Language：English   Publishing type：Research paper (scientific journal)  

We simulate the nonequilibrium ensemble dynamics of a biomolecule using the weighted ensemble method, which was introduced in molecular dynamics simulations by Huber and Kim and further developed by Zuckerman and co-workers. As the order parameters to characterize its conformational change, we here use the coordinates derived from the diffusion map (DM) method, one of the manifold learning techniques. As a concrete example, we study the kinetic properties of a small peptide, chignolin in explicit water, and calculate the conformational change between the folded and misfolded states in a nonequilibrium way. We find that the transition time scales thus obtained are comparable to those using previously employed hydrogen-bond distances as the order parameters. Since the DM method only uses the 3D Cartesian coordinates of a peptide, this shows that the DM method can extract the important distance information of the peptide without relying on chemical intuition. The time scales are compared well with the previous results using different techniques, non-Markovian analysis and core-set milestoning for a single long trajectory. We also find that the most significant DM coordinate turns out to extract a dihedral angle of glycine, and the previously studied relaxation modes are well correlated with the most significant DM coordinates.

DOI： 10.1063/1.5049420

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：eLife Sciences Publications Ltd  

The multidrug transporter AcrB transports a broad range of drugs out of the cell by means of the proton-motive force. The asymmetric crystal structure of trimeric AcrB suggests a functionally rotating mechanism for drug transport. Despite various supportive forms of evidence from biochemical and simulation studies for this mechanism, the link between the functional rotation and proton translocation across the membrane remains elusive. Here, calculating the minimum free energy pathway of the functional rotation for the complete AcrB trimer, we describe the structural and energetic basis behind the coupling between the functional rotation and the proton translocation at atomic resolution. Free energy calculations show that protonation of Asp408 in the transmembrane portion of the drug-bound protomer drives the functional rotation. The conformational pathway identifies vertical shear motions among several transmembrane helices, which regulate alternate access of water in the transmembrane as well as peristaltic motions that pump drugs in the periplasm.

DOI： 10.7554/eLife.31715

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Performing comprehensive quantum-chemical calculations, a vibrational Hamiltonian of acetylbenzonitrile is constructed, on the basis of which a quantum-mechanical "tier model" is developed that describes the vibrational dynamics following excitation of the CN stretch mode. Taking into account 36 vibrational modes and cubic and quartic anharmonic couplings between up to three different modes, the tier model calculations are shown to qualitatively reproduce the main findings of the experiments of Rubtsov and coworkers (2011), including the energy relaxation of the initially excited CN mode and the structure dependent vibrational transport. Moreover, the calculations suggest that the experimentally measured cross-peak among the CN and CO modes does not correspond to direct excitation of the CO normal mode but rather reflects excited low-frequency vibrations that anharmonically couple to the CO mode. Complementary quasiclassical trajectory calculations are found to be in good overall agreement with the quantum calculations. (C) 2016 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.chemphys.2016.09.010

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DOI： 10.1016/j.bpj.2015.11.2799

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Language：English   Publisher：Frontiers Media S.A.  

Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration.

DOI： 10.3389/fbioe.2015.00125

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.54.S256_3

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.54.S152_3

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.54.S242_4

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

We propose a novel path sampling method based on the Onsager-Machlup (OM) action by generalizing the multiscale enhanced sampling technique suggested by Moritsugu and co-workers [J. Chem. Phys. 133, 224105 (2010)]. The basic idea of this method is that the system we want to study (for example, some molecular system described by molecular mechanics) is coupled to a coarse-grained (CG) system, which can move more quickly and can be computed more efficiently than the original system. We simulate this combined system (original + CG system) using Langevin dynamics where different heat baths are coupled to the two systems. When the coupling is strong enough, the original system is guided by the CG system, and is able to sample the configuration and path space with more efficiency. We need to correct the bias caused by the coupling, however, by employing the Hamiltonian replica exchange, where we prepare many path replicas with different coupling strengths. As a result, an unbiased path ensemble for the original system can be found in the weakest coupling path ensemble. This strategy is easily implemented because a weight for a path calculated by the OM action is formally the same as the Boltzmann weight if we properly define the path "Hamiltonian." We apply this method to a model polymer with Asakura-Oosawa interaction, and compare the results with the conventional transition path sampling method. (C) 2013 AIP Publishing LLC.

DOI： 10.1063/1.4817209

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.53.S219_5

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.53.S118_5

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PUBLIC LIBRARY SCIENCE  

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.

DOI： 10.1371/journal.pcbi.1002555

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We propose a generalization of the intrinsic reaction coordinate (IRC) for quantum many-body systems described in terms of the mass-weighted ring polymer centroids in the imaginary-time path integral theory. This novel kind of reaction coordinate, which may be called the "centroid IRC," corresponds to the minimum free energy path connecting reactant and product states with a least amount of reversible work applied to the center of masses of the quantum nuclei, i.e., the centroids. We provide a numerical procedure to obtain the centroid IRC based on first principles by combining ab initio path integral simulation with the string method. This approach is applied to NH3 molecule and N2H5- ion as well as their deuterated isotopomers to study the importance of nuclear quantum effects in the intramolecular and intermolecular proton transfer reactions. We find that, in the intramolecular proton transfer (inversion) of NH3, the free energy barrier for the centroid variables decreases with an amount of about 20% compared to the classical one at the room temperature. In the intermolecular proton transfer of N2H5-, the centroid IRC is largely deviated from the "classical" IRC, and the free energy barrier is reduced by the quantum effects even more drastically. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4709723]

DOI： 10.1063/1.4709723

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

Febuxostat, a drug recently approved in the US, European Union and Japan for treatment of gout, inhibits xanthine oxidoreductase (XOR)-mediated generation of uric acid during purine catabolism. It inhibits bovine milk XOR with a K-i in the picomolar-order, but we found that it is a much weaker inhibitor of Rhodobacter capsulatus XOR, even though the substrate-binding pockets of mammalian and bacterial XOR are well-conserved as regards to catalytically important residues and three-dimensional structure, and both permit the inhibitor to be accommodated in the active site, as indicated by computational docking studies. To clarify the reason for the difference of inhibitory potency towards the two XORs, we performed molecular dynamics simulations. The results indicate that differences in mobility of hydrophobic residues that do not directly interact with the substrate account for the difference in inhibitory potency.

DOI： 10.1038/srep00331

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.52.S128_3

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.52.S101_3

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.52.S40_2

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.52.S98_1

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Language：English   Publishing type：Part of collection (book)   Publisher：WILEY-BLACKWELL  

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Language：English   Publishing type：Part of collection (book)   Publisher：WILEY-BLACKWELL  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

For sampling multiple pathways in a rugged energy landscape, we propose a novel action-based path sampling method using the Onsager-Machlup action functional. Inspired by the Fourier-path integral simulation of a quantum mechanical system, a path in Cartesian space is transformed into that in Fourier space, and an overdamped Langevin equation is derived for the Fourier components to achieve a canonical ensemble of the path at a finite temperature. To avoid "path trapping" around an initially guessed path, the path sampling method is further combined with a powerful sampling technique, the replica exchange method. The principle and algorithm of our method is numerically demonstrated for a model two-dimensional system with a bifurcated potential landscape. The results are compared with those of conventional transition path sampling and the equilibrium theory, and the error due to path discretization is also discussed.

DOI： 10.1063/1.3372802

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Language：English   Publisher：CELL PRESS  

DOI： 10.1016/j.bpj.2009.12.3111

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.50.S94_3

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.50.S137_4

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.50.S150_3

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DOI： 10.2142/biophys.50.S110_5

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JOHN WILEY & SONS INC  

Employing extensive quantum-chemical calculations at the DFT/B3LYP and MP2 level, quartic force fields of isolated N-methylacetamide are constructed. Taking into account 24 vibrational degrees of freedom, the model is employed to perform numerically exact vibrational configuration interaction calculations of the vibrational energy relaxation of the amide 1 mode. It is found that the energy transfer pathways may sensitively depend on details of the theoretical description. Moreover, the exact reference calculations were used to Study the applicability and accuracy of (i) the quasiclassical trajectory method, (ii) time-dependent second-order perturbation theory, and (iii) the instantaneous normal mode description of frequency fluctuations. Based on the results, several strategies to describe vibrational energy relaxation in biomolecular systems are discussed. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 109:2047-2057, 2009.

DOI： 10.1002/qua.22061

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The mode-specific vibrational energy relaxation of the amide I' and amide II' modes in NMA-d(1)/(D(2)O)(n) (n = 0-3) clusters were studied using the time-dependent perturbation theory at the B3LYP/aug-cc-pvdz level. The amide modes were identified for each cluster based on the potential energy distribution of each mode. The vibrational population relaxation time constants were derived for the amide I' and II' modes. Results for the amide I' mode relaxation of NMA-d(1)/(D(2)O)(3) agree well with previous experimental results. The energy relaxation pathways were identified, and both intra- and inter-molecular mechanisms were found to be important. The amide II' mode was identified in the energy transfer pathways from the excited amide I' mode of NMA-d(1)(D(2)O)(n) (n = 1-3) clusters. The modes associated with methyl group deformation were found to play a role in the mechanism of energy transfer from both excited amide I' and II' modes. The kinetics of energy flow in the cluster were examined by solving a master equation describing the vibrational energy relaxation process from excited system mode as a multistep reaction with the third order Fermi resonance parameters as the reaction rate constants. The intramolecular energy transfer mechanism was found to dominate the short time energy flow dynamics, whereas the intermolecular mechanism was found to be dominant at longer times.

DOI： 10.1021/jp8109995

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The time scales and mechanisms of mode-specific vibrational energy relaxation in imidazole ligated ferrous iron porphine were studied using a non-Markovian time-dependent perturbation theory and density functional theory calculation. Seven normal modes, including nu(4), nu(7), and five Fe out-of-plane modes (Fe-oop), were treated as the relaxing system mode coupled to all other modes forming the bath. The derived cooling time constants for the nu(4) and nu(7) modes agree well with the results of previous experimental studies. The pathways for energy transfer from each system mode were identified. The gamma(7) mode, associated with Fe-oop motion with frequency similar to 350 cm(-1), was observed to couple strongly through its overtone with the nu(7) porphine in-plane vibration. This suggests a possible mechanism for the excitation of the nu(7) mode, which is distinct from the direct excitation together with Fe-oop motion of the nu(4) mode. Four other Fe-oop motions were observed to couple to low frequency modes including those involving significant imidazole ligand motions. Through these couplings, excitation following ligand photodissociation may be efficiently transferred from the heme doming mode to the protein backbone motions essential to conformational changes associated with the protein's function.

DOI： 10.1063/1.3055277

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.49.S156_3

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

The rotating-wave approximation and its validity in multi-state quantum systems are studied through analytic approaches. Their applicability is also verified from the viewpoint of generic states by the use of direct numerical integrations of the Schrodinger equation. First, we introduce an extension of the rotating-wave approximation for multi-state systems. Under an assumption that a smooth transition is induced by the optimal field, we obtain three types of analytic control fields to demonstrate their validity and deficiency for generic systems represented by random matrices. Through the comparison, we conclude that the analytic field based on our coarse-grained approach outperforms the other ones for generic quantum systems with a large number of states. Finally, the further extension of the analytic field is introduced for realistic chaotic systems and its validity is shown in banded random matrix systems.

DOI： 10.1080/09500340802296331

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.49.S154_5

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A computational approach to describe the energy relaxation of a high-frequency vibrational mode in a fluctuating heterogeneous environment is outlined. Extending previous work [H. Fujisaki, Y. Zhang, and J. E. Straub, J. Chem. Phys. 124, 144910 (2006)], second-order time-dependent perturbation theory is employed which includes the fluctuations of the parameters in the Hamiltonian within the vibrational adiabatic approximation. This means that the time-dependent vibrational frequencies along a molecular dynamics trajectory are obtained via a partial geometry optimization of the solute with fixed solvent and a subsequent normal mode calculation. Adopting the amide I mode of N-methylacetamide in heavy water as a test problem, it is shown that the inclusion of dynamic fluctuations may significantly change the vibrational energy relaxation. In particular, it is found that relaxation occurs in two phases, because for short times (less than or similar to 200 fs) the spectral density appears continuous due to the frequency-time uncertainty relation, while at longer times the discrete nature of the bath becomes apparent. Considering the excellent agreement between theory and experiment, it is speculated if this behavior can explain the experimentally obtained biphasic relaxation the amide I mode of N-methylacetamide. (C) 2008 American Institute of Physics.

DOI： 10.1063/1.2985606

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.48.S29_1

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

With use of a time-dependent perturbation theory, vibrational energy relaxation (VER) of isotopically labeled amide I modes in cytochrome c solvated with water is investigated. Contributions to the VER are decomposed into two contributions from the protein and water. The VER pathways are visualized by using radial and angular excitation functions for resonant normal modes. Key differences of VER among different amide I modes are demonstrated, leading to a detailed picture of the spatial anisotropy of the VER. The results support the experimental observation that amide I modes in proteins relax with subpicosecond time scales, while the relaxation mechanism turns out to be sensitive to the environment of the amide I mode.

DOI： 10.1021/jp072651o

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

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 accuracy 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. (c) 2007 Published by Elsevier B.V.

DOI： 10.1016/j.cplett.2007.06.067

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The time scale and mechanism of vibrational energy relaxation of the heme moiety in myoglobin was studied using molecular dynamics simulation. Five different solvent models, including normal water, heavy water, normal glycerol, deuterated glycerol and a nonpolar solvent, and two forms of the heme, one native and one lacking acidic side chains, were studied. Structural alteration of the protein was observed in native myoglobin glycerol solution and native myoglobin water solution. The single-exponential decay of the excess kinetic energy of the heme following ligand photolysis was observed in all systems studied. The relaxation rate depends on the solvent used. However, this dependence cannot be explained using bulk transport properties of the solvent including macroscopic thermal diffusion. The rate and mechanism of heme cooling depends upon the detailed microscopic interaction between the heme and solvent. Three intermolecular energy transfer mechanisms were considered: (i) energy transfer mediated by hydrogen bonds, (ii) direct vibration-vibration energy transfer via resonant interaction, and (iii) energy transfer via vibration-translation or vibration-rotation interaction, or in other words, thermal collision. The hydrogen bond interaction and vibration-vibration interaction between the heme and solvent molecules dominates the energy transfer in native myoglobin aqueous solution and native myoglobin glycerol solutions. For modified myoglobin, the vibration-vibration interaction is also effective in glycerol solution, different from aqueous solution. Thermal collisions form the dominant energy transfer pathway for modified myoglobin in water solution, and for both native myoglobin and modified myoglobin in a nonpolar environment. For native myoglobin in a nonpolar solvent solution, hydrogen bonds between heme isopropionate side chains and nearby protein residues, absent in the modified myoglobin nonpolar solvent solution, are key interactions influencing the relaxation pathways.

DOI： 10.1021/jp065877k

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMERICAN PHYSICAL SOC  

We examine random matrix systems driven by an external field in view of optimal control theory (OCT). By numerically solving OCT equations, we can show that there exists a smooth transition between two states called "moving bases" which are dynamically related to initial and final states. In our previous work [J. Phys. Soc. Jpn. 73, 3215 (2004); Adv. Chem. Phys. 130A, 435 (2005)], they were assumed to be orthogonal, but in this paper, we introduce orthogonal moving bases. We can construct a Rabi-oscillation-like representation of a wave packet using such moving bases, and derive an analytic optimal field as a solution of the OCT equations. We also numerically show that the newly obtained optimal field outperforms the previous one.

DOI： 10.1103/PhysRevE.75.0336219

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：AMER INST PHYSICS  

An analytic approach for controlling quantum states, which was originally applied to fully random matrix systems [T. Takami and H. Fujisaki, Phys. Rev. E 75, 036219 (2007)], is extended to deal with more realistic quantum systems with a banded random. matrix (BRM). The validity of the new analytic field is confirmed by directly solving the Schrodinger equation with a BRM interaction. We find a threshold of the width of the BRM for the quantum control to be successful.

DOI： 10.1063/1.2836218

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

DOI： 10.1021/ja061328g

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

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. (c) 2006 American Institute of Physics.

DOI： 10.1063/1.2191038

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

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.

DOI： 10.1073/pnas.040983102

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DOI： 10.1002/0471712531.ch9

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DOI： 10.1002/0471712531.ch15

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.45.S6_2

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PHYSICAL SOC JAPAN  

DOI： 10.1143/JPSJ.73.3215

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMERICAN PHYSICAL SOC  

We investigate entanglement between electronic and nuclear degrees of freedom for a model nonadiabatic system. We find that entanglement (measured by the von Neumann entropy of the subsystem for the eigenstates) becomes nearly maximum when the system shows "nonadiabatic chaos" behavior which was found in our previous work [ Phys. Rev. E 63, 066221 (2001) ], but the reverse is not necessarily the case.

DOI： 10.1103/PhysRevA.70.012313

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

A nonadiabatic transition system which exhibits "quantum chaotic" behavior [H. Fujisaki and K. Takatsuka, Phys. Rev. E 63, 066221 (2001)] is investigated from quasiclassical aspects. Since such a system does not have a naive classical limit, we take the mapping approach [Stock and Thoss, Phys. Rev. Lett. 78, 578 (1997)] to represent the quasiclassical dynamics of the system. We numerically show that there is a sound correspondence between the quantum chaos and classical chaos for the system.

DOI： 10.1103/PhysRevE.69.037201

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PHYSICAL SOC JAPAN  

We investigate how the dynamical production of quantum entanglement for weakly coupled mapping systems is influenced by the chaotic dynamics of the corresponding classical system. We derive a general perturbative formula for the entanglement production rate which is defined by using the linear entropy of the subsystem. This formula predicts that the increment in the strength of chaos does not enhance the production rate of entanglement when the coupling is weak enough and the subsystems are strongly chaotic. The prediction is confirmed by numerical experiments for coupled kicked tops and rotors. We also discuss the entanglement production using the Husimi representation of the reduced density matrix.

DOI： 10.1143/JPSJ.72.111

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

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 in 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.

DOI： 10.1103/PhysRevE.67.066201

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DOI： 10.1103/PhysRevE.67.066201

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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 in 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. © 2003 The American Physical Society.

DOI： 10.1103/PhysRevE.67.066201

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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. © 2002 The American Physical Society.

DOI： 10.1103/PhysRevE.66.045201

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DOI： 10.1103/PhysRevE.66.045201

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

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.

DOI： 10.1103/PhysRevE.66.045201

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

Chaos in the multimode nonadiabatic system constructed by Heller [J. Chem. Phys. 92, 1718 (1990)], which consists of two diabatic two-dimensional harmonic potentials with the Condon coupling, is studied. A thorough investigation is carried out by scanning the magnitudes of the Condon coupling and the Duschinsky angle. To elucidate mechanisms that can cause chaos in this quantum system, the statistical properties of the energy levels and eigenfunctions of the system are investigated. We find an evidence in terms of the nearest-neighbor spacing distribution of energy levels and other measures that a certain class of chaos is purely induced by the nonadiabatic interaction due to breakdown of the Born-Oppenheimer approximation. Since the nonadiabatic transition can induce repeated bifurcation and merging of a wave packet around the region of quasicrossing between two potential surfaces, and since this interaction does not have a counterpart in the lower adiabatic system, the present chaos deserves being called "nonadiabatic chaos.'' Another type of chaos in a nonadiabatic system was previously identified [D. M. Leitner et al., J. Chem. Phys. 104, 434 (1996)] that reflects the inherent chaos of a corresponding adiabatic potential. We present a comparative study to establish the similarity and difference between these kinds of chaos.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

We study the characteristics of vibronic eigenfunctions of a multidimensional nonadiabatic system and their consequences in the quantum spectra. As an illustrative example, we investigate the properties of highly excited eigenfunctions of Heller's multimode nonadiabatic system. The system consists of two diabatic states and two-dimensional (two-mode) harmonic potentials that are nonadiabatically coupled with the Condon approximation and with an appropriate magnitude of the Duschinsky angle. "Quantum chaos" thus produced has no classical counterpart. In addition to rather characterless chaotic eigenfunctions that are uniformly widespread in configuration space, we have found highly excited localized eigenfunctions of two extreme types which favor either the diabatic picture or adiabatic picture. As a result, the features of the associated quantum spectra are strongly affected by the initial preparation of a wave packet. This finding suggests that one can control the rate of nonadiabatic transitions such as that for electron transfer by using laser techniques or by choosing appropriate solvents. (C) 2001 American Institute of Physics.

DOI： 10.1063/1.1337801

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMERICAN PHYSICAL SOC  

From the microscopic quantum Langevin equations (QLEs) we derive the effective semiconductor QLEs and the associated noise correlations which are valid at a low-injection level and in real devices. Applying the semiconductor QLEs to semiconductor light-emitting devices (LEDs), we obtain a formula for the Fano factor of photons that gives the photon-number statistics as a function of the pump statistics and several parameters of LEDs. Key ingredients are nonradiative processes, carrier-number dependence of the radiative and nonradiative lifetimes, and multimodeness of LEDs. The formula is applicable to the actual cases where the quantum efficiency eta differs from the differential quantum efficiency eta(d), whereas previous theories implicitly assumed eta = eta(d). It is also applicable to the cases where photons in each mode of the cavity are emitted and/or detected inhomogeneously. When eta(d) < eta at a running point, in particular, our formula predicts that even a Poissonian pump can produce sub-Poissonian light. This mechanism for generation of sub-Poissonian light is completely different from those of previous theories, which assumed sub-Poissonian statistics for the current injected into the active layers of LEDs. Our results agree with recent experiments. We also discuss frequency dependence of the photon statistics.

DOI： 10.1103/PhysRevA.57.3074

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PHYSICAL SOC JAPAN  

We study the photon statistics of semiconductor light-emitting devices at a low-injection level, using quantum Langevin equations which take account of nonradiative processes and carrier-number dependence of lifetimes. Assuming the noise correlations which are consistent with the fluctuatian-dissipation theorem, we derive new formulae for the photon Fano factor, which represents the photon statistics as a function of the pump (injection) statistics. The formulae are applicable to the general cases when the quantum efficiency eta differs from the differential quantum efficiency eta(d) and when emission efficiency and/or detection efficiency of photons are different among different photon modes. The formulae agree with recent experimental results, which cannot be explained by the previous theories. It is also shown that a Poissonian pump can produce either sub-Poissonian light (if eta(d) < eta at the running point) or super-Poissonian light (if eta(d) > eta).

DOI： 10.1143/JPSJ.66.34

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Language：Japanese   Publisher：日本医科大学  

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Language：Japanese   Publisher：京都大学数理解析研究所  

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Language：Japanese   Publisher：京都大学数理解析研究所  

本稿では、生体分子におけるレアイベントの意義、Onsager-Machlup作用の定義と導出、それを用いたパスサンプリング手法、拡張アンサンブルや再重みつけ法との組み合わせなどについて解説する。また今後の展望についても述べる。Here we describe the meaning of rare events for computational biophysics, and explain the definition and derivation of the Onsager-Machlup (OM) action, path sàmpling methods using the OM action, and how to combine the OM action method with extended ensemble methods and reweighting methods. Finally we describe the future prospects on the computational use of the OM action.

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：CELL PRESS  

DOI： 10.1016/j.bpj.2016.11.2407

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Language：Japanese   Publisher：分子シミュレーション研究会  

本稿では化学反応，構造変化，リガンド結合などに関わる速度論（キネティックス）を記述する量であるレートを分子レベルで計算する手法として，ノンマルコフな軌道解析法，重み付きアンサンブル法，遷移パスサンプリング法などについて解説する．最後にキネティックスを計算する際にまだ残っている問題点や今後の展望について述べる．

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.57.040

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Language：Japanese   Publisher：一般社団法人 日本物理学会  

<p>編集後記</p>

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Language：Japanese   Publisher：The Physical Society of Japan  

<p>生体分子の機能を調べるためには構造変化のダイナミクス、特にその分子的な詳細を調べなければならない。現在は計算機も高速になり、小さな系であれば構造変化をサンプルすることも可能になりつつあるが、その際にどの反応座標で反応を解析するかということに関してはまだ経験的であり、最適な手法は見つかっていない。ここでは拡散マップ法を用いて、転移温度上のシニョリンのダイナミクスから、どのように反応座標が抜き出されるか調べたい。</p>

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Language：Japanese   Publisher：日本医科大学  

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Language：Japanese   Publisher：一般社団法人 日本痛風・核酸代謝学会  

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Language：Japanese   Publisher：The Physical Society of Japan  

<p>アミノ酸の中でもプロリンをターゲットにするプロリン異性化酵素は、そのペプチド結合を異性化することでターゲットタンパク質の構造安定性に甚大な影響を与える。ただし、酵素反応とは言っても分子シミュレーションで計算するには遅い時間スケールで進行するので、その反応の分子的な詳細はよく分かっていない。ここではプロリン異性化タンパク質PIN1にリン酸化された基質を相互作用させたときのプロリンの異性化をストリング法のような構造変化を計算するのに適した手法を用いて計算し、そのメカニズムについて調べる。</p>

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Language：Japanese   Publisher：The Physical Society of Japan  

<p>キサンチン酸化還元酵素（XOR）は、痛風のターゲットタンパク質である。XORは細菌からヒトまで存在し、その3次元構造は全ての生物種で酷似しているが、XORのStructure-Based inhibitorであるBOFは、哺乳類に対しては阻害するが、バクテリアには阻害しない。この差異に関してXORの静的な構造では理解することが難しいが、動的な構造で理解することが可能であることを示す。</p>

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Language：Japanese   Publisher：The Physical Society of Japan  

DOI： 10.11316/jpsgaiyo.71.1.0_3181

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Language：Japanese   Publisher：分子シミュレーション研究会  

前回に引き続き，化学反応や構造変化，リガンド結合などに関わる速度論 (kinetics) を記述する量である，レート (rate) を分子レベルで計算する手法について解説する．今回は最近よく用いられるようになってきている，マルコフ状態モデル (Markov state model) とマイルストーン (milestoning) 法について取り上げる.

DOI： 10.11436/mssj.17.175

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Language：Japanese   Publisher：一般社団法人 日本物理学会  

DOI： 10.11316/jpsgaiyo.70.1.0_3244

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Language：Japanese   Publisher：分子シミュレーション研究会  

ここでは，化学反応や構造変化，リガンド結合などに関わる速度論(kinetics) を記述する量である，レート(rate)を分子レベルで計算する手法について解説する．特に，もっとも基本的な手法である，反応流束法や遷移状態理論，Kramers の理論などを取り上げる．

DOI： 10.11436/mssj.17.55

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DOI： 10.11316/jpsgaiyo.70.1.0_2847

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Language：Japanese   Publisher：統計数理研究所  

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要旨なし生体高分子の揺らぎとダイナミクス－シミュレーションと実験の統計解析－その他・前書き

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Language：Japanese   Publisher：統計数理研究所  

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要旨あり生体高分子の揺らぎとダイナミクス－シミュレーションと実験の統計解析－研究詳解

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Language：Japanese   Publisher：日本医科大学  

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DOI： 10.11436/mssj.16.8

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Language：Japanese   Publisher：分子シミュレーション研究会  

遷移パスサンプリングは分子動力学などを使ってベイスン間をホップするような軌道を取り出す有用な手法である．通常の分子動力学がベイスン内をサンプルすることに重点を置いているのと異なり，ベイスン間の軌道は本質的に非平衡なものであり，その取扱いには非平衡統計力学の枠組みを使わなければならない．本稿ではパスサンプリングの基本的な概念を解説し，その問題点や分子系に適用するときの注意点を挙げる．

DOI： 10.11436/mssj.16.8

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DOI： 10.1272/manms.9.202

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Language：Japanese   Publisher：The Medical Association of Nippon Medical School  

I review several theoretical and computational approaches for calculating the conformational change of biomolecules, which is a key biomolecular event in cells. After discussing the motivation for the study of conformational change, I describe the path search algorithms in simple terms and discuss the application of the string method, a powerful path search method, to the calculation of minimum free energy pathways in an enzyme, adenylate kinase, which plays a role in converting ADP to AMP and ATP in cells. Finally I briefly mention a more advanced topic of path sampling for biomolecules.<br>

DOI： 10.1272/manms.9.202

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Language：Japanese   Publisher：The Medical Association of Nippon Medical School  

We review theoretical and computational approaches to ligand binding, one of the most relevant biomolecular events in a cell. Starting from a kinetic description of ligand binding, which is summarized by the use of the dissociation constant, we discuss simple docking simulations, the Molecular Mechanics/Poisson-Boltzmann Surface Area (Generalized Born Surface Area) approximation for binding free energy (intermediate level of approximation) , and more rigorous free energy profile calculations, which will be used in the near future for designing and discovering drugs.<br>

DOI： 10.1272/manms.9.135

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Language：Japanese   Publisher：一般社団法人 日本痛風・核酸代謝学会  

DOI： 10.6032/gnam.37.19

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Language：Japanese   Publisher：日本医科大学. 1980-  

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DOI： 10.1272/manms.8.222

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DOI： 10.1016/j.bpj.2011.11.145

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We review our recent collaborative study, performed by computational physicists and biochemists, of the enzyme effects due to the drug called febuxostat. Febuxostat, which was recently approved in the US, European Union and Japan for treatment of gout, inhibits xanthine oxidoreductase (XOR)-mediated generation of uric acid during purine catabolism. Experiments have shown that febuxostat has strong effects on mammalian XOR but not on bacterial XOR, although the two enzymes have similar three-dimensional structures. To clarify the difference in the inhibitory power of febuxostat, we performed docking and molecular dynamics simulations for mammalian and bacterial XORs. We found that the static structures are not sufficient to explain the binding difference and that important interactions occur between febuxostat and the active region of the enzymes which suggests a better strategy for drug design.<br>

DOI： 10.1272/manms.8.222

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Other Link： http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100641427

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DOI： 10.11436/mssj.11.2_25

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Language：English   Publisher：一般社団法人 日本生物物理学会  

DOI： 10.2142/biophys.47.S210_4

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Language：English   Publisher：物性研究刊行会  

Our recent studies on vibrational energy relaxation (VER) and collective motions in proteins are summarized. As a first topic, we discuss the validity of Fermi&#039;s golden rule for VER problems in proteins, and to get over this limitation, we apply the finite-time perturbation theory due to Okazaki&#039;s group to our VER problem of a localized mode in a protein. As a second topic, we discuss the dynamical effects of solvent water on the collective protein dynamics, employing several time series analysis methods such as principal component analysis and the power spectra of kinetic energies.

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この論文は国立情報学研究所の電子図書館事業により電子化されました。

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