Deep tissue fluorescence imaging with time-reversed light

Advances in optical techniques have enabled many breakthroughs in biology and medicine. However, light scattering by biological tissues remains a great obstacle, restricting the use of optical methods to thin ex vivo sections or superficial layers in vivo. In this thesis, we present two related methods that overcome the optical depth limit—digital time reversal of ultrasound encoded light (digital TRUE) and time reversal of variance-encoded light (TROVE). These two techniques share the same principle of using acousto-optic beacons for time reversal optical focusing within highly scattering media, like biological tissues. Ultrasound, unlike light, is not significantly scattered in soft biological tissues, allowing for ultrasound focusing. In addition, a fraction of the scattered optical wavefront that passes through the ultrasound focus gets frequency-shifted via the acousto-optic effect, essentially creating a virtual source of frequency-shifted light within the tissue. The scattered ultrasound-tagged wavefront can be selectively measured outside the tissue and time-reversed to converge at the location of the ultrasound focus, enabling optical focusing within deep tissues. In digital TRUE, we time reverse ultrasound-tagged light with an optoelectronic time reversal device (the digital optical phase conjugate mirror, DOPC). The use of the DOPC enables high optical gain, allowing for high intensity optical focusing and focal fluorescence imaging in thick tissues at a lateral resolution of 36 µm by 52 µm. The resolution of the TRUE approach is fundamentally limited to that of the wavelength of ultrasound. The ultrasound focus (~ tens of microns wide) usually contains hundreds to thousands of optical modes, such that the scattered wavefront measured is a linear combination of the contributions of all these optical modes. In TROVE, we make use of our ability to digitally record, analyze and manipulate the scattered wavefront to demix the contributions of these spatial modes using variance encoding. In essence, we encode each spatial mode inside the scattering sample with a unique variance, allowing us to computationally derive the time reversal wavefront that corresponds to a single optical mode. In doing so, we uncouple the system resolution from the size of the ultrasound focus, demonstrating optical focusing and imaging between highly diffusing samples at an unprecedented, speckle-scale lateral resolution of ~ 5 µm. Our methods open up the possibility of fully exploiting the prowess and versatility of biomedical optics in deep tissues.

Geological evolution of two crustal scale shear zones. Part I. The Rand thrust complex, northwestern Mojave Desert, California. Part II. The Magdalena metamorphic core complex, north central Sonora, Mexico

The geology and structure of two crustal scale shear zones were studied to understand the partitioning of strain within intracontinental orogenic belts. Movement histories and regional tectonic implications are deduced from observational data. The two widely separated study areas bear the imprint of intense Late Mesozoic through Middle Cenozoic tectonic activity. A regional transition from Late Cretaceous-Early Tertiary plutonism, metamorphism, and shortening strain to Middle Tertiary extension and magmatism is preserved in each area, with contrasting environments and mechanisms. Compressional phases of this tectonic history are better displayed in the Rand Mountains, whereas younger extensional structures dominate rock fabrics in the Magdalena area.

In the northwestern Mojave desert, the Rand Thrust Complex reveals a stack of four distinctive tectonic plates offset along the Garlock Fault. The lowermost plate, Rand Schist, is composed of greenschist facies metagraywacke, metachert, and metabasalt. Rand Schist is structurally overlain by Johannesburg Gneiss (= garnet-amphibolite grade orthogneisses, marbles and quartzites), which in turn is overlain by a Late Cretaceous hornblende-biotite granodiorite. Biotite granite forms the fourth and highest plate. Initial assembly of the tectonic stack involved a Late Cretaceous? south or southwest vergent overthrusting event in which Johannesburg Gneiss was imbricated and attenuated between Rand Schist and hornblende-biotite granodiorite. Thrusting postdated metamorphism and deformation of the lower two plates in separate environments. A post-kinematic stock, the Late Cretaceous Randsburg Granodiorite, intrudes deep levels of the complex and contains xenoliths of both Rand Schist and mylonitized Johannesburg? gneiss. Minimum shortening implied by the map patterns is 20 kilometers.

Some low angle faults of the Rand Thrust Complex formed or were reactivated between Late Cretaceous and Early Miocene time. South-southwest directed mylonites derived from Johannesburg Gneiss are commonly overprinted by less penetrative north-northeast vergent structures. Available kinematic information at shallower structural levels indicates that late disturbance(s) culminated in northward transport of the uppermost plate. Persistence of brittle fabrics along certain structural horizons suggests a possible association of late movement(s) with regionally known detachment faults. The four plates were juxtaposed and significant intraplate movements had ceased prior to Early Miocene emplacement of rhyolite porphyry dikes.

In the Magdalena region of north central Sonora, components of a pre-Middle Cretaceous stratigraphy are used as strain markers in tracking the evolution of a long lived orogenic belt. Important elements of the tectonic history include: (1) Compression during the Late Cretaceous and Early Tertiary, accompanied by plutonism, metamorphism, and ductile strain at depth, and thrust driven? syntectonic sedimentation at the surface. (2) Middle Tertiary transition to crustal extension, initially recorded by intrusion of leucogranites, inflation of the previously shortened middle and upper crustal section, and surface volcanism. (3) Gravity induced development of a normal sense ductile shear zone at mid crustal levels, with eventual detachment and southwestward displacement of the upper crustal stratigraphy by Early Miocene time.

Elucidation of the metamorphic core complex evolution just described was facilitated by fortuitous preservation of a unique assemblage of rocks and structures. The "type" stratigraphy utilized for regional correlation and strain analysis includes a Jurassic volcanic arc assemblage overlain by an Upper Jurassic-Lower Cretaceous quartz pebble conglomerate, in turn overlain by marine strata with fossiliferous Aptian-Albian limestones. The Jurassic strata, comprised of (a) rhyolite porphyries interstratified with quartz arenites, (b) rhyolite cobble conglomerate, and (c) intrusive granite porphyries, are known to rest on Precambrian basement north and east of the study area. The quartz pebble conglomerate is correlated with the Glance Conglomerate of southeastern Arizona and northeastern Sonora. The marine sequence represents part of an isolated arm? of the Bisbee Basin.

Crosscutting structural relationships between the pre-Middle Cretaceous supracrustal section, younger plutons, and deformational fabrics allow the tectonic sequence to be determined. Earliest phases of a Late Cretaceous-Early Tertiary orogeny are marked by emplacement of the 78 ± 3 Ma Guacomea Granodiorite (U/Pb zircon, Anderson et al., 1980) as a sill into deep levels of the layered Jurassic series. Subsequent regional metamorphism and ductile strain is recorded by a penetrative schistosity and lineation, and east-west trending folds. These fabrics are intruded by post-kinematic Early Tertiary? two mica granites. At shallower crustal levels, the orogeny is represented by north directed thrust faulting, formation of a large intermontane basin, and development of a pronounced unconformity. A second important phase of ductile strain followed Middle Tertiary? emplacement of leucogranites as sills and northwest trending dikes into intermediate levels of the deformed section (surficial volcanism was also active during this transitional period to regional extension). Gravitational instabilities resulting from crustal swelling via intrusion and thermal expansion led to development of a ductile shear zone within the stratigraphic horizon occupied by a laterally extensive leucogranite sill. With continued extension, upper crustal brittle normal faults (detachment faults) enhanced the uplift and tectonic denudation of this mylonite zone, ultimately resulting in southwestward displacement of the upper crustal stratigraphy.

Strains associated with the two ductile deformation events have been successfully partitioned through a multifaceted analysis. R_f/Ø measurements on various markers from the "type" stratigraphy allow a gradient representing cumulative strain since Middle Cretaceous time to be determined. From this gradient, noncoaxial strains accrued since emplacement of the leucogranites may be removed. Irrotational components of the postleucogranite strain are measured from quartz grain shapes in deformed granites; rotational components (shear strains) are determined from S-C fabrics and from restoration of rotated dike and vein networks. Structural observations and strain data are compatable with a deformation path of: (1) coaxial strain (pure shear?), followed by (2) injection of leucogranites as dikes (perpendicular to the minimum principle stress) and sills (parallel to the minimum principle stress), then (3) southwest directed simple shear. Modeling the late strain gradient as a simple shear zone permits a minimum displacement of 10 kilometers on the Magdalena mylonite zone/detachment fault system. Removal of the Middle Tertiary noncoaxial strains yields a residual (or pre-existing) strain gradient representative of the Late Cretaceous-Early Tertiary deformation. Several partially destrained cross sections, restored to the time of leucogranite emplacement, illustrate the idea that the upper plate of the core complex bas been detached from a region of significant topographic relief. 50% to 100% bulk extension across a 50 kilometer wide corridor is demonstrated.

Late Cenozoic tectonics of the Magdalena region are dominated by Basin and Range style faulting. Northeast and north-northwest trending high angle normal faults have interacted to extend the crust in an east-west direction. Net extension for this period is minor (10% to 15%) in comparison to the Middle Tertiary detachment related extensional episode.

The Equation of State and Petrogenesis of Komatiite

(1) Equation of State of Komatiite

The equation of state (EOS) of a molten komatiite (27 wt% MgO) was detennined in the 5 to 36 GPa pressure range via shock wave compression from 1550°C and 0 bar. Shock wave velocity, U_S, and particle velocity, U_P, in km/s follow the linear relationship U_S = 3.13(±0.03) + 1.47(±0.03) U_P. Based on a calculated density at 1550°C, 0 bar of 2.745±0.005 glee, this U_S-U_P relationship gives the isentropic bulk modulus K_S = 27.0 ± 0.6 GPa, and its first and second isentropic pressure derivatives, K'_S = 4.9 ± 0.1 and K"_S = -0.109 ± 0.003 GPa^-1.

The calculated liquidus compression curve agrees within error with the static compression results of Agee and Walker [1988a] to 6 GPa. We detennine that olivine (FO₉₄) will be neutrally buoyant in komatiitic melt of the composition we studied near 8.2 GPa. Clinopyroxene would also be neutrally buoyant near this pressure. Liquidus garnet-majorite may be less dense than this komatiitic liquid in the 20-24 GPa interval, however pyropic-garnet and perovskite phases are denser than this komatiitic liquid in their respective liquidus pressure intervals to 36 GPa. Liquidus perovskite may be neutrally buoyant near 70 GPa.

At 40 GPa, the density of shock-compressed molten komatiite would be approximately equal to the calculated density of an equivalent mixture of dense solid oxide components. This observation supports the model of Rigden et al. [1989] for compressibilities of liquid oxide components. Using their theoretical EOS for liquid forsterite and fayalite, we calculate the densities of a spectrum of melts from basaltic through peridotitic that are related to the experimentally studied komatiitic liquid by addition or subtraction of olivine. At low pressure, olivine fractionation lowers the density of basic magmas, but above 14 GPa this trend is reversed. All of these basic to ultrabasic liquids are predicted to have similar densities at 14 GPa, and this density is approximately equal to the bulk (PREM) mantle. This suggests that melts derived from a peridotitic mantle may be inhibited from ascending from depths greater than 400 km.

The EOS of ultrabasic magmas was used to model adiabatic melting in a peridotitic mantle. If komatiites are formed by >15% partial melting of a peridotitic mantle, then komatiites generated by adiabatic melting come from source regions in the lower transition zone (≈500-670 km) or the lower mantle (>670 km). The great depth of incipient melting implied by this model, and the melt density constraint mentioned above, suggest that komatiitic volcanism may be gravitationally hindered. Although komatiitic magmas are thought to separate from their coexisting crystals at a temperature =200°C greater than that for modern MORBs, their ultimate sources are predicted to be diapirs that, if adiabatically decompressed from initially solid mantle, were more than 700°C hotter than the sources of MORBs and derived from great depth.

We considered the evolution of an initially molten mantle, i.e., a magma ocean. Our model considers the thermal structure of the magma ocean, density constraints on crystal segregation, and approximate phase relationships for a nominally chondritic mantle. Crystallization will begin at the core-mantle boundary. Perovskite buoyancy at > 70 GPa may lead to a compositionally stratified lower mantle with iron-enriched mangesiowiistite content increasing with depth. The upper mantle may be depleted in perovskite components. Olivine neutral buoyancy may lead to the formation of a dunite septum in the upper mantle, partitioning the ocean into upper and lower reservoirs, but this septum must be permeable.

(2) Viscosity Measurement with Shock Waves

We have examined in detail the analytical method for measuring shear viscosity from the decay of perturbations on a corrugated shock front The relevance of initial conditions, finite shock amplitude, bulk viscosity, and the sensitivity of the measurements to the shock boundary conditions are discussed. The validity of the viscous perturbation approach is examined by numerically solving the second-order Navier-Stokes equations. These numerical experiments indicate that shock instabilities may occur even when the Kontorovich-D'yakov stability criteria are satisfied. The experimental results for water at 15 GPa are discussed, and it is suggested that the large effective viscosity determined by this method may reflect the existence of ice VII on the Rayleigh path of the Hugoniot This interpretation reconciles the experimental results with estimates and measurements obtained by other means, and is consistent with the relationship of the Hugoniot with the phase diagram for water. Sound waves are generated at 4.8 MHz at in the water experiments at 15 GPa. The existence of anelastic absorption modes near this frequency would also lead to large effective viscosity estimates.

(3) Equation of State of Molybdenum at 1400°C

Shock compression data to 96 GPa for pure molybdenum, initially heated to 1400°C, are presented. Finite strain analysis of the data gives a bulk modulus at 1400°C, K'_S. of 244±2 GPa and its pressure derivative, K'_OS of 4. A fit of shock velocity to particle velocity gives the coefficients of U_S = C_O+S U_P to be C_O = 4.77±0.06 km/s and S = 1.43±0.05. From the zero pressure sound speed, C_O, a bulk modulus of 232±6 GPa is calculated that is consistent with extrapolation of ultrasonic elasticity measurements. The temperature derivative of the bulk modulus at zero pressure, θK_OSθT|_P, is approximately -0.012 GPa/K. A thermodynamic model is used to show that the thermodynamic Grüneisen parameter is proportional to the density and independent of temperature. The Mie-Grüneisen equation of state adequately describes the high temperature behavior of molybdenum under the present range of shock loading conditions.

Particle fluid mechanics in shear flows, acoustic waves, and shock waves

Three different categories of flow problems of a fluid containing small particles are being considered here. They are: (i) a fluid containing small, non-reacting particles (Parts I and II); (ii) a fluid containing reacting particles (Parts III and IV); and (iii) a fluid containing particles of two distinct sizes with collisions between two groups of particles (Part V).

Part I

A numerical solution is obtained for a fluid containing small particles flowing over an infinite disc rotating at a constant angular velocity. It is a boundary layer type flow, and the boundary layer thickness for the mixture is estimated. For large Reynolds number, the solution suggests the boundary layer approximation of a fluid-particle mixture by assuming W = W_p. The error introduced is consistent with the Prandtl’s boundary layer approximation. Outside the boundary layer, the flow field has to satisfy the “inviscid equation” in which the viscous stress terms are absent while the drag force between the particle cloud and the fluid is still important. Increase of particle concentration reduces the boundary layer thickness and the amount of mixture being transported outwardly is reduced. A new parameter, β = 1/Ω τ_v, is introduced which is also proportional to μ. The secondary flow of the particle cloud depends very much on β. For small values of β, the particle cloud velocity attains its maximum value on the surface of the disc, and for infinitely large values of β, both the radial and axial particle velocity components vanish on the surface of the disc.

Part II

The “inviscid” equation for a gas-particle mixture is linearized to describe the flow over a wavy wall. Corresponding to the Prandtl-Glauert equation for pure gas, a fourth order partial differential equation in terms of the velocity potential ϕ is obtained for the mixture. The solution is obtained for the flow over a periodic wavy wall. For equilibrium flows where λ_v and λ_T approach zero and frozen flows in which λ_v and λ_T become infinitely large, the flow problem is basically similar to that obtained by Ackeret for a pure gas. For finite values of λ_v and λ_T, all quantities except v are not in phase with the wavy wall. Thus the drag coefficient C_D is present even in the subsonic case, and similarly, all quantities decay exponentially for supersonic flows. The phase shift and the attenuation factor increase for increasing particle concentration.

Part III

Using the boundary layer approximation, the initial development of the combustion zone between the laminar mixing of two parallel streams of oxidizing agent and small, solid, combustible particles suspended in an inert gas is investigated. For the special case when the two streams are moving at the same speed, a Green’s function exists for the differential equations describing first order gas temperature and oxidizer concentration. Solutions in terms of error functions and exponential integrals are obtained. Reactions occur within a relatively thin region of the order of λ_D. Thus, it seems advantageous in the general study of two-dimensional laminar flame problems to introduce a chemical boundary layer of thickness λ_D within which reactions take place. Outside this chemical boundary layer, the flow field corresponds to the ordinary fluid dynamics without chemical reaction.

Part IV

The shock wave structure in a condensing medium of small liquid droplets suspended in a homogeneous gas-vapor mixture consists of the conventional compressive wave followed by a relaxation region in which the particle cloud and gas mixture attain momentum and thermal equilibrium. Immediately following the compressive wave, the partial pressure corresponding to the vapor concentration in the gas mixture is higher than the vapor pressure of the liquid droplets and condensation sets in. Farther downstream of the shock, evaporation appears when the particle temperature is raised by the hot surrounding gas mixture. The thickness of the condensation region depends very much on the latent heat. For relatively high latent heat, the condensation zone is small compared with Ʌ_D.

For solid particles suspended initially in an inert gas, the relaxation zone immediately following the compression wave consists of a region where the particle temperature is first being raised to its melting point. When the particles are totally melted as the particle temperature is further increased, evaporation of the particles also plays a role.

The equilibrium condition downstream of the shock can be calculated and is independent of the model of the particle-gas mixture interaction.

Part V

For a gas containing particles of two distinct sizes and satisfying certain conditions, momentum transfer due to collisions between the two groups of particles can be taken into consideration using the classical elastic spherical ball model. Both in the relatively simple problem of normal shock wave and the perturbation solutions for the nozzle flow, the transfer of momentum due to collisions which decreases the velocity difference between the two groups of particles is clearly demonstrated. The difference in temperature as compared with the collisionless case is quite negligible.

Steady surface wave pattern in a shear flow

The subject under investigation concerns the steady surface wave patterns created by small concentrated disturbances acting on a non-uniform flow of a heavy fluid. The initial value problem of a point disturbance in a primary flow having an arbitrary velocity distribution (U(y), 0, 0) in a direction parallel to the undisturbed free surface is formulated. A geometric optics method and the classical integral transformation method are employed as two different methods of solution for this problem. Whenever necessary, the special case of linear shear (i.e. U(y) = 1+ϵy)) is chosen for the purpose of facilitating the final integration of the solution.

The asymptotic form of the solution obtained by the method of integral transforms agrees with the leading terms of the solution obtained by geometric optics when the latter is expanded in powers of small ϵ r.

The overall effect of the shear is to confine the wave field on the downstream side of the disturbance to a region which is smaller than the wave region in the case of uniform flows. If U(y) vanishes, and changes sign at a critical plane y = y_cr (e.g. ϵy_cr = -1 for the case of linear shear), then the boundary of this asymmetric wave field approaches this critical vertical plane. On this boundary the wave crests are all perpendicular to the x-axis, indicating that waves are reflected at this boundary.

Inside the wave field, as in the case of a point disturbance in a uniform primary flow, there exist two wave systems. The loci of constant phases (such as the crests or troughs) of these wave systems are not symmetric with respect to the x-axis. The geometric optics method and the integral transform method yield the same result of these loci for the special case of U(y) = U_o(1 + ϵy) and for large Kr (ϵr ˂˂ 1 ˂˂ Kr).

An expression for the variation of the amplitude of the waves in the wave field is obtained by the integral transform method. This is in the form of an expansion in small ϵr. The zeroth order is identical to the expression for the uniform stream case and is thus not applicable near the boundary of the wave region because it becomes infinite in that neighborhood. Throughout this investigation the viscous terms in the equations of motion are neglected, a reasonable assumption which can be justified when the wavelengths of the resulting waves are sufficiently large.