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.

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.

Structural Systematics of the Anhydrous 1:1 Proton-Transfer Compounds of 3,5-Dinitrosalicylic Acid with Aniline and Monosubstituted Anilines

The crystal structures of the proton-transfer compounds of 3,5-dinitrosalicylic acid (DNSA) with a series of aniline-type Lewis bases [aniline, 2-hydroxyaniline, 2-methoxyaniline, 3-methoxyaniline, 4-fluoroaniline, 4-chloroaniline and 2-aminoaniline] have been determined and their hydrogen-bonding systems analysed. All are anhydrous 1:1 salts: [(C6H8N)+(C7H3N2O7)-], (1), [(C6H8NO)+(C7H3N2O7)-], (2), [(C7H10NO)+(C7H3N2O7)-], (3), [(C7H10NO)+(C7H3N2O7)-], (4), [(C6H7FN)+(C7H3N2O7)-], (5), [(C6H7ClN)+(C7H3N2O7)-], (6), and [(C6H9N2)+(C7H3N2O7)-], (7) respectively. Crystals of 1 and 6 are triclinic, space group P-1 while the remainder are monoclinic with space group either P21/n (2, 4, 5 and 7) or P21 (3). Unit cell dimensions and contents are: for 1, a = 7.2027(17), b = 7.5699(17), c = 12.9615(16) Å, α = 84.464(14), β = 86.387(15), γ = 75.580(14)o, Z = 2; for 2, a = 7.407(3), b = 6.987(3), c = 27.653(11) Å, β = 94.906(7)o, Z = 4; for 3, a = 8.2816(18), b = 23.151(6), c = 3.9338(10), β = 95.255(19)o, Z = 2; for 4, a = 11.209(2), b = 8.7858(19), c = 15.171(3) Å, β = 93.717(4)o, Z = 4; for 5, a = 26.377(3), b = 10.1602(12), c = 5.1384(10) Å, β = 91.996(13)o, Z = 4; for 6, a = 11.217(3), b = 14.156(5), c = 4.860(3) Å, α = 99.10(4), β = 96.99(4), γ = 76.35(2)o, Z = 2; for 7, a = 12.830(4), b = 8.145(3), c = 14.302(4) Å, β = 102.631(6)o, Z = 4. In all compounds at least one primary linear intermolecular N+-H…O(carboxyl) hydrogen-bonding interaction is present which, together with secondary hydrogen bonding results in the formation of mostly two-dimensional network structures, exceptions being with compounds 4 and 5 (one-dimensional) and compound 6 (three-dimensional). In only two cases [compounds 1 and 4], are weak cation-anion or cation-cation π-π interactions found while weak aromatic C-H…O interactions are insignificant. The study shows that all compounds fit the previously formulated classification scheme for primary and secondary interactive modes for proton-transfer compounds of 3,5-dinitrosalicylic acid but there are some unusual variants.

Molecular structural studies of the amorphous mineral pitticite Fe, AsO4, SO4, H2O

Some minerals are colloidal and show no X-ray diffraction patterns. Vibrational spectroscopy offers one of the few methods for the assessment of the structure of these types of mineral. Among this group of minerals is pitticite simply described as Fe, AsO4, SO4, H2O. The objective of this research is to determine the molecular structure of the mineral pitticite using vibrational spectroscopy. Raman microscopy offers a useful method for the analysis of such colloidal minerals. Raman and infrared bands are attributed to the , and water stretching vibrations. The Raman spectrum is dominated by a very intense sharp band at 983 cm−1 assigned to the symmetric stretching mode. A strong Raman band at 1041 cm−1 is observed and is assigned to the antisymmetric stretching mode. Low intensity Raman bands at 757 and 808 cm−1 may be assigned to the antisymmetric and symmetric stretching modes. Raman bands observed at 432 and 465 cm−1 are attributable to the doubly degenerate ν2(SO4)2- bending mode.

A nanoscratch method for measuring hardness of thin films

Thin solid films were extensively used in the making of solar cells, cutting tools, magnetic recording devices, etc. As a result, the accurate measurement of mechanical properties of the thin films, such as hardness and elastic modulus, was required. The thickness of thin films normally varies from tens of nanometers to several micrometers. It is thus challenging to measure their mechanical properties. In this study, a nanoscratch method was proposed for hardness measurement. A three-dimensional finite element method (3-D FEM) model was developed to validate the nanoscratch method and to understand the substrate effect during nanoscratch. Nanoindentation was also used for comparison. The nanoscratch method was demonstrated to be valuable for measuring hardness of thin solid films.

Inactivation and structural changes of E. Cloacae and B. Subtilis Endospores during IR laser water treatment

IR radiation has been studied for micro-organism inactivation of bacterial spores on metal substrates [1] and on metal and paper substrates [2]. A near-point near infrared laser water treatment apparatus for use in dental hand-pieces was also developed [3]. To date water sterilisation research using a mid-IR laser technique is very rare. According to the World Health Organisation [4], examinations for faecal indicator bacteria remain the most sensitive and specific way of assessing the hygienic quality of water. Bacteria that fall into this group are E. coli, other coliform bacteria (including E. cloacae) and to a lesser extent, faecal streptococci [5]. Protozoan cysts from organisms which cause giardiasis are the most frequently identified cause of waterborne diseases in developed countries [6,7]. The use of aerobic bacterial endospores to monitor the efficiency of various water treatments has been shown to provide a reliable and simple indicator of overall performance of water treatment[8,9].The efficacy of IR radiation for water disinfection compared to UV treatment has been further investigated in the present study. In addition FTIR spectroscopy in conjunction with Principle Component Analysis was used to characterise structural changes within the bacterial cells and endospores following IR laser treatment. Changes in carbohydrate content of E. cloacae following IR laser treatment were observed.

On the oscillatory behavior of transient Rayleigh Benard convection of air for 2D channel flow at moderate Rayleigh numbers

Unsteady numerical simulation of Rayleigh Benard convection heat transfer from a 2D channel is performed. The oscillatory behavior is attributed to recirculation of ascending and descending flows towards the core of the channel producing organized rolled motions. Variation of the parameters such as Reynolds number, channel outlet flow area and inclination of the channel are considered. Increasing Reynolds number (for a fixed Rayleigh number), delays the generation of vortices. The reduction in the outflow area leads to the later and the less vortex generation. As the time progresses, more vortices are generated, but the reinforced mean velocity does not let the eddies to enter the core of the channel. Therefore, they attach to the wall and reduce the heat transfer area. The inclination of the channel (both positive and negative) induces the generated vortices to get closer to each other and make an enlarged vortex.

Travel behavior of workers in Dhaka and their attitude towards road pricing

Dhaka, the capital of Bangladesh, is facing severe traffic congestion. Owing to the flaws in past land use and transport planning decisions, uncontrolled population growth and urbanization, Dhaka’s traffic condition is worsening. Road space is widely regarded in the literature as a utility, so a common view of transport economists is that its usage ought to be charged. Road pricing policy has proven to be effective in managing travel demand, in order to reduce traffic congestion from road networks in a number of cities including London, Stockholm and Singapore. Road pricing as an economic mechanism to manage travel demand can be more effective and user-friendly when revenue is hypothecated into supply alternatives such as improvements to the transit system. This research investigates the feasibility of adopting road pricing in Dhaka with respect to a significant Bus Rapid Transit (BRT) project. Because both are very new concepts for the population of Dhaka, public acceptability would be a principal issue driving their success or failure. This paper explores the travel behaviour of workers in Dhaka and public perception toward Road Pricing with regards to work trips- based on worker’s travel behaviour. A revealed preference and stated preference survey has been conducted on sample of workers in Dhaka. They were asked limited demographic questions, their current travel behaviour and at the end they had been given several hypothetical choices of integrated BRT and road pricing to choose from. Key finding from the survey is the objective of integrated road pricing; subsidies Bus rapid Transit by road pricing to get reduced BRT fare; cannot be achieved in Dhaka. This is because most of the respondent stated that they would choose the cheapest option Walk-BRT-Walk, even though this would be more time consuming and uncomfortable as they have to walk from home to BRT station and also from BRT station to home. Proper economic analysis has to be carried out to find out the appropriate fare of BRT and road charge with some incentive for the low income people.