Benchmark results in vector atmospheric radiative transfer

In this paper seven vector radiative transfer codes are inter-compared for the case of underlying black surface. They include three techniques based on the discrete ordinate method (DOM), two Monte-Carlo methods, the successive orders scattering method, and a modified doubling-adding technique. It was found that all codes give very similar results. Therefore, we were able to produce benchmark results for the Stokes parameters both for reflected and transmitted light in the cases of molecular, aerosol and cloudy multiply scattering media. It was assumed that the single scattering albedo is equal to one. Benchmark results have been provided by several studies before, including Coulson et al. [22], Garcia and Siewert [7], [8], Wauben and Hovenier [10], and Natraj et al. [11] among others. However, the case of the elongated phase functions such as for a cloud and with a high angular resolution is presented here for the first time. Also in difference with other studies, we make inter-comparisons using several codes for the same input dataset, which enables us to quantify the corresponding errors more accurately.     

Matrix formulations of radiative transfer including the polarization effect in a coupled atmosphere-ocean system

A vector radiative transfer model has been developed for a coupled atmosphere-ocean system. The radiative transfer scheme is based on the discrete ordinate and matrix operator methods. The reflection/transmission matrices and source vectors are obtained for each atmospheric or oceanic layer through the discrete ordinate solution. The vertically inhomogeneous system is constructed using the matrix operator method, which combines the radiative interaction between the layers. This radiative transfer scheme is flexible for a vertically inhomogeneous system including the oceanic layers as well as the ocean surface. Compared with the benchmark results, the computational error attributable to the radiative transfer scheme has been less than 0.1% in the case of eight discrete ordinate directions. Furthermore, increasing the number of discrete ordinate directions has produced computations with higher accuracy. Based on our radiative transfer scheme, simulations of sun glint radiation have been presented for wavelengths of 670 nm and 1.6 μm. Results of simulations have shown reasonable characteristics of the sun glint radiation such as the strongly peaked, but slightly smoothed radiation by the rough ocean surface and depolarization through multiple scattering by the aerosol-loaded atmosphere. The radiative transfer scheme of this paper has been implemented to the numerical model named Pstar as one of the OpenCLASTR/STAR radiative transfer code systems, which are widely applied to many radiative transfer problems, including the polarization effect.     

Evaluation of binding affinity of protein-mutant dna complexes in solution by laser spray mass spectrometry

We have applied laser spray mass spectrometry developed by Hiraoka et al. to investigate the binding affinity of protein-mutant DNA complexes. The results were compared with our previous data of collision-induced dissociation (CID) experiments using electrospray ionization mass spectrometry (ESI-MS). Systematic experiments were carried out on the complexes of the c-Myb DNA binding domain (c-Myb DBD) bound to eight kinds of 16- or 22-mer point mutant double-stranded DNA (dsDNA), whose solution K(d) values are different in the range from 10(-9) M to 10(-7) M. The dissociation curve as a function of laser power was plotted for each complex, and the laser power where 50% of complex was dissociated (E(50%)) in population was obtained. The correlation coefficient between E(50%) and the relative binding free-energy change (DeltaDeltaG) of each complex formation in solutions was 0.9808, which is much better than the coefficient obtained by the previous ESI-CID experiments that was 0.859. In addition, complexes of the c-Myb DBD with five other mutant dsDNA were also examined to confirm that laser spray can be used to estimate the K(d) values of a DNA-protein complex in solutions if an appropriate calibration curve is available. In the process of laser spray, dissociations of these noncovalent complexes occur in solutions, but not in the gas phase. This differs greatly from ESI-CID. Laser spray mass spectrometry has been found to be better than ESI-CID in evaluating binding affinity of a protein to various mutant DNA.     

An efficient in silico screening method based on the protein-compound affinity matrix and its application to the design of a focused library for cytochrome P450 (CYP) ligands

A new method has been developed to design a focused library based on available active compounds using protein-compound docking simulations. This method was applied to the design of a focused library for cytochrome P450 (CYP) ligands, not only to distinguish CYP ligands from other compounds but also to identify the putative ligands for a particular CYP. Principal component analysis (PCA) was applied to the protein-compound affinity matrix, which was obtained by thorough docking calculations between a large set of protein pockets and chemical compounds. Each compound was depicted as a point in the PCA space. Compounds that were close to the known active compounds were selected as candidate hit compounds. A machine-learning technique optimized the docking scores of the protein-compound affinity matrix to maximize the database enrichment of the known active compounds, providing an optimized focused library.     

Multiattribute utility analysis for policy selection and financing for the preservation of the forest

In this paper, we examine effective policies for financing and activities for the preservation of the forest on Mount Ryuoh in the city of Higashi-Hiroshima by multiattribute utility analysis. In multiattribute utility analysis, we deal with decision making problems with multiple attributes and select the most effective solution among several alternatives by deriving preference of the decision maker. Although in our decision making problem, the decision maker is a representative of a hypothetical nonprofit organization established for the preservation of the forest, the decision maker gives serious consideration to intentions of several groups of people receiving the benefit from the mountain, and then from this viewpoint, our problem can be interpreted as a group decision making problem.     

Solid-phase combinatorial synthesis of aeruginosin derivatives and their biological evaluation

A 24-member combinatorial library based on the structure of aeruginosin 298-A (1a) was synthesized utilizing solid-phase, and their inhibitory activity against trypsin was evaluated. Among the library, we found that D-Hpla-D-Leu-L-Choi-Agma (1h) is 300 times more potent than the parent natural product 1a.     

Radical polymerization of muconic acid and ethyl muconate

Muconic acid (Mu-acid) was found to polymerize to trans-1,4-poly(Mu-acid) with the use of azobisisobutyronitrile (AIBN) as an initiator. Similarly, a muconic acid derivative, ethyl muconate (EMu), was readily polymerized through a trans-1,4 addition mechanism by the use of a radical or anionic catalyst, but did not polymerize when a cationic catalyst such as boron trifluoride etherate was used. Moreover, the copolymerization of Mu-acid and EMu with various comonomers such as styrene, acryronitrile, and 2-vinylpyridine was carried out and Q–e values of Mu-acid and EMu are discussed. These substituted diene monomers always polymerized through trans-1,4 addition with all catalysts and any comonomers.