Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?

The determination of a protein''s folding nucleus, i.e. a set of native contacts playing an important role during its folding process, remains an elusive yet essential problem in biochemistry. In this work, we investigate the mechanical properties of 70 protein structures belonging to 14 protein families presenting various folds using coarse-grain Brownian dynamics simulations. The resulting rigidity profiles combined with multiple sequence alignments show that a limited set of rigid residues, which we call the consensus nucleus, occupy conserved positions along the protein sequence. These residues'' side chains form a tight interaction network within the protein''s core, thus making our consensus nuclei potential folding nuclei. A review of experimental and theoretical literature shows that most (above 80%) of these residues were indeed identified as folding nucleus member in earlier studies.     

Electrical and optical properties of semi-insulating polycrystalline silicon thin films: the role of microstructure and doping

We have investigated the relationship between microstructure and electrical conductivity in semi-insulating polycrystalline silicon (SIPOS) with oxygen concentrations in the 2–35 at.% range and the effect of doping with boron, phosphorus, arsenic and erbium by ion implantation. SIPOS thin films are mixtures of silicon and silicon oxide phases. The chemical and morphological evolution of these phases upon annealing is emphasized. Electrical conductivity measurements are interpreted in terms of a physical model containing few free parameters related to the material microstructure. A direct extension of this model explains also the conductivity increase in SIPOS doped with elements of the third or the fifth group. In the last part of the paper, data of electroluminescence at 1.54 μm in Er-implanted SIPOS due to intra-4f transitions of the Er³⁺ ion are shown and discussed.     

Transgenerational effects of the holocaust: Externalization of aggression in second generation of holocaust survivors.

Examined the psychological characteristics of the children of holocaust survivors. 38 males and females in their late 20's were interviewed; the parents of 19 Ss were holocaust survivors, and the parents of the other 19 Ss were in Israel during World War II and did not suffer directly. It was hypothesized that reactions of the children of the holocaust survivors would include guilt rather than external aggression and a tendency not to externalize aggressive impulses in reaction to frustrating events. The Ss' reactions to a projective test were analyzed, and the responses provide support for the major hypothesis. Results show that sons and daughters of holocaust survivors were less likely to externalize aggression than were those in a control group. This finding is supported by the content analysis of the structured interview conducted with the Ss in both groups. (20 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A Constraint-based Approach for Annotating Music Scores with Gestural Information

The physical gestures that operate music instruments are responsible for the qualities of the sound being produced in a performance. Gestural information is thereby crucial for a model of music performance, paired with a model of sound synthesis where this information is applied. The highly constrained nature of performers gestures makes this task suitable to be modeled via a constraint-based approach, coupled with a strategy aimed at maximizing the gestural comfort of performers. We illustrate the problem representation, the search strategy and a validation of the model against human performance.     

Xylene Isomerization in a ZSM-5/SS Membrane Reactor

A membrane reactor containing different types of ZSM-5/porous SS membranes was used to perform the xylene isomerization reaction. The parent Na-ZSM-5 layer was synthesized by secondary growth on top of porous stainless steel tubes. The xylene isomerization reaction was carried out at different temperatures in the membrane reactor and in a fixed-bed reactor of identical geometry for comparison. Two different kinds of membranes were prepared by ion exchange: a Pt/H-ZSM-5 catalytic membrane and two Ba-ZSM-5 composites with different Ba²⁺ concentration. The p-xylene production using 100% exchanged Ba-membrane was about 28% higher than the fixed-bed reactor at 370 °C, when m-xylene was fed.     

Maturation ponds, rock filters and reedbeds in the UK: statistical analysis of winter performance.

Wastewater treatment technologies suitable for serving large populations are generally reliable and reasonably cost-effective, yet they are almost always financially inappropriate for small communities (< 2,000 p.e.). Comparative cost data suggests that waste stabilization ponds should be an attractive option for small communities, yet perceptions relating to land costs, climate and effluent quality have limited their application in the UK. This paper details typical UK land costs, climate and winter performance data for a pilot-scale waste stabilization pond with various upgrading technologies: system A, two tertiary maturation ponds in series; B, two tertiary maturation ponds in series followed by a reed bed channel; C, a control rock filter; D, an aerated rock filter; and E, a constructed wetland. System D was found to perform best, closely followed by system B.     

A methodology for the performance evaluation of data querystrategies in universal mobile telecommunication systems (UMTS)

The anticipated emergence of third-generation mobile systems, referred to as universal mobile telecommunication systems (UMTS), raises the problem of reconsidering the design of the databases destined to contain the user information. In particular, it is expected that the key concepts of the new database architectures will be high distribution and fast updating of information. So far, the problem of determining the most appropriate distributed database (DDB) architectures for third-generation mobile systems has not been widely dealt with in literature. This paper presents a methodology for evaluating hierarchical DDB architectures by means of an analytical model of the data querying operation. This methodology allows for structural alternatives, differing on account of the number of levels and branches in the hierarchy, to be evaluated in terms of query loads and mean response times, according to a given user mobility characterization and a given search protocol operation. By way of illustration, the paper discusses a case study, concerning a query operation arising from a location updating procedure and applied to a hierarchical tree-like DDB in which some structural alternatives are considered     

Molecular dynamics simulations of polyphosphazenes: poly[bis(chloro)phosphazene][NPCl2] n

Suitable parameter sets for the CHARMm force field were derived for the structural units in polychlorophosphazene [P=N, P N, P Cl] using the Dinur Hagler energy second derivative procedure based on quantum mechanical SCI calculations using the 6–31G^* basis set. To validate the reliability of the parameter set, structural results obtained with CHARMm for the adopted model compounds (OP₂NCl₅ and OP₃N₂Cl₅) were compared with those derived fromab initio quantum mechanics using the 6–31G^* basis set. Application of molecular dynamics (MD) simulations in combinatioin with the available X-ray diffraction data provided structural and conformational information on the polymer. The calculation made using the periodic boundary conditions (PBC) agree well with the polychlorophosphazene ordered in a monoclinic unit cell (a=5.98,b=12.99,c=4.92 A; β=111.7). This model was stabilized mainly by the image atoms contribution to the electrostatic energy term and had aquasi-planar conformation of the backbone chain (glide symmetry). The MD calculations also provided evidence that the difference between single and double PN bonds is less marked than that measured experimentally. This result is, however, in agreement with more recent and accurate X-ray studies on poly(methylphosphazene). Validation of the polymer model provided a complete picture, otherwise experimentally inaccessible, of the internal fluctuations of the polymeric chains.     

Water absorption properties of phosphate glass fiber‐reinforced poly‐ϵ‐caprolactone composites for craniofacial bone repair

The moisture uptake of polymers and composites has increasing significance where these materials are specified for invasive, long‐term medical applications. Here we analyze mass gain and the ensuing degradation mechanisms in phosphate glass fiber reinforced poly‐?‐caprolactone laminates. Specimens were manufactured using in situ polymerization of ?‐caprolactone around a bed of phosphate glass fibers. The latter were sized with 3‐aminopropyltriethoxysilane to control the rate of modulus degradation. Fiber content was the main variable in the study, and it was found that the moisture diffusion coefficient increased significantly with increasing fiber volume fraction. Diffusion, plasticization, and leaching of constituents appear to be the dominant aspects of the process over these short‐term tests. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2008