The automation of protein crystal presentation for X ray diffraction experiments using standing acoustic waves in a microfluidic chip environment

As the pressure continues to grow on Diamond and the world's synchrotrons for higher throughput of diffraction experiments, new and novel techniques are required for presenting micron dimension crystals to the X ray beam. Currently this task is both labour intensive and primarily a serial process. Diffraction measurements typically take milliseconds but sample preparation and presentation can reduce throughput down to 4 measurements an hour. With beamline waiting times as long as two years it is of key importance for researchers to capitalize on available beam time, generating as much data as possible. Other approaches detailed in the literature [1] [2] [3] are very much skewed towards automating, with robotics, the actions of a human protocols. The work detailed here is the development and discussion of a bottom up approach relying on SSAW self assembly, including material selection, microfluidic integration and tuning of the acoustic cavity to order the protein crystals.

Efficient Computation of Electromagnetic Waves in Hydrocarbon Exploration Using the Improved Numerical Mode Matching (NMM) Method

In this study, we developed and improved the numerical mode matching (NMM) method which has previously been shown to be a fast and robust semi-analytical solver to investigate the propagation of electromagnetic (EM) waves in an isotropic layered medium. The applicable models, such as cylindrical waveguide, optical fiber, and borehole with earth geological formation, are generally modeled as an axisymmetric structure which is an orthogonal-plano-cylindrically layered (OPCL) medium consisting of materials stratified planarly and layered concentrically in the orthogonal directions.

In this report, several important improvements have been made to extend applications of this efficient solver to the anisotropic OCPL medium. The formulas for anisotropic media with three different diagonal elements in the cylindrical coordinate system are deduced to expand its application to more general materials. The perfectly matched layer (PML) is incorporated along the radial direction as an absorbing boundary condition (ABC) to make the NMM method more accurate and efficient for wave diffusion problems in unbounded media and applicable to scattering problems with lossless media. We manipulate the weak form of Maxwell's equations and impose the correct boundary conditions at the cylindrical axis to solve the singularity problem which is ignored by all previous researchers. The spectral element method (SEM) is introduced to more efficiently compute the eigenmodes of higher accuracy with less unknowns, achieving a faster mode matching procedure between different horizontal layers. We also prove the relationship of the field between opposite mode indices for different types of excitations, which can reduce the computational time by half. The formulas for computing EM fields excited by an electric or magnetic dipole located at any position with an arbitrary orientation are deduced. And the excitation are generalized to line and surface current sources which can extend the application of NMM to the simulations of controlled source electromagnetic techniques. Numerical simulations have demonstrated the efficiency and accuracy of this method.

Finally, the improved numerical mode matching (NMM) method is introduced to efficiently compute the electromagnetic response of the induction tool from orthogonal transverse hydraulic fractures in open or cased boreholes in hydrocarbon exploration. The hydraulic fracture is modeled as a slim circular disk which is symmetric with respect to the borehole axis and filled with electrically conductive or magnetic proppant. The NMM solver is first validated by comparing the normalized secondary field with experimental measurements and a commercial software. Then we analyze quantitatively the induction response sensitivity of the fracture with different parameters, such as length, conductivity and permeability of the filled proppant, to evaluate the effectiveness of the induction logging tool for fracture detection and mapping. Casings with different thicknesses, conductivities and permeabilities are modeled together with the fractures in boreholes to investigate their effects for fracture detection. It reveals that the normalized secondary field will not be weakened at low frequencies, ensuring the induction tool is still applicable for fracture detection, though the attenuation of electromagnetic field through the casing is significant. A hybrid approach combining the NMM method and BCGS-FFT solver based integral equation has been proposed to efficiently simulate the open or cased borehole with tilted fractures which is a non-axisymmetric model.

The microphysics of collisionless shock waves

Collisionless shocks, that is shocks mediated by electromagnetic processes, are customary in space physics and in astrophysics. They are to be found in a great variety of objects and environments: magnetospheric and heliospheric shocks, supernova remnants, pulsar winds and their nebulæ, active galactic nuclei, gamma-ray bursts and clusters of galaxies shock waves. Collisionless shock microphysics enters at different stages of shock formation, shock dynamics and particle energization and/or acceleration. It turns out that the shock phenomenon is a multi-scale non-linear problem in time and space. It is complexified by the impact due to high-energy cosmic rays in astrophysical environments. This review adresses the physics of shock formation, shock dynamics and particle acceleration based on a close examination of available multi-wavelength or in situ observations, analytical and numerical developments. A particular emphasis is made on the different instabilities triggered during the shock formation and in association with particle acceleration processes with regards to the properties of the background upstream medium. It appears that among the most important parameters the background magnetic field through the magnetization and its obliquity is the dominant one. The shock velocity that can reach relativistic speeds has also a strong impact over the development of the micro-instabilities and the fate of particle acceleration. Recent developments of laboratory shock experiments has started to bring some new insights in the physics of space plasma and astrophysical shock waves. A special section is dedicated to new laser plasma experiments probing shock physics.

Breaking Waves on the Ocean Surface

Thesis (Ph.D.)--University of Washington, 2016-08

On the sound waves propagation in the Persian Gulf

In this research I focused on the propagation of acoustic rays in shallow water areas then I selected the Persian Gulf and described sound transmission in this region with emphasize on physical properties of water masses and of sediments. Finally I studied on the sound speed variations and sound attention with data collected from this area (NE of Farsi Island & 50 kilometers south of Delware). Sound speed deviation in western part of Strait of Hormuz in winter is between 20-30 m/s and it is between 5-20 m/s in the Oman Sea. Minimum sound speed deviation is at 23-24 degree north & 60-62 degree east. In spring, this deviation varies from 25-35 m/s, which is greater than in winter. In winter, at east of 56 degree east, greater speed are in shallow water coastal areas. In summer, sound speeds are greater than in spring and vary from 35 to 55 m/s at western part of Strait of Hormuz and 20 to 40 m/s in Oman Sea. Finally in autumn, sound speed deviation is 30-45 m/s west of 56 degree east and in Oman Sea is the same. The greatest attenuation rate caused by absorption in Bandar Dayer is between 17 to 27 meters depth, which is from water masses with different densities.

The effects of permeable bed on waves setup

Generally the flow properties of rivers, estuaries and coastal seas are highly dependent on the bed morphology. These include mainly three flow parameters, as bed shear stress, velocity profile and turbulent fluctuations. Here we investigate the effects of permeate of the bed on these flow properties We consider the effects of suction (W0) injection (W0) on these flow properties particularly the bottom stress. Four types of bottom permeability with different size of sand have been tested. The results indicate a substantial reduction and enhancement of the bed stress under respectively injection and suction as has been observed by others on wave motion in shallow seas. We consider 5 waves to shore with this rang of wave steepness ( 0/015 < so < 0/05 ) . Cr Calculated used of mansard method (1980). We search the stream line of current in bed with a video camera and looking this. Near the surface and the deep of bed and consider V=W (in or su)/ U(ru or rd) and bottom stress for 6 period of this study with Canly and Inman studies (1994). All these results are shown by curves with the effects of permeable bed.

Interaction between wind waves and swell in the Persian Gulf

The effect of swell on wind wave growth has been a topic of active research for many years with inconsistent results. The details are often contradictory among investigations. Further more, there remain a variety of competing theories to explain these phenomena. In this research, we consider waves and wind and temperature data in the Persian Gulf (Busher region) in years 1995, 1996 and 1999. This study provides estimations of wave conditions and the atmosphere stability that has an influence on wind wave. Results are also compared with data that have been recorded by a buoy in Caspian Sea (Neka region) during 1989. In the second part of this work we estimate non- dimensional energy and non-dimensional peak frequencies as a function of the non- dimensional fetch and Bulk Richardson numbers for the Persian Gulf (Busher region).This results also agree well with similar results for the Caspian Sea. The acquired relations can be used to compute the wind wave parameters. Also the results for the Persian Gulf show that the relationship of non-dimensional energy to as a function of wave age is independent of presence of swell. Finally the WAM model was run for the Persian Gulf during 3-8 September of 2002. The results show that swell on the Persian Gulf reduces the energy density of wind waves by up to 10%, but the growth rate at peak frequency is only reduced by up to 4%, and the spectral peak frequency is increased by only 1%.

Wind Waves in the Arctic Seas: Envisat and AltiKa Data Analysis

Wind-generated waves in the Kara, Laptev, and East-Siberian Seas are investigated using altimeter data from Envisat RA-2 and SARAL-AltiKa. Only isolated ice-free zones had been selected for analysis. Wind seas can be treated as pure wind-generated waves without any contamination by ambient swell. Such zones were identified using ice concentration data from microwave radiometers. Altimeter data, both significant wave height (SWH) and wind speed, for these areas were further obtained for the period 2002-2012 using Envisat RA-2 measurements, and for 2013 using SARAL-AltiKa. Dependencies of dimensionless SWH and wavelength on dimensionless wave generation spatial scale are compared to known empirical dependencies for fetch-limited wind wave development. We further check sensitivity of Ka- and Ku-band and discuss new possibilities that AltiKa's higher resolution can open.

The transport of nitric oxide in the upper atmosphere by planetary waves and the zonal mean circulation

U of I Only

Ocean bottom pressure records from the Cascadia array and short surface gravity waves

The ocean bottom pressure records from eight stations of the Cascadia array are used to investigate the properties of short surface gravity waves with frequencies ranging from 0.2 to 5 Hz. It is found that the pressure spectrum at all sites is a well-defined function of the wind speed U10 and frequency f, with only a minor shift of a few dB from one site to another that can be attributed to variations in bottom properties. This observation can be combined with the theoretical prediction that the ocean bottom pressure spectrum is proportional to the surface gravity wave spectrum E(f) squared, times the overlap integral I(f) which is given by the directional wave spectrum at each frequency. This combination, using E(f) estimated from modeled spectra or parametric spectra, yields an overlap integral I(f) that is a function of the local wave age inline image. This function is maximum for f∕fPM = 8 and decreases by 10 dB for f∕fPM = 2 and f∕fPM = 30. This shape of I(f) can be interpreted as a maximum width of the directional wave spectrum at f∕fPM = 8, possibly equivalent to an isotropic directional spectrum, and a narrower directional distribution toward both the dominant low frequencies and the higher capillary-gravity wave frequencies.

Ocean waves across the Arctic: attenuation due to dissipation dominates over scattering for periods longer than 19 s

The poorly understood attenuation of surface waves in sea ice is generally attributed to the combination of scattering and dissipation. Scattering and dissipation have very different effects on the directional and temporal distribution of wave energy, making it possible to better understand their relative importance by analysis of swell directional spreading and arrival times. Here we compare results of a spectral wave model – using adjustable scattering and dissipation attenuation formulations – with wave measurements far inside the ice pack. In this case, scattering plays a negligible role in the attenuation of long swells. Specifically, scattering-dominated attenuation would produce directional wave spectra much broader than the ones recorded, and swell events arriving later and lasting much longer than observed. Details of the dissipation process remain uncertain. Average dissipation rates are consistent with creep effects but are 12 times those expected for a laminar boundary layer under a smooth solid ice plate.

The impact of tides and waves on near-surface suspended sediment concentrations in the English Channel

Numerous ecological problems of continental shelf ecosystems require a refined knowledge of the evolution of suspended sediment concentrations (SSC). The present investigation focuses on the spatial and temporal variabilities of near-surface SSC in coastal waters of the English Channel (western Europe) by exploiting numerical predictions from the Regional Ocean Modeling System ROMS. Extending previous investigations of ROMS performances in the Channel, this analysis refines, with increased spatial and temporal resolutions, the characterization of near-surface SSC patterns revealing areas where concentrations are highly correlated with evolutions of tides and waves. Significant tidal modulations of near-surface concentrations are thus found in the eastern English Channel and the French Dover Strait while a pronounced influence of waves is exhibited in the Channel Islands Gulf. Coastal waters present furthermore strong SSC temporal variations, particularly noticeable during storm events of autumn and winter, with maximum near-surface concentrations exceeding 40 mg l−1 and increase by a factor from 10 to 18 in comparison with time-averaged concentrations. This temporal variability strongly depends on the granulometric distribution of suspended sediments characterized by local bi-modal contributions of silts and sands off coastal irregularities of the Isle of Wight, the Cotentin Peninsula and the southern Dover Strait.

Accelerating wide-angle converging waves in the near field

We show that a wide-angle converging wave may be transformed into a shape-preserving accelerating beam having a beam-width near the diffraction limit. For that purpose, we followed a strategy that is particularly conceived for the acceleration of nonparaxial laser beams, in contrast to the well-known method by Siviloglou et al (2007 Phys. Rev. Lett. 99 213901). The concept of optical near-field shaping is applied to the design of non-flat ultra-narrow diffractive optical elements. The engineered curvilinear caustic can be set up by the beam emerging from a dynamic assembly of elementary gratings, the latter enabling to modify the effective refractive index of the metamaterial as it is arranged in controlled orientations. This light shaping process, besides being of theoretical interest, is expected to open up a wide range of broadband application possibilities.

Gravimetric and density profiling using the combination of surface acoustic waves and neutron reflectivity

A new approach is described herein, where neutron reflectivity measurements that probe changes in the density profile of thin films as they absorb material from the gas phase have been combined with a Love wave based gravimetric assay that measures the mass of absorbed material. This combination of techniques not only determines the spatial distribution of absorbed molecules, but also reveals the amount of void space within the thin film (a quantity that can be difficult to assess using neutron reflectivity measurements alone). The uptake of organic solvent vapours into spun cast films of polystyrene has been used as a model system with a view to this method having the potential for extension to the study of other systems. These could include, for example, humidity sensors, hydrogel swelling, biomolecule adsorption or transformations of electroactive and chemically reactive thin films. This is the first ever demonstration of combined neutron reflectivity and Love wave-based gravimetry and the experimental caveats, limitations and scope of the method are explored and discussed in detail.

Resonant metamaterials for the control of Rayleigh waves

Since their emergence, locally resonant metamaterials have found several applications for the control of surface waves, from micrometer-sized electronic devices to meter-sized seismic barriers. The interaction between Rayleigh-type surface waves and resonant metamaterials has been investigated through the realization of locally resonant metasurfaces, thin elastic interfaces constituted by a cluster of resonant inclusions or oscillators embedded near the surface of an elastic waveguide. When such resonant metasurfaces are embedded in an elastic homogeneous half-space, they can filter out the propagation of Rayleigh waves, creating low-frequency bandgaps at selected frequencies. In the civil engineering context, heavy resonating masses are needed to extend the bandgap frequency width of locally resonant devices, a requirement that limits their practical implementations. In this dissertation, the wave attenuation capabilities of locally resonant metasurfaces have been enriched by proposing (i) tunable metasurfaces to open large frequency bandgaps with small effective inertia, and by developing (ii) an analytical framework aimed at studying the propagation of Rayleigh waves propagation in deep resonant waveguides. In more detail, inertial amplified resonators are exploited to design advanced metasurfaces with a prescribed static and a tunable dynamic response. The modular design of the tunable metasurfaces allows to shift and enlarge low-frequency spectral bandgaps without modifying the total inertia of the metasurface. Besides, an original dispersion law is derived to study the dispersive properties of Rayleigh waves propagating in thick resonant layers made of sub-wavelength resonators. Accordingly, a deep resonant wave barrier of mechanical resonators embedded inside the soil is designed to impede the propagation of seismic surface waves. Numerical models are developed to confirm the analytical dispersion predictions of the tunable metasurface and resonant layer. Finally, a medium-size scale resonant wave barrier is designed according to the soil stratigraphy of a real geophysical scenario to attenuate ground-borne vibration.