Office of Information Technology University of São Paulo

Rice University

Blue Gene/P

In 2012, USP and William Marsh Rice University have signed a deal to promote the development of research and other academic and cultural activities, included an agreement  for academic cooperation and an agreement for the shared use of a supercomputer.

In the academic agreement it is foreseen the interchange of teachers and researchers , the ensemble elaboration of research projects; the organization of scientific and cultural events; the interchange of academic  scientific information and publications, student interchange, interchange of technical and administrative people; shared courses and curricula. The agreement previews the shared administrations and use of a Blue Gene supercomputer with 24576 nuclei (86 TeraFlops).

This machine should help to construct a sinergistic scientifc colaboration between the two universities. By this agreement USP´s share accounts to 30% of the supercomputer usage, in studies related to engineering, physiscs, material strucutre, astronomy, weather forecast, atmospheric sciences, climate studies, environment, pharmacy products design and biotechnology.

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Academic Works

Articles Published
Cucchieri, Attilio; Mendes, Tereza, Ghost sector and geometry in minimal Landau gauge: further constraining the infinite-volume limit,   Phys.Rev. D88 (2013) 114501, 22 pags.

Eleno, Luiz T.F.; Errico, Leonardo A.; Gonzales-Ormeño, Pablo G.; Petrilli, Helena M.; Schön, Cláudio G. Ordering phase relationships in ternary iron aluminides. Calphad 44 (2013) 70.

Gustavo G. Rondina and Juarez L. F. Da Silva, Revised Basin Hopping Monte Carlo Algorithm for Structure Optimization of Clusters and Nanoparticles, dx.doi.org/10.1021/ci400224z | J. Chem. Inf. Model. 2013, 53, 2282−2298.

L.F. Martins, L. P. Antunes, R.C. Pascon, J.C. Franco de Oliveira, L.A. Digiampietri, D. Barbosa, B.M. Peixoto, M.A. Vallim, C. Viana-Niero, E.H. Ostroski, G.P. Telles, Z. Dias, J.B. da Cruz, L. Juliano, S. Verjovski-Almeida, A.M. da Silva, J.C. Setubal. Metagenomic analysis of a tropical composting operation at the São Paulo Zoo Park reveals diversity of biomass degradation functions and organisms. PLoS ONE, 8(4):e61928, 2013.

Rondina, G. G.; Da Silva, J. L. F. Revised Basin-Hopping Monte Carlo algorithm for structure optimization of clusters and nanoparticles. Journal of Chemical Information and Modeling, v. 53, n. 9, p. 2282–2298, 2013.

Symmetry Breaking and Bose-Ghost Propagator in Lattice Minimal Landau Gauge Attilio Cucchieri, David Dudal, Tereza Mendes e Nele Vandersickel Phys. Rev. D90 (2014), 051501(R)

Presentations of work
Rosset, L. M.; Nardin, L. G. & Sichman, J. S. Use of high performance computing in agent-based social simulation: A case study on trust-based coalition formation Anais do VII Workshop-Escola de Sistemas de Agentes, seus Ambientes e apliCações (WESAAC’13), 2013, 161-163

Rosset, L. M.; Nardin, L. G. & Sichman, J. S. Simulação de parcerias entre agentes autônomos Anais do 21o Simpósio Internacional de Iniciação Científica (SIICUSP), Universidade de São Paulo, 2013

Cucchieri,  Attilio; Dudal, David; Mendes , Tereza,  e Vandersickel, Nele , Evidence of BRST-Symmetry Breaking in Lattice Minimal Landau Gauge , PoS LATTICE2014 (2015) 347

Cucchieri,  Attilio e Mendes , Tereza,  Crossing the Gribov horizon: an unconventional study of geometric properties of gauge-configuration space in Landau gauge, PoS LATTICE2013 (2014) 367 BRST

Vequi-Suplicy, C.C.; Rusu, V. H.; Lins, R. D.; Coutinho, K. Characterization of structural and electronic properties of 2’-palmitoyluridine (2UP) and 3’- palmitoyluridine (3UP) in vacuum and in solvents, apresentado na School on Computational Trends in Solvation and Transport in Liquids

L. T. Rangel and J.C. Setubal. Analysis of Proteobacteria Genomes Using Phylogenomic Networks. Poster apresentado no Brazilian Symposium on Bioinformatics, 2012.

L.T. Rangel and J.C. Setubal. Horizontal Gene Transfer and Nitrogen Fixation Genes in Gamma- and Beta-proteobacteria. Poster apresentado no workshop RECOMB-CG, Lyon, França, 2012.

Master´s Thesis
Rondina, Gustavo Garcia. Novas ideias para o Método de Basin-Hopping Monte Carlo aplicado à otimização global de Clusters e Nanopartículas [online]. São Carlos : Instituto de Física de São Carlos, Universidade de São Paulo, 2013. Dissertação de Mestrado em Física Aplicada. Disponível em: <http://www.teses.usp.br/teses/disponiveis/76/76132/tde-17012014-161604/>

PhD. Thesis
Franco-Soto, D.C. (2014). Modelos Birnbaum-Saunders para sobrevivência com dados longitudinais. Departamento de Estatística, Instituto de Matemática e Estatística, Universidade de São Paulo (coorientação com Antonio Carlos Pedroso de Lima)

Ricardo Oliveira dos Santos Soares, Processos preliminares da infecção viral: estudo estereoquímico da proteína E do Dengue,  Faculdade de Ciências Farmacêuticas de Ribeirão Preto, orientador Prof. Dr. Antonio Caliri

Works in progress or accepted for publication

Articles
Cucchieri,  Attilio e Mendes , Tereza, “Crossing the Gribov horizon: an unconventional study of geometric properties of gauge-configuration space in Landau gauge” a ser publicado nos anais PoS LATTICE2013 (2013)

Cucchieri,  Attilio; Dudal, David; Mendes , Tereza,  e Vandersickel, Nele ,  “BRST-Symmetry Breaking and Bose-Ghost Propagator in Lattice Minimal Landau Gauge” a ser submetido ao Phys. Rev. Lett.

Cucchieri,  Attilio e Mendes , Tereza,, Numerical Evaluation of the Bose-Ghost Propagator in Minimal Landau Gauge a ser a ser submetido para publicação no Phys. Rev. D

Diego G. Sobrinho, Maurício J. Piotrowski, and Juarez L. F. Da Silva, The effects of environment effects in the stability of Pt and Au nanoclusters, manuscript in preparation.

Diego G. Sobrinho, Ricardo K. Nomiyama, Anderson S. Chaves, Maurício J. Piotrowski, and Juarez L. F. Da Silva, The stability of Platinum-based nanoalloys: A DFT investigation, manuscript in preparation.

Nardin, L. G.; Rosset, L. M. & Sichman, J. S. Adamatti, D. F.; Dimuro, G. P. & Coelho, H. (Eds.) Scale and topology effects on agent-based simulation: A trust-based coalition formation case study Interdisciplinary applications of agent-based social simulation and modeling, IGI Global, In the press

Scientific Initiation
Jacy Ellen Guimarães Silva (Metallurgical Engineering)

Master´s degree
Thaícia Stona de Almeida (Metallurgical Engineering)

Doctoral Degree
Diego Guedes Sobrinho – start in 2013.