HPC Endorsements

We also express our gratitude for UCI HPC assistance and especially Dr. Harry Mangalam and Garr Updegraff for their generous support, and the UCI Research Computing group especially Allen Schiano and Dana Roode. This work was supported by an NSF Fellowship (NRSG), NIH AG029378 and AG16573 (MBJ), and generous donors to the UCI Sue and Bill Gross Stem Cell Research Center.

Pediatrics
— Anita Lakatos

I also want to thank you both for the incredible, extraordinary and vital work that you are doing for research computing at UCI, and that you’ve done for me personally. The computing resource that you have built, with a truly shameful budget, has been one of the most impressive things I’ve witnessed in my 12 years at UCI. Thanks for the help you’ve provided me and my students over the years.

Epidemiology
— Chad Garner

It was the question of waiting several days on my little 30-core cluster or about an hour on HPC. Plus the advantage of HPC is that, as long as it’s not busy, if I make a mistake, I find that mistake in an hour, rather than a few days later.

ICS
— Wayne Hayes

I do think it is great for other people to be able do HPC work, even if they [don’t buy hardware]. All of the work that you’ve put into the system seems to balance not wasting resources that may otherwise lay idle with giving priority to those who bought the machines. A nice side effect [of the Free Q] is that some potentially heavy users can get a little taste of what the HPC can do, and might just buy in in the future. I think this may have happened with one of my faculty colleagues. Anyway, I think it is a great system. And I appreciate how much work it must take. Thanks!

Ecology & Evolutionary Biology
— JJ Emerson

[The] study ran FreeSurfer on 362 subjects, i.e., 8,688 compute hours. The image analysis was completed in a single day on the HPC. It would have taken a full month on my 12 node server. The HPC enables me to be competitive with imaging researchers at other institutions.

Psychiatry & Human Behavior
— Theo van Erp

[HPC] was very beneficial for me even though our lab did not own any private nodes on the cluster. For my recent work (in review), I was able to simulate 1154 separate simulated windows within 2 weeks using the HPC FreeQ. It would have taken more than a month on our local server.

Chemical Engineering & Materials Science
— Quynh Vo

The value of HPC lies not only in the hardware — whose computing power dwarfs what can be achieved with the resources of a single lab — but also in its associated staff, who are always responsive and willing to go out of their way to help and accommodate needs even when those needs are out of the ordinary. HPC significantly lowers the barrier to entry for labs that do not have computational expertise, and allows labs that already have that expertise to tackle questions that would be far beyond their reach otherwise. HPC is one of the most important campus resources that my lab has come to rely on. I hope it receives the support it well deserves.

Developmental & Cell Biology
— Olivier Cinquin

I think the HPC is very well managed. I’m very happy generally and not sure what else to say - the support is excellent, both personal support and online content with tips and advice. I remember my first experience with using the HPC was very smooth. In terms of resources, I have used a number of different programs and they are updated regularly. I have no suggestions for improvement.

Ecology and Evolutionary Biology
— Gilbert Smith

Publications

School of Medicine

Pediatics

Submitted by: Anita Lakatos
  • Anita Lakatos, Natalie R. S. Goldberg, Mathew Blurton-Jones. Integrated analysis of genetic, behavioral, and biochemical data implicates neural stem cell-induced changes in immunity, neurotransmission and mitochondrial function in Dementia with Lewy Body mice. Acta Neuropathol Commun. 2017; 5: 21. <doi:10.1186/s40478-017-0421-0> Link

Public Health

Submitted by: Mariam Girguis
  • Girguis MS, Strickland MJ, Hu X, Liu Y, Bartell SM, Vieira VM. Maternal exposure to traffic-related air pollution and birth defects in Massachusetts. Environ Res. 2016 Apr;146: 1-9. Epub 2015 Dec 17. PubMed PMID: 26705853.

Dept of Anatomy And Neurobiology

Submitted by: Theo van Erp
  • van Erp TG, Greve DN, Rasmussen J, Turner J, Calhoun VD, Young S, Mueller B, Brown GG, McCarthy G, Glover GH, Lim KO, Bustillo JR, Belger A, McEwen S, Voyvodic J, Mathalon DH, Keator D, Preda A, Nguyen D, Ford JM, Potkin SG, Fbirn. A multi-scanner study of subcortical brain volume abnormalities in schizophrenia. Psychiatry Res. 2014;222(1-2):10-6.
    <doi:10.1016/j.pscychresns.2014.02.011>
    http://www.sciencedirect.com/science/article/pii/S0925492714000535

Submitted by: Calvin Schneider
  • Calvin J. Schneider, Marianne Bezaire, Ivan Soltesz (2012). Toward a full-scale computational model of the rat dentate gyrus. Frontiers in neural circuits, Vol. 6 (2012),
    <doi:10.3389/fncir.2012.00083>
    Key: citeulike:11745559

Submitted by: Richard Samuel Leopold Stein
  • A kinetic, quaternary complex model, based on a system of coupled linear first-order differential equations, accounts for the binding attributes of the ligand, receptor, G protein and two types of guanine nucleotide (GDP and GTP) as well as for GTPase activity. We solved the model numerically to predict the extents of G protein activation, receptor occupancy by ligand and receptor coupling that result from varying the ligand concentration, presence of GDP and/or GTP, the ratio of G protein to receptor and the equilibrium constants governing receptor pre-coupling and constitutive activity. Our model shows that agonist-induced G protein activation can occur with either a net decrease or increase in total receptor-G protein coupling. LINK

Dept of Physiology and Biophysics

Submitted by: Stephen H. White
  • Bondar AN, del Val C, Freites JA, Tobias DJ, & White SH (2010). Dynamics of SecY translocons with translocation-defective mutations. Structure 18:847-857.

  • Andersson M, Freites JA, Tobias DJ, & White SH (2011). Structural dynamics of the S4 voltage-sensor helix in lipid bilayers lacking phosphate groups. J Phys Chem B. 115:8732-8738.

  • Bondar AN & White SH (2012). Hydrogen bond dynamics in membrane protein function. Biochim Biophys Acta 1818:942-950. PDF

Donald Bren School of Information & Computer Sciences

Dept of Computer Science

Submitted by: Wayne B Hayes
  • Darren Davis and Wayne Hayes “SpArcFiRe: Scalable Automated Detection of Spiral GalaxyArm Segments” The Astrophysical Journal 790:87, 14pp (2014).

  • Darren R. Davis and Wayne Hayes. “Automated Quantitative Description of Spiral Galaxy Arm-Segment Structure.” Computer Vision and Pattern Recognition (CVPR) 2012. Providence, Rhode Island, June 16–21, 2012.

  • Wayne Hayes, Kai Sun, Nataˇsa Prˇzulj. Graphlet-based measures are suitable for biological network comparison. Bioinformatics doi:10.1093/bioinformatics/bts729 (2013).

Submitted by: Nam Duong
  • Nam Duong, Dali Zhao, Taesu Kim, Rosario Cammarota, Mateo Valero and Alexander V. Veidenbaum. Improving cache management policies using dynamic reuse distances. Proceedings of the 45th Annual IEEE/ACM International Symposium on Microarchitecture (MICRO), December 2012.

  • Nam Duong, Taesu Kim, Dali Zhao, and Alexander V. Veidenbaum. Revisiting level-0 caches in embedded processors. Proceedings of the International Conference on Compilers, Architecture and Synthesis for Embedded Systems (CASES), October 2012.

  • Nam Duong and Alexander V. Veidenbaum. Compiler-assisted, selective out-of-order commit. IEEE Computer Architecture Letters (CAL), May 2012.

  • Nam Duong, Rosario Cammarota, Dali Zhao, Taesu Kim, and Alexander V. Veidenbaum. SCORE: A score-based memory cache replacement policy. The 1st JILP Workshop on Computer Architecture Competitions (JWAC), June 2010.

Submitted by: Santanu Sarma
  • S.Sarma and N.Dutt, "Cross-Layer Exploration of Heterogeneous Multicore Processor Configurations", Proceedings of the International Conference on VLSI Design (VLSID), Jan 2015.

  • S. Sarma, N Dutt, P Gupta, N Venkatasubramanian, and A Nicolau "CyberPhysical-System-On-Chip (CPSoC) : A Self-Aware MPSoC Paradigm with Cross-Layer Virtual Sensing and Actuation" DATE 2015, Grenoble, France, March 2015.

The Henry Samueli School of Engineering

Dept of Engineering, Mechanical And Aerospace

Submitted by M. Plecnik
  • M. Plecnik, J. M. McCarthy, and C. W. Wampler, "Kinematic Synthesis of a Watt I Six-Bar Linkage for Body Guidance", Advances in Robot Kinematics, Springer International Publishing, 2014, 317-325.

Submitted by: Marc Carreras Sospedra
  • Emission estimates of HCFCs and HFCs in California from the 2010 CalNex study. Barletta B., Carreras-Sospedra M., Cohan A., Nissenson P., Dabdub D., Meinardi S., Atlas E., Lueb R., Holloway J.S., Ryerson T.B., Pederson J., VanCuren R.A., Blake D.R. J. Geophys. Res. 118, (2013) 2019-2030. doi: 10.1002/jgrd.50209 PDF

  • Secondary organic aerosol formation from naphthalene roadway emissions in the South Coast Air Basin of California. Cohan, A., Eiguren-Fernandez, A., Miguel, A.H., Dabdub, D. Int. J. of Environ. & Pollution 52, (2013) 206-224. doi: 10.1504/IJEP.2013.058461 PDF

  • Images reveal that atmospheric particles can undergo liquid-liquid phase separations. You Y., Renbaum-Wolff L., Carreras-Sospedra, M., Hanna, S.J., Hiranuma N., Kamal S., Smith M.L., Zhang X.L., Weber R.J., Shilling J.E., Dabdub, D., Martin S.T., Bertram A.K. Proc. Natl. Acad. Sci. 109, (2012) 13188-13193. doi: 10.1073/pnas.1206414109 PDF

  • Future impacts of distributed power generation on ambient ozone and particulate matter concentrations in the San Joaquin Valley of California. Vutukuru S., Carreras-Sospedra M., Brouwer J. and Dabdub D. J. Air & Waste Manage. Assoc. 61, (2011) 1319-1333. doi: 10.1080/10473289.2011.603990 PDF

  • Projecting full build-out environmental impacts and roll-out strategies associated with viable hydrogen fueling infrastructure strategies. Stephens-Romero S.D., Brown T.M., Carreras-Sospedra M., Kang J.E., Brouwer J., Dabdub D., Recker W.W. and Samuelsen G.S. International Journal of Hydrogen Energy 36, (2011) 14309-14323. doi: 10.1016/j.ijhydene.2011.08.005 PDF

  • HFC-152a and HFC-134a emission estimates and characterization of CFCs, CFC replacements, and other halogenated solvents measured during the 2008 ARCTAS campaign (CARB phase) over the South Coast Air Basin of California. Barletta B., Nissenson P., Meinardi S., Dabdub D., Rowland F., VanCuren R. A., Pederson J. and Blake D. R. Atmospheric Chemistry and Physics 10 , (2011) 2655-2669. doi: 10.5194/acp-11-2655-2011 PDF Support Info

  • High-resolution pollutant transport in the San Pedro Bay of California. Cohan A., Wu J. and Dabdub D. Atmospheric Pollution Research 2, (2011) 237-246. doi: 10.5094/APR.2011.030 PDF

  • Central power generation versus distributed generation - an air quality assessment in the South Coast Air Basin of California. Carreras-Sospedra M., Vutukuru S., Brouwer J. and Dabdub D. Atmospheric Environment 44 , (2010) 3215-3223. doi: 10.1016/j.atmosenv.2010.05.017 PDF

  • Partitioning phase preference for secondary organic aerosol in an urban atmosphere. Chang W. L., Griffin R. J. and Dabdub D. Proc. Natl. Acad. Sci. 107, (2010) 6705-6710. doi: 10.1073/pnas.0911244107 PDF

  • Impacts of electronically photo-excited NO2 on air pollution in the South Coast Air Basin of California. Ensberg J.J., Carreras-Sospedra M. and Dabdub D. Atmospheric Chemistry and Physics 10 , (2010) 1171-1181. doi: 10.5194/acp-10-1171-2010 PDF

  • Determining air quality and greenhouse gas impacts of hydrogen infrastructure and fuel cell vehicles. Stephens-Romero S., Carreras-Sospedra M., Brouwer J., Dabdub D. and Samuelsen S. Environmental Science & Technology 43 , (2009) 9022-9029. doi: 10.1021/es901515y PDF

  • Potential for atmospheric driven lead paint degradation in the South Coast Air Basin of California. Cohan A. J., Edwards R. D., Kleinman M. T. and Dabdub D. Environmental Science & Technology 43 , (2009) 8881-8887. doi: 10.1021/es901360j PDF

  • Chlorine activation indoors and outdoors via surface-mediated reactions of nitrogen oxides with hydrogen chloride. Raff J. D., Njegic B., Chang W. L., Gordon M. S., Dabdub D., Gerber R. B. and Finlayson-Pitts B. J. Proc. Natl. Acad. Sci. 106 , (2009) 13647-13654. doi: 10.1073/pnas.0904195106 PDF

  • Influence of the public transportation system on the air quality of a major urban center. A case study: Milan, Italy. Meinardi S., Nissenson P., Barletta B., Dabdub D., Rowland F. S. and Blake D. R. Atmospheric Environment 42 , (2008) 7915-7923. doi: 10.1016/j.atmosenv.2008.07.046 PDF

  • Sensitivity and uncertainty analysis of the mechanism of gas-phase chlorine production from NaCl aerosols in the MAGIC model. Nissenson P., Thomas J.L., Finlayson-Pitts B. J. and Dabdub D. Atmospheric Environment 42 , (2008) 6934-6941. doi: 10.1016/j.atmosenv.2008.04.041 PDF

  • Air quality impacts of distributed energy resources implemented in the Northeastern United States. Carreras-Sospedra M., Dabdub D., Brouwer J., Knipping E., Kumar N., Darrow K., Hampson A. and Hedman B. J. Air & Waste Manage. Assoc. , 58, (2008) 902-912. doi: 10.3155/1047-3289.58.7.902 PDF

  • Modeling the effects of ship emissions on coastal air quality: A case study of southern California. Vutukuru S. and Dabdub D. Atmospheric Environment 42, (2008) 3751-3764. doi: 10.1016/j.atmosenv.2007.12.073 PDF

  • Influence of sea-salt activated chlorine and surface-mediated renoxification on the weekend effect in the South Coast Air Basin of California. Cohan A., Chang W., Carreras-Sospedra M. and Dabdub D. Atmospheric Environment 42 , (2008) 3115-3129. doi: 10.1016/j.atmosenv.2007.11.046 PDF

  • Rethinking ozone production. Wennberg P. O. and Dabdub D. Science 319, (2008) 1624-1625. doi: 10.1126/science.1155747 PDF

  • Air quality impacts of distributed power generation in the South Coast Air Basin of California 2: Model uncertainty and sensitivity analysis. Rodriguez M. A., Brouwer J., Samuelsen G. S. and Dabdub D. Atmospheric Environment 41 , (2007) 5618-5635. doi: 10.1016/j.atmosenv.2007.02.049 PDF

  • Contribution of gas phase oxidation of volatile organic compounds to atmospheric carbon monoxide levels in two areas of the United States. Griffin R.J., Chen J., Carmody K., Vutukuru S. and Dabdub D. J. Geophys. Res. 112, D10S17, (2007) doi: 10.1029/2006JD007602 PDF

  • Air quality impacts of distributed power generation in the South Coast Air Basin of California 1: Scenario development and modeling analysis. Rodriguez M. A., Carreras-Sospedra M., Medrano M., Brouwer J., Samuelsen G. S. and Dabdub D. Atmospheric Environment 40 , (2006) 5508-5521. doi: 10.1016/j.atmosenv.2006.03.054 PDF

  • Air Quality Modeling in the South Coast Air Basin of California: What do the numbers really mean? Carreras-Sospedra M., Dabdub D., Rodriguez M. and Brouwer J. J. Air & Waste Manage. Assoc. , 56 , (2006) 1184-1195. doi: 10.1080/10473289.2006.10464530 PDF

  • Simulation and analysis of secondary organic aerosol dynamics in the South Coast Air Basin of California. Vutukuru S., Griffin R. J. and Dabdub D. J. Geophys. Res. 111, D10S12, (2006) doi: 10.1029/2005JD006139 PDF

  • Calculation of incremental secondary organic aerosol reactivity. Carreras-Sospedra, M., Griffin R. J. and Dabdub D. Environ. Sci. Technol. 39, (2005) 1724-1730. doi: 10.1021/es0495359 PDF

Submitted by: Mark Mathew Plecnik
  • M. Plecnik, J. M. McCarthy, and C. W. Wampler, “Kinematic Synthesis of a Watt I Six-Bar Linkage for Body Guidance,” Advances in Robot Kinematics, Springer International Publishing, 2014, 317-325. PDF

Dept of Civil And Environmental Engineering

Submitted by: Brett F. Sanders
  • Pau, J.C. and Sanders, B.F. Performance of Parallel Implementations of an Explicit Finite-Volume Shallow-Water Model, ASCE Journal of Computing in Civil Engineering, 20(2), 99-110,2006. LINK

  • Sanders, B.F., Schubert, J.E. and Detwiler, R.L. ParBreZo: A parallel, unstructured grid, Godunov-type, shallow-water code for high-resolution flood inundation modeling at the regional scale, Advances in Water Resources, 33, 1456-1467,2010. LINK

  • Gallegos, H.A., Schubert, J.E. and Sanders, B.F. Structural damage prediction in a high-velocity urban dam-break flood: a field-scale assessment of predictive skill, ASCE Journal of Engineering Mechanics, 138(10), 1249-1262,2012. LINK

Submitted by: Russell L. Detwiler
  • Ameli, P., J.E. Elkhoury, J.P. Morris, and R.L. Detwiler (2014), Fracture permeability alteration due to chemical and mechanical processes: A coupled high-resolution model, Rock Mechanics and Rock Engineering., doi:10.1007/s00603-014-0575-z.

  • Elkhoury, J.E., P. Ameli, and R.L. Detwiler (2013), Dissolution and deformation in fractured carbonates caused by flow of CO2-rich brine under reservoir conditions, International Journal of Greenhouse Gas Control, doi:10.1016/j.ijggc.2013.02.023.

  • Zafarani, A. and R.L. Detwiler (2013), An efficient time-domain approach for simulating Pe-dependent transport through fracture intersections, Advances in Water Resources, doi:10.1016/j.advwatres.2012.11.011.

School of Physical Sciences

Dept Of Physics and Astronomy

Submitted by: Calvin Lau
  • Calvin Lau (1), Po-Chun Yeh (1), Onnie Luk (1), Joseph McClenaghan (1), Toshikazu Ebisuzaki (2), Toshiki Tajima (1) corresponding author: calvin.lau@uci.edu, (2014). Ponderomotive Acceleration by Relativistic Waves. (1) Dept. of Physics and Astronomy, University of California, Irvine, CA
    (2) RIKEN, Wako, Saitama, Japan) http://arxiv.org/abs/1407.0768

Francisco J. Ayala School of Biological Sciences

Dept of Developmental Biology

Submitted by: Ira Blitz
  • Chiu WT, Charney Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, Cho KW. (2014). Genome-wide view of TGFΒ/Foxh1 regulation of the early mesendoderm program. Development. 2014 Dec;141(23):4537-47. doi: 10.1242/dev.107227. Epub 2014 Oct 30. Direct Link. PMID:25359723

  • Blitz IL, Paraiso KD, Patrushev I, Chiu WT, Cho KW, Gilchrist MJ. (2016) A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo. Dev Biol. 2016 Jul 27. pii: S0012-1606(16)30118-X. doi: 10.1016/j.ydbio.2016.07.002. [Epub ahead of print] PMID:27475627

  • Forouzmand E, Owens ND, Blitz IL, Paraiso KD, Khokha MK, Gilchrist MJ, Xie X, Cho KW. (2016). Developmentally regulated long non-coding RNAs in Xenopus tropicalis. Dev Biol. 2016 Jul 12. pii: S0012-1606(16)30120-8. doi: 10.1016/j.ydbio.2016.06.016. [Epub ahead of print] PMID:27418388

Dept of Ecology and Evolutionary Biology

Submitted by: Kevin R. Thornton
  • Thornton, K. R. (2014) A C++ template library for efficient forward-time population genetic simulation of large populations. Genetics 98:157-166
    PMID: 24950894

  • Rogers, R. L., J. M. Cridland, L. Shao, T. T. Hu, P. Andolfatto and K. R. Thornton (2014) Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans. Molecular Biology and Evolution 31: 1750-1766
    PMID 24710518

  • Rogers, R. L., L. Shao, J. Sanjak, P. Andolfatto and K. R. Thornton (Accepted) Sex-biased expression in the Drosophila melanogaster group. G3: Genes, Genomes, Genetics.
    doi:10.1534/g3.114.013532

Submitted by: Anthony D. Long
  • Burke MK, Liti G, Long AD. Standing Genetic Variation Drives Repeatable Experimental Evolution in Outcrossing Populations of Saccharomyces cerevisiae. Mol Biol Evol. 2014 Dec;31(12):3228-39.
    doi: 10.1093/molbev/msu256.
    Epub 2014 Aug 28.
    PubMed PMID: 25172959
    PubMed Central PMCID: PMC4245818.

  • King EG, Sanderson BJ, McNeil CL, Long AD, Macdonald SJ. Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity. PLoS Genet. 2014 May 8;10(5):e1004322.
    doi:10.1371/journal.pgen.1004322.
    eCollection 2014 May.
    PubMed PMID: 24810915;
    PubMed Central PMCID: PMC4014434.

  • Baldwin-Brown JG, Long AD, Thornton KR. The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms. Mol Biol Evol. 2014 Apr;31(4):1040-55.
    doi: 10.1093/molbev/msu048.
    Epub 2014 Jan 18.
    PubMed PMID: 24441104;
    PubMed Central PMCID: PMC3969567.

  • Burke MK, King EG, Shahrestani P, Rose MR, Long AD. Genome-wide association study of extreme longevity in Drosophila melanogaster. Genome Biol Evol. 2014 Jan;6(1):1-11.
    doi: 10.1093/gbe/evt180.
    PubMed PMID: 24259311;
    PubMed Central PMCID: PMC3914684.

  • Thornton KR, Foran AJ, Long AD. Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect. PLoS Genet. 2013;9(2):e1003258.
    doi: 10.1371/journal.pgen.1003258.
    Epub 2013 Feb 21.
    PubMed PMID: 23437004;
    PubMed Central PMCID: PMC3578756.

Submitted by: Gilbert Smith
  • Smith, G., Chen, Y. R., Blissard, G. W., & Briscoe, A. D. (2014). Complete dosage compensation and sex-biased gene expression in the moth Manduca sexta. Genome biology and evolution, 6(3), 526-537.

  • Smith, G., Macias-Muñoz, A., & Briscoe, A. D. (2014). Genome sequence of a novel iflavirus from mRNA sequencing of the butterfly Heliconius erato.Genome announcements, 2(3), e00398-14.