X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures

The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 A resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable variation in their quaternary association, although the DNA-binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but could be related to variation in protein stability. Molecular-dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype Escherichia coli SSB and the individual subunits of both proteins. Together, the X-ray studies and molecular-dynamics simulations yield information on the relatively rigid and flexible regions of the molecule and on the effect of oligomerization on flexibility. The simulations provide insight into the changes in subunit structure on oligomerization. They also provide insight into the stability and time evolution of the hydrogen bonds/water bridges that connect the two pairs of monomers in the tetramer.

A nonhelical, multiple β-turn conformation in a glycine-rich heptapeptide fragment of trichogin A IV containing a single central α-aminoisobutyric acid residue

The conformational properties of the protected seven-residue C-terminal fragment the lipopeptaibol antibiotic Trichogin A IV (Boc-Gly-Gly-Leu-Aib-Gly-Ile-Leu-OMe) has been examined in CDCl3 and (CD3)2SO by 1H-nmr. Evidence for a multiple β-turn conformation [type I′ at Gly(1)-Gly(2), type II at Leu(3)-Aib(4), and a type I′ at Aib(4)-Gly(5)] suggests that Leu(3) has preferred an extended or semiextended conformation over a helical conformation in CDCl3. This structure is thus in contrast to earlier observations of seven-residue peptides containing a single central Aib preferring helical conformations in both solution and crystalline slates. A structural transition to a frayed right-handed helix is absented in (CD3)2SO. These results suggest that nonhelical conformations may be important in Gly-rich peptides containing Aib. Further, the presence of amino acids with contradictory influences on backbone conformational freedom can lead to well-defined conformational transitions even in small peptides

Ions in water: Role of attractive interactions in size dependent diffusivity maximum

A molecular dynamics study of model ions in water is reported. The van der Waals diameter of both the cations and anions is varied. We have carried out two sets of simulations-with and without dispersion interaction-between the ion and water. Self-diffusivity of the ions exhibits an anomalous maximum as a function of the van der Waals diameter for both these sets. This existence of a maximum in self-diffusivity when there is no dispersion interaction between the ion and the water is attributed to the attractive term from electrostatic interactions. Detailed analysis of this effect shows that the solvent shell is more strongly defined in the presence of dispersion interactions. A smaller ion exhibits biexponential decay while a single exponential decay is seen for the ion with maximum diffusivity in the self-part of the intermediate scattering function. The solvent structure around the ion appears to determine much of the dynamics of the ion. Interesting trends are seen in the activation energies and these can be understood in terms of the levitation effect. (C) 2010 American Institute of Physics. doi:10.1063/1.3481656]

The Single Langmuir Probe under Orbital-Limited Conditions in a Low-Density Collisional Plasma

The cylindrical Langmuir probe under orbital-limited conditions was used to determine the charge density in a low-density collisional plasma. The Langmuir's theory was applied to both electron and ion saturation currents in their respective accelerating regions. Present study indicates that the length of the probe significantly affects the probe characteristics. A probe of suitable length under orbital-limited conditions may be useful under the experimental conditions where the radius of the probe is much smaller than the Debye lengt.

Surface recombination at semiconductor electrodes: a single level study

The recombination and the faradaic fluxes are shown to be sensitive to the location of a single level recombination center, when it is located near the band edges. As the surface level is shifted deeper into the band gap from either of the band edges, the back emission terms are dominated by electron capture and hole capture terms, and the occupancy of the surface level is no longer determined by its location in the band gap. However, when one of the back emission terms determines the surface state occupancy, it is shown that there exists a simple relation between the value of the surface level and the recombination and the faradaic fluxes respectively. Expressions to this effect are derived and verified in the case of the recombination flux, which characterized by the potential at which it attains its maximum value. For the faradaic flux the results are qualitative.

Polarization studies in electromagnetic scattering by small Solar-system particles

In remote-sensing studies, particles that are comparable to the wavelength exhibit characteristic features in electromagnetic scattering, especially in the degree of linear polarization. These features vary with the physical properties of the particles, such as shape, size, refractive index, and orientation. In the thesis, the direct problem of computing the unknown scattered quantities using the known properties of the particles and the incident radiation is solved at both optical and radar spectral regions in a unique way. The internal electromagnetic fields of wavelength-scale particles are analyzed by using both novel and established methods to show how the internal fields are related to the scattered fields in the far zone. This is achieved by using the tools and methods that were developed specifically to reveal the internal field structure of particles and to study the mechanisms that relate the structure to the scattering characteristics of those particles. It is shown that, for spherical particles, the internal field is a combination of a forward propagating wave with the apparent wavelength determined by the refractive index of the particle, and a standing wave pattern with the apparent wavelength the same as for the incident wave. Due to the surface curvature and dielectric nature of the particle, the incident wave front undergoes a phase shift, and the resulting internal wave is focused mostly at the forward part of the particle similar to an optical lens. This focusing is also seen for irregular particles. It is concluded that, for both spherical and nonspherical particles, the interference at the far field between the partial waves that originate from these concentrated areas in the particle interior, is responsible for the specific polarization features that are common for wavelength-scale particles, such as negative values and local extrema in the degree of linear polarization, asymmetry of the phase function, and enhancement of intensity near the backscattering direction. The papers presented in this thesis solve the direct problem for particles with both simple and irregular shapes to demonstrate that these interference mechanisms are common for all dielectric wavelength-scale particles. Furthermore, it is shown that these mechanisms can be applied to both regolith particles in the optical wavelengths and hydrometeors at microwave frequencies. An advantage from this kind of study is that it does not matter whether the observation is active (e.g., polarimetric radar) or passive (e.g., optical telescope). In both cases, the internal field is computed for two mutually perpendicular incident polarizations, so that the polarization characteristics can then be analyzed according to the relation between these fields and the scattered far field.

Interfacial Phenomena in Pharmaceutical Low Moisture Content Powder Processing

Powders are essential materials in the pharmaceutical industry, being involved in majority of all drug manufacturing. Powder flow and particle size are central particle properties addressed by means of particle engineering. The aim of the thesis was to gain knowledge on powder processing with restricted liquid addition, with a primary focus on particle coating and early granule growth. Furthermore, characterisation of this kind of processes was performed. A thin coating layer of hydroxypropyl methylcellulose was applied on individual particles of ibuprofen in a fluidised bed top-spray process. The polymeric coating improved the flow properties of the powder. The improvement was strongly related to relative humidity, which can be seen as an indicator of a change in surface hydrophilicity caused by the coating. The ibuprofen used in the present study had a d50 of 40 μm and thus belongs to the Geldart group C powders, which can be considered as challenging materials in top-spray coating processes. Ibuprofen was similarly coated using a novel ultrasound-assisted coating method. The results were in line with those obtained from powders coated in the fluidised bed process mentioned above. It was found that the ultrasound-assisted method was capable of coating single particles with a simple and robust setup. Granule growth in a fluidised bed process was inhibited by feeding the liquid in pulses. The results showed that the length of the pulsing cycles is of importance, and can be used to adjust granule growth. Moreover, pulsed liquid feed was found to be of greater significance to granule growth in high inlet air relative humidity. Liquid feed pulsing can thus be used as a tool in particle size targeting in fluidised bed processes and in compensating for changes in relative humidity of the inlet air. The nozzle function of a two-fluid external mixing pneumatic nozzle, typical for small scale pharmaceutical fluidised bed processes, was studied in situ in an ongoing fluidised bed process with particle tracking velocimetry. It was found that the liquid droplets undergo coalescence as they proceed away from the nozzle head. The coalescence was expected to increase droplet speed, which was confirmed in the study. The spray turbulence was studied, and the results showed turbulence caused by the event of atomisation and by the oppositely directed fluidising air. It was concluded that particle tracking velocimetry is a suitable tool for in situ spray characterisation. The light transmission through dense particulate systems was found to carry information on particle size and packing density as expected based on the theory of light scattering by solids. It was possible to differentiate binary blends consisting of components with differences in optical properties. Light transmission showed potential as a rapid, simple and inexpensive tool in characterisation of particulate systems giving information on changes in particle systems, which could be utilised in basic process diagnostics.

Impurity diffusion in bismuth single-crystals

Measurements of impurity diffusion of 86Rb, 90Sr, 133Ba, and 137Cs in single crystal Bi were carried out. Diffusion samples were prepared from single crystal Bi by ion implantation. About 1012-1013 ions were implanted, resulting in surface activities approx =104 cpm. After implantation, specimens were annealed for specified times at 220-265 deg C, and tracer penetration profiles were determined by an electrolytic method. A typical penetration profile for 137Cs in Bi showed a linear relationship for log C vs x in with Fick's law for volume diffusion. Laws of grain boundary diffusion were not obeyed and the order of magnitude of the penetration distances was much less than on a grain boundary mechanism. Results were interpreted in terms of a modified Fischer analysis using a kinetic trapping term. Effective half lengths for trapping at a twin boundary were determined for each impurity.

A Resonant Integrator Based PLL and AC Current Controller for Single Phase Grid Connected PWM-VSI

Grid connected PWM-VSIs are being increasingly used for applications such as Distributed Generation (DG), power quality, UPS etc. Appropriate control strategies for grid synchronisation and line current regulation are required to establish such a grid interconnection and power transfer. Control of three phase VSIs is widely reported in iterature. Conventionally, dq control in Synchronous Reference Frame(SRF) is employed for both PLL and line current control where PI-controllers are used to track the DC references. Single phase systems do not have defined direct (d) and quadrature (q) axis components that are required for SRF transformation. Thus, references are AC in nature and hence usage of PI controllers cannot yield zero steady state errors. Resonant controllers have the ability to track AC references accurately. In this work, a resonant controller based single phase PLL and current control technique are being employed for tracking grid frequency and the AC current reference respectively. A single phase full bridge converter is being operated as a STATCOM for performance evaluation of the control scheme.

A homotopy approach for stabilizing single-input systems with control structure constraints

A linear state feedback gain vector used in the control of a single input dynamical system may be constrained because of the way feedback is realized. Some examples of feedback realizations which impose constraints on the gain vector are: static output feedback, constant gain feedback for several operating points of a system, and two-controller feedback. We consider a general class of problems of stabilization of single input dynamical systems with such structural constraints and give a numerical method to solve them. Each of these problems is cast into a problem of solving a system of equalities and inequalities. In this formulation, the coefficients of the quadratic and linear factors of the closed-loop characteristic polynomial are the variables. To solve the system of equalities and inequalities, a continuous realization of the gradient projection method and a barrier method are used under the homotopy framework. Our method is illustrated with an example for each class of control structure constraint.

Local texture and microstructure in cube-oriented nickel single crystal deformed by equal channel angular extrusion

Local texture and microstructure was investigated to study the deformation mechanisms during equal channel angular extrusion of a high purity nickel single crystal of initial cube orientation. A detailed texture and microstructure analysis by various diffraction techniques revealed the complexity of the deformation patterns in different locations of the billet. A modeling approach, taking into account slip system activity, was used to interpret the development of this heterogeneous deformation.

Theory of the effects of destruction of localization by inelastic scattering in the resistivity of pure thin potassium wires

Measurements of the electrical resistivity of thin potassium wires at temperatures near 1 K have revealed a minimum in the resistivity as a function of temperature. By proposing that the electrons in these wires have undergone localization, albeit with large localization length, and that inelastic-scattering events destroy the coherence of that state, we can explain both the magnitude and shape of the temperature-dependent resistivity data. Localization of electrons in these wires is to be expected because, due to the high purity of the potassium, the elastic mean free path is comparable to the diameters of the thinnest samples, making the Thouless length lT (or inelastic diffusion length) much larger than the diameter, so that the wire is effectively one dimensional. The inelastic events effectively break the wire into a series of localized segments, whose resistances can be added to obtain the total resistance of the wire. The ensemble-averaged resistance for all possible segmented wires, weighted with a Poisson distribution of inelastic-scattering lengths along the wire, yields a length dependence for the resistance that is proportional to [L3/lin(T)], provided that lin(T)?L, where L is the sample length and lin(T) is some effective temperature-dependent one-dimensional inelastic-scattering length. A more sophisticated approach using a Poisson distribution in inelastic-scattering times, which takes into account the diffusive motion of the electrons along the wire through the Thouless length, yields a length- and temperature-dependent resistivity proportional to (L/lT)4 under appropriate conditions. Inelastic-scattering lifetimes are inferred from the temperature-dependent bulk resistivities (i.e., those of thicker, effectively three-dimensional samples), assuming that a minimum amount of energy must be exchanged for a collision to be effective in destroying the phase coherence of the localized state. If the dominant inelastic mechanism is electron-electron scattering, then our result, given the appropriate choice of the channel number parameter, is consistent with the data. If electron-phason scattering were of comparable importance, then our results would remain consistent. However, the inelastic-scattering lifetime inferred from bulk resistivity data is too short. This is because the electron-phason mechanism dominates in the inelastic-scattering rate, although the two mechanisms may be of comparable importance for the bulk resistivity. Possible reasons why the electron-phason mechanism might be less effective in thin wires than in bulk are discussed.