安藤 耕司

Abstract Molecular dynamics simulations were performed to investigate the medaka fish taste receptor protein T1r2a-T1r3 complexed with four different amino acid ligands, L-glutamate, L-glutamine, L-alanine, and glycine. We focused on the structure and dynamics of water clusters in the ligand-binding pocket of T1r2a, as previous experimental studies have shown that T1r2a has a higher ligand specificity than T1r3. The simulation revealed that a number of water molecules dynamically formed alternating hydrogen bonds with the α-substituents of the amino acid ligands. The water cluster with the ligands L-glutamine and L-alanine showed similar distance and angle distributions as well as time-correlation functions of the number of hydrogen bonds. As these ligands are known to exhibit higher affinity to the receptor than the others, our results seem to imply that the characteristics of the water cluster in the ligand binding pocket is related to the affinity.

Molecular dynamics (MD) simulations were used to analyze the effect of the odorant molecule eugenol on the olfactory receptor protein mOR-EG and the dynamic correlation between amino acid residues around the binding site due to ligand binding. When eugenol hydrogen-bonded with Ser 113 of mOR-EG, the dynamic correlation with amino acid residues 213-218 on the adjacent α-helix increased within 10 ps. In particular, the correlation between Ser 113 and Leu 217 showed characteristic oscillations between 10 ps and 30 ps. The correlation with Leu 217 shifted toward residues closer to the G protein over time. Correlation with amino acids on the other side of the membrane was also observed, suggesting the contribution of collective protein motion.

High-harmonic generation (HHG) spectrum from a LiH molecule induced by an intense laser pulse is computed and analyzed with potential energy surfaces for electron motion (ePES) constructed from a model of localized electron wave packets (EWP) with valence-bond spin-coupling. The molecule has two valence ePES with binding energies of 0.39 hartree and 1.1 hartree. The HHG spectrum from an electron dynamics on the weaker bound valence ePES, virtually assigned to Li 2s, exhibits a dominant peak at the first harmonic without plateau and cut-off. This compares with the free electron spectrum under oscillating laser field and is comprehensive with the shape and depth of the ePES. The other valence ePES, assingned to H 1s, is deeper bound such that the overall profile of the wave function is well approximated by a Gaussian of the width comparable to the Li-H bond length. However, a small fraction, less than $10^{-3}$, of the probability density amplitude tunnels out from the bound potential with high wave number, and spreads over tens of nm's with parts recombining to the molecule due to the laser field oscillation. This minor portion of the electronic wave function is the major origin of the HHG extending up to 50 harmonic orders. Nonlinear dynamics within the potential well induced by the laser field oscillation also contributes to the HHG up to 30 harmonic orders.

<p>The recently developed quantum molecular dynamics method including nuclear quantum effects demonstrated that supercooled hydrogens exhibit intrinsic properties including a precursor of superfluidity which neither normal hydrogen liquid nor solid possesses.</p>

A mixed quantal-semiquantal theory is presented in which the semiquantal squeezed-state wave packet describes the heavy degrees of freedom. We first derive mean-field equations of motion from the time-dependent variational principle. Then, in order to take into account the interparticle correlation, in particular the 'quantum backreaction' beyond the mean-field approximation, we introduce the stochastic particle description for both the quantal and semiquantal parts. A numerical application on a model of O2 scattering from a Pt surface demonstrates that the proposed scheme gives correct asymptotic behavior of the scattering probability, with improvement over the mixed quantum-classical scheme with Bohmian particles, which is comprehended by comparing the Bohmian and the stochastic trajectories.