Dynamics of fluorescent proteins
In fact, excited state dynamics in general has been puzzling many chemists for over decades already, and we still have much to learn to understand the fascinating phenomona in a satisfactory manner. Practically also, through such understanding, we can even have capabilities of suggesting directions for newly designing additional variations for many interesting photoprotein systems.

Chromophore dynamics in the electronically excited state leads to changes in emission properties of many fluorescent proteins. For example, the blue fluorescent protein (BFP) loses its emission when the chromophore twists as shown in the figure. Protein-chromophore interaction can modulate this dynamics and accurate potential description can pin point what factors contribute importantly for such modulations. For details, you can read J. Phys. Chem. B 116, 11137 (2012).
Quantum effects in photosynthetic systems
In this project, we have been examining the detailed dynamics within photosynthetic complexes. Our major point of view is to include all atomistic details in the examination. For this, we have been treating a series of prototypical systems such as the famous Fenna-Matthews-Olson (FMO) complex. Treating the transfer dynamics with all-atom details actually requires different techniques than conventional classical mechanics based approaches (which are often called "MD" approaches). Thus, we apply nonadiabatic semiclassical techniques, and we are heavily developing practical and reliable schemes that can be newly applied for relevant systems. Ultimately, we would love to get to a stage where we can understand the dynamics of protein complexes or supercomplexes with many proteins, even in their embedding membrane. This will indeed be a huge challenge in various respects for quite some time in the future. (However, who doesn't love a challenge?!?) Through this study, we expect that we will be able to elucidate the fundamentals of quantum mechanical behaviors of various biological systems, and thus gain comprehensive pictures that we can use as a guidance in the future.

During the energy transfer process in the FMO complex (cartoon drawing at the top panel), cross-talking between chromophores lasts for a long time even with noisy protein environment (bottom panel). Why and how that happens is a puzzle, and tackling that question with theoretical means is also a challenge. For details, you can read J. Phys. Chem. Lett. 2, 808 (2011) and J. Am. Chem. Soc. 134, 11640 (2012).
Bioluminescence: From a molecular view point
In this project, we are attempting to analyze the chromophore-luciferase interactions and their effect on luminescence by combining both quantum chemical and statistical approaches. We also simulate the dynamics of the chromophore-luciferase complex to reveal the real picture of this interesting biochemical phenomenon. For this, we often develop models of interesting bioluminescent systems and perform molecular dynamics simulations. Interestingly, but not surprisingly, we almost always experience that chemical intuition is much more important than any model or any computation during the analysis of our data!

Oxyluciferin, the luminophore of firefly bioluminescence, can be affected by various factors such as electrostatic interactions with neighboring protein side chains and a water molecule in the active pocket of the luciferase enzyme. One single type of oxyluciferin may emit from green to red with these factors. Moreover, oxyluciferin may even be chemically modified through tautomerization to attain a further diversified repotoire of emission colors. Explaining its full detail is a challenging but interesting topic in chemistry. For details, you can read J. Am. Chem. Soc. 133, 12040 (2011) and J. Phys. Chem. B 117, 7260 (2013) .