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12 Sep

Publications 2018-2019

Thanks to everyone that reported your publications supported by the UPR HPCf. From October 2018 to September 2019 we supported 45 publications!

Please remember the HPCf runs mainly with external funding, please acknowledge our active awards. You can use

Research reported in this publication was supported by National Institute for General Medical Sciences (NIGMS) of the National Institutes of Health under award number P20GM103475. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

7 publications with PMCID Complete & Acknowledge HPCf or INBRE grant

  1. Vélez V, Carrasquillo K, Santini J, Ramos Y, Vázquez L, Roche A, Rodríguez J, Parés E. Modelling and molecular docking studies of the cytoplasmic domain of Wsc-family, full-length Ras2p, and therapeutic antifungal compounds. Comput Biol Chem. 2019 Feb; 78:338-352 PMCID: PMC6377308. (BIRC, ADM & CRI) Impact Factor: 1.41
  2. Chorna N.E., Chornyy A.P. (2019) Metabolomics Analysis of Glutamate Receptor Function. In: Burger C., Velardo M. (eds) Glutamate Receptors. Methods in Molecular Biology, vol 1941. Humana Press, New York, NY. PMCID: PMC6413523 (BIRC, CRI) Book Chapter
  3. Forestier-Román IS, López-Rivas A, Sánchez-Vázquez MM, Rohena-Rivera K,Nieves-Burgos G, Ortiz-Zuazaga H, Torres-Ramos CA, Martínez-Ferrer M. Andrographolide induces DNA damage in prostate cancer cells. Oncotarget. 2019 Feb 1;10(10):1085-1101. doi: 10.18632/oncotarget.26628. eCollection 2019 Feb 1. PubMed PMID: 30800220; PubMed Central PMCID: PMC6383681. Impact Factor: 4.78
  4. Pedraza-Marrón CDR, Silva R, Deeds J, Van Belleghem SM, Mastretta-Yanes A, Domínguez-Domínguez O, Rivero-Vega RA, Lutackas L, Murie D, Parkyn D, Bullock LH, Foss K, Ortiz-Zuazaga H, Narváez-Barandica J, Acero A, Gomes G, Betancur-R R. Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation. Proc Biol Sci. 2019 Apr 10;286(1900):20182924. doi:10.1098/rspb.2018.2924. PubMed PMID: 30940064; PubMed Central PMCID: PMC6501682. Impact Factor: 4.30
  5. Ribeiro E, Davis AM, Rivero-Vega RA, Ortí G, Betancur-R R. Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes. Proc Biol Sci. 2018 Dec 19;285(1893):20182010. doi: 10.1098/rspb.2018.2010. PubMed PMID: 30963906; PubMed Central PMCID: PMC6304066 Impact Factor: 4.30
  6. Pagán-Jiménez M, Ruiz-Calderón JF, Dominguez-Bello MG, García-Arrarás JE. Characterization of the intestinal microbiota of the sea cucumber Holothuria glaberrima. PLoS One. 2019 Jan 30;14(1):e0208011. doi:10.1371/journal.pone.0208011. eCollection 2019. PubMed PMID: 30699110; PubMed Central PMCID: PMC6353073. (BIRC, DRPP, CRI) Impact Factor: 2.77
  7. Morales-Ortíz J, Deal V, Reyes F, Maldonado-Martínez G, Ledesma N, Staback F, Croft C, Pacheco A, Ortiz-Zuazaga H, Yost CC, Rowley JW, Madera B, John AS, Chen
  8. J, Lopez J, Rondina MT, Hunter R, Gibson A, Washington AV. Platelet-derived TLT-1 is a prognostic indicator in ALI/ARDS and prevents tissue damage in the lungs in a mouse model. Blood. 2018 Dec 6;132(23):2495-2505. doi:10.1182/blood-2018-03-841593. Epub 2018 Oct 3. PubMed PMID: 30282800; PubMed Central PMCID: PMC6284217. (BIRC, ADM) Impact Factor: 16.52

3 Publications with PMCID in process that acknowledge HPCf or INBRE

  1. Rincon-Sandoval M, Betancur-R R, Maldonado-Ocampo JA. Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers. Mol Ecol. 2019 Mar;28(5):1096-1115. doi:10.1111/mec.15036. PubMed PMID: 30714250. Impact Factor: 5.85
  2. Betancur-R R, Arcila D, Vari RP, Hughes LC, Oliveira C, Sabaj MH, Ortí G. Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes. Evolution. 2019 Feb;73(2):329-345. doi: 10.1111/evo.13649. Epub 2018 Dec 4. PubMed PMID: 30426469 Impact Factor: 3.57
  3. Yan Gao,a Yuee Xie,a Yuanping Chen, Jinxing Gub and Zhongfang Chen. Spindle nodal chain in three-dimensional α′ boron. Phys. Chem. Chem. Phys., 2018,20, 23500-23506. PMID: 30183022 Impact Factor: 3.56

9 Publications that acknowledge HPCf or INBRE

  1. D. Derilus, A. Forestil, J. Fortuné, O. Polyanska, C. Louime, G. Gervais, and S. E. Massey. (2019). Functional Metagenomics Characterization of an Anaerobic Saltwater Bioreactor. Journal of Renewable Energy Volume 2019, Article ID 4527628. https://doi.org/10.1155/2019/4527628 Impact Factor: 1.51
  2. Shijun YuanHui, DingJinlan Wang, Zhongfang Chen. Extraordinary Magnetoresistance in Janus Monolayer MoTeB2: A Theoretical Prediction. 2018. J. Phys. Chem. C20181224928423-28430. Impact Factor: 2.83
  3. Gu, J., Magagula, S., Zhao, J., Chen, Z., Boosting ORR/OER Activity of Graphdiyne by Simple Heteroatom Doping. Small Methods 2019, 1800550. https://doi.org/10.1002/smtd.201800550. Impact Factor: 8.64
  4. Xiangyu Guo, Jinxing Gu, Xuemin Hu, Shengli Zhang, Zhongfang Chen, Shiping Huang, Coordination tailoring towards efficient single-atom catalysts for N2 fixation: A case study of iron-nitrogen-carbon (Fe@N-C) systems, Catalysis Today, 2019. Impact Factor: 4.88
  5. Sandra C. Albarracín-Suazo, Yomaira J. Pagán-Torres, and María C. Curet-Arana. DFT Study on the Effect of Aluminum Position in Zn-Exchanged MFI on Methane Activation. The Journal of Physical Chemistry C 2019 123 (26), 16164-16171 DOI: 10.1021/acs.jpcc.9b02487. Impact Factor: 2.83
  6. Brian D. Montejo-Valencia and María C. Curet-Arana. Periodic DFT Study of the Opening of Fructose and Glucose Rings and the Further Conversion of Fructose to Trioses Catalyzed by M-BEA (M = Sn, Ti, Zr, or Hf). The Journal of Physical Chemistry C. 2019 123 (6), 3532-3540. DOI: 10.1021/acs.jpcc.8b10211 Impact Factor: 2.83
  7. Jovadell Cruz, Luis Raúl Pericchi. 2018. Sequential Bayesian Tests and the Hypothesis of independent or naive Bayes. Rev. Fac. Cienc., Volumen 7, Número 1, p. 112-123, 2018. ISSN electrónico 2357-5549. ISSN impreso 0121-747X. DOI: https://doi.org/10.15446/rev.fac.cienc.v7n1.67107
  8. Zhao, Y., Zhang, J.‐J., Yuan, S., Chen, Z., Nonvolatile Electrical Control and Heterointerface‐Induced Half‐Metallicity of 2D Ferromagnets. Adv. Funct. Mater. 2019, 29, 1901420. https://doi.org/10.1002/adfm.201901420. Impact Factor: 15.62
  9. Rodriguez, I. F., Megret, R., Acuna, E., Agosto-Rivera, J. L., & Giray, T. (2018). Recognition of Pollen-Bearing Bees from Video Using Convolutional Neural Network. Proceedings – 2018 IEEE Winter Conference on Applications of Computer Vision, WACV 2018, 2018-January, 314–322. https://doi.org/10.1109/WACV.2018.00041. Impact Factor: 3.55

20 Publications supported by HPCf (no acknowledgment)

  1. Pérez Claudio E, Rodriguez-Cruz Y, Arslan OC, Giray T, Agosto Rivera JL, Kence M, Wells H, Abramson CI. Appetitive reversal learning differences of two honey bee subspecies with different foraging behaviors. PeerJ. 2018 Nov 21;6:e5918. doi: 10.7717/peerj.5918. eCollection 2018. PubMed PMID: 30498631; PubMed Central
    PMCID: PMC6252072
  2. Ana M. Chicas-Mosier, Christopher W. Dinges, Jose L. Agosto-Rivera, Tugrul Giray, Devrim Oskay, Charles I. Abramson. Honey bees (Apis mellifera spp.) respond to increased aluminum exposure in their foraging choice, motility, and circadian rhythmicity. PLoS One. 2019; 14(6): e0218365. Published online 2019 Jun 27. doi: 10.1371/journal.pone.0218365 PMCID: PMC6597069
  3. Vega-Bellido GI, DeLaCruz-Araujo RA, Kretzschmar I, Córdova-Figueroa UM. Self-assembly of magnetic colloids with shifted dipoles. Soft Matter. 2019 May 22;15(20):4078-4086. doi: 10.1039/c8sm02591f. PubMed PMID: 30942785
  4. JianLvab, MeilingXua, ShiruLineXuecheng, ShaoaXinyuZhanga, YanhuiLiud, YanchaoWanga, ZhongfangChene, YanmingMaac. 2018. Direct-gap semiconducting tri-layer silicene with 29% photovoltaic efficiency. Science Direct. Nano Energy Volume 51, September 2018, Pages 489-495
  5. Li F, Chen Z. Cu dimer anchored on C(2)N monolayer: low-cost and efficient Bi-atom catalyst for CO oxidation. Nanoscale. 2018 Aug 23;10(33):15696-15705. doi: 10.1039/c8nr03394c. PubMed PMID: 30091768.
  6. Josell Ramirez-Paz, Manoj Saxena, Louis J. Delinois, Freisa M. Joaquín-Ovalle, Shiru Lin, Zhongfang Chen, Virginia A. Rojas-Nieves, Kai Griebenow. Site-specific PEGylation crosslinking of L-asparaginase subunits to improve its therapeutic efficiencybioRxiv 317040; doi: https://doi.org/10.1101/317040
  7. Fengyu Li, Fuzhao Yi, Junfeng Gao, Haijun Zhang, and Zhongfang Chen, Modulating the electronic properties of perovskite via σ–π interfacial interactions: A computational study. APL Materials 6, 114203 (2018); https://doi.org/10.1063/1.5044453
  8. Ya Wang,abc Jeffrey Comer, Zhongfang Chen, Jingwen Chen and James C. Gumbart, Exploring adsorption of neutral aromatic pollutants onto graphene nanomaterials via molecular dynamics simulations and theoretical linear solvation energy relationships. Environ. Sci.: Nano, 2018,5, 2117-2128
  9. Jia ZhaoJingxiang Zhao, Fengyu LiZhongfang Chen, Copper Dimer Supported on a C2N Layer as an Efficient Electrocatalyst for CO2 Reduction Reaction: A Computational Study. 2018. J. Phys. Chem. C20181223419712-19721
  10. C.-X. Liu, W.-H. Zhang, N. Wang, P. Guo, M. Muhler, Y. Wang, S. Lin, Z. Chen, G. Yang, Highly Efficient Photocatalytic Degradation of Dyes by a Copper–Triazolate Metal–Organic Framework. Chem. Eur. J. 2018, 24, 16804. PMID: 30133022.
  11. Lv X, Li F, Gong J, Chen Z. The dimensional and hydrogenating effect on the electronic properties of ZnSe nanomaterials: a computational investigation. Phys Chem Chem Phys. 2018 Oct 7;20(37):24453-24464. doi: 10.1039/c8cp04472d. Epub 2018 Sep 17. PubMed PMID: 30221293.
  12. Qiao M, Liu J, Wang Y, Li Y, Chen Z. PdSeO(3) Monolayer: Promising Inorganic 2D Photocatalyst for Direct Overall Water Splitting Without Using Sacrificial Reagents and Cocatalysts. J Am Chem Soc. 2018 Sep 26;140(38):12256-12262. doi: 10.1021/jacs.8b07855. Epub 2018 Sep 12. PubMed PMID: 30169028
  13. Chen W, Liu Z, Zhao Y, Yi X, Chen Z, Zheng A. To Be or Not To Be Protonated:cyclo-N(5)(-) in Crystal and Solvent. J Phys Chem Lett. 2018 Dec 20;9(24):7137-7145. doi: 10.1021/acs.jpclett.8b02841. Epub 2018 Dec 13. PubMed PMID: 30395479.
  14. Chen, Z., Zhao, J., Cabrera, C. R., Chen, Z., Computational Screening of Efficient Single‐Atom Catalysts Based on Graphitic Carbon Nitride (g‐C3N4) for Nitrogen Electroreduction.Small Methods 2019, 3, 1800368. https://doi.org/10.1002/smtd.201800368
  15. Zhe Chen, Jingxiang Zhao,Lichang Yin and Zhongfang Chen. 2019.B-terminated (111) polar surfaces of BP and BAs: promising metal-free electrocatalysts with large reaction regions for nitrogen fixation. J. Mater. Chem. A, 2019,7, 13284-13292
  16. Chunmei Zhang, Tianwei He, Sri Kasi Matta, Ting Liao, Liangzhi Kou, Zhongfang Chen, and Aijun Du. Predicting Novel 2D MB2 (M = Ti, Hf, V, Nb, Ta) Monolayers with Ultrafast Dirac Transport Channel and Electron-Orbital Controlled Negative Poisson’s Ratio The Journal of Physical Chemistry Letters 2019 10 (10), 2567-2573. DOI: 10.1021/acs.jpclett.9b00762
  17. Jun Long, Jinxing Gu, Zhanhong Yang, Jianfeng Mao,b Junnan Hao, Zhongfang Chen and Zaiping Guo. 2019. Highly porous, low band-gap NixMn3−xO4 (0.55 ≤ x ≤ 1.2) spinel nanoparticles with in situ coated carbon as advanced cathode materials for zinc-ion batteries. J. Mater. Chem. A, 2019,7, 17854-17866
  18. Benjamin, D. J., Berger, J. O., Johannesson, M., Nosek, B. A., Wagenmakers, E. J., Berk, R., … Johnson, V. E. (2018). Redefine statistical significance. Nature Human Behaviour, 2(1), 6-10. https://doi.org/10.1038/s41562-017-0189-z
  19. Jiménez, R. , Thurner, S. , Pericchi, L. R. and Klimek, P. (2019). Fraud Detection, Electoral. In Wiley StatsRef: Statistics Reference Online (eds N. Balakrishnan, T. Colton, B. Everitt, W. Piegorsch, F. Ruggeri and J. L. Teugels). doi:10.1002/9781118445112.stat08006
  20. M. J. Bayarri, James O. Berger, Woncheol Jang, Surajit Ray, Luis R. Pericchi & Ingmar Visser (2019) Prior-based Bayesian information criterion, Statistical Theory and Related Fields, 3:1, 2-13, DOI: 10.1080/24754269.2019.1582126

6 In press or Submitted that acknowledge HPCf or INBRE

  1. Electron confinement and magnetism of (LaTiO3)1/(SrTiO3)5 heterostructure: A diffusion quantum Monte Carlo study, , J. A. Santana,J. T. Krogel, S. Okamoto, and F. A. Reboredo1, J. Chem. Theory Comput. (2019)
  2. DFT calculations of the electrochemical adsorption of sulfuric acid anions on the Pt(110) and Pt(100) surfaces, J. A. Santana and Y. Ishikawa, J. Phys. Chem. C, (2019)
  3. Linear correlation models for the redox potential of organic molecules in aqueous solutions, J. C. Ortiz-Rodríguez, J. A. Santana and D. D. Méndez-Hernández, J. Molecular Modeling, (2019)
  4. Dieunel Derilus, Zillur Rahman, Fernando Pinero, and Steven Massey. The Black Queen, the Proteomic Constraint, and the dynamics of genome reduction in the photosynthetic picoeukaryotes. Applied and Environmental microbiology (AEM01616-19 )
  5. Dieunel Derilus , Filipa Godoy-Vitorino, Hebe Rosado Rivera, Edgardo Agosto, Maria Gloria Dominguez Bello , Humberto Cavallin. Unraveling the bacterial microcosms of a C-section operating room. Journal: PLOS Biology
  6. Oxygen Evolution Reaction on 2D Ferromagnetic Fe3GeTe2: Boosting the Reactivity by the Self-Reduction of Surface Hydroxy Yinghe Zhao, Jinxing Gu, and Zhongfang Chen*

18 Jul

Boqueron /work Unexpected Downtime Resolved

Boqueron’s /work file system recently experienced unexpected downtime due to a hardware issue. Our colleagues at Central Administration provided us with the replacement hardware we needed, and the issue seems to have finally been resolved. As far as we can tell, there has not been any data loss; however, we still encourage users to connect to Boqueron and verify the integrity of their files. We’d also like to take this opportunity to remind our users that, per our Usage Policies, the /work directory in Boqueron is specifically built for performance and not for reliability, and that, as such, data in users’ /work directory is not and will not be backed up. Users are responsible for maintaining their own backups of any data they keep in their /work.

We apologize for any delay in communication regarding this issue. The HPCf has been understaffed these past two weeks, precisely when the hardware problem popped up. All HPCf staff should be back at the office starting Monday July 23.

We apologize for the inconvenience this issue has no doubt caused, and we thank you for your patience and continued support for the HPCf. As always, you may direct any questions or comments to help@hpcf.upr.edu.

About

The High Performance Computing facility of the University of Puerto Rico is presently developing a technology and service infrastructure for the research and education community of the University.  This infrastructure is built from the following components:

  • Advanced Research Network
  • Core High Performance Computational Resources
  • Services in Support of Users of Computational Resources
  • Standards and Architecture
  • Evaluation of Emerging Technologies

Some common tasks:

Use of HPCf resources requires that you acknowledge our sponsoring institutions: the University of Puerto Rico and the Institutional Development Award (IDeA) INBRE grant P20 GM103475 from the National Institute for General Medical Sciences (NIGMS), a component of the National Institutes of Health (NIH) and the Bioinformatics Research Core of INBRE.