Large-scale biological simulations using supercomputers

Apr.1 (Wed.)- 2 (Thur.), 2015, RIKEN


The simposium will be hled at RIKEN Advanced Institute for Computational Science (AICS), 6F auditorium.
(Please refer to RIKEN website for the location.)

Scientific Program

April 1st (Wednesday)

13:00 - 13:15 Opening talk by Kimihiko Hirao (RIKEN)
Session 1: Cellular-scale simulations by multi-scale models (Chair: Yuji Sugita)
13:15 - 14:00 Zaida Luthey-Schulten (University of Illinois)

GPU-based Simulations of Cellular Processes: From Single Cells to Colonies
14:00 - 14:45 Leihan Tang (Hong Kong Baptist University and Beijing Computational Science Research Center)

Acetate overflow in bacteria: a manifestation of growth-regulated proteome coordination?
14:45 - 15:15 Koichi Takahashi (RIKEN)

Simulating intracellular biochemical networks at the molecular resolution

<< Coffee Break (15:15 - 15:30) >>

<< K tour & MD GRAPE4 (15:30 - 16:30) >>
Session 2: Large-scale MD simulations in life science (Chair: Makoto Taiji)
16:30 - 17:15 Klaus Schulten (University of Illinois)

Data-guided and Advanced Sampling Molecular Dynamics Simulations to Resolve Large Scale Structure and Dynamics of Biomolecules
17:15 - 17:45 Jin Yu (Beijing Computational Science Research Center)

Fluctuation and fidelity control in T7 RNA polymerase transcription
17:45 - 18:15 Yuji Sugita (RIKEN)

Molecular Dynamics Simulations of Atomic Models of Bacterial Cytoplasm

April 2nd (Thursday)

Session 3: Simulations of molecular machinery in biological systems (Chair: Tadashi Ando)
09:15 - 09:45 Osamu Miyashita (RIKEN)

Effect of Crystal Packing on Protein Conformations and Dynamics
09:45 - 10:15 Haiguang Liu (Beijing Computational Science Research Center)

Computational challenges in analysis of data from X-ray free electron laser
10:15 - 10:45 Florence Tama (RIKEN & Nagoya University)

Hybrid approaches to characterize structure and dynamics of biomolecular systems from single molecule experiments

<< Coffee Break (10:45 - 11:00) >>
Session 4: MD simulations using special-purpose machines (Chair: Yasuhiro Matsunaga)
11:00 - 11:45 Yibing Shan (D.E.Shaw Research & Beijing Computational Science Research Center)

Structural Biology of Protein Kinases by Large-scale Molecular Dynamics Simulation
11:45 - 12:15 Makoto Taiji (RIKEN)

MDGRAPE-4: the special-purpose computer system for MD simulations
12:15 - 12:20 Closing remarks by Makoto Taiji (RIKEN)


Yuji Sugita (RIKEN), Makoto Taiji (RIKEN)


For any questions regarding the workshop, please send an email to the secretary Ms. Hiromi Kano (hkano "at" (please change "at" to @)).