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We performed a coarse-grained simulation of Pseudomonas Aeruginosa azurin using the implementation of Go model. We probe the unfolding dynamics of oxidized structure of copper-containing H117G (Cu-H117G) azurin. In vitro, the kinetic experiments have shown that both of the wild type and H117G azurins fold in apparent two-state reactions. Here we analyze the transition state of azurin based on energy landscape theory. The transition state which is indicated by free energy barrier between the denatured state and native state has been found on the simulation near the folding temperature. We simulated for several fixed temperature and found that mutated azurin unfolds faster than wild-type azurin. Moreover, we also calculated the [lowercase_phi_synonym]-value which is widely used in experimental studies for reconstructing protein-folding transition state and is most powerful when in combination with simulation. By this analysis, we determine which region of azurin folds faster than others and compare the results with experimental data. [ABSTRACT FROM AUTHOR]

The equation of state of diamond was studied using laser-driven shock waves in a terapascal region between 0.5 and 2 TPa. Strong shock waves were generated by direct irradiation of a 2.5 ns laser pulse on an Al driver plate. The shock wave velocities in the diamond and Al were measured optically. Particle velocities and pressures were obtained using impedance matching and the known Al Hugoniot. The dependence of UsDia(upDia) obtained for single crystalline diamond is well-approximated by UsDia=11.2+1.2upDia for the obtained Hugoniot data, all previous experimental data, and the bulk sound velocity. © 2006 American Institute of Physics [ABSTRACT FROM AUTHOR]

The backbone dynamics of azurin has been observed by 3.0 ns molecular dynamics simulation at 300K. The local correlation function and the spectral density are derived form the torsion and bending motion of NH bond existed in peptide plane of protein. We have presented the square order parameter S2 which is comparable value with NMR experiment. © 2004 American Institute of Physics [ABSTRACT FROM AUTHOR]

Azurin is a relatively small metalloprotein of the mononuclear blue copper protein found in plants and bacteria. In this study, we investigate the vibrational motion of the active site of azurin by molecular dynamics (MD) calculations and estimatethe Resonance Raman(RR) spectrum of azurin from the analysis of the time correlation function, and compare the experimentally measured RR spectrum with one obtained from MD calculations. © 2004 American Institute of Physics [ABSTRACT FROM AUTHOR]

We investigate the oxygen rearrangement model by using a cluster model of the copper oxide. The potential energy surface is estimated by the semiempirical molecular orbital calculation (AM1). We discuss the jumping of oxygen ions in the Cu-O chain in relation to the possibility of the laser control of the oxygen ion. © 2004 American Institute of Physics [ABSTRACT FROM AUTHOR]

Stimulated Raman adiabatic passage method (STIRAP) is well known to be a very effective method for the efficient and selective transition between two molecular eigenstates in molecule. In this study, we generalize the STIRAP to be able to treat the transition to the non-stationary state in the hydrogen bonded model system. © 2004 American Institute of Physics [ABSTRACT FROM AUTHOR]

Stimulated Raman adiabatic passage method (STIRAP) is well known to be a very effective method for the efficient and selective transition between two molecular eigenstates in molecule. In this study, we generalize the STIRAP to be able to complete transfer between all-trans and 11-cis in the retinal. © 2004 American Institute of Physics [ABSTRACT FROM AUTHOR]

Recently, the quantum computer (QC) using the nano-devices have significantly attracted attention, because a large-scale extention of the qubits could be easily realized in the nano-devices. However, some problems for the realization of the QC with nano-devices arise from the short decoherence time and the interaction of qubits only between nearest-neighbor qubits. Therefore, we try to design the optimal quantum circuit of the quantum Fourier transform in various network system by means of the genetic algorithm (GA). © 2004 American Institute of Physics [ABSTRACT FROM AUTHOR]