A model for the generation of fundamental frequency contours (F0contours) of spoken, sentences is presented for the purpose of elucidating the relationship between the sentence F0 contour and the linguistic and non-linguistic information. It is based on a quantitative formulation of the process whereby the logarithmic fundamental frequency is controlled in proportion to the sum of two components corresponding respectively to the effects of phrase and accent. The model's parameters were determined to give the best approximation to an observed F0 contour on the basis of the mean squared error. Analysis of natural utterances of various declarative sentences of Japanese revealedthat the model can generate close approximations to observed F0 contours from a set of discrete commands and a small number of parameters. The extracted parameters were found to be closely related to linguistic factors and factors constituting thenaturalness of speech. These results provide a means for generating natural F0contours from a small set of parameters and rules for synthesis.

Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme.

We investigate how the dynamical production of quantum entanglement for weakly coupled, composite quantum systems is influenced by the chaotic dynamics of the corresponding classical system, using coupled kicked tops. The linear entropy for the subsystem (a kicked top) is employed as a measure of entanglement. A perturbative formula for the entanglement production rate is derived. The formula contains a correlation function that can be evaluated only from the information of uncoupled tops. Using this expression and the assumption that the correlation function decays exponentially which is plausible for chaotic tops, it is shown that the increment of the strength of chaos does not enhance the production rate of entanglement when the coupling is weak enough and the subsystems (kicked tops) are strongly chaotic. The result is confirmed by numerical experiments. The perturbative approach is also applied to a weakly chaotic region, where tori and chaotic sea coexist in the corresponding classical phase space, to reexamine a recent numerical study that suggests an intimate relationship between the linear stability of the corresponding classical trajectory and the entanglement production rate.

Without invoking the Markov approximation, we derive formulas for vibrational energy relaxation (VER) and dephasing for an anharmonic system oscillator using a time-dependent perturbation theory. The system-bath Hamiltonian contains more than the third order coupling terms since we take a normal mode picture as a zeroth order approximation. When we invoke the Markov approximation, our theory reduces to the Maradudin-Fein formula which is used to describe the VER properties of glass and proteins. When the system anharmonicity and the renormalization effect due to the environment vanishes, our formulas reduce to those derived by and Mikami and Okazaki [J. Chem. Phys. 121, 10052 (2004)] invoking the path-integral influence functional method with the second order cumulant expansion. We apply our formulas to VER of the amide I mode of a small amino-acid like molecule, N-methylacetamide, in heavy water.

An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied by using two theoretical approaches. One approach is the equilibrium simulation approach with quantum correction factors, and the other is the reduced model approach, which describes the protein as an ensemble of normal modes interacting through nonlinear coupling elements. Both methods result in similar estimates of the VER time (subpicoseconds) for a CD stretching mode in the protein at room temperature. The theoretical predictions are in accord with previous experimental data. A perspective on directions for the detailed study of time scales and mechanisms of VER in proteins is presented.W hen a protein is excited by ligand binding, ATP attachment, or laser pulses, vibrational energy relaxation (VER) occurs. Energy initially ''injected'' into a localized region flows to the rest of the protein and surrounding solvent. VER in large molecules (including proteins) is an important problem for chemical physics (1,2). Even more significant is the challenge to relate VER to fundamental reaction processes, such as a conformational change or electron transfer of a protein, associated with protein functions. The development of an accurate understanding of VER in proteins is an essential step toward the goal of controlling protein dynamics (3).Because of the advance of laser technology, there have been many experimental studies of VER in proteins (4-17). These experimental works are impressive, but it is difficult to derive detailed information from the experimental data alone. Theoretical approaches, including atomic-scale simulations, can provide more detailed information. In turn, experimental data can be used to refine simulation methods and empirical force fields. This combination of experimental and theoretical studies of protein structures and dynamics has begun to blossom. As experimental methods develop further and theoretical approaches grow in accuracy, the relationship will become fruitful.There have been many theoretical tools (see Theories) developed to analyze VER in proteins. Some aspects of VER in proteins can be explained by perturbative formulas based on the equilibrium condition of the bath (see Cyt c), but the use of the perturbative formulas may be too restrictive to describe protein dynamics generally at room temperature. In this article, we not only discuss the success of such established methods but also present a perspective on the study of VER in proteins. TheoriesIn this section, we present a selective overview of theories appropriate for the study of VER in proteins. For the most part, these theories have been developed to deal with VER in liquids, solids, or glasses. For recent reviews, see refs. 18-20. We refer to two distinct categories; one is based on equilibrium dynamics and Fermi's golden rule, whereas the other is based on nonequilibrium dynamical models.Fermi's Golden Rule. If (i) there is a clear separation between the system and bath, (...

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The production of quantum entanglement between weakly coupled mapping systems, whose classical counterparts are both strongly chaotic, is investigated. In the weak-coupling regime, it is shown that time-correlation functions of the unperturbed systems determine the entanglement production. In particular, we elucidate that the increment of the nonlinear parameter of coupled kicked tops does not accelerate the entanglement production in the strongly chaotic region. An approach to the dynamical inhibition of entanglement is suggested.

Vibrational energy transfer of the amide I mode of N-methylacetamide (NMA) is studied theoretically using the vibrational configuration interaction method. A quartic force field of NMA is constructed at the B3LYP/6-31G+(d) level of theory and its accuarcy is checked by comparing the resulting anharmonic frequencies with available theoretical and experimental values. Quantum dynamics calculations for the amide I mode excitation clarify the dominant energy transfer pathways, which sensitively depend on the anharmonic couplings among vibrational modes. A ratio of the anharmonic coupling to the frequency mismatch is employed to predict and interpret the dominant energy flow pathways.