Nanocomposites refer to the materials in which the defining characteristic size of inclusions is in the order of 10-100nm. There are several types of nanoparticle inclusions with different structures: metal clusters, fullerenes particles and molybdenum selenide, Our research focus is on polymer nanocomposites with inorganic clay particles as inclusions, in particular we used sodium montmorillonite polymer nanocomposite. In our study, modeling and simulations of sodium montmorillonite (Na+-MMT) is currently being investigated as an inorganic nanocomposite material. Na+-MMT clay consists of platelets, one nanometer thick with large lateral dimensions, which can be used to achieve efficient reinforcement of polymer matrices. This nanocomposite has different applications such as a binder of animal feed, a plasticizing agent in cement, brick and ceramic, and a thickener and stabilizer of latex and rubber adhesives. In this study, sodium montmorillonite called Na+-MMT structure is built with the bulk system and the layered system which includes from 1 to 12 layers by using Crystal Builder of Cerius2. An isothermal and isobaric ensemble is used for calculation of thermodynamic properties such as specific heat capacities and isothermal expansion coefficients of Na+-MMT. A canonical ensemble which holds a fixed temperature, volume and number of molecules is used for defining exfoliation kinetics of layered structures and surface formation energies for Na+-MMT layered structures are calculated by using a canonical ensemble. Mechanical properties are used to help characterize and identify the Na+-MMT structure. Several elastic properties such as compliance and stiffness matrices, Young's, shear, and bulk modulus, volume compressibility, Poisson's ratios, Lamé constants, and velocities of sound are calculated in specified directions. Another calculation method is the Vienna Ab-initio Simulation Package (VASP). VASP is a complex package for performing ab-initio quantum-mechanical calculations and molecular dynamic (MD) simulations using pseudopotentials and a plane wave basis set. Cut off energy is optimized for the unit cell of Na+-MMT by using different cut off energy values. Experimental and theoretical cell parameters are compared by using cell shape and volume optimization and root mean square (RMS) coordinate difference is calculated for variation of cell parameters. Cell shape and volume optimization are done for calculating optimum expansion or compression constant.

A variety of organic reactions provide experimental observations that are not explained by current models of reactivity and selectivity. This dissertation describes a combination of experimental and theoretical studies of such reactions. In the ene reaction of singlet oxygen with tetramethylene, it is found that standard statistical rate theories fail to account for the observed kinetic isotope effects, particularly with regard to their broad temperature independence. Dynamics trajectories are found to account for the observed isotope effects. In the dimerization of cyclopentadiene, novel "dynamic" isotope effects are observed on the 13C distribution in the product, and a method for the prediction of these isotope effects is developed here. In the cycloaddition of diazomethane with dimethylfulvene, it is found that the current model of the mechanism as a [6 + 4] cycloaddition is incorrect, and a new mechanism is proposed. Isotope effects have been measured for the recently reported unusual "on water" quadricyclane cycloadditions, and the implications of these observations toward the mechanism are discussed.

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The performance of the ensemble Kalman filter (EnKF) in forced, dissipative flow under imperfect model conditions is investigated through simultaneous state and parameter estimation where the source of model error is the uncertainty in the model parameters. Two numerical models with increasing complexity are used with simulated observations. For lower complexity, a two-dimensional, nonlinear, hydrostatic, non-rotating, and incompressible sea breeze model is developed with buoyancy and vorticity as the prognostic variables. Model resolution is 4 km horizontally and 50 m vertically. The ensemble size is set at 40. Forcing is maintained through an explicit heating function with additive stochastic noise. Simulated buoyancy observations on land surface with 40-km spacing are assimilated every 3 hours. Up to six model parameters are successfully subjected to estimation attempts in various experiments. The overall EnKF performance in terms of the error statistics is found to be superior to the worst-case scenario (when there is parameter error but no parameter estimation is performed) with an average error reduction in buoyancy and vorticity of 40% and 46%, respectively, for the simultaneous estimation of six parameters. The model chosen to represent the complexity of operational weather forecasting is the Pennsylvania State University-National Center for Atmospheric Research MM5 model with a 36-km horizontal resolution and 43 vertical layers. The ensemble size for all experiments is chosen as 40 and a 41st member is generated as the truth with the same ensemble statistics. Assimilations are performed with a 12-hour interval with simulated sounding and surface observations of horizontal winds and temperature. Only single-parameter experiments are performed focusing on a constant inserted into the code as the multiplier of the vertical eddy mixing coefficient. Estimation experiments produce very encouraging results and the mean estimated parameter value nicely converges to the true value exhibiting a satisfactory level of variability.

Changes in follicular dynamics were monitored in forty-four Brahman multiparous (n=30) and primiparous (n=14) cows randomly assigned to control (n=22) and once-daily suckling (n=22) treatments. Daily transrectal ultrasonography images were taken from d 21 through 88 post-calving or detection of first estrus. Suckling treatment was introduced on d 28 post-calving. Follicular waves were profiled and characterized by development and regression of a variable number of small and medium sized (2-9 mm) follicles before one of the follicles differentiated and became the dominant follicle. Primiparous cows had 34% more (P<0.04) follicular waves (4.8 + 0.6) than did the multiparous cows (3.1 + 0.4) prior to first ovulation (FO). Once-daily suckled multiparous cows had 37% fewer (P<0.03) follicular waves (2.4 + 0.5) prior to FO than controls. Interval from calving to FO was reduced (P < 0.05) by an average of 12 d by once-daily suckling in multiparous cows. Primiparous cows developed 30% more (P<0.02) dominant follicles (6.3 + 0.6) from d 21 to estrus than did the multiparous cows (4.3 + 0.4). Ovulation before d 88 occurred in 42 of 44 (95%) cows. Behavioral estrus was not detected in 40 of 42 (95%) cows at FO. The length of the subsequent estrous cycle was short (<17 days) in 39 of 42 (93%) cows. We can conclude from these data that ovarian function is resumed shortly after parturition and ovulation of a dominant follicle ends postpartum anestrous. Primiparous cows experienced more follicular waves and therefore grew more dominant follicles prior to first estrus. Once-daily suckling hastened return to estrus and reduced the number of follicular waves prior to first post-partum estrus in multiparous cows. The incidence of first ovulation being associated with behavioral estrus was low. Short cycles followed first ovulation. It appears obligatory that postpartum Brahman cows experience a silent ovulation with formation of functional luteal tissue prior to resumption of normal estrous cyclicity.

Phosphofructokinase from Escherichia coli (EcPFK) is allosterically regulated by MgADP and phosphoenolpyruvate (PEP), which act to activate or inhibit, respectively, by changing the substrate (Fru-6-P) affinity of the enzyme. Both ligands bind to the same allosteric site in EcPFK. Therefore, the questions we want to address are how these two molecules regulate EcPFK and how the allosteric signal is propagated throughout the enzyme. EcPFK has 28 potential site-site interactions. These interactions in turn derive from multiple copies of 6 potentially unique homotropic interactions and 4 potentially unique heterotropic interactions. Making hybrid tetramer of EcPFK is used to isolate a single heterotropic interaction. To improve the yield of the 1:3 hybrid, the in vivo hybrid formation method was developed. Four heterotropic interactions were isolated by this manner and re-evaluated. The same kinetics characteristics were obtained for each 1:3 hybrid from both the in vivo and in vitro method. To address the question of how the allosteric signal is transmitted throughout EcPFK, we identified residues (G184, Asp59 and S157) that are important for the allosteric regulation for both PEP inhibition and MgADP activation. The impact of each mutation on individual interaction is unique and also suggests that the structural basis for PEP inhibition is different from that for MgADP activation. Most importantly, since the sum of each heterotropic interaction with a modification in only one subunit is equal to the total heterotropic interaction with a modification in all four subunits, this result indicates that the heterotropic allosteric signal transmission is realized in a single subunit. The 23Ã heterotropic interaction, which contributes the most to the PEP inhibition, was chosen to study the dynamic properties. Fluorescence was used to study the dynamic perturbations of the 23Ã interaction upon ligand binding. Taking advantage of the hybrid formation strategy and the tryptophan-shift mutagenesis method, a tryptophan residue can be placed at different individual locations throughout the native subunit containing the 23Ã heterotropic interaction. The steady-state anisotropy and lifetime measurement at each tryptophan position indicate that the 23Ã allosteric interaction involves the perturbation of side-chain dynamics both near and quite far away from the respective ligand binding sites.

Past educational studies reveal that students have difficulty making the connection between the mathematical and analytical models used to describe building behavior and the behavior itself. This thesis examines the development and use of visual simulation software as a tool to help students create connections between abstract mathematical models and the real world. A framework for the software was designed and implemented, enabling students to interactively construct, analyze, and evaluate models within a single environment. The software was tested by students in an undergraduate dynamics course to assess its effectiveness as a learning tool. Results are presented through scenarios that demonstrate the extensibility and flexibility of the framework and an analysis of student responses from the Student Assessment of Learning Gains instrument.

Through methodology unique for tropical cyclones in peer-reviewed literature, this study explores how the dynamics of moist convection affects the predictability of tropical cyclogenesis. Mesoscale models are used to perform short-range ensemble forecasts of a non-developing disturbance in 2004 and Hurricane Humberto in 2007; both of these cases were highly unpredictable. Taking advantage of discrepancies between ensemble members in short-range ensemble forecasts, statistical correlation is used to pinpoint sources of error in forecasts of tropical cyclone formation and intensification. Despite significant differences in methodology, storm environment and development, it is found in both situations that high convective instability (CAPE) and mid-level moisture are two of the most important factors for genesis. In the gulf low, differences in CAPE are related to variance in quasi-geostrophic lift, and in Humberto the differences are related to the degree of interaction between the cyclone and a nearby front. Regardless of the source of CAPE variance, higher CAPE and mid-level moisture combine to yield more active initial convection and more numerous and strong vortical hot towers (VHTs), which incrementally contribute to a stronger vortex. In both cases, strength differences between ensemble members are further amplified by differences in convection that are related to oceanic heat fluxes. Eventually the WISHE mechanism results in even larger ensemble spread, and in the case of Humberto, uncertainty related to the time of landfall drives spread even higher. It is also shown that initial condition differences much smaller than current analysis error can ultimately control whether or not a tropical cyclone forms. Furthermore, even smaller differences govern how the initial vortex is built. Differences in maximum winds and/or vorticity vary nonlinearly with initial condition differences and depend on the timing and intensity of small mesoscale features such as VHTs and cold pools. Finally, the strong sensitivity to initial condition differences in both cases exemplifies the inherent uncertainties in hurricane intensity prediction. This study illustrates the need for implementing advanced data analysis schemes and ensemble prediction systems to provide more accurate and event-dependent probabilistic forecasts.