IUPAB2024 CHARMM-GUI/GENESIS Program
Day 1: 30 June 2024 (Sun) |
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| 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 |
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Lecturer: Chigusa Kobayashi (RIKEN)
TA: Kiyoshi Yagi, Yangyang Zhang, Diego Ugarte La Torre, Cheng Tan, Shingo Ito |
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| 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 |
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Lecturer: Wonpil Im (Lehigh University)
TA: TBD |
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| 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) |
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| 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 |
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Lecturer: Nathan Kern (Lehigh University)
TA: TBD |
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| 16:45 – 17:15 | Multi-component assembler |
| 17:15 – 18:00 | Hands-on multi-component assembler |
Day 3: 02 July 2024 (Tue) |
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| 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 |
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Lecturer: Shingo Ito (RIKEN)
TA: Kiyoshi Yagi, Yangyang Zhang, Diego Ugarte La Torre, Chigusa Kobayashi, Jaewoon Jung, Cheng Tan |
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| 13:30 – 15:00 | Generalized-ensemble simulations using GENESIS |
| 15:00 – 15:30 | BREAK |
| CHARMM-GUI | Hands-on Part 3 |
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Lecturer: Donghyuk Suh (Lehigh University)
TA: TBD |
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| 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
