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NERSC Science Highlights December 2017

Science Highlights December 2017 AstrophysicsObservations + computer models confirm that kilonovas produce heavy elements. NERSC PI: Kasen, Berkeley Lab. Nature

NuclearPhysicsAnalysis shows for the first time that the Earth stops high-energy neutrinos. NERSC PI: Palczewski, Berkeley Lab. Nature

MaterialsScienceScientists take big step towards making practical next-generation “memristor” memory devices. NERSC PI: Batista, Yale Univ. Nature Materials

FusionScienceAnalysis show how plasma ‘blobs’ cause problems in fusion reactors. NERSC PI: Chang, PPPL. Plasma Physics and Controlled Fusion

HighEnergyPhysicsSimulations show how the first supernovae seeded the universe with heavy elements. NERSC PI: Chen, EACOA. The Astrophysical Journal

BiologicalScienceAnalyzing cryo-EM images provides insight in immune system function.. NERSC PI: Nogales, UC Berkeley. Science

BioscienceSimulations reveal how bacteria react to environmental stress. NERSC PI: Palsson, UC San Diego. Proc Nat. Acad. Sci.

ScientificAchievementInastudypublishedinNature,opticalandinfraredsignalsfromaneutronstarmergerwerefoundtobeconsistentwithcomputermodelpredictionsofakilonova,aneventthatis1,000timesbrighterthanaclassicalnova.TheobservationsfollowedthedetectionofgravitationalwavesfromtheneutronstarmergerGW170817.

OriginofHeavyElements

NERSCProjectPI:D.Kasen,BerkeleyLab

Kasenet.al,Nature551,80–84(Nov.2,2017)doi:10.1038/nature24453

TheoreticalcalculationoftheevolutionofthespectrumoflightfromakilonovasuchasthatassociatedwithgravitationalwavesignalGW170817.Therightpanelshowsanillustrationoftheexpandingradioactivedebriscloudthatproducestheobservedradiation.Credit:DanKasen

ResearchDetailsTheresearchersused4,000computecorestorunthegeneralrelativisticmagnetohydrodynamicalcodeHARMPIandtheradiationtransportcodeSEDONAtoproducehighlyresolvedsimulationsofthelong-termaftermathandobservablelightfromneutronstarmergers.

SCProgram:HighEnergyPhysics

SignificanceandImpactPhysicistshavelongdiscussedhowelementsheavierthanironcouldbeproducedandsimulationsofneutronstarmergershavepredictedthatkilonovasareprimecandidates.Theobservationsinthispaperarethefirsttoprovidestrongevidencetosupportthistheory.

ScientificAchievementComputationalanalysisofcryo-electronmicroscopy(cryo-EM)imageshelpedbiologistsresolvethestructureofaringofproteinsusedbytheimmunesystemtotodetectandrespondtoabacterialattack.

SignificanceandImpactThestudy,ledbyBerkeleyLabandUCBerkeleyresearchers,usedcryo-EMtocapturehigh-resolutionimagesofaproteinringcalledan“inflammasome”asitwasboundtoflagellin,aproteinfromthewhipliketailusedbybacteriatopropelthemselves.Thisapproachprovidesnewinsightintopotentialstrategiesforprotectionfrombacterialinfections.

TowardBetterProtectionsfromPathogens

NERSCProjectPI:E.Nogales,BerkeleyLab

J.Tenthorey,etal,ScienceNov.172017,Vol.358,Issue6365

doi:10.1126/science.aao1140

Usingcryo-electronmicroscopy,researchershaverevealedthestructureofamulti-proteincomplexcalledtheNAIP5-NLRC4inflammasome,whichhelpsidentifyinvadingbacteria.Credit:NicoleHaloupek,UCBerkeley/HowardHughesMedicalInstitute

ResearchDetailsUsingNERSCresources,theresearcherswereabletoscaleuptheirstructure-determinationpipelineandquicklydetermineatomicstructuresofmacromolecularcomplexeswithawiderangeoffunctionsinmicrobesandplants.Theyalsominedthestructuralinformationtounderstandhowgenomicdataistranslatedintofunctionalcapabilitiesandareusingthisdatabaseasapipelineformodelingbiologicalfunction.

SCProgram:BasicEnergySciences:ChemicalSciences,Geosciences,andBiosciencesDivision

ScientificAchievementTheIceCubeCollaborationshowedforthefirsttimethathigh-energyneutrinosareabsorbedbyEarthaspredictedbytheStandardModelofparticlephysics.Neutrinosinteractrarelywithnormalmatter,buttheEarthislargeenoughtostopsomeofthem,andIceCubewasabletomeasurethateffect.

SignificanceandImpactTheresultsnotonlysupporttheStandardModel,butareinconsistentwithsomemorespeculativetheories.Adetailedunderstandingofhowhigh-energyneutrinosinteractwithEarth’smatterwillalsoallowresearcherstoprobethecompositionofEarth’scoreandmantel.

StoppingNeutrinosInTheirTracks

SCProgram:NuclearPhysics

IllustrationofhowamuoninteractsintheIceCubedetectorarray.Credit:IceCubeCollaboration

NERSCPI:T.Palczewski,BerkeleyLab

ResearchDetails•  SimulationstosupporttheanalysiswererunatNERSC;theIceCube

projectusesNERSC’sCori,Edison&PDSFsystemsfordataanalysisandsimulations.

•  HistoricaldataisarchivedatNERSC.

TheIceCubeCollaboration,Nature551,596–600(Nov.2017)doi:10.1038/nature24459

ScientificAchievementAninternationalteamofastronomersandcosmologistsranmulti-scale,multi-physics2Dand3DsimulationsatNERSCtoshowhowelementsexpelledfromthefirstsupernovaehelpedpopulationsofstarsintheearlyuniversestarttoevolvefromextremelymassiveandhotobjectstowardsonelikethoseseeninourgalaxytoday.

How1stSupernovaeAlteredEarlyStarFormation

SCProgram:HighEnergyPhysics

NERSCProjectPI:K.Chen,EACOA

ResearchDetailsTheteamransmall-scale,high-resolutionsimulationsofthechemicalenrichmentofadarkmatterhaloswithelementsproducedinanearbysupernovaexplosion.TheyusedNERSCcomputerstoproduceaseriesof2Dand3Dsimulationsthathelpedthemexaminetheroleofdarkmatterhalophotoevaporationintheearlyformationofstarsandtheassemblyoflatergalaxies.

SignificanceandImpactThisstudydemonstratedanewmethodologythatcombinessmall,stellar-scalesimulations(typicalofastrophysics)andlarge,galactic-scalesimulations(typicalofcosmology)toprovidemoreinsightintotheformationoftheearlyuniverse. Thissimulationshowstheturbulentgaswhena

supernovacollideswithanearbystar-forminghalo.Credit:KenChen,EACOA

K.Chen,etal,TheAstrophysicalJournal,844:111,August2017,

doi:10.3847/1538-4357/aa7b34

ScientificAchievementInarecentNatureMaterialsarticleresearchersdescribeanewrobust“memristor”deviceandtheoreticalinsightsintowhyithasthesize,stability,reproducibility,andendurancetosupplantflashmemorytechnologiesinfuturegenerationsofdigitaldevices.

HPCforBetterComputerMemoryTechnologies

NERSCProjectPI:VictorBatista,YaleUniv.

S.Goswami,etal,NatureMaterials,Oct.23,2017,doi:10.1038/NMAT5009

Aninternationalteamofresearchershasdevelopedthin,molecularfilmsthatcanstoreinformation,withpotentialapplicationsinthecomputerindustry.Credit:YaleUniversity

ResearchDetailsTheresearchersusedacomputationalmethodologythatcombineslarge-scaledensityfunctionaltheorymoleculardynamicsandsimulationsofelectronicrelaxationtoaccuratelydescribetheelectronicrelaxationprocessesinfunctionalizedtitanium-dioxidesurfaces.

SignificanceandImpactTheteamperformedcalculationsatNERSCtogainanunderstandingofwhytheirdevice,basedonaspin-coatedactivelayerofatransitionmetalcomplex,performssowell.Theinsightmayacceleratethedeploymentoforganicresistivememorydevicesandthefindingshavewiderapplicabilityforothersemiconductormaterials,particularlythoseusedinneuromorphicandlogiccircuits.

SCProgram:BasicEnergySciences:ChemicalSciences,Geosciences,andBiosciencesDivision

ScientificAchievementUsingNERSCsupercomputers,physicistsatPrincetonPlasmaPhysicsLaboratoryhavegainednewunderstandingoftheturbulent“bubbles”(blobs)thatpercolatewithintheplasmaedgeduringafusionreactionandhowtheycannegativelyimpactperformance.

SignificanceandImpactBlobsplayanimportantroleintheoutwardmovementofparticlesinplasmaandtheycouldcause50%oftheparticlelossattheplasmaedge.Thisstudygivesfusionscientistsabetterunderstandingofhowheatmovesfromplasmatothewalls,potentiallycausingdamage.

ResearchDetailsThePPPLteamtransferredTerabytesofsimulationdatafromOakRidge,whereitwasproduced,toNERSCforanalysis.Theanalysis,whichwasperformedonNERSC’sEdisonsupercomputer,usedablobdetectionandtrackingmethodtorevealhowtheblobsmovetotheplasmaedgeandinteractwiththewalls.

TheBlobthatAtetheTokamak

SCProgram:FusionEnergySciences

Normalizeddensitycontour(red)atasinglepoloidalplane,withfluctuatingpotentialcontourlinesoverlaidtoshowpositivepotential(solidblack)andnegativepotential(dashedblack).Adetecteddensityblobisoutlinedinthethickredcontourline.Credit:PPPL

R.M.Churchill,etal,PlasmaPhys.ControlFusion59(2017),105014doi:10.1088/1361-6587/aa7c03

NERSCProjectPI:C.S.Chang,PPPL

ScientificAchievementResearchersattheUniversityofCaliforniaSanDiegodevelopedagenome-scalecomputationalmodel,FoldME,thatcanaccuratelypredicthowE.colibacteriarespondtotemperaturechangesandgeneticmutationsandthenreallocatetheirresourcestostabilizeproteins.

SignificanceandImpactThisworkandtheFoldMEmodelprovideacomprehensive,systems-levelunderstandingofhowcellsadaptunderenvironmentalstress,withstatisticaldescriptionsofmultiscalecellularresponseconsistentwithmanydatasets.Themodelcouldaidindesigningengineeredorganismsforbiofuelproductionandpatient-specifictreatmentsforbacterialinfections.

HowBacteriaAdapttoEnvironmentalStress

SCProgram:Biological&EnvironmentalResearch:BiologicalSystemsScienceDivision

NERSCProjectPI:B.Palsson,UCSD

ResearchersatUCSanDiegodevelopedagenome-scalemodelthatcanaccuratelypredicthowE.colibacteriarespondtoenvironmentalstress.Credit:NIAIDResearchDetails

ThissteadyusedcomputationalresourcesofNERSCtorunlarge-scalesimulationswithparametersampling.ThesupercomputingservicesprovidedbyNERSCallowedtheresearcherstoeitherrunmanyofthesetechniquesinparallelforhundredsofproteins,speedingupwhatwouldotherwisebeweek-longsimulationsofthesecomplexproblems.

K.Chen,etal,PNAS,vol.114no.43,11548–11553,doi:10.1073/pnas.1705524114

National Energy Research Scientific Computing Center

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