2D association and integrative omics analysis in rice provides systems biology view in trait analysis.

The interactions among genes and between genes and environment contribute significantly to the phenotypic variation of complex traits and may be possible explanations for missing heritability. However, to our knowledge no existing tool can address the two kinds of interactions. Here we propose a novel linear mixed model that considers not only the additive effects of biological markers but also the interaction effects of marker pairs. Interaction effect is demonstrated as a 2D association. Based on this linear mixed model, we developed a pipeline, namely PATOWAS. PATOWAS can be used to study transcriptome-wide and metabolome-wide associations in addition to genome-wide associations. Our case analysis with real rice recombinant inbred lines (RILs) at three omics levels demonstrates that 2D association mapping and integrative omics are able to provide a systems biology view into the analyzed traits, leading toward an answer about how genes, transcripts, proteins, and metabolites work together to produce an observable phenotype

Nonlinear Flow Characteristics and Horizontal Well Pressure Transient Analysis for Low-Permeability Offshore Reservoirs

Threshold pressure gradient (TPG) and stress sensitivity which cause the nonlinear flow in low permeability reservoirs were carried out by experiments. Firstly, the investigation of existing conditions of TPG for oil flow in irreducible water saturation low-permeability reservoirs was conducted and discussed, using the cores from a real offshore oilfield in China. The existence of TPG was proven. The relationship between TPG and absolute permeability was obtained by laboratory tests. TPG increases with decreasing absolute permeability. Then, stress sensitivity experiment was carried out through depressurizing experiment and step-up pressure experiment. Permeability modulus which characterizes stress sensitivity increases with decreasing absolute permeability. Consequently, a horizontal well pressure transient analysis mathematical model considering threshold pressure gradient and stress sensitivity was established on the basis of mass and momentum conservation equations. The finite element method (FEM) was presented to solve the model. Influencing factors, such as TPG, permeability modulus, skin factor, wellbore storage, horizontal length, horizontal position, and boundary effect on pressure and pressure derivative curves, were also discussed. Results analysis demonstrates that the pressure transient curves are different from Darcy’s model when considering the nonlinear flow characteristics. Both TPG and permeability modulus lead to more energy consumption and the reservoir pressure decreases more than Darcy’s model

Computing the Newton Potential in the Boundary Integral Equation for the Dirichlet Problem of the Poisson Equation

Evaluating the Newton potential is crucial for efficiently solving the boundary integral equation of the Dirichlet boundary value problem of the Poisson equation. In the context of the Fourier-Garlerkin method for solving the boundary integral equation, we propose a fast algorithm for evaluating Fourier coefficients of the Newton potential by using a sparse grid approximation. When the forcing function of the Poisson equation expressed in the polar coordinates has mth-order bounded mixed derivatives, the proposed algorithm achieves an accuracy of order (n-m log3 n), with requiring (n log2 n) number of arithmetics for the computation, where n is the number of quadrature points used in one coordinate direction. With the help of this algorithm, the boundary integral equation derived from the Poisson equation can be efficiently solved by a fast fully discrete Fourier-Garlerkin method

Climate Change, Water Supply, and Agriculture in the Arid Western United States: Eighty Years of Agricultural Census Observations from Idaho

As the population and agricultural development in the U.S. expanded west throughout the 20th century, major water infrastructure projects were initiated in order to meet irrigation demand and to reduce the risk and uncertainty associated with highly variable water supplies.2 Agriculture in the arid and semi-arid western U.S. is particularly vulnerable to variability in water supply, and has evolved to rely heavily on major water infrastructure projects.3 In 2007, of the 57 million acres of irrigated cropland and pastureland in the U.S., nearly three-quarters was in the 17 western-most contiguous states; in 2008, irrigated agriculture applied 91.2 million acre-feet of water, with over four-fifths being used in the arid west

Dynamics in a Fermi lattice gas

We use 40K atoms trapped in a cubic optical lattice to simulate the Fermi-Hubbard model. The work in this thesis focuses on investigating dynamics in the Fermi-Hubbard model and developing techniques for engineering Hamiltonians beyond the minimal Hubbard model. We discussed three experiments. In the first, we investigated the transport properties of a Fermi lattice gas by directly measuring the transport lifetime at various interaction strengths and temperatures. The resistivity is inferred from the measured transport lifetime. We observe anomalous transport behavior, which is analogous to bad-metal behavior in strongly correlated electronic materials. The second experiment presents the first realization of correlated, density-dependent tunneling in a Fermi-Hubbard optical lattice model by applied Raman laser fields. This correlated tunneling involves spin-flips and the generation of doublons, which have been observed experimentally. We also confirmed that the amplitude of correlated tunneling is suppressed when neighboring lattice sites are unoccupied. The last experiment explores the possibility to introduce long-range interactions for fermions trapped in optical lattices via Rydberg-dressed states. We developed a novel velocity-selective spectroscopy method to measure the transition between the 5P_1/2 and Rydberg states via electromagnetically induced transparency. This measurement is a first step toward inducing Rydberg-dressed interactions in optical lattices