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Computational Information Chemistry Lab
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A lab that develops quantum chemical and molecular dynamics computational methods to uncover how molecules work.
AboutAbout the lab
Developing theories and computational methods to understand how molecules work.
The Yagi-Matsui Lab (Computational Information Chemistry) uses quantum chemical calculations, molecular dynamics simulations, and information science to study the structure, reaction mechanisms, and functions of molecules.
The lab devises new theories and computational methods and develops its own programs.
Focusing mainly on biomolecules and functional polymers, the lab works to understand molecular interactions, optical functions, and chemical reactions, and also takes on the design of new molecules.
On the lab's website, it is introduced under the name "Yagi-Matsui Lab."
Key terms
- Quantum chemical calculation
- A calculation that determines the behavior of electrons in molecules using quantum mechanics. In the QM/MM method, it handles the high-accuracy part
- QM/MM method
- A method that treats the region of interest with high-accuracy quantum chemical calculations and the environment, such as solvent and biomolecules, with low-cost classical force-field calculations
- Density functional theory
- A theory widely used in quantum chemical calculations. How to determine its many parameters is a challenge
ResearchResearch themes
This lab develops new theories and computational methods in quantum chemical calculations, molecular dynamics simulations, information science, and the fields where they merge. Using these techniques, it investigates the structures, reaction mechanisms, and functions of complex molecules, and feeds challenges that arise in applications back into method development.
*Illustrative imageTheory for studying the vibrations of complex molecules
The lab develops theory for calculating the vibrational states of molecules. Because the computational cost becomes enormous as the number of atoms increases, it has developed efficient solution methods and released them in its own program, SINDO.
*Illustrative imageAccelerating QM/MM molecular dynamics simulations
The lab implemented the QM/MM method in the molecular dynamics program GENESIS and integrated it with QSimulate-QM, achieving calculations more than 10 times faster than before. It is currently developing methods to obtain free energies efficiently.
*Illustrative imageDensity functional theory based on molecular information
The lab developed a method that determines the parameters of density functional theory from theoretical constraints, without relying on experiments or high-accuracy calculations, and combined it with machine-learning fitting. It is currently developing a procedure for constructing new functionals.
*Illustrative imageQuantum transport theory focused on molecular topology
The lab treats electrical and thermal conduction at the molecular scale by linking quantum transport theory based on the nonequilibrium Green's function method with graph theory, which describes molecular topology. It is building a theory that relates molecular structure to electron and heat transport.
MembersFaculty
The members of the Yagi-Matsui Lab are faculty, doctoral, master's, and undergraduate students, and visiting graduate students.As of 2026
- ProfessorKiyoshi Yagi
- Associate ProfessorToru Matsui
- Assistant ProfessorKazuki Okazawa
- Project Assistant ProfessorKazuya Okita
VoicesStudent voices
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “Model molecular àcid salicílic” Joel Gonzàlez / CC BY-SA 4.0 (cropped)
- Theory for studying the vibrations of complex molecules: “1-Undecanol molecular model” RandomKatze / CC0 (cropped)
- Accelerating QM/MM molecular dynamics simulations: “The catalyst high performance computing (HPC)” ENERGY.GOV / Public domain (cropped)
- Density functional theory based on molecular information: “Carbon dioxide molecular orbital” ChiralJon / CC BY 2.0 (cropped)
- Quantum transport theory focused on molecular topology: “Bucked kit” _sarchi / CC BY 2.0 (cropped)
- Related lab (超分子化学): “Osmium Host-Guest Assembly” Dslate2123 / CC BY-SA 3.0 (cropped)
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