Using Quasi-elastic Events to Measure Neutrino Oscillations with MINOS Detectors in the NuMI Neutrino Beam

MINOS (Main Injector Neutrino Oscillation Search) experiment has been designed to search for a change in the avor composition of a beam of muon neutrinos as they travel between the Near Detector at Fermi National Accelerator Laboratory and the Far Detector in the Soudan mine in Minnesota, 735 km from the target. The MINOS oscillation analysis is mainly performed with the charged current (CC) events and sensitive to constrain high-delta m2 values. However, the quasi-elastic (QEL) charged current interaction is dominant in the energy region important to access low-delta m2 values. For further improvement, the QEL oscillation analysis is performed in this dissertation. A data sample based on a total of 2.50 x 1020 POT is used for this analysis. In summary, 55 QEL-like events are observed at the Far detector while 87.06 +/- 13.17 (syst:) events are expected with null oscillation hypothesis. These data are consistent with vm disappearance via oscillation with delta m2 = 2.10 +/- 0.37 (stat:) +/- 0.24 (syst:) eV2 and the maximal mixing angle

Reaction-diffusion kinetics on lattice at the microscopic scale

Lattice-based stochastic simulators are commonly used to study biological reaction-diffusion processes. Some of these schemes that are based on the reaction-diffusion master equation (RDME), can simulate for extended spatial and temporal scales but cannot directly account for the microscopic effects in the cell such as volume exclusion and diffusion-influenced reactions. Nonetheless, schemes based on the high-resolution microscopic lattice method (MLM) can directly simulate these effects by representing each finite-sized molecule explicitly as a random walker on fine lattice voxels. The theory and consistency of MLM in simulating diffusion-influenced reactions have not been clarified in detail. Here, we examine MLM in solving diffusion-influenced reactions in 3D space by employing the Spatiocyte simulation scheme. Applying the random walk theory, we construct the general theoretical framework underlying the method and obtain analytical expressions for the total rebinding probability and the effective reaction rate. By matching Collins-Kimball and lattice-based rate constants, we obtained the exact expressions to determine the reaction acceptance probability and voxel size. We found that the size of voxel should be about 2% larger than the molecule. MLM is validated by numerical simulations, showing good agreement with the off-lattice particle-based method, eGFRD. MLM run time is more than an order of magnitude faster than eGFRD when diffusing macromolecules with typical concentrations in the cell. MLM also showed good agreements with eGFRD and mean-field models in case studies of two basic motifs of intracellular signaling, the protein production-degradation process and the dual phosphorylation cycle. Moreover, when a reaction compartment is populated with volume-excluding obstacles, MLM captures the non-classical reaction kinetics caused by anomalous diffusion of reacting molecules

Optical dispersions through intracellular inhomogeneities

Transport of intensity equation (TIE) exhibits a non-interferometric correlation between intensity and phase variations of intermediate fields (e.g., light and electron) in biological imaging. Previous TIE formulations have generally assumed a free space propagation of monochromatic coherent field functions crossing phase distributions along a longitudinal direction. Here, we modify the TIE with fractal (or self-similar) organization models based on intracellular refractive index turbulence. We then implement the TIE simulation over a broad range of fractal dimensions and wavelengths. Simulation results show how the intensity propagation through the spatial fluctuation of intracellular refractive index interconnects fractal-dimensionality with intensity dispersion (or transmissivity) within the picometer to micrometer wavelength range. In addition, we provide a spatial-autocorrelation of phase derivatives which allows the direct measurement and reconstruction of intracellular fractal profiles from optical and electron microscopy imaging.Comment: 22 pages, 18 figures, 4 table

A computational framework for bioimaging simulation

Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding how higher level functions emerge from the combined action of biomolecules. However, there still remain formidable challenges in bridging the gap between bioimaging and mathematical modeling. Generally, measurements using fluorescence microscopy systems are influenced by systematic effects that arise from stochastic nature of biological cells, the imaging apparatus, and optical physics. Such systematic effects are always present in all bioimaging systems and hinder quantitative comparison between the cell model and bioimages. Computational tools for such a comparison are still unavailable. Thus, in this work, we present a computational framework for handling the parameters of the cell models and the optical physics governing bioimaging systems. Simulation using this framework can generate digital images of cell simulation results after accounting for the systematic effects. We then demonstrate that such a framework enables comparison at the level of photon-counting units.Comment: 57 page

Functional Interplay between P5 and PDI/ERp72 to Drive Protein Folding

The physiological functions of proteins are destined by their unique three-dimensional structures. Almost all biological kingdoms share conserved disulfide-catalysts and chaperone networks that assist in correct protein folding and prevent aggregation. Disruption of these networks is implicated in pathogenesis, including neurodegenerative disease. In the mammalian endoplasmic reticulum (ER), more than 20 members of the protein disulfide isomerase family (PDIs) are believed to cooperate in the client folding pathway, but it remains unclear whether complex formation among PDIs via non-covalent interaction is involved in regulating their enzymatic and chaperone functions. Herein, we report novel functional hetero complexes between PDIs that promote oxidative folding and inhibit aggregation along client folding. The findings provide insight into the physiological significance of disulfide-catalyst and chaperone networks and clues for understanding pathogenesis associated with disruption of the networks.P5 is one of protein disulfide isomerase family proteins (PDIs) involved in endoplasmic reticulum (ER) protein quality control that assists oxidative folding, inhibits protein aggregation, and regulates the unfolded protein response. P5 reportedly interacts with other PDIs via intermolecular disulfide bonds in cultured cells, but it remains unclear whether complex formation between P5 and other PDIs is involved in regulating enzymatic and chaperone functions. Herein, we established the far-western blot method to detect non-covalent interactions between P5 and other PDIs and found that PDI and ERp72 are partner proteins of P5. The enzymatic activity of P5-mediated oxidative folding is up-regulated by PDI, while the chaperone activity of P5 is stimulated by ERp72. These findings shed light on the mechanism by which the complex formations among PDIs drive to synergistically accelerate protein folding and prevents aggregation. This knowledge has implications for understanding misfolding-related pathology