Seismic full waveform inversion (waveform tomography) is a method to reconstruct the underground velocity field in high resolution using seismic data. The method was first introduced during the 1980’s and became computationally feasible during the late 1990’s when the method was implemented in the frequency domain. This work presents three case studies and one synthetic benchmark of full waveform inversion applications. Two of the case studies are focused on time-lapse cross-well and 2D reflection seismic data sets acquired at the Ketzin CO2 geological storage site. These studies are parts of the CO2SINK and CO2MAN projects. The results show that waveform tomography is more effective than traveltime tomography for the CO2 injection monitoring at the Ketzin site for the cross-well geometry. For the surface data sets we find it is difficult to recover the true value of the velocity anomaly due to the injection using the waveform inversion method, but it is possible to qualitatively locate the distribution of the injected CO2. The results agree well with expectations based upon conventional 2D CDP processing methods and more extensive 3D CDP processing methods in the area. A further investigation was done to study the feasibility and efficiency of seismic full waveform inversion for time-lapse monitoring of onshore CO2 geological storage sites using a reflection seismic geometry with synthetic data sets. The results show that waveform inversion may be a good complement to standard CDP processing when monitoring CO2 injection. The choice of method and strategy for waveform inversion is quite dependent on the goals of the time-lapse monitoring of the CO2 injection. The last case study is an application of the full waveform inversion method to two crooked profiles at the Forsmark site in eastern central Sweden. The main goal of this study was to help determine if the observed reflections are mainly due to fluid filled fracture zones or mafic sills. One main difficulty here is that the profiles have a crooked line geometry which corresponds to 3D seismic geometry, but a 2D based inversion method is being used. This is partly handled by a 3D to 2D coordinate projection method from traveltime inversion. The results show that these reflections are primarily due to zones of lower velocity, consistent with them being generated at water filled fracture zones.

A robotic microscope was designed using a microcontroller to take time-lapse digital photographs of developing salamander embryos. The microcontroller operated three stepper motors to control three-axis movement accurately, and two six mega-pixel digital cameras to capture through-focus time-lapse digital pictures of six views of Ambystoma mexicanum embryos (axolotl, a salamander). The device is designed to take images every five minutes for 80 hours of early development, from fertilization to stage 20, when the neural tube closes to form the brain and spinal column. Techniques to enhance the embryo images were investigated including image fusion to get in-focus views from a stack of images. In the early embryo surface epithelial cells differentiate to form neural tissue and external skin tissue. Observing the whole embryo surface at cellular level will give a better idea of the stress and strain each cell undergoes and what physical forces are involved in cell differentiation. / May 2007

Expanded polyglutamine proteins are known to be the causative agents of a number of human neurodegenerative diseases but the molecular basis of their cytoxicity is still poorly understood. Polyglutamine tracts may impede the activity of the proteasome, and evidence from single cell imaging suggests that the sequestration of polyglutamine proteins into inclusion bodies can reduce the proteasomal burden and promote cell survival, at least in the short term. The presence of misfolded protein also leads to activation of stress kinases such as p38MAPK, which can be cytotoxic. The relationships of these systems are not well understood. We have used fluorescent reporter systems imaged in living cells, and stochastic computer modeling to explore the relationships of expanded polyglutamine proteins, p38MAPK activation, generation of reactive oxygen species (ROS), proteasome inhibition, and inclusion body formation. In cells expressing a polyglutamine protein, inclusion body formation was preceded by proteasome inhibition but cytotoxicity was greatly reduced by administration of a p38MAPK inhibitor. Computer simulations suggested that without the generation of ROS, the proteasome inhibition and activation of p38MAPK would have significantly reduced toxicity. Our data suggest a vicious cycle of stress kinase activation and proteasome inhibition that is ultimately lethal to cells. There was close agreement between experimental data and the predictions of a stochastic computer model, supporting a central role for proteasome inhibition and p38MAPK activation in inclusion body formation and ROS-mediated cell death.

The objective of this work is to investigate the elastic modulus of gastrula-stage avian embryos and the effect of substrate stiffness on presumptive precardiac cell fate. Our overall hypothesis is that the mechanical microenvironment, specifically, tissue modulus and substrate stiffness, influences gastrulation and cardiac induction. Large-scale morphogenetic movements during early embryo development are driven by complex changes in biochemical and biophysical factors. Current models for amniote primitive streak morphogenesis and gastrulation take into account numerous genetic pathways but largely ignore the role of mechanical forces. Here, we used atomic force microscopy (AFM) to obtain for the first time precise biomechanical properties of the early avian embryo. Our data reveal that the primitive streak is significantly stiffer than neighboring regions of the epiblast, and that it is stiffer than the pre-primitive streak epiblast. To test our hypothesis that these changes in mechanical properties are due to a localized increase of actomyosin contractility, we inhibited actomyosin contractility via the Rho kinase (ROCK) pathway using the small-molecule inhibitor Y-27632. Our results using several different assays show the following: 1) primitive streak formation was blocked; 2) the time-dependent increase in primitive streak stiffness was abolished; and 3) convergence of epiblast cells to the midline was inhibited. Taken together, our data suggest that actomyosin contractility is necessary for primitive streak morphogenesis, and specifically, ROCK plays a critical role. To better understand the underlying mechanisms of this fundamental process, future models should account for the findings presented in this study. As presumptive cardiac cells traverse the course of differentiation into cardiac myocytes during cardiogenesis, the sequence, magnitude, and spatiotemporal map of biomechanical and biochemical signals has not been fully explored. There have been many studies detailing the induction of cardiogenesis on a variety of substrates and extracellular matrix (ECM) proteins, but none have completed a rigorous study of the effects of substrate stiffness on the induction of precardiac cells prior to the onset of cardiac gene expression (smooth muscle alpha actin [SMAA] at stage 5.) We investigate the effects of the mechanical environment on precardiac cell behaviors in an in vitro setting to elucidate the effect of substrate stiffness and inducing factors on precardiac tissue and the potential connection between them. The cells in the anterior portion of the primitive streak are fated to form the heart, and we show differing levels of SMAA expression on substrates of differing moduli, which suggests that substrate stiffness may play a role in cardiac differentiation. We cannot determine the physical mechanisms during morphogenesis without understanding the response of precardiac cells to changes in their mechanical environment.

While geophysical reservoir characterization has been an area of research for the last three decades, geophysical reservoir monitoring, time-lapse studies, have recently become an important geophysical application. Generally speaking, the main target is to detect, estimate, and discriminate the changes in subsurface rock properties due to production. This research develops various sensitivity and feasibility analyses to investigate the effects of production-induced time-lapse changes on geophysical measurements including seismic and controlled-source electromagnetic (CSEM) data. For doing so, a realistic reservoir model is numerically simulated based on a prograding near-shore sandstone reservoir. To account for the spatial distribution of petrophysical properties, an effective porosity model is first simulated by Gaussian geostatistics. Dispersed clay and dual water models are then efficiently combined with other well-known theoretical and experimental petrophysical correlations to consistently simulate reservoir model parameters. Next, the constructed reservoir model is subjected to numerical simulation of multi-phase fluid flow to replicate a waterflooding scenario of a black oil reservoir and to predict the spatial distributions of fluid pressure and saturation. A modified Archie’s equation for shaly sandstones is utilized to simulate rock resistivity. Finally, a geologically consistent stress-sensitive rock physics model, combined with the modified Gassmann theory for shaly sandstones, is utilized to simulate seismic elastic parameters. As a result, the comprehensive petro-electro-elastic model developed in this dissertation can be efficiently utilized in sensitivity and feasibility analyses of seismic/CSEM data with respect to petrophysical properties and, ultimately, applied to reservoir characterization and monitoring research. Using the resistivity models, a base and two monitor time-lapse CSEM surveys are simulated via accurate numerical algorithms. 2.5D CSEM modeling demonstrates that a detectable time-lapse signal after 5 years and a strong time-lapse signal after 10 years of waterflooding are attainable with the careful application of currently available CSEM technology. To simulate seismic waves, I employ different seismic modeling algorithms, one-dimensional (1D) acoustic and elastic ray tracing, 1D full elastic reflectivity, 2D split-step Fourier plane-wave (SFPW), and 2D stagger grid explicit finite difference (FD). My analyses demonstrate that acoustic modeling of an elastic medium is a good approximation up to ray parameter (p) equal to 0.2 sec/km. However, at p=0.3 sec/km, differences between elastic and acoustic wave propagation is the more dominant effect compared to internal multiples. Here, converted waves are also generated with significant amplitudes compared to primaries and internal multiples. I also show that time-lapse modeling of the reservoir using SFPW approach is very fast compared to FD, 100 times faster for my case here. It is capable of handling higher frequencies than FD. It provides an accurate image of the waterflooding process comparable to FD. Consequently, it is a powerful alternative for time-lapse seismic modeling. I conclude that both seismic and CSEM data have adequate but different sensitivities to changes in reservoir properties and therefore have the potential to quantitatively map production-induced time-lapse changes. / text

Time-lapse seismic monitoring repeats 3D seismic imaging over a reservoir to map fluid movements in a reservoir. During hydrocarbon production, the fluid saturation, pressure, and temperature of a reservoir change, thereby altering the acoustic properties of the reservoir. Time-lapse seismic analysis can illuminate these dynamic changes of reservoir properties, and therefore has strong potential for improving reservoir management. However, the response of a reservoir depends on many parameters and can be diffcult to understand and predict. Numerical modeling results integrating streamline fluid flow simulation, rock physics, and ray-Born seismic modeling address some of these problems. Calculations show that the sensitivity of amplitude changes to porosity depend on the type of sediment comprising the reservoir. For consolidated rock, high-porosity models show larger amplitude changes than low porosity models. However, in an unconsolidated formation, there is less consistent correlation between amplitude and porosity. The rapid time-lapse modeling schemes also allow statistical analysis of the uncertainty in seismic response associated with poorly known values of reservoir parameters such as permeability and dry bulk modulus. Results show that for permeability, the maximum uncertainties in time-lapse seismic signals occur at the water front, where saturation is most variable. For the dry bulk-modulus, the uncertainty is greatest near the injection well, where the maximum saturation changes occur. Time-lapse seismic methods can also be applied to monitor CO2 sequestration. Simulations show that since the acoustic properties of CO2 are very different from those of hydrocarbons and water, it is possible to image CO2 saturation using seismic monitoring. Furthermore, amplitude changes after supercritical fluid CO2 injection are larger than liquid CO2 injection. Two seismic surveys over Teal South Field, Eugene Island, Gulf of Mexico, were acquired at different times, and the numerical models provide important insights to understand changes in the reservoir. 4D seismic differences after cross-equalization show that amplitude dimming occurs in the northeast and brightening occurs in the southwest part of the field. Our forward model, which integrates production data, petrophysicals, and seismic wave propagation simulation, shows that the amplitude dimming and brightening can be explained by pore pressure drops and gas invasion, respectively.

With burgeoning world demand and a limited rate of discovery of new reserves, there is increasing impetus upon the industry to optimize recovery from already existing fields. 4D, or time-lapse, seismic imaging is an emerging technology that holds great promise to better monitor and optimise reservoir production. The basic idea behind 4D seismic is that when multiple 3D surveys are acquired at separate calendar times over a producing field, the reservoir geology will not change from survey to survey but the state of the reservoir fluids will change. Thus, taking the difference between two 3D surveys should remove the static geologic contribution to the data and isolate the timevarying fluid flow component. However, a major challenge in 4D seismic is that acquisition and processing differences between 3D surveys often overshadow the changes caused by fluid flow. This problem is compounded when 4D effects are sought to be derived from vintage 3D data sets that were not originally acquired with 4D in mind. The goal of this study is to remove the acquisition and imaging artefacts from a 4D seismic difference cube using Curvelet processing techniques.

We present an alternative method of extracting production related differences from time-lapse seismic data sets. Our method is not based on the actual subtraction of the two data sets, risking the enhancement of noise and introduction of artifacts due to local phase rotation and slightly misaligned events. Rather, it mutes events of the monitor survey with respect to the baseline survey based on the magnitudes of coefficients in a sparse and local atomic decomposition. Our technique is demonstrated to be an effective tool for enhancing the time-lapse signal from surveys which have been cross-equalized

No description available.

A robotic microscope was designed using a microcontroller to take time-lapse digital photographs of developing salamander embryos. The microcontroller operated three stepper motors to control three-axis movement accurately, and two six mega-pixel digital cameras to capture through-focus time-lapse digital pictures of six views of Ambystoma mexicanum embryos (axolotl, a salamander). The device is designed to take images every five minutes for 80 hours of early development, from fertilization to stage 20, when the neural tube closes to form the brain and spinal column. Techniques to enhance the embryo images were investigated including image fusion to get in-focus views from a stack of images. In the early embryo surface epithelial cells differentiate to form neural tissue and external skin tissue. Observing the whole embryo surface at cellular level will give a better idea of the stress and strain each cell undergoes and what physical forces are involved in cell differentiation.