Numerical and experimental investigations of dependence of photoacoustic signals from gold nanoparticles on the optical properties

Gold nanoparticles (AuNPs) are used as a contrast agent of the photoacoustic (PA) imaging. The efficiency of AuNPs has been discussed with the absorption cross section. However, the effects of the scattering of the light by AuNPs and surrounding medium on the PA signal from AuNPs have not been discussed. The PA signals from the aqueous solution of AuNPs were examined in the numerical simulation and the experiment. In the numerical simulation, the absorption and scattering cross sections of spherical and polyhedral AuNPs were calculated by Mie theory and discrete dipole approximation. Monte Carlo simulation calculated the absorbed light energy in the aqueous solution of AuNPs. Based on the PA wave equation, the PA signals were simulated. In the experiment, the PA signal from the aqueous solution of AuNP was measured by use of a piezoelectric film and a Q-switched Nd:YAG laser operated at 532 nm. The results of the numerical simulation and the experiment agreed well. In the numerical simulation and the experiment, a single Au nanocube with 50-nm edge generated the peak value of the PA signal significantly. It was approximately 350 times and twice as large as the peak values of the spherical AuNPs with 10- and 50-nm diameters, respectively. The peak value of the PA signal depended on both the absorption and scattering coefficients of the AuNPs and the surrounding medium. The peak value increased with the scattering coefficient in a quadratic manner. The character of the temporal profile of the PA signal such as full width at half maximum depended on the scattering coefficient of the AuNPs.     

Efficient free energy calculation of water across lipid membranes

An efficient free energy (FE) calculation of a water molecule to go across lipid membranes is presented. Both overlapping distribution and cavity insertion Widom methods are complementarily used. The former is useful for a dense region where water molecules are found, i.e., from the interfacial to bulk water region, while the latter works well in the low density region, i.e., the hydrocarbon region. Since both methods evaluate the excess chemical potential of water, the obtained FE profile is free from the fitting problem usually arisen when a FE difference method is used. A diphytanyl phosphatidylcholine bilayer is used for our test calculations. An excellent and fast convergence of the chemical potential is obtained when each method is applied for the appropriate region. The estimated FE barrier using the Ewald method for the electrostatic interaction is approximately 7.2 kcal/mol, which is higher than that using the interaction cutoff of 20 A by about 0.9 kcal/mol.     

Nagelamide J, a novel dimeric bromopyrrole alkaloid from a sponge Agelas species

A novel dimeric bromopyrrole alkaloid, nagelamide J (1), with antimicrobial activity has been isolated from an Okinawan marine sponge Agelas species, and the structure and stereochemistry were elucidated from spectroscopic data. Nagelamide J (1) is the first bromopyrrole alkaloid possessing a cyclopentane ring fused to an amino imidazole ring.     

Exciton lifetime in quantum well with vicinal high-density excitons

Radiative lifetime of an exciton in a GaAs quantum well (QW) is controlled by high-density excitons, which restrict the exciton coherence through scattering. In order to circumvent the phase space filling effect of high-density excitons, we have prepared a QW structure in such a way that a reservoir for high-density excitons is separated from the QW. The lifetime increases (up to 30%) with the exciton density in the reservoir and saturates at 1×10¹⁷/cm³. The upper bound lifetime is determined by the excitonic relative motion.     

Computationally efficient canonical molecular dynamics simulations by using a multiple time‐step integrator algorithm combined with the particle mesh Ewald method and with the fast multipole method

An efficient implementation of the canonical molecular dynamics simulation using the reversible reference system propagator algorithm (r‐RESPA) combined with the particle mesh Ewald method (PMEM) and with the macroscopic expansion of the fast multipole method (MEFMM) was examined. The performance of the calculations was evaluated for systems with 3000, 9999, 30,000, 60,000, and 99,840 particles. For a given accuracy, the optimal conditions for minimizing the CPU time for the implementation of the Ewald method, the PMEM, and the MEFMM were first analyzed. Using the optimal conditions, we evaluated the performance and the reliability of the integrated methods. For all the systems examined, the r‐RESPA with the PMEM was about twice as fast as the r‐RESPA with the MEFMM. The difference arose from the difference in the numerical complexities of the fast Fourier transform in the PMEM and from the transformation of the multipole moments into the coefficients of the local field expansion in the MEFMM. Compared with conventional methods, such as the velocity‐verlet algorithm with the Ewald method, significant speedups were obtained by the integrated methods; the speedup of the calculation was a function of system size, and was a factor of 100 for a system with 3000 particles and increased to a factor of 700 for a system with 99,840 particles. These integrated calculations are, therefore, promising for realizing large‐scale molecular dynamics simulations for complex systems. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 201–217, 2000