Preprocessed visualization of large scale unsteady flow simulations

In some cases, conventional CFD visualization techniques do not give us sufficient information of the flowfield, especially when the flowfield is unsteady, and there is a need for a new postprocessing technique. In the present paper, one of such new post-processing techniques is proposed. In the present technique, raw result of CFD simulation is pre-processed by frequency filters, and then processed secondary data set is visualized. The idea is applied to two examples. The examples show that the present method visualizes each frequency mode separately, and gives clear view of the temporal variation of the whole flowfield. The results indicate that the present method improves the understandings of the flow mechanism.     

Morphology control of polypropylene by crystallization under carbon dioxide

We investigated the crystalline morphology of isotactic polypropylene obtained by melt crystallization under carbon dioxide (CO₂) at various pressures. Spherulites consisting of regularly arranged fibrils without subsidiary lamellae were obtained by crystallization under CO₂ below 2 MPa, whereas large spherulites consisting of irregularly arranged fibrils with subsidiary lamellae were obtained under ambient pressure. Distorted domain crystals with uniform optical anisotropy consisting of α‐form were found to be obtained under CO₂ above 2 MPa, and needle crystals consisting of γ‐form were obtained above 12 MPa. Transmission electron micrographs showed that straight and thick lamellae are regularly arranged in both the distorted domain crystals and the needle crystals. The uniformly thick lamellae were confirmed by differential scanning calorimetry thermograms; that is, the melting temperature is higher and the melting peak is sharper than those obtained under ambient pressure. Such characteristic crystalline morphologies obtained under CO₂ may be attributed to local ordering in the melt state. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 2738–2746, 2004     

Studies of micro-brownian motion of a polymer chain by the fluorescence polarization method. II. Segmental motions in concentrated polymer solutions

The fluorescence polarization method has been used to study the micro-Brownian motion of a terminal segement of a polymer chain in concentrated solutions. A new apparatus for determining the fluorescence intensity and its polarization degree was designed. By using this apparatus, the rotational relaxation time 〈ρ〉 of the terminal segment of the fluorescent conjugates of polyacrylamide in aqueous polyacrylamide solutions was obtained as a function of polymer concentration from 0 to 65%, molecular weight of the conjugate from 3.5 × 10⁴ to 3 × 10⁵, and temperature from 10 to 30°C. The logarithm of 〈ρ〉 increased approximately linearly with increasing polymer concentration. This increase in 〈ρ〉, amounting to a factor of 20 times, was less marked than that in macroscopic viscosity. At concentrations less than 30%, 〈ρ〉 depended appreciably on the molecular weight of the conjugate.     

Third virial coefficient of polystyrene in benzene

Second virial coefficients A₂ and third virial coefficients A₃ for benzene solutions of ten polystyrene fractions ranging in weight-average molecular weight M_w from 10⁴ to 2 × 10⁷ at 25°C were determined by light scattering. The third coefficient is represented approximately by A₃ = 8.0 × 10^?6 M mol g^?3 cm⁶ for M_w above 10⁵. In this molecular weight region, the factor g defined by A₃/AM_w/ This trend of g is consistent with predictions of early two-parameter theories but not with those of renormalization group theories. In particular, quantitative agreement is observed between the present experiments (for M_w ? 2 × 10⁵) and the mean-field two-parameter theory of Stockmayer and Casassa.     

Nanoindentation of biodegradable cellulose diacetate‐graft‐poly(L‐lactide) copolymers: Effect of molecular composition and thermal aging on mechanical properties

Nanoindentation of cellulose diacetate‐graft‐poly(lactide)s (CDA‐g‐PLLAs) synthesized by ring opening graft copolymerization of L ‐lactide in bulk onto the residual hydroxyl positions on CDA were conducted to investigate the effect of the molecular composition and thermal aging on mechanical properties and creep behavior. Continuous stiffness measurement (CSM) technique was used to obtained hardness and elastic modulus. These material properties were expressed as a mean value from 100 to 300 nm depths and an unloading value at final indentation depth. The hardness and elastic modulus in all CDA‐g‐PLLAs were higher than those in pure CDA, indicating that the introduction of PLLA increases the hardness and elastic modulus. With an increase of crystallinity by thermal aging, the hardness and elastic modulus were increased in both CDA‐g‐PLLA and PLLA. The creep test performed by CSM showed that the creep strain of CDA was decreased by the grafting of PLLA. Thermal aging decreased the creep strain of CDA‐g‐PLLA and PLLA. With an increase of holding time, hardness was decreased, whereas elastic modulus was kept almost constant. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 1114–1121, 2007     

Computational Design of Single-Peptide Nanocages with Nanoparticle Templating

Protein complexes perform a diversity of functions in natural biological systems. While computational protein design has enabled the development of symmetric protein complexes with spherical shapes and hollow interiors, the individual subunits often comprise large proteins. Peptides have also been applied to self-assembly, and it is of interest to explore such short sequences as building blocks of large, designed complexes. Coiled-coil peptides are promising subunits as they have a symmetric structure that can undergo further assembly. Here, an α-helical 29-residue peptide that forms a tetrameric coiled coil was computationally designed to assemble into a spherical cage that is approximately 9 nm in diameter and presents an interior cavity. The assembly comprises 48 copies of the designed peptide sequence. The design strategy allowed breaking the side chain conformational symmetry within the peptide dimer that formed the building block (asymmetric unit) of the cage. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) techniques showed that one of the seven designed peptide candidates assembled into individual nanocages of the size and shape. The stability of assembled nanocages was found to be sensitive to the assembly pathway and final solution conditions (pH and ionic strength). The nanocages templated the growth of size-specific Au nanoparticles. The computational design serves to illustrate the possibility of designing target assemblies with pre-determined specific dimensions using short, modular coiled-coil forming peptide sequences.     

Consensus scoring with feature selection for structure-based virtual screening

The evaluation of ligand conformations is a crucial aspect of structure-based virtual screening, and scoring functions play significant roles in it. While consensus scoring (CS) generally improves enrichment by compensating for the deficiencies of each scoring function, the strategy of how individual scoring functions are selected remains a challenging task when few known active compounds are available. To address this problem, we propose feature selection-based consensus scoring (FSCS), which performs supervised feature selection with docked native ligand conformations to select complementary scoring functions. We evaluated the enrichments of five scoring functions (F-Score, D-Score, PMF, G-Score, and ChemScore), FSCS, and RCS (rank-by-rank consensus scoring) for four different target proteins: acetylcholine esterase (AChE), thrombin (thrombin), phosphodiesterase 5 (PDE5), and peroxisome proliferator-activated receptor gamma (PPARgamma). The results indicated that FSCS was able to select the complementary scoring functions and enhance ligand enrichments and that it outperformed RCS and the individual scoring functions for all target proteins. They also indicated that the performances of the single scoring functions were strongly dependent on the target protein. An especially favorable result with implications for practical drug screening is that FSCS performs well even if only one 3D structure of the protein-ligand complex is known. Moreover, we found that one can infer which scoring functions significantly enrich active compounds by using feature selection before actual docking and that the selected scoring functions are complementary.     

Interaction of albumin with polysaccharides containing ionic groups

It is very important to clarify the mechanisms of the interaction between components of organisms. In this report, the interaction between bovine serum albumin (BSA) and ionic polysaccharides were discussed. The fluorescence spectrum of tryptophan (Trp) in BSA changed as its conformation changed. On adding polysaccharide containing sulfonic acid residues (sulfonic‐type) at pH 7.4, a remarkable blue shift of the emission maximum (λ_em) of Trp was observed. This blue shift was decreased by adding NaCl. In contrast, polysaccharide containing carboxylic acid residues (carboxy‐type) scarcely changed Trp fluorescence at the same pH. At a pH lower than the isoelectric point (PI = 4.7–4.9) of BSA, a remarkable blue shift was observed not only by adding sulfonic‐type polysaccharide but also by adding carboxy‐type polysaccharide. Moreover, using the energy transfer method, in the pH region higher than the PI of BSA, carboxylic‐type polysaccharides may interact relatively weakly with the binding site II of BSA, but sulfonic‐type ones can selectively interact with binding site I weakly and with binding site II strongly. And in the pH region lower than the PI of BSA, carboxylic‐type polysaccharides interact with binding site II strongly. On the other hand, sulfonic‐type polysaccharides are bound to both binding site I and binding site II very strongly. Copyright © 1999 John Wiley & Sons, Ltd.