Correlations between designability and various structural characteristics of protein lattice models

Using six kinds of lattice types (4×4 ,5×5 , and6×6 square lattices;3×3×3 cubic lattice; and2+3+4+3+2 and4+5+6+5+4 triangular lattices), three different size alphabets (HP ,HNUP , and 20 letters), and two energy functions, the designability of proteinstructures is calculated based on random samplings of structures and common biased sampling (CBS) of proteinsequence space. Then three quantities stability (average energy gap),foldability, and partnum of the structure, which are defined to elucidate the designability, are calculated. The authors find that whatever the type of lattice, alphabet size, and energy function used, there will be an emergence of highly designable (preferred) structure. For all cases considered, the local interactions reduce degeneracy and make the designability higher. The designability is sensitive to the lattice type, alphabet size, energy function, and sampling method of the sequence space. Compared with the random sampling method, both the CBS and the Metropolis Monte Carlo sampling methods make the designability higher. The correlation coefficients between the designability, stability, and foldability are mostly larger than 0.5, which demonstrate that they have strong correlation relationship. But the correlation relationship between the designability and the partnum is not so strong because the partnum is independent of the energy. The results are useful in practical use of the designability principle, such as to predict the proteintertiary structure.

Experimental investigation of the governing parameters in the electrospinning of poly(3-hydroxybutyrate) scaffolds : structural characteristics of the pores

We sought to determine the impact of electrospinning parameters on a trustworthy criterion that could evidently improve the maximum applicability of fibrous scaffolds for tissue regeneration. We used an image analysis technique to elucidate the web permeability index (WPI) by modeling the formation of electrospun scaffolds. Poly(3-hydroxybutyrate) (P3HB) scaffolds were fabricated according to predetermined conditions of levels in a Taguchi orthogonal design. The material parameters were the polymer concentration, conductivity, and volatility of the solution. The processing parameters were the applied voltage and nozzle-to-collector distance. With a law to monitor the WPI values when the polymer concentration or the applied voltage was increased, the pore interconnectivity was decreased. The quality of the jet instability altered the pore numbers, areas, and other structural characteristics, all of which determined the scaffold porosity and aperture interconnectivity. An initial drastic increase was observed in the WPI values because of the chain entanglement phenomenon above a 6 wt % P3HB content. Although the solution mixture significantly (p < 0.05) changed the scaffold architectural characteristics as a function of the solution viscosity and surface tension, it had a minor impact on the WPI values. The solution mixture gained the third place of significance, and the distance was approved as the least important factor.

Molecular dynamics simulation of structural characteristics in metal cluster deposition on surfaces

The deposition of small metal clusters (Cu, Au and Al) on f.c.c. metals (Cu, Au and Ni) has been studied by molecular dynamics simulation using Finnis–Sinclair (FS) potential. The impact energy varied from 0.01 to 10 eV/atom. First, the deposition of single cluster was simulated. We observed that, even at much lower energy, a small cluster with (Ih) icosahedral symmetry was reconstructed to match the substrate structure (f.c.c.) after deposition. Next, clusters were modeled to drop, one after the other, on the surface. The nanostructure was found by soft landing of Au clusters on Cu with increasing coverage, where interfacial energy dominates. While at relatively higher deposition energy (a few eV), the ordered f.c.c.-like structure was observed in the first adlayer of the film formed by Al clusters depositing on Ni substrate. This characteristic is mainly attributive to the ballistic collision. Our results indicate that the surface morphology synthesized by cluster deposition could be controlled by experimental parameters, which will be helpful for controlled design of nanostructure.

Structural characteristics of a giant tropical liana and its mode of canopy spread in an alien environment

To circumvent the practical difficulties in research on tropical rainforest lianas in their natural habitat due to prevailing weather conditions, dense camouflaging vegetation and problems in transporting equipment for experimental investigations, Entada pursaetha DC (syn. Entada scandens Benth., Leguminosae) was grown inside a research campus in a dry subtropical environment. A solitary genet has attained a gigantic size in 17 years, infesting crowns of semi-evergreen trees growing in an area roughly equivalent to 1.6 ha. It has used aerially formed, cable-like stolons for navigating and spreading its canopy across tree gaps. Some of its parts which had remained unseen in its natural habitat due to dense vegetation are described. The attained size of this liana in a climatically different environment raises the question as to why it is restricted to evergreen rainforests. Some research problems for which this liana will be useful are pointed out.

Structural characteristics affecting functions of two actin regulating proteins

Structural biology is a branch of science that concentrates on the relationship between the structure and function of biological macromolecules. The prevalence of a large number of three dimensional structures offers effective tools for bio-scientists to understand the living world. Actin is the most abundant cellular protein and one of its main functions is to produce movement in living cells. Actin forms filaments that are dynamic and which are regulated by a number of different proteins. A class of these regulatory proteins contains actin depolymerizing factor homology (ADF-H) domains. These directly interact with actin through their ADF-H domains. Although ADF-H domains possess very similar three dimensional structures to one another, they vary in their functional properties. One example of this is the ability to bind to actin monomers or filaments. During the work for this thesis two structures of ADF-H domains were solved by nuclear magnetic resonance spectroscopy (NMR). The elucidated structures help us understand the binding specificities of the ADF-H family members.

Effect of V2O5 on the Surface and Structural Characteristics of Potassium Lithium Niobate

It has been suggested that materials with interesting and useful bulk non-linear optical properties might result by substituting vanadium, the lightest element in the group V of periodic table, for Nb or Ta atoms along with Li and three oxygens. It is with this motivation that we have been making attempts to grow single crystals of LiNbO3 doped with various concentrations of V2O5. Unfortunately the results obtained on the ceramic samples of this material have not been very encouraging, owing to their hygroscopic nature. However, our attempts to prepare both ceramic and single-crystalline samples of potassium lithium niobate (K3Li2Nb5O15; KLN) doped V2O5 were successful. In this letter we report the preliminary results concerning our studies on the effect of V2O5 doping on the structural as well as topographic features of both ceramic and single-crystalline samples of KLN.

Crystallization of amorphous Si films by pulsed laser annealing and their structural characteristics

Nanocrystalline silicon (nc-Si) films were prepared by pulsed laser annealed crystallization of amorphous silicon (alpha-Si) films on SiO2-coated quartz or glass substrates. The effect of laser energy density on structural characteristics of nc-Si films was investigated. The Ni-induced crystallization of the a-Si films was also discussed. The surface morphology and microstructure of these films were characterized by scanning electron microscopy, high-resolution electron microscopy, atomic force microscopy and Raman scattering spectroscopy. The results show that not only can the alpha-Si films be crystallized by the laser annealing technique, but also the size of Si nanocrystallites can be controlled by varying the laser energy density. Their average size is about 4-6 nm. We present a surface tension and interface strain model used for describing the laser annealed crystallization of the alpha-Si films. The doping of Ni atoms may effectively reduce the threshold value of laser energy density to crystallize the alpha-Si films, and the flocculent-like Si nanostructures could be formed by Ni-induced crystallization of the alpha-Si films.

Structural characteristics and redox behaviors of Ce1-xCuxOy solid solutions

Nanosized Ce1-xCuxOy materials were prepared by complexation-combustion method. The structural characteristics and redox behaviors were investigated using X-ray diffraction (XRD), temperature programmed reduction (H-2-TPR), UV-Vis, and Raman spectroscopies. In XRD patterns, no evidence of CuO diffraction peaks are observed for the Ce1-xCuxOy samples calcinated at 650 degreesC for 5 h, until the Cu/(Ce + Cu) ratio is higher than 0.4. The stepwise decrease of the 2theta value of CeO2 in Ce1-xCuxOy with the increasing of Cu concentration suggests that the CU2+ ions incorporate into the CeO2 lattice to form Ce1-xCuxOy solid solutions for low Cu/(Ce + Cu) ratios (x less than or equal to 0.1). The CuO phase begins to segregate from the solid solutions with the further increasing of Cu/(Ce+Cu) ratio. The Raman mode at 1176 cm(-1) ascribed to the enhanced defects appears for CeO2 and the Ce0.9Cu0.1Oy solid solution. Compared with CeO2 alone, the Raman mode of cubic CeO2 shifts from 462 to 443 cm(-1) for the Ce0.9Cu0.1Oy solid solution. The H-2 consumption of the fresh Ce0.95Cu0.05Oy is 1.65 times higher than that needed to reduce CuO to Cu, and it increases to 2.4 after a reoxidation of the partially reduced Ce0.95Cu0.05Oy at 300 degreesC, which indicates that the CeO2 phase is also extensively reduced. Compared with the high Cu/(Ce+Cu) ratio sample Ce0.7Cu0.3Oy, the Ce0.9Cu0.1Oy solid solution shows high and stable redox property even after different reoxidation temperatures. When the reoxidation temperature exceeds 200 degreesC, the a peak (similar to170 degreesC) ascribed to the reduction of surface oxygen disappears, and the P peak (similar to190 degreesC) ascribed to the reduction of Cu2+ species and the partial reduction of bulk CeO2 shifts to higher temperatures with the H-2 consumption 1.16 times higher than that for fresh sample. The result demonstrates that the redox property of the CeO2 is Significantly improved by forming the Ce1-xCuxOy solid solutions.

Structural characteristics and thermal properties of plasticized poly(L-lactide)-silica nanocomposites synthesized by sol-gel method

Plasticized poly(L-lactide)-silica nanocomposite materials have been successfully synthesized by sol-gel process. The resultant nanocomposites were characterized by infrared spectra (IR), X-ray diffraction (XRD), thermogravimetry (TG), Tensile testing and scanning electron microscope (SEM). IR measurements show that vibration of C-O-C group is confined by silica network. Also the crystallization of poly (L-lactide) is partly confined by silica network. The presence of even small amount of silica largely improves the tensile strength of the samples, TGA results reveal that the thermal stability of samples is improved with silica loading.

Mechanical and structural characteristics of phenolphthalein poly(ether sulfone) ultra-high molecular weight polyethylene blends

Mechanical and structural properties of blends of phenolphthalein poly(ether sulfone) (PBS-C) with ultra-high molecular weight polyethylene (UHMWPE) were investigated using tensile and bending testing, scanning electron microscopy and transition electron microscopy. The incorporation of minor amounts of UHMWPE (2 wt.-%) into PES-C has a reinforcement effect. With higher concentrations of UHMWPE, the mechanical properties decrease gradually. Structural studies demonstrated that the blends are multiphasic in the whole composition range. The minor UHMWPE, dispersed uniformly and oriented along the flow direction, as well as the strong interfacial adhesion contribute to the increase of the mechanical performance of the blends. The domain size of the UHMWPE phase was found to increase with the increase of its concentration.