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

We propose a new adaptive QM/MM method, the size-consistent multipartitioning (SCMP) QM/MM scheme, which enables stable and computationally efficient QM/MM simulations. A number of partitionings with identical size of the QM and the MM regions are considered with a new adaptive scheme in order to (1) realize smooth QM/MM switching, (2) introduce a conserved quantity (total energy, Hamiltonian), (3) avoid spurious artificial forces on the QM/MM border, and (4) allow for an efficient parallel implementation. Benchmark simulations performed for "QM water in MM water" show that energy conservation can be significantly improved and the computational efficiency allows treating also larger QM regions, for which previous methods had to face an intractable increase in computer time.

DOI： 10.1021/ct5005593

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

Channelrhodopsins (ChRs) are light-gated cation channels that mediate ion transport across membranes in microalgae (vectorial catalysis). ChRs gain increasing attention as useful tools for the analysis of neural networks in tissues and living animals (optogenetics). In fact, various mutagenesis approaches have realized practical applications with high reliability by enhancement of the expression level, channel kinetics control, and color tuning. Furthermore, the recently published x-ray structure has provided valuable information for further atomistic studies and engineering ChRs for a wider application. The present study is a computational attempt to describe the functional mechanism at the atomic level based on the x-ray structure. We present several structural characteristics that are highly involved in ion channel gating and ion transport, including (1) water distribution, (2) cation binding sites, (3) intrahelical hydrogen bond, (4) DC gate, and (5) active site. (C) 2013 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.jmb.2013.01.033

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

Channelrhodopsins (ChRs) are light-gated cation channels that mediate ion transport across membranes in microalgae (vectorial catalysis). ChRs are now widely used for the analysis of neural networks in tissues and living animals with light (optogenetics). For elucidation of functional mechanisms at the atomic level, as well as for further engineering and application, a detailed structure is urgently needed. In the absence of an experimental structure, here we develop a structural ChR model based on several molecular computational approaches, capitalizing on characteristic patterns in amino acid sequences of ChR1, ChR2, Volvox ChRs, Mesostigma ChR, and the recently identified ChR of the halophilic alga Dunaliella salina. In the present model, we identify remarkable structural motifs that may explain fundamental electrophysiological properties of ChR2, ChR1, and their mutants, and in a crucial validation of the model, we successfully reproduce the excitation energy predicted by absorption spectra.

DOI： 10.1074/jbc.M111.320309

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

A Variational Quantum Algorithm for Generalized Eigenvalue Problems and Its Application to Finite Element Method

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

DOI： 10.1039/C3CP44181D

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

Simulating Time Evolution with Fully Optimized Single-Qubit Gates

DOI： 10.1103/PhysRevA.105.062421

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

DOI： 10.1140/epjs/s11734-021-00087-z

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

Applications of quantum computing for investigations of electronic transitions in phenylsulfonyl-carbazole TADF emitters
<title>Abstract</title>A quantum chemistry study of the first singlet (<italic>S</italic>₁) and triplet (<italic>T</italic>₁) excited states of phenylsulfonyl-carbazole compounds, proposed as useful thermally activated delayed fluorescence (TADF) emitters for organic light emitting diode (OLED) applications, was performed with the quantum Equation-Of-Motion Variational Quantum Eigensolver (qEOM-VQE) and Variational Quantum Deflation (VQD) algorithms on quantum simulators and devices. These quantum simulations were performed with double zeta quality basis sets on an active space comprising the highest occupied and lowest unoccupied molecular orbitals (HOMO, LUMO) of the TADF molecules. The differences in energy separations between <italic>S</italic>₁ and <italic>T</italic>₁ (Δ<italic>E</italic>_{<italic>S</italic><italic>T</italic>}) predicted by calculations on quantum simulators were found to be in excellent agreement with experimental data. Differences of 17 and 88 mHa with respect to exact energies were found for excited states by using the qEOM-VQE and VQD algorithms, respectively, to perform simulations on quantum devices without error mitigation. By utilizing state tomography to purify the quantum states and correct energy values, the large errors found for unmitigated results could be improved to differences of, at most, 4 mHa with respect to exact values. Consequently, excellent agreement could be found between values of Δ<italic>E</italic>_{<italic>S</italic><italic>T</italic>} predicted by quantum simulations and those found in experiments.

DOI： 10.1038/s41524-021-00540-6

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

The nitrogen-vacancy (NV) center in diamond is a quantum sensor with exceptional quality for highly sensitive nanoscale analysis of nuclear magnetic resonance (NMR) spectra and thermometry. In this study, nanoscale phase change detection of lipid bilayers is investigated utilizing ensemble-averaged nuclear spin detection from small volume ≈(6 nm)3, which is determined by the depth of the NV center. Analysis of nanoscale NMR signal confirms thickness of lipid bilayer to be 6.2 nm ± 3.4 nm with proton density of 65 protons per nm3 on top of diamond sample. The result of the correlation spectroscopy from nanoscale volume is compared with the 2D molecular diffusion model constructed by Monte Carlo simulation combined with results from molecular dynamics (MD) simulation. There is a change in diffusion constant from 1.5 ± 0.25 nm2 µs−1 to 3.0 ± 0.5 nm2 µs−1 when the temperature changes from 26.5 to 36.0 °C. The results demonstrate that the multi-parameter detection of changes in translational diffusion and temperature is possible in label-free measurements using nanoscale diamond magnetometry. The method paves the way for label-free imaging of cell membranes for understanding their phase composition and dynamics.

DOI： 10.1002/qute.202000106

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

Mutational analysis of the conserved carboxylates of anion channelrhodopsin-2 (ACR2) expressed in Escherichia coli and their roles in anion transport

DOI： 10.2142/biophysico.15.0_179

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

For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol.

DOI： 10.3390/molecules23081882

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

DOI： 10.1073/pnas.1717048114

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

In the cyanobacterial photosystem II (PSII), the O4-water chain in the D1 and CP43 proteins, a chain of water molecules that are directly H-bonded to O4 of the Mn4Ca cluster, is linked with a channel that connects the protein bulk surface along with a membrane-extrinsic protein subunit, PsbU (O4-PsbU channel). The cyanobacterial PSII structure also shows that the O1 site of the Mn4Ca cluster has a chain of H-bonded water molecules, which is linked with the channel that proceeds toward the bulk surface via PsbU and PsbV (O1-PsbU/V channel). Membrane-extrinsic protein subunits PsbU and PsbV in cyanobacterial PSII are replaced with PsbP and PsbQ in plant PSII. However, these four proteins have no structural similarity. It remains unknown whether the corresponding channels also exist in plant PSII, because water molecules are not identified in the plant PSII cryo-electron microscopy (cryo-EM) structure. Using the cyanobacterial and plant PSII structures, we analyzed the channels that proceed from the Mn4Ca cluster. The cyanobacterial O4-PsbU and O1-PsbU/V channels were structurally conserved as the channel that proceeds along PsbP toward the protein bulk surface in the plant PSII (O4-PsbP and O1-PsbP channels, respectively). Calculated protonation states indicated that in contrast to the original geometry of the plant cryo-EM structure, protonated PsbP-Lys166 may form a salt-bridge with ionized D1-Glu329 and protonated PsbP-Lys173 may form a salt-bridge with ionized PsbQ-Asp28 near the O1-PsbP channel. The existence of these channels might explain the molecular mechanism of how PsbP can interact with the Mn4Ca cluster.

DOI： 10.1007/s11120-017-0347-1

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

In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics. Thus, a quantum mechanical (QM) molecular description is required for both solute and solvent to incorporate these properties. However, it is challenging to conduct molecular dynamics (MD) simulations for condensed systems of sufficient scale when adapting QM potentials. To overcome this problem, we recently developed the size-consistent multi-partitioning (SCMP) quantum mechanics/molecular mechanics (QM/MM) method and realized stable and accurate MD simulations, using the QM potential to a benchmark system. In the present study, as the first application of the SCMP method, we have investigated the structures and dynamics of Na+, K+, and Ca2+ solutions based on nanosecond-scale sampling, a sampling 100-times longer than that of conventional QM-based samplings. Furthermore, we have evaluated two dynamic properties, the diffusion coefficient and difference spectra, with high statistical certainty. Furthermore the calculation of these properties has not previously been possible within the conventional QM/MM framework. Based on our analysis, we have quantitatively evaluated the quantum chemical solvation effects, which show distinct differences between the cations.

DOI： 10.1039/c7cp01708a

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

Origins of water molecules in the photosystem II crystal structure

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

In MtrF, an outer-membrane multiheme cytochrome, the 10 heme groups are arranged in heme binding domains II and IV along the pseudo-C-2 axis, forming the electron transfer (ET) pathways. Previous reports based on molecular dynamics simulations showed that the redox potential (Em) values for the heme pairs located in symmetrical positions in domains II and IV were similar, forming bidirectional ET pathways [Breuer M, Zarzycki P, Blumberger J, Rosso KM (2012) J Am Chem Soc 134(24): 9868-9871]. Here, we present the Em values of the 10 hemes in MtrF, solving the linear Poisson-Boltzmann equation and considering the protonation states of all titratable residues and heme propionic groups. In contrast to previous studies, the Em values indicated that the ET is more likely to be downhill from domain IV to II because of localization of acidic residues in domain IV. Reduction of hemes in MtrF lowered the Em values, resulting in switching to alternative downhill ET pathways that extended to the flavin binding sites. These findings present an explanation of how MtrF serves as an electron donor to extracellular substrates.

DOI： 10.1073/pnas.1617615114

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

Quantum effects in solute-solvent interactions, such as the many-body effect and the dipole-induced dipole, are known to be critical factors influencing the infrared spectra of species in the liquid phase. For accurate spectrum evaluation, the surrounding solvent molecules, in addition to the solute of interest, should be treated using a quantum mechanical method. However, conventional quantum mechanics/molecular mechanics (QM/MM) methods cannot handle free QM solvent molecules during molecular dynamics (MD) simulation because of the diffusion problem. To deal with this problem, we have previously proposed an adaptive QM/MM "size-consistent multipartitioning (SCMP) method''. In the present study, as the first application of the SCMP method, we demonstrate the reproduction of the infrared spectrum of liquid-phase water, and evaluate the quantum effect in comparison with conventional QM/MM simulations.

DOI： 10.1039/c5cp07136d

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

DOI： 10.1039/C6SC00468G

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

In hydrophilic protein-protein associations, the dehydration penalty, which can cause the formation of a reaction barrier, must be canceled out; however, its mechanism has not been clarified. Here, we explored the possible mechanism through investigation of the dimerization of nucleotide binding domains (NBDs). We assessed the different dimerization processes by molecular dynamics simulations with and without thermal fluctuations in each NBD. Consequently, the reaction barriers of the former and latter were estimated to be similar to 100 and similar to 15 kcal/mol, respectively, suggesting that thermal fluctuations in the proteins facilitate the exclusion of water molecules from the interfacial region, thereby lowering the barrier. (C) 2015 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2015.11.014

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

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

The field of optogenetics uses channelrhodopsins (ChRs) for light-induced neuronal activation. However, optimized tools for cellular inhibition at moderate light levels are lacking. We found that replacement of E90 in the central gate of ChR with positively charged residues produces chloride-conducting ChRs (ChloCs) with only negligible cation conductance. Molecular dynamics modeling unveiled that a high-affinity Cl--binding site had been generated near the gate. Stabilizing the open state dramatically increased the operational light sensitivity of expressing cells (slow ChloC). In CA1 pyramidal cells, ChloCs completely inhibited action potentials triggered by depolarizing current injections or synaptic stimulation. Thus, by inverting the charge of the selectivity filter, we have created a class of directly light-gated anion channels that can be used to block neuronal output in a fully reversible fashion.

DOI： 10.1126/science.1249375

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

DOI： 10.1002/jcc.23119

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

We examined the shift of absorption maxima between the chlamydomonas-type channelrhodopsins (ChRs) and bacteriorhodopsin (BR). Starting from the BR X-ray structure, we modeled the color tuning in the binding pockets of the ChRs by mutating up to 28 amino acids in the vicinity of the chromophore. By applying the efficient self-consistent charge density functional tight binding (SCC-DFTB) method in a quantum mechanical/molecular mechanical (QM/MM) framework, including explicit polarization and calculating excitation energies with the semiempirical OM2/MRCI method and the ab initio SORCI method, we have shown that multiple mutations in the binding pocket of BR causes large hypsochromic shifts that are of the same order as the experimentally observed shifts of the absorption maxima between BR and the ChRs. This study further demonstrates that mutations in the proximity of the Schiff base and complex counterion lead to a stronger but more flexible interaction with the retinal, which could serve as a possible explanation for the spectral patterns found in the ChRs.

DOI： 10.1021/jp2085457

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

Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin.

DOI： 10.2142/biophysics.6.67

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

Bacteriorhodopsin is a prototype of efficient molecular machinery functioning as a light-activated proton pump. Among the five distinct intermediates (K, L, M, N, and O) of the photocycle, there is less structural information on the later stages compared with the early intermediates. Here, we report the structural modeling of the O-intermediate for which the determination of experimental structure remains difficult. Hypothetical conformational change of the molecule from the light-adapted state to the O-intermediate state was simulated by gradually changing the protonation state of two residues. To achieve accurate molecular modeling, we carefully constructed a realistic system of the native purple membrane. The modeled structure of the O-intermediate has some implications about proton transfer in the later stages of the photocycle and the structural response of bacteriorhodopsin to the inner charge distribution.

DOI： 10.1002/prot.22221

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

We report a theoretical study on the optical properties of a small, water-soluble photosensory receptor, photoactive yellow protein (PYP). A hierarchical ab initio molecular orbital calculation accurately evaluated the optical absorption maximum of the wild-type, as well as the lambda(max) values of 12 mutants. Electronic excitation of the chromophore directly affects the electronic state of nearby atoms in the protein environment. This effect is explicitly considered in the present study. Furthermore, the spectral tuning mechanism of PYP was investigated at the atomic level. The static disorder of a protein molecule is intimately related to the complex nature of its energy landscape. By using molecular dynamics simulation and quantum mechanical structure optimization, we obtained multiple minimum energy conformations of PYP. The statistical distribution of electronic excitation energies of these minima was compared with the hole-burning experiment (Masciangioli, T. 120001 Photochem. Photobiol. 72, 639), a direct observation of the distribution of excitation energies.

DOI： 10.1562/2006-06-16-RA-930

Event date： 2024.12

Language：Japanese   Presentation type：Poster presentation  

Venue：アクリエひめじ, 兵庫   Country：Japan  

Event date： 2022.10

Language：Japanese  

Country：Other  

Full optimazation of a single-qubit gate on the generalized sequential quantum optimizer

Event date： 2022.9

Language：Japanese  

Country：Other  

Event date： 2022.5

Language：Japanese  

Country：Other  

Event date： 2021.12

Language：Japanese  

Country：Other  

Event date： 2021.9

Language：Japanese  

Country：Other  

Event date： 2021.9

Language：Japanese  

Country：Other  

Event date： 2021.9

Language：Japanese  

Country：Other  

Event date： 2019.12

Language：Japanese  

Country：Other  

Development of molecular dynamics simulation method to incorporate solation quantum chemical effects and its Applications to Biosystem

Event date： 2019.12

Language：Japanese  

Country：Other  

Proton transfer by Solute adaptive QM/MM method

Event date： 2015.11

Language：Japanese  

Venue：朱鷺メッセ, 新潟   Country：Other  

Language：Japanese  

Venue：盛岡   Country：Other  

Language：Japanese  

Venue：岡山大学   Country：Other  

バクテリオロドプシンO中間体の構造モデリング

Language：English  

Venue：名古屋大学   Country：Other  

Theoretical modeling of the O-intermediate structure of bacteriorhodopsin

Language：English  

Venue：福岡国際会議場   Country：Other  

Language：English  

Venue：名古屋大学   Country：Other  

On the spectral properties of retinal proteins --inhomogeneity and static disorder--

Language：Japanese  

Venue：札幌   Country：Other  

Language：Japanese  

Venue：熊本大学   Country：Other  

Language：English  

Venue：アスティ徳島   Country：Other  

Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin

Language：Japanese  

Venue：名古屋中小企業振興会館   Country：Other  

Language：English  

Venue：Muenchen, Germany   Country：Other  

Structural model of Channelrhodopsin

Language：English  

Venue：Huenfeld, Germany   Country：Other  

Structural model of CHannelrhodopsin

Language：English  

Venue：Berlin   Country：Other  

Color tuning of Channelrhodopsins

Language：English  

Country：Other  

Computational study of channelrhodopsins - Simulations lead to novel insights of channel mechanism -

Language：English  

Venue：札幌   Country：Other  

Theoretical approach toward an understanding molecular functions of channelrhodopsin

Language：English  

Venue：名古屋工業大学, 名古屋   Country：Other  

Theoretical approach toward an understanding molecular functions of channelrhodopsin

Language：English  

Venue：長浜ロイヤルホテル, 長浜   Country：Other  

Theoretical approach toward an understanding molecular functions of channelrhodopsin

Language：Japanese  

Venue：仙台市民会館, 仙台   Country：Other  

Language：Japanese  

Venue：理化学研究所, 和光   Country：Other  

Size-Consistent Multipartitioning QM/MM method

Language：English  

Venue：金沢大学, 金沢   Country：Other  

The first application of adaptive quantum mechanics/molecular mechanics method for infrared spectra of liquid water

Language：English  

Venue：Honolulu, USA   Country：Other  

Size-Consistent Multipartitioning QM/MM method

Language：Japanese  

Venue：東京大学, 駒場   Country：Other  

Structural analysis of channelrhodopsin and its appliaction to optogenetics

Language：Japanese  

Venue：早稲田大学, 東京   Country：Other  

Language：Japanese  

Venue：東北大学, 仙台   Country：Other  

Analysis of channelrhodopsin and development of infrared spectrum calculation

Language：English  

Venue：国際会議場, 筑波   Country：Other  

Strategic modeling of channelrhodopsins and MtrF based on the correlation between protein structures and functions

Language：Japanese  

Venue：分子科学研究所   Country：Other  

Cation solvation based on quantum mechanical potential by size-consistent multipartitioning quantum mechanics/molecualr mechanics method

Language：Japanese  

Venue：京都大学   Country：Other  

Language：English  

Venue：国際センター, 仙台   Country：Other  

Electron transfer pathways in a multi-heme cytochrome MtrF

Language：English  

Venue：The Univerisity of East Anglia, England   Country：Other  

Electron transfer pathway in a multiheme MtrF

Language：Japanese  

Venue：東北大学, 仙台   Country：Other  

Language：English  

Venue：熊本大学   Country：Other  

Cation solvation with quantum mechanical effect incorporated by size-consistent multi-partitioning quantum mechanics/molecular mechanics method

Language：English  

Country：Other  

Quantum chemical effects on solvation incorporated by size-consistent multipartitioning quantum mechanics/molecular mechanics method

Language：Japanese  

Country：Other  

Improvement of size-consistent multipartitioning method toward a practical application

Language：English  

Country：Other  

Structural modeling and molecular simulations provide insights into the functional mechanism of anion channelrhodpsin-2

Language：English  

Country：Other  

Recent progress and development toward incorporation of quantum chemical effects by size-consistent multipartitioning quantum mechanical/ molecular mechanical method

Language：English  

Country：Other  

Developments and applications of molecular dynamics simulation with quantum chemical effect of solvent

Language：Japanese  

Venue：理化学研究所   Country：Other  

Toward incorporation of quantum chemical effects of solvent into molecular dynamics simulation

Language：English  

Venue：京都大学   Country：Other  

Quantitative analysis of QM/MM artifacts and its correction in adaptive QM/MM

Language：English  

Venue：Bostonn University   Country：Other  

Toward incorporation of quantum chemical effects of solvent into molecular dynamics simulation

Language：English  

Venue：Orland   Country：Other  

Incorporation of quantum chemical effects of solvent into molecular dynamics simulation

Language：English  

Country：Other  

The development and the applications of the seamless analysis of protein dynamics with incorporated quantum chemical effect

Language：Japanese  

Venue：東北大学   Country：Other  

Molecular dynamics simulation for proton transfer in bulk phase

Language：English  

Venue：韓国 済州島   Country：Other  

Toward Incorporation of Quantum Chemical effect of Solvation into Molecular dynamics simulations: Stable and efficient adaptive QM/MM

Language：Japanese  

Country：Other  

Language：Others  

Country：Other  

Language：Japanese  

Country：Other  

Language：English  

Country：Other  

Proton transfer dynamics simulation using adaptive QM/MM method

Language：English  

Country：Other  

Optimizing Parameterized Quantum Circuits with Free-Axis Selection

Language：English  

Country：Other  

Optimizing Parameterized Quantum Circuits with Free-Axis Selection

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