Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be $18.3\pm 3.5$ kcal mol$^{-1}$ for MP2/cc-pVDZ and $19.3\pm 3.6$ for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.Comment: SI not attache

Beta decay of rb86

Measuring of rubidium 86 beta decay using lithium drifted surface barrier silicon detector

The Urbane

A thesis presented to the faculty of the Caudill College of Humanities at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Arts in English by Kenneth H. Casper on May 8, 1997

Hybrid RHF/MP2 geometry optimizations with the Effective Fragment Molecular Orbital Method

The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by chorismate mutase, where the substrate is treated at the MP2 level of theory while the rest of the system is treated at the RHF level. MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile. For double zeta basis sets the increase in CPU time relative to RHF is roughly a factor of two.Comment: 11 pages, 3 figure

Timesharing performance as an indicator of pilot mental workload

Attentional deficits (workloads) were evaluated in a timesharing task. The results from this and other experiments were incorporated into an expert system designed to provide workload metric selection advice to non-experts in the field interested in operator workload

Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program

An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy gradients and is parallelized. For large molecules such as ubiquitin a reasonable speedup (up to a factor of six) is observed for up to 16 cores. The SCF convergence is greatly improved by PCM for proteins compared to the gas phase

A New Time Domain Formulation for Broadband Noise Predictions

A new analytic result in acoustics called "Formulation 1B," proposed by Farassat, is used to compute the loading noise from an unsteady surface pressure distribution on a thin airfoil in the time domain. This formulation is a new solution of the Ffowcs Williams-Hawkings equation with the loading source term. The formulation contains a far field surface integral that depends on the time derivative and the surface gradient of the pressure on the airfoil, as well as a contour integral on the boundary of the airfoil surface. As a first test case, the new formulation is used to compute the noise radiated from a flat plate, moving through a sinusoidal gust of constant frequency. The unsteady surface pressure for this test case is analytically specied from a result based on linear airfoil theory. This test case is used to examine the velocity scaling properties of Formulation 1B and to demonstrate its equivalence to Formulation 1A of Farassat. The new acoustic formulation, again with an analytic surface pressure, is then used to predict broadband noise radiated from an airfoil immersed in homogeneous, isotropic turbulence. The results are compared with experimental data previously reported by Paterson and Amiet. Good agreement between predictions and measurements is obtained. Finally, an alternative form of Formulation 1B is described for statistical analysis of broadband noise

Broadband Noise Prediction When Turbulence Simulation Is Available - Derivation of Formulation 2B and Its Statistical Analysis

We show that a simple modification of Formulation 1 of Farassat results in a new analytic expression that is highly suitable for broadband noise prediction when extensive turbulence simulation is available. This result satisfies all the stringent requirements, such as permitting the use of the exact geometry and kinematics of the moving body, that we have set as our goal in the derivation of useful acoustic formulas for the prediction of rotating blade and airframe noise. We also derive a simple analytic expression for the autocorrelation of the acoustic pressure that is valid in the near and far fields. Our analysis is based on the time integral of the acoustic pressure that can easily be obtained at any resolution for any observer time interval and digitally analyzed for broadband noise prediction. We have named this result as Formulation 2B of Farassat. One significant consequence of Formulation 2B is the derivation of the acoustic velocity potential for the thickness and loading terms of the Ffowcs Williams-Hawkings (FW-H) equation. This will greatly enhance the usefulness of the Fast Scattering Code (FSC) by providing a high fidelity boundary condition input for scattering predictions