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.

Effect of modular neck variation on bone and cement mantle mechanics around a total hip arthroplasty stem

Background Total hip arthroplasty carried out using cemented modular-neck implants provides the surgeon with greater intra-operative flexibility and allows more controlled stem positioning. Methods In this study, finite element models of a whole femur implanted with either the Exeter or with a new cemented modular-neck total hip arthroplasty (separate, neck and stem components) were developed. The changes in bone and cement mantle stress/strain were assessed for varying amounts of neck offset and version angle for the modular-neck device for two simulated physiological load cases: walking and stair climbing. Since the Exeter is the gold standard for polished cemented total hip arthroplasty stem design, bone and cement mantle stresses/strains in the modular-neck finite element models were compared with finite element results for the Exeter. Findings For the two physiological load cases, stresses and strains in the bone and cement mantle were similar for all modular-neck geometries. These results were comparable to the bone and cement mechanics surrounding the Exeter. These findings suggest that the Exeter and the modular neck device distribute stress to the surrounding bone and cement in a similar manner. Interpretation It is anticipated that the modular-neck device will have a similar short-term clinical performance to that of the Exeter, with the additional advantages of increased modularity.

Spectroscopic and structural characterization of pascoite

Pascoite mineral having yellow-orange colour of Colorado, USA origin has been characterized by EPR, optical and NIR spectroscopy. The colour dark red-orange to yellow-orange colour of the pascoite indicates that the mineral contain mixed valency of vanadium. The optical spectrum exhibits a number of electronic bands due to presence of VO(II) ions in the mineral. From EPR studies, the parameters of g, A are evaluated and the data confirm that the ion is in distorted octahedron. Optical absorption studies reveal that two sets of VO(II) is in distorted octahedron. The bands in NIR spectra are due to the overtones and combinations of water molecules.

Are the ‘cave’ minerals archerite (K,NH4)H2PO4 and biphosphammite (K,NH4)H2PO4 identical? A molecular structural study

The molecular structure of the mineral archerite ((K,NH4)H2PO4) has been determined and compared with that of biphosphammite ((NH4,K)H2PO4). Raman spectroscopy and infrared spectroscopy has been used to characterise these ‘cave’ minerals. Both minerals originated from the Murra-el-elevyn Cave, Eucla, Western Australia. The mineral is formed by the reaction of the chemicals in bat guano with calcite substrates. Raman and infrared bands are assigned to H2PO4-, OH and NH stretching vibrations. The Raman band at 981 cm-1 is assigned to the HOP stretching vibration. Bands in the 1200 to 1800 cm-1 region are associated with NH4+ bending modes. The molecular structure of the two minerals appear to be very similar, and it is therefore concluded that the two minerals are identical.

Rademacher and Gaussian complexities: Risk bounds and structural results

We investigate the use of certain data-dependent estimates of the complexity of a function class, called Rademacher and Gaussian complexities. In a decision theoretic setting, we prove general risk bounds in terms of these complexities. We consider function classes that can be expressed as combinations of functions from basis classes and show how the Rademacher and Gaussian complexities of such a function class can be bounded in terms of the complexity of the basis classes. We give examples of the application of these techniques in finding data-dependent risk bounds for decision trees, neural networks and support vector machines.