IUPAB2024 CHARMM-GUI/GENESIS Program

Day 1: 30 June 2024 (Sun)

8:40 – 9:00 Registration
9:00 – 9:10 Welcome address by Wonpil Im (Lehigh University)
 
Session 1 Molecular Dynamics Theories and Methods (chair: Yasuhiro Matsunaga)
9:10 – 9:40 Helmut Grubmüller (Max Planck Institute for Multidisciplinary Sciences)
Constant pH Simulations with FMM and solvation shell entropies
9:40 – 10:10 Kei Moritsugu (Osaka Metropolitan University)
Weighted Ensemble for Biomolecules
10:10 – 10:40 Ana Damjanovic , Juyong Lee, Bernard Brooks (NIH)
Constant pH Replica-Exchange Methods
10:40 – 11:00 COFFEE BREAK
 
Session 2 Enzyme Mechanisms (chair: Kiyoshi Yagi)
11:00 – 11:30 Kwangho Nam (The University of Texas at Arlington)
Advancements in multiscale QM/MM and free simulation methods for enzyme modeling
11:30 – 12:00 Youngmin Rhee (KAIST)
Following photodynamics in biology: non-adiabatic dynamics simulations with conventional MD packages
12:10 – 13:30 LUNCH
13:30 – 18:00 Scientific Discussion (6F, 8F)
 
GENESIS  Hands-on Part 1
Lecturer: Chigusa Kobayashi (RIKEN)
TA: Kiyoshi Yagi, Yangyang Zhang, Diego Ugarte La Torre, Cheng Tan, Shingo Ito
13:30 – 14:30 GENESIS basics and GENESIS on Fugaku
14:30 – 15:00 Hands-on GENESIS
15:00 – 15:20 BREAK
 
CHARMM-GUI  Hands-on Part 1
Lecturer: Wonpil Im (Lehigh University)
TA: TBD
15:20 – 16:20 Introduction of CHARMM-GUI and Membrane Builder
16:20 – 17:20 Hands-on CHARMM-GUI
17:20 – 18:00 BREAK
18:00 – BANQUET (all on-site participants)

Day 2: 01 July 2024 (Mon)

Session 3 Membrane Biology (chair: Florence Tama)
9:00 – 9:30 Chen Song (Peking University)
Gating mechanism of the mechanosensitive ion channel NOMPC: new insights from molecular dynamics simulations
9:30 – 10:00 Jana Shen (University of Maryland)
Drug-membrane partitioning and crossing from unbiased molecular dynamics coupled with proton titration
10:00 – 10:30 Ben Corry (Australian National University)
Molecular simulation of membrane channels, transporters, and receptors
10:30 – 10:50 COFFEE BREAK
 
Session 4 Modeling of Cellular Components, Part I (chair: Yasuhiro Matsunaga)
10:50 – 11:20 Jianhan Chen (University of Massachusetts)
Coarse-grained simulations of protein and RNA phase separation
11:20 – 11:50 Michael Feig (Michigan State University)
Multi-scale modeling of biomolecular condensates
11:50 – 13:15 LUNCH
13:15 – 18:00 Scientific Discussion (6F, 8F)
 
Fugaku Tour Instructor: Chigusa Kobayashi
13:15 – 14:20 GROUP 1
13:55 – 14:55 GROUP 2
 
GENESIS  Hands-on Part 2
14:30 – 15:30
Lecturer: Cheng Tan (RIKEN)
TA: Diego Ugarte La Torre, Yangyang Zhang, Kiyoshi Yagi, Shingo Ito
Coarse-grained simulations in GENESIS (Lecture + Hands-on)
15:30 – 16:30
Lecturer: Jaewoon Jung (RIKEN)
TA: Diego Ugarte La Torre, Yangyang Zhang, Kiyoshi Yagi, Chigusa Kobayashi, Shingo Ito
High-performance computation with GENESIS (Lecture + Hands-on)
16:30 – 16:45 BREAK
   
CHARMM-GUI  Hands-on Part 2
Lecturer: Nathan Kern (Lehigh University)
TA: TBD
16:45 – 17:15 Multi-component assembler
17:15 – 18:00 Hands-on multi-component assembler

Day 3: 02 July 2024 (Tue)

Session 5 Modeling of Cellular Components, Part II (chair: Kei Moritsugu)
9:00 – 9:30 Gerhard Hummer (Max Planck Institute of Biophysics)
Integrating molecular dynamics simulations and experiments
9:30 – 10:00 Naoto Hori (University of Nottingham)
Coarse-grained simulations of RNA folding and misfolding
10:00 – 10:20 COFFEE BREAK
10:20 – 10:50 Alberto Perez (University of Florida)
Synergizing simulations and experiments: faster exploration of biologically relevant states
10:50 – 11:20 Florence Tama (RIKEN)
Unraveling the Structure and Dynamics of Biomolecules via Integrative Modeling
11:20 – 11:50 Yasuhiro Matsunaga (Saitama University)
Integrative Modeling of Protein Dynamics from High-speed Atomic Force Microscopy and Molecular Dynamics Simulations
 
11:50 – 12:00 Closing Remarks to the morning sessions by Yuji Sugita (RIKEN)
12:00 – 13:30 LUNCH
13:30 – 17:10 Scientific Discussion (6F, 8F)
 
GENESIS  Hands-on Part 3
Lecturer: Shingo Ito (RIKEN)
TA: Kiyoshi Yagi, Yangyang Zhang, Diego Ugarte La Torre, Chigusa Kobayashi, Jaewoon Jung, Cheng Tan
13:30 – 15:00 Generalized-ensemble simulations using GENESIS
15:00 – 15:30 BREAK
 
CHARMM-GUI  Hands-on Part 3
Lecturer: Donghyuk Suh (Lehigh University)
TA: TBD
15:30 – 16:00 Enhanced sampler
16:00 – 17:00 Hands-on enhanced sampler
17:00 – 17:10 Yuko Okamoto (Nagoya University)
Closing Remarks
 

Food Maps

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