Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.

The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not contacted by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through multiple X-ray structures and binding properties of Fis-DNA complexes containing base analogs that the 2-amino group on guanine is the primary molecular determinant controlling minor groove widths. Molecular dynamics simulations of free-DNA targets with canonical and modified bases further demonstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the presence of purine 2-amino groups. We also provide evidence that protein-mediated phosphate neutralization facilitates minor groove compression and is particularly important for binding to non-optimally shaped DNA duplexes

Method of fabricating a twisted composite superconductor

A method of producing a twisted, stabilized wire or tube superconductor which can be used to wind electromagnets, armatures, rotors, field windings for motors and generators, and other magnetic devices which use a solenoid, toroidal, or other type winding is reported. At least one groove is formed along the length of a wire substrate which is then twisted into a helix and a layer of intermetallic superconducting material is formed in the groove. This layer can be formed by depositing the desired intermetallic compound into the groove or by diffusing one component of the superconductor into the groove formed in a substrate composed of the other component. The superconductor prepared by this method comprises a non-superconductor wire twisted into the shape of a helix, having at least one groove containing a layer of superconductor material along the length of the wire

Modelling and Analysis Using GROOVE

In this paper we present case studies that describe how the graph transformation tool GROOVE has been used to model problems from a wide variety of domains. These case studies highlight the wide applicability of GROOVE in particular, and of graph transformation in general. They also give concrete templates for using GROOVE in practice. Furthermore, we use the case studies to analyse the main strong and weak points of GROOVE

Anisotropic Wetting Property of Superhydrophobic Surfaces and Electrokinetic Flow on Liquid-Filled Surfaces

Understanding the wetting property of rough surface is critical in guiding droplets and novel superhydrophobic surface design. The Cassie-Baxter model and Wenzel model are always used to describe the totally non-wetting and completely wetting states, however, there were few discussions about the intermediate state. Through measuring the contact angles of groove patterned surfaces in different groove orientations, the anisotropic wetting properties of groove patterned superhydrophobic surface were investigated. The degree of water penetration into the grooves was experimentally observed and it was found that the degree of water penetration was different with groove orientations, which would affect the corresponding contact angle. Besides guiding droplets, superhydrophobic surfaces are also very important in microfluidic due to their ability to generate fluid slip and flow enhancement. After a deeper understanding of the wetting property of groove patterned superhydrophobic surface, I further investigated its important role in microfluidics. In this dissertation, I mainly focus on electrokinetics on groove patterned surface and liquid-filled slippery surfaces, a new kind of surface by filling low surface tension oil into the interstices of groove patterned surfaces. I experimentally measured the streaming potential on flat parylene surface, air-filled groove patterned surface and liquid-filled surfaces and compared their effects in streaming potential enhancement. The liquid-filled surfaces were shown to be able to enhance the generated streaming potential due to its slippery property and liquid-oil interface charges. As the electrokinetic on liquid-filled surfaces is a new phenomenon, the underlying physics is still not clear. I further investigated the influences of filled oil properties and groove orientation on streaming potentials and fluid slip. Oils with different densities, viscosities, dielectric constant, conductivities and surface tensions were filled into the interstices of groove patterned surfaces to make different types of liquid-filled surfaces. The streaming potentials on liquid-filled surfaces with different oils were experimentally measured. An empirical relationship between streaming potential and oil properties was found and the effects of electrical properties, such as interface charge density and dielectric constant of filled oil, on fluid slip were also studied. Finally, the groove orientation was varied to study the tensorial effects on streaming potential. Through both streaming potential measurement and theoretical analysis, it was found that the streaming potential at 45° was always smaller than the arithmetic mean of those at 0° and 90°, and the pressure gradient in the transvers direction generated by tensorial effects was important in the streaming potential modification. My work will be important in guiding droplets, flow patterning, lab-on-chip devices and the development of electrokientic based power sources

Spiral groove seal

Mating flat surfaces inhibit leakage of a fluid around a stationary shaft. A spiral groove produces a pumping action toward the fluid when the shaft rotates. This prevents leakage while a generated hydraulic lifting force separates the mating surfaces to minimize wear. Provision is made for placing these spiral grooves in communication with the fluid to accelerate the generation of the hydraulic lifting force

Continuous self-locking spiral wound seal

A spiral wound seal for effecting a seal between two surfaces is described. The seal consists of a strip of gasket material wound into a groove machined into one of the surfaces. The gasket strip is wider than the groove is deep so that a portion of the gasket material protrudes from the groove. The seal is effected by clamping the second surface onto the first surface and compressing the protruding gasket material

Transient behavior of surface plasmon polaritons scattered at a subwavelength groove

We present a numerical study and analytical model of the optical near-field diffracted in the vicinity of subwavelength grooves milled in silver surfaces. The Green's tensor approach permits computation of the phase and amplitude dependence of the diffracted wave as a function of the groove geometry. It is shown that the field diffracted along the interface by the groove is equivalent to replacing the groove by an oscillating dipolar line source. An analytic expression is derived from the Green's function formalism, that reproduces well the asymptotic surface plasmon polariton (SPP) wave as well as the transient surface wave in the near-zone close to the groove. The agreement between this model and the full simulation is very good, showing that the transient "near-zone" regime does not depend on the precise shape of the groove. Finally, it is shown that a composite diffractive evanescent wave model that includes the asymptotic SPP can describe the wavelength evolution in this transient near-zone. Such a semi-analytical model may be useful for the design and optimization of more elaborate photonic circuits whose behavior in large part will be controlled by surface waves.Comment: 12 pages, 10 figure

Adsorption of mono- and multivalent cat- and anions on DNA molecules

Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modelled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands, in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major groove cationic charge is independent on the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salt. Simulations for a larger ion radii, which mimic the effect of the ion hydration, indicate an increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure