Rare Event Sampling and Related Topics II

March 27-28, 2015

The Institute of Statistical Mathematics

Tachikawa, Tokyo

ACCESS

Seminar Room 5 / floor 3

Organizers
Yukito Iba (ISM)
Hiroshi Fujisaki (Nippon Medical School)

Aim and Scope

The art of realization of rare events in computer simulation and calculation of their probabilities are important in many fields of science and engineering. The aim of this series of symposiums is to give a coherent perspective on this subject, focusing on novel computational techniques and their applications to highly complex and nonlinear systems.

A field of rare event sampling of recent interest is sampling rare events in molecular simulation. A typical example is numerical studies on transition paths of conformational changes of a protein molecule. In this symposium, a lecture by Dr. Daniel M Zuckerman (University of Pittsburgh) is scheduled.

Further, there are a number of application fields of rare event sampling, and recent introduction and innovative use of Markov chain Monte Carlo (MCMC) and sequential Monte Carlo (SMC) open the door of a variety of novel applications. Some interesting examples are found in theoretical studies on chaotic dynamical system, random matrices, and counting combinatorial objects, as well as practical problems such as rare event sampling in meteorology. In this symposium, we also treat these subjects as well as algorithms developed for them.

March 27 (Seminar Room 5 / floor 3)

13:30-15:00
Jorge Cardoso Leitao (Max Planck Institute) Invited Talk
Monte Carlo sampling in chaotic systems
see, for example, this paper

(short break)

15:15-16:00
Yukito Iba (ISM)
Rare event sampling using Markov chain Monte Carlo and sequential Monte Carlo

16:00-16:45
Shinichi Takayanagi (SOKENDAI) and Yukito Iba (ISM)
Sampling time-reversed path ensembles using sequential Monte Carlo

March 28 (Seminar Room 5 / floor 3)

10:00-11:30
Daniel M Zuckerman (University of Pittsburgh) Invited Lecture
Sampling rare events in biomolecular and cell-scale models based on statistical physics
Part I: Basic theory and weighted ensemble simulation
Zuckerman Lab. webpage

(lunch break)

12:30-13:30
Daniel M Zuckerman (University of Pittsburgh) Invited Lecture
Sampling rare events in biomolecular and cell-scale models based on statistical physics
Part II: Advanced theory and future challenges

(short break)

14:00-15:00
Tetsuya Morishita (AIST)
Logarithmic mean-force dynamics for sampling rare events

15:00-16:00
Yasuhiro Matsunaga (RIKEN AICS)
Drug extrusion mechanism of multidrug transporter AcrB studied by molecular dynamics simulations

16:00-17:00
Hiroshi Fujisaki (Nippon Medical School)
Extracting free energy profile and diffusion coefficients using the Onsager-Machlup action principle

iba at ism.ac.jp