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SUMMARY:Dialogues in the Midst: Accessing Long Time and Large Length Scale
 s: Coarse-Grained Simulations
DTSTART:20260327T063000Z
DTEND:20260327T130000Z
DTSTAMP:20260619T164300Z
UID:indico-event-252@indico.truba.gov.tr
CONTACT:ncc@ulakbim.gov.tr
DESCRIPTION:\n\nLimited to 25 people. \n\nDate: March 27\, 2026\n\nEvent T
 ype: Training\n\nFormat: Face-to-face (Sabancı University- Altunizade D
 igital Campus\, İstanbul)\n\nTopic: Computational Biology\n\nOverview: 
  \n\nIn the theory session\, we will introduce the transition from atomist
 ic molecular dynamics simulations to coarse-grained (CG) models and discus
 s how coarse-graining enables accession to longer time and larger length s
 cales. The session will include an overview of the Martini force field\, b
 asic mapping strategies\, and the use of GROMACS for the system setup and 
 simulation. An introduction to ligand parameterization within the Martini 
 framework will also be provided.\n\nIn the hands-on session\, participants
  will set up and run coarse-grained simulations using GROMACS. Practical e
 xercises will include trajectory analysis\, dynamics evaluation\, and an 
 introduction to backmapping from coarse-grained to atomistic resolution.\n
 \nAgenda: The training will consist of two sections: morning and afternoon
  sessions. Registration will start at 9:30 AM\, and the first session will
  begin at 10:00 AM.\n\nLevel: Intermediate\n\nLanguage: English\n\nDurati
 on: 6 Hours\n\nTarget Audience: Academia\n\nPrerequisite(s): Basic famil
 iarity with molecular dynamics and working in Linux environment is recomme
 nded. Prior experience with coarse-grained simulations is not required.  
           \n\nAbout the instructor: \n\nÖzge Şensoy received her B.
 Sc. degrees in Molecular Biology and Genetics and Chemistry from İstanbul
  Technical University in 2005. She completed her M.Sc. and Ph.D. at Koç U
 niversity\, where she focused on protein dynamics for development of pepti
 de-based materials. She carried out her postdoctoral research at Weill Cor
 nell Medical College between 2011 and 2015. Since 2015\, she has been a fa
 culty member in the Department of Biomedical Engineering at İstanbul Medi
 pol University. Her research centers on the structural and dynamic mechani
 sms underlying biased G protein–coupled receptor signaling\, RAS protein
  dynamics\, posttranslational modifications and antibiotic resistance. Usi
 ng computational approaches\, she aims to understand how small therapeutic
  molecules modulate protein dynamics and signaling pathways\, with the goa
 l of development of targeted therapeutic strategies. \n\nModerator: Dr. C
 anan Atılgan\n\nApplication Due: March 27\, 2026\n\nContact: ncc@ulakbim
 .gov.tr\n\nThis course is offered free of charge\n\nNotes:\n\nRegistration
  based on the principle of "first come – first served"\n\nPlease cancel 
 your registration if you won't be able to attend so that others may attend
 .\n\nParticipants will use their own laptop or computer for the hands-on s
 ession.\n\n-------\n\nDisclaimer\n\nSadece EuroHPC JU katılımcı ülkele
 rinde  (Türkiye gibi) yaşayan ve çalışan katılımcılar etkinliğe
  katılım sağlayabilir.( https://eurohpc-ju.europa.eu/about/discover-eu
 rohpc-ju_en)\n\nYalnızca resmi e-posta adresleri (çalıştığınız kur
 um e-posta adresi veya edu uzantılı üniversite e-posta adresleri) kayı
 t için kabul edilmektedir\; kişisel veya jenerik e-posta adresleri (gmai
 l\, hotmail\, yahoo gibi) kabul edilmemektedir.\n\n------\n\nBizi X ve Lin
 kedIn hesaplarımızdan takip edebilirsiniz. YouTube kanalımıza abone ol
 mayı unutmayın!\n\n- Twitter: https://twitter.com/EuroCC_Turkey \n\n-
  LinkedIN: https://www.linkedin.com/company/eurocc-turkey\n\n- YouTube:
  https://www.youtube.com/c/EuroCCTurkey\n\n \n\nAcknowledgments\n\nThis 
 event is supported by the EuroCC 2 and EuroCC4SEE projects\, which receive
 d funding from the European High-Performance Computing Joint Undertaking (
 JU) under grant agreements No. 101101903 and No. 101191697\, respectively.
  The JU receives support from the Digital Europe Programme and Germany\, B
 ulgaria\, Austria\, Croatia\, Cyprus\, Czech Republic\, Denmark\, Estonia\
 , Finland\, Greece\, Hungary\, Ireland\, Italy\, Lithuania\, Latvia\, Pola
 nd\, Portugal\, Romania\, Slovenia\, Spain\, Sweden\, France\, Netherlands
 \, Belgium\, Luxembourg\, Slovakia\, Norway\, Türkiye\, Republic of North
  Macedonia\, Iceland\, Montenegro\, Serbia. \n\n    \n          
                                           \n\n\nFoll
 ow us on Twitter and LinkedIn. Subscribe to our YouTube Channel\n\nhttps:/
 /twitter.com/EuroCC_Turkey\n\nhttps://www.linkedin.com/company/eurocc-turk
 ey\n\nhttps://www.youtube.com/channel/UC-qaWnbbTl6OPiPasUf4t8w/playlists\n
 \n \n\n \n\n                             \n\nhttps://ind
 ico.truba.gov.tr/event/252/
LOCATION:Classrooms G08-G09 (Sabancı University Altunizade Digital Campus
 \, Istanbul)
URL:https://indico.truba.gov.tr/event/252/
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