792 research outputs found

    HP-sequence design for lattice proteins - an exact enumeration study on diamond as well as square lattice

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    We present an exact enumeration algorithm for identifying the {\it native} configuration - a maximally compact self avoiding walk configuration that is also the minimum energy configuration for a given set of contact-energy schemes; the process is implicitly sequence-dependent. In particular, we show that the 25-step native configuration on a diamond lattice consists of two sheet-like structures and is the same for all the contact-energy schemes, (−1,0,0);(−7,−3,0);(−7,−3,−1);(−7,−3,1){(-1,0,0);(-7,-3,0); (-7,-3,-1); (-7,-3,1)}; on a square lattice also, the 24-step native configuration is independent of the energy schemes considered. However, the designing sequence for the diamond lattice walk depends on the energy schemes used whereas that for the square lattice walk does not. We have calculated the temperature-dependent specific heat for these designed sequences and the four energy schemes using the exact density of states. These data show that the energy scheme (−7,−3,−1)(-7,-3,-1) is preferable to the other three for both diamond and square lattice because the associated sequences give rise to a sharp low-temperature peak. We have also presented data for shorter (23-, 21- and 17-step) walks on a diamond lattice to show that this algorithm helps identify a unique minimum energy configuration by suitably taking care of the ground-state degeneracy. Interestingly, all these shorter target configurations also show sheet-like secondary structures.Comment: 19 pages, 7 figures (eps), 11 tables (latex files

    Novel framework for secure mobile financial services

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    The financial sector is always looking for new services delivery platforms to improve customer confidence and satisfaction. To achieve this, the banking service delivery platform must provide end-to-end security to safeguard the financial information exchanged between the bank and the customer. Today a number of banks offer mobile banking service to their customers. However, still banks have been adopting the generic user authentication systems that were developed for the desktop environment based on two-factor authentication with a number of user intrusive activities. This paper presents a novel authentication and authorization framework for secure mobile banking applications based on the user SIM and mobile credentials

    A study on the diversity and production of microbial extracellular nucleases :potential anti-biofilm enzymes

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    PhD ThesisMicroorganisms have been viewed as planktonic, free living single cells but predominantly they exist as sessile multispecies communities in the natural environment forming ‘biofilms’. Biofilms are beneficial for organisms to survive in natural environment as well as for biotechnological applications such as microbial fuel cells and bioremediation. However, biofilms are associated with disease persistence and biofouling and are comprised of adhered microbes within a hydrated matrix rich in polysaccharides, proteins and extracellular DNA (eDNA). eDNA is an important structural component and its degradation by deoxyribonucleases may be a novel approach to eradicate biofilm related problems. The present work was undertaken in this context to discover and produce microbial nucleolytic enzymes for applications for the control of harmful biofilms. Eighty six out of 260 bacterial isolates which included thermophilic and psychrophilic strains, showed deoxyribonuclease activity. The diversity and function of extracellular nucleases was also investigated throughout the microbial world using bioinformatics tools. Sequence driven analysis suggested that major bacterial lineages contain diverse extracellular nucleases with biological function related to nitrogen, phosphate and carbohydrate metabolism, protection, survival and virulence. Production optimisation for one specific extracellular nuclease, NucB, from Bacillus licheniformis EI-34-6 was carried out. This enzyme was previously known to cleave eDNA causing biofilm dispersal, and may therefore be used commercially to remove biofilms. The understanding of B. licheniformis physiology was applied in order to enhance NucB production 10-fold. For further characterisation of the enzyme and to Abstract iv understand its biological mechanism in breaking down biofilms, NucB was expressed in the SURE expression host B. subtilis NZ8900. This allowed a 68-fold increase in protein yield. NucB protein has been purified to high degree purity with specific nuclease activity of 15000 U/mg of protein. Biophysical characterisation showed that the protein was thermally stable and could reversibly refold. Statistical optimisation of extracellular nucleases production in diverse bacteria grown at different temperatures was demonstrated as a promising methodology for enhancing key enzyme secretion. The effectiveness of biofilm disruption by NucB was successfully tested with different single species biofilms grown on polystyrene, glass, and stainless steel surfaces. Biofilm dispersal efficiency of other microbial nucleases ranged between 60 – 95 % of removal after 1 h. The results presented in this thesis demonstrate that bacteria were able to produce nucleases across broad temperature range. In context to biofilm dispersal, bioinformatic analysis speculates the ecological implication of secreted diverse microbial extracellular nuclease-like genes were to decide the fate of eDNA and play pivotal role in nutrient cycling of the eco-system. Bioprocess development confirmed process optimisation can reliably produce functional and well-folded recombinant NucB at levels suitable for applications where biofilm removal is needed. Production optimisation of extracellular nucleases from diverse bacteria expanded the availability of different nucleases with wide range of anti-biofilm properties. Evidence is also presented to show that extracellular nucleases can disperse preformed microbial biofilms on different substrata. Microbial extracellular nucleases therefore appear to be a rich and unexplored source of anti-biofilm enzymes

    Hydrodynamic aspects of airlift contactors

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    This study deals with gas void fraction, liquid circulation velocity and liquid mixing in airlift contactors. Experimental measurements of gas holdup, liquid velocity, mixing and circulation times, Bodenstein number and liquid phase axial dispersion coefficient were obtained with various Newtonian and non-Newtonian fluids using different reactor configurations. The experimental data were obtained in two distinct laboratory scale draft tube internal loop airlift devices (52 L) and an external loop airlift contactor (35 L).The effect of superficial gas velocity (low to intermediate range), liquid properties (salt concentration and liquid viscosity), two immiscible liquid phases (oil/water) and reactor geometry on the gas holdup, liquid velocity and liquid mixing in airlift vessels were examined. Gas holdup was observed to increase with increasing gas velocity, liquid phase electrolyte concentration and Newtonian and pseudoplastic non-Newtonian liquid viscosity. The effect of the two immiscible liquid phases on gas holdup was relatively complex. Initially, on addition of oil to the continuous phase (water) there was a sharp increase in gas holdup. As the concentration of oil-in-water emulsion increased the gas holdup was observed to decrease and then increase as the pure oil limit was reached. The liquid velocity and liquid phase mixing in the airlift vessel improved with increasing gas flow rate. But, with an increase in electrolyte concentration, liquid viscosity and oil-in-water emulsion concentration the superficial liquid velocity decreased. Hence, the liquid mixing was found to deteriorate with increasing salt concentration, liquid viscosity and oil-in-water emulsion concentration. For a fixed gas velocity, the local Bodenstein numbers and axial dispersion coefficients indicated that the mixing in the airlift contactor was not uniform in the different regions of the vessel. The downcomer section gave considerably higher axial dispersion coefficient values compared to the riser section for a given gas flow rate. The riser and downcomer Bo numbers indicated that the liquid flow in the riser section approached plug flow, while the flow in the downcomer section was reasonably well mixed. The liquid mixing in the reactor as a whole was somewhere in- between the mixing in the riser and downcomer sections. A hydrodynamic model was employed to estimate the riser gas holdup and liquid velocity in the airlift vessels. This model was developed using a drift flux model together with an energy balance over an airlift loop. Model predictions were compared with experimental data obtained in this study. In addition, suitable experimental data available in previous literature were used. The applicability of the model to a broad range of airlift reactor types (split-cylinder and draft tube internal loops; external loop) and scales (0.033 m3 ≤ V ≤ 1.058 m3; 1.220 m ≤ Ht ≤ 5.076 m; 0.11 ≤ Ad/Ar ≤ 1.45) and with various Newtonian and non-Newtonian liquids is demonstrated. For non-Newtonian media in airlift vessels, a correlation for average shear rate was also developed. This relationship considers the effect of gas holdup, liquid velocity and flow behaviour index on shear rate. A higher apparent liquid viscosity gave a lower average shear rate in the vessel than a lower apparent viscosity, at a given superficial gas velocity
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