. Mira, Zavala, M., Gövert, S., Kok, J., Vázquez, M., and Houzeaux, G., Coupling approach to account for heat losses in a practical combustor, 15th International Conference on Numerical Combustion. Avignon (F), 2015.
H. Owen, Houzeaux, G., Vázquez, M., Samaniego, C., and Calmet, H., Coupling free surface turbulent fluid flow and rigid body motion with the Parallel Finite Element code Alya. 2013.
R. Tolosana-Delgado, Soret, A., Jorba, O., Baldasano, J. M., and Sánchez-Arcilla, A., Coupling of WRF meteorological model to WAM spectral wave model through sea surface roughness at the Balearic Sea: impact on wind and wave forecasts, 9th European Geosciences Union Conference (EGU) General Assembly. Geophysical Research Abstracts, vol. 14. European Geosciences Union (EGU), 22-27 April, 2012. Viena, Austria, 2012.
I. Rivalcoba, DeGyves, O., Rudomin, I., and Pelechano, N., Coupling pedestrians with a simulated virtual crowd, GRAPP 2014. SciTePress, Lisboa, Portugal, pp. 312–321, 2014.
Coupling Protein Dynamics with Active Site Chemistry: a MM and QM tale, ICPP8 International Conference on Porphyrins and Phtalocyanines, Istanbul, Turkey. 2014.
V. Guallar, Coupling Protein Dynamics with Active Site Chemistry: a MM and QM tale, ICPP8 International Conference on Porphyrins and Phtalocyanines, Istanbul, Turkey. 2014.
C. Luque, Moretó, M., Cazorla, F., Gioiosa, R., Buyuktosunoglu, A., and Valero, M., CPU Accounting for Multicore Processors, IEEE Transactions on Computers, vol. 61. pp. 251–264, 2012.
C. Luque, Moreto, M., Cazorla, F., Gioiosa, R., Buyuktosunoglu, A., and Valero, M., CPU accounting in CMP Processors. In IEEE Computer Architecture Letters. Volume 9, 2009.
J. Carlos Rui Luque, CPU Accounting in Multi-Threaded Processors, 2014.

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