In visual systems and fluorescent proteins, controlling the photo-absorption/emission energy (color tuning) of the chromophore is the essentials to furnish a protein with the photo-functionality. Depending on the protein environment, the chromophores show a variety of colors, which are relevant to the character of the excited states and to the interactions between the chromophore and the environment. Here we summarize our recent studies on the spectral tuning mechanism of the human visual cone pigments and the fluorescent proteins. These studies elucidated a common feature in the color tuning, which also suggests a strategy to artificially control the color of proteins. We also explain our recent progress in developing the symmetry-adapted cluster-configuration interaction (SAC-CI) method and hybrid quantum mechanical/molecular mechanical (QM/MM) method particularly for studying the photo-functional proteins.

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Two novel electronics based on molecular conductors are discussed. One is a crystalline supramolecular nanowire comprising conducting cation-radical molecules and halogen-bonded insulating networks. The way to utilize this nanowire for nano-size wiring in high-density memory is proposed. The other is a field effect transistor with highly correlated electrons on the conducting molecules. The Mott insulating state of organic interface is transformed into a metallic-like state by electrostatic doping, or band-filling control due to the capacitive effect of the transistor configuration. The Mott-transition transistor can be a new type of transistor driven by a phase transition.

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Amphiphilic molecules form self-assemblies (e.g. micelles, spherical or tubular vesicles) in water and these self- assemblies exhibit elastic response towards an external field, spontaneous movements coupled with chemical reactions, self-reproduction upon the addition of an amphiphilic precursor. If a self-replication of an informational molecule (e.g. DNA) proceeds in a self-reproducing vesicle, such a supramolecular system can be regarded as an artificial cell. A lipid world, in which abovementioned dynamics are occurring, serves a non-linear and open system that can be explored by modern molecular science.

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Flagellar motor is a nano-sized rotary machine. Despite of 40-year research on the flagella, the physic-chemical principle of torque generation in the motor is not clear. Even the conventional technique for measuring torque has a flaw as an experimental method. Image of the flagellar motor is extensively changing at the moment. Updated information on the flagellar motor is presented.

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