workshop “trends in computational molecular biophysics” · interaction between transcription...

RIKENCenterforComputationalScience,InstituteforTransformativeBiomolecules(Nagoyauniversity),NanoLifeScience

Institute(Kanazawauniversity)

Workshop“TrendsinComputationalMolecular

Biophysics”

AlexanderMikhailov(WPI-NanoLSI),OsamuMiyashita(RIKEN),

FlorenceTama(RIKENandWPI-ITbM)

TheFourthHighSchoolMemorialMuseumofCulturalExchange,Kanazawa

https://nanolsi.kanazawa-u.ac.jp/en/en-workshop-201811/

Saturday,November3rd10:30 Opening10:45 J.Yu(BeijingComputationalScienceResearchCenter)jinyu@csrc.ac.cnTranscriptionstudiedinanutshellonT7RNApolymeraseratchetingalongDNAwithfidelitycontrolandburstingactivity11:20 T.Uchihashi(Nagoyauniversity)uchihast@d.phys.nagoya-u.ac.jpConnectionbetweenAFMdataandcomputationalsimulation11:55 T.Komatsuzaki(Hokkaidouniversity)tamiki@es.hokudai.ac.jpRevisittransitionstatetheory:Past,Present,Future12:30–14:30 Lunch14:30 S.Takada(Kyotouniversity)takada@biophys.kyoto-u.ac.jpTowardsintegrationofhigh-speedAFMdatawithbiomolecularsimulations15:05 H.Kodera(Kanazawauniversity) nkodera@staff.kanazawa-u.ac.jpInterpretationofHS-AFMimagesusingcoarse-grainedmoleculardynamicssimulation15:40 L.Dai(BeijingComputationalScienceResearchCenter)dailiq@csrc.ac.cnDecipheringintrinsicinter-subunitcouplingsthatleadtosequentialhydrolysisofF1-ATPasering16:00–16:30Break

16:30 N.Koga(InstituteofMolecularScience)nkoga@ims.ac.jpDBTLinproteindesign17:05 K.Okazaki(InstituteofMolecularScience)keokazaki@ims.ac.jpMechanismofNa+/H+antiporterfromtransition-pathsimulations:Makingfastertransporterbasedonmechanism17:40 Y.Kawasaki(KyushuUniversity)y-kawasaki@bioreg.kyushu-u.ac.jpIntegrativeapproachcombiningelectronmicroscopyandhigh-speedAFMrevealedthedynamicconformationalexchangeoftheoligosaccharyltransferaseinlipidbilayers18:00 C.Tan(KyotoUniversity)tan@nick.biophys.kyoto-u.ac.jpInteractionbetweentranscriptionfactorsandthenucleosomestudiedbymoleculardynamicssimulations.Sunday,November4th9:00 J.Noel(MaxDelbrückCenterforMolecularMedicine,Berlin)jknoel@gmail.comMesoscopicpolymer-likemodelfordynamicsofdynaminfilamentsondeformablemembranetubes9:35 Y.Togashi(Hiroshimauniversity)togashi@hiroshima-u.ac.jpTowardmesoscalemodelsofchromatin:consideringthestateandshapeofmolecules10:10 G.Brandani(KyotoUniversity)g.brandani88@gmail.comMoleculardynamicssimulationsofspontaneousandactivenucleosomeassembly10:30–11:00Break11:00 H.Kitahata(Chibauniversity)kitahata@chiba-u.jpHydrodynamiccollectiveeffectsofactiveproteinsinbiologicalsystems11:35 T.Nagai(Nagoyauniversity)tnagai@nagoya-u.jpTowardhybridmodelingofXFELsingleparticleexperimentbyGaussianmixturemodel12:10 B.Dasgupta(NagoyaUniversity)dasgupta.bhaskar@k.mbox.nagoya-u.ac.jpModellinglow-resolutionmolecularvolumeofproteinsfromAtomic-ForceMicroscopyimagebyadaptiveGaussiankernels12:30–14:00Lunch14:00 H.Flechsig(Kanazawauniversity)flechsig@staff.kanazawa-u.ac.jpAreducedmodelofmyosinVmotordynamicstounderstandthemechanismofprocessivesteppingobservedinhigh-speedAFMexperiments

14:35 T.Sumikama(Kanazawauniversity)sumi@staff.kanazawa-u.ac.jpTowardselucidatingthephysicaloriginofforceinAFMmeasurementsandamethodanalyzingdynamicsobservedbyHS-AFM15:10 L.Yang(Kanazawauniversity)l.yang@staff.kanazawa-u.ac.jpAgeneralapproachcombiningmoleculardynamicsandmachinelearningtobridgethegapbetweenAFMimageandrealstructure15:45 Y.Koyano(Chibauniversity)y.koyano@chiba-u.jpCooperativeDynamicsofActiveDimers16:05 Closing

The workshop will take place in the historical building of the Fourth High School constructed in 1891. Today it accomodates The Fourth High School Memorial Museum of Cultural Exchange and The Ishikawa Modern Literature Museum. This building is located in the center of the city, next to the Kanazawa castle. The conference room is Room 4 on the second floor.

Please take a KANAZAWA LOOP BUS (Left Loop) at Kanazawa Station East Gate Bus Terminal #7, or Line 18 (Terminal #3), Line 13 or 90 or 92-95 (Terminal #6), Line 30-33 or 35 (Terminal #8), Line 41 or 42 or 44-46 (Terminal #9), Line 20-22 (Terminal #10) , or Line 51 or 54 or 56 (Terminal #11), and get off at the Korinbo bus stop. The trip is about 10 minutes and the fare is 200 yen.