Kuniyoshi Ebina

Quantum chemical approach to the gibbs energy of ion transfer between two immiscible liquids

Abstract The linear dependence of the standard ion transfer potential Δ O W φ ° of polyanions on their surface field strength E is elucidated on the basis of Mullikens charge-transfer (CT) complex theory. Quantum chemical considerations based on a simple model, where an electron in the 2p orbital (HOMO) of the surface oxygen atom of the polyanion partially transfers to the 4a 1 molecular orbital (LUMO) of water, have shown that the CT interaction energy per primary solvent is a function of E , approximately a quadratic equation. This leads to the apparent linear dependence of Δ O W φ ° (exactly, the charge-dependent part) on E . The theoretically estimated coefficient of the linear term is in fair agreement with the experimental value, suggesting that the CT interaction plays the most important role in the linear dependence. In this paper, comments on Aokis theory of 1995 (J. Electroanal. Chem., 386 (1995) 17) are also offered.

Study of the aggregation mechanism of polyglutamine peptides using replica exchange molecular dynamics simulations

Polyglutamine (polyQ, a peptide) with an abnormal repeat length is the causative agent of polyQ diseases, such as Huntington’s disease. Although glutamine is a polar residue, polyQ peptides form insoluble aggregates in water, and the mechanism for this aggregation is still unclear. To elucidate the detailed mechanism for the nucleation and aggregation of polyQ peptides, replica exchange molecular dynamics simulations were performed for monomers and dimers of polyQ peptides with several chain lengths. Furthermore, to determine how the aggregation mechanism of polyQ differs from those of other peptides, we compared the results for polyQ with those of polyasparagine and polyleucine. The energy barrier between the monomeric and dimeric states of polyQ was found to be relatively low, and it was observed that polyQ dimers strongly favor the formation of antiparallel β-sheet structures. We also found a characteristic behavior of the monomeric polyQ peptide: a turn at the eighth residue is always present, even when the chain length is varied. We previously showed that a structure including more than two sets of β-turns is stable, so a long monomeric polyQ chain can act as an aggregation nucleus by forming several pairs of antiparallel β-sheet structures within a single chain. Since the aggregation of polyQ peptides has some features in common with an amyloid fibril, our results shed light on the mechanism for the aggregation of polyQ peptides as well as the mechanism for the formation of general amyloid fibrils, which cause the onset of amyloid diseases.

Reduced minimum model for the photosynthetic induction processes in photosystem I.

Photosystem I (PS I) is one of the most important protein complexes for photosynthesis, which is present in plants, algae and cyanobacteria. A variety of mechanisms for environmental response in and around PS I have been elucidated experimentally and theoretically. During the photosynthetic induction time, the congestion of electron occurs in PS I and then the over-reduced PS I states are realized. This means that the degree of freedom of the redox states of PS I becomes large and thus the understanding of phenomena based on the model describing PS I in the state space becomes difficult. To understand the phenomena intuitively, we have reduced the complicated PS I model which has the multi-timescale property for electron and excitation-energy transfer processes into a simple one which has only the mono-timescale property through the use of hierarchical coarse-graining (HCG) method. The coarse-grained model describes the state of PS I by seven variable states, while the original model describes the PS I by 3×2(7)(=384) states. Based on the derived model, the I820 (820nm transmittance signal) curve in photosynthetic induction term, which indicates the accumulations of P700(+) and Pc(+), is simulated and analyzed in comparison with experiment. With respect to this signal curve, it is revealed that the initial increase up to the shoulder at 10(-3) s, the increase from that point to the peak at 2 ×10(-2) s, and the decay after that peak reflect the accumulations of P700(+), Pc(+) and P700FA(-)FB(-) (PS I state in which P700,FA(-) and FB(-) are observed.), respectively. Besides, the important role of the charge recombination processes from P700(+)A0A(-) and P700(+)A1A(-) states for the dissipation of the extra absorbed energy in photosynthetic induction period is confirmed.

Anisotropic structures of metallic hydrogen

Abstract We analyze the mechanism of formation of anisotropic structures of metallic hydrogen using the structural expansion in the static approximation. We demonstrate the importance of the curvature in the energy-wavevector characteristics. Among the rhombohedral structures, a planar structure is stabilized in the second-order regime and a filamentary one in the third-order regime. The same mechanism works to stabilize the isotropic structures in the case of helium.

Systems approach to excitation-energy and electron transfer reaction networks in photosystem II complex: model studies for chlorophyll a fluorescence induction kinetics

Photosystem II (PS II) is a protein complex which evolves oxygen and drives charge separation for photosynthesis employing electron and excitation-energy transfer processes over a wide timescale range from picoseconds to milliseconds. While the fluorescence emitted by the antenna pigments of this complex is known as an important indicator of the activity of photosynthesis, its interpretation was difficult because of the complexity of PS II. In this study, an extensive kinetic model which describes the complex and multi-timescale characteristics of PS II is analyzed through the use of the hierarchical coarse-graining method proposed in the authors׳ earlier work. In this coarse-grained analysis, the reaction center (RC) is described by two states, open and closed RCs, both of which consist of oxidized and neutral special pairs being in quasi-equilibrium states. Besides, the PS II model at millisecond scale with three-state RC, which was studied previously, could be derived by suitably adjusting the kinetic parameters of electron transfer between tyrosine and RC. Our novel coarse-grained model of PS II can appropriately explain the light-intensity dependent change of the characteristic patterns of fluorescence induction kinetics from O-J-I-P, which shows two inflection points, J and I, between initial point O and peak point P, to O-J-D-I-P, which shows a dip D between J and I inflection points.

Hierarchical coarse-graining model for photosystem II including electron and excitation-energy transfer processes

We propose a hierarchical reduction scheme to cope with coupled rate equations that describe the dynamics of multi-time-scale photosynthetic reactions. To numerically solve nonlinear dynamical equations containing a wide temporal range of rate constants, we first study a prototypical three-variable model. Using a separation of the time scale of rate constants combined with identified slow variables as (quasi-)conserved quantities in the fast process, we achieve a coarse-graining of the dynamical equations reduced to those at a slower time scale. By iteratively employing this reduction method, the coarse-graining of broadly multi-scale dynamical equations can be performed in a hierarchical manner. We then apply this scheme to the reaction dynamics analysis of a simplified model for an illuminated photosystem II, which involves many processes of electron and excitation-energy transfers with a wide range of rate constants. We thus confirm a good agreement between the coarse-grained and fully (finely) integrated results for the population dynamics.

Three-body interaction between adsorbates

Abstract We investigate the three-body interaction between adsorbates via conduction electron of the substrate through the nonlinear electric susceptibility. The second-order nonlinear susceptibility has a step-function-like singularity as a function of the wavevectors. Due to this singularity, oscillatory behavior is expected in the three-body interaction. We calculate the three-body interaction numerically and examine the oscillatory behavior, which is not dominated by a single wavevector component.

A lattice model for cytoskeletons’ dynamics: analysis of growth and shrinkage

We analyze growth–shrinkage dynamics of cytoskeletons by using a lattice model in two dimensions. The behavior of the length of a chain corresponding to one cytoskeleton immersed in a “gas” of the basic units of cytoskeletons is simulated for low and intermediate concentrations, which shows the characteristic behavior of dynamic instability. We calculate the mean long-time velocity for several low concentrations and find that the length dynamics is sensitive to the concentration, which suggests the existence of a critical concentration. We also calculate the mean velocity for several short time spans and the probability distribution functions (PDFs) of the length difference with different time lags Δt. We find that the PDFs have a shoulder at around zero and a peak in the positive velocity region and the central parts of the PDF are essentially independent of Δt.

Spectral hole burning in NMR : experimental test of relaxation theories by using well-characterized noise fields

An experimental approach for the verification of relaxation theories is presented. Spectral hole burning in the proton NMR line in water was observed, and the hole shape was investigated in well-characterized noise fields. Motional narrowing of the hole shape is demonstrated. Power broadening of the hole shape was observed, and a violation of the Bloch equations in the saturation regime is studied.

Phase relaxation in a well-defined noise field: A two-state pulse noise field

Abstract Phase relaxation times of proton NMR in water were measured in a well-defined noise field to test relaxation theories. Here two-state pulse noise was studied. The applicability of the conventional stochastic theory was examined, and a nonlinear theory, which well explains the experimental results, was developed.