Eiji Yamamoto

Protein conformational fluctuations are highly complex and exhibit long-term correlations. Here, molecular dynamics simulations of small proteins demonstrate that these conformational fluctuations directly affect the protein's instantaneous diffusivity D_{I}. We find that the radius of gyration R_{g} of the proteins exhibits 1/f fluctuations that are synchronous with the fluctuations of D_{I}. Our analysis demonstrates the validity of the local Stokes-Einstein-type relation D_{I}∝1/(R_{g}+R_{0})

A molecular simulation pipeline for determining the mode of interaction of pleckstrin homology (PH) domains with phosphatidylinositol phosphate (PIP)-containing lipid bilayers is presented. We evaluate our methodology for the GRP1 PH domain via comparison with structural and biophysical data. Coarse-grained simulations yield a 2D density landscape for PH/membrane interactions alongside residue contact profiles. Predictions of the membrane localization and interactions of 13 PH domains reveal can

Pleckstrin homology (PH) domains are membrane-binding lipid recognition proteins that interact with phosphatidylinositol phosphate (PIP) molecules in eukaryotic cell membranes. Diffusion of PH domains plays a critical role in biological reactions on membrane surfaces. Although diffusivity can be estimated by long-time measurements, it lacks information on the short-time diffusive nature. We reveal two diffusive properties of a PH domain bound to the surface of a PIP-containing membrane using mol

Association of peripheral proteins with lipid bilayers regulates membrane signaling and dynamics. Pleckstrin homology (PH) domains bind to phosphatidylinositol phosphate (PIP) molecules in membranes. The effects of local PIP enrichment on the interaction of PH domains with membranes is unclear. Molecular dynamics simulations allow estimation of the binding energy of GRP1 PH domain to PIP₃-containing membranes. The free energy of interaction of the PH domain with more than two PIP<sub>

Effects of general anesthesia can be controllable by the ambient pressure. We perform molecular dynamics simulations for a 1-palmitoyl-2-oleoyl phosphatidylethanolamine lipid bilayer with or without xenon molecules by changing the pressure to elucidate the mechanism of the pressure reversal of general anesthesia. According to the diffusive nature of xenon molecules in the lipid bilayer, a decrease in the orientational order of the lipid tails, an increase in the area and volume per lipid molecul

Pleckstrin homology (PH) domains are lipid-binding modules present in peripheral membrane proteins which interact with phosphatidyl-inositol phosphates (PIPs) in cell membranes. We use multiscale molecular dynamics simulations to characterize the localization and anomalous dynamics of the DAPP1 PH domain on the surface of a PIP-containing lipid bilayer. Both translational and rotational diffusion of the PH domain on the lipid membrane surface exhibit transient subdiffusion, with an exponent α ≈

Water molecules at interfaces of materials exhibit enigmatic properties. A variety of spectroscopic studies have observed a high-frequency motion in these water molecules, represented by a blueshift, at both hydrophobic and hydrophilic interfaces. However, the molecular mechanism behind this blueshift has remained unclear. Using Raman spectroscopy and ab initio molecular dynamics simulations, we reveal the molecular mechanism of the blueshift of water molecules around six monosaccharide isomers.

Aquaporins (AQPs), which transport water molecules across cell membranes, are involved in many physiological processes. Recently, it is reported that the water-water interactions within the channel are broken at the aromatic/arginine selectivity filter (ar/R region), which prevents proton transportation [U. K. Eriksson et al., Science 340, 1346 (2013)]. However, the effects of the conformational fluctuations of amino acids on water transportation remain unclear. Using all-atom molecular dynamics

Cell membranes provide unique local environments for biological reactions, where the diffusion of biomolecules as well as water molecules plays critical roles. Translational and rotational motions of water molecules near membranes are known to be slower than those in bulk. Using all-atom molecular dynamics simulations of a membrane, we show that the temperature dependence of the water molecular motions on the membrane surface is different from that in bulk. Decreasing temperature enhances the wa

Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although water structures and diffusivities near the membrane surfaces have been extensively studied, hydration dynamics on the surfaces has remained an open question. Here we investigate residence time statistics of water molecules on the surface of lipid membranes using all-atom molecular dynamics simulations. We show that hydration dynamics on th

A calculation method for tunable twin-guide (TTG) laser tuning characteristics and the threshold current density depending on the modulation layer band-gap wavelength is presented. Experimental results for a 1.5 µm range TTG laser fabricated by all MOVPE are given for the first time. The optimized band-gap wavelength of the modulation layer is approx. 1.3 µm ∼1.4 µm and the maximum tuning range is approx. 9 nm by analysis. In the preliminary fabrication, the threshold current was 23 mA and the t

The characteristics for a twin-guide (TG) laser modulated by a reverse bias are studied for the first time. The extinction ratio and the wavelength shift are 20 dB with only 1 V bias and −0.4 nm, respectively. Further, the characteristics of a TG modulator itself (that has the same structure as the TG laser) are measured under a driving current lower than the threshold. The possibility of integrating a TG modulator with a tunable twin-guide (TTG) laser is presented.

We propose a new type of tunable laser, the complementary twin-active-guide (CTAG) laser, and present the preliminary experimental results of its tuning characteristics. A wide continuous tuning range over 4 nm is obtained for the CTAG laser. In the CTAG laser, not only power reduction but also spectral line-width broadening during tuning are greatly improved in comparison to conventional TTG lasers and three-section DBR lasers.

Tunable twin-guide distributed feedback (TTG-DFB) lasers are fabricated by the all-metalorganic vapor phase epitaxy (MOVPE) process. A very wide continuous tuning range (4.9 nm/25 mA) with single-mode operation is obtained by improving the efficiency of current-injection into the modulation layer. The side-mode suppression ratio (SMSR) is larger than 20 dB in the tuning range up to 4.3 nm.The threshold current is 16 mA and maximum output power is 5 mW.