Torsional path integral Monte Carlo method for calculating the absolute quantum free energy of large molecules

A new technique for evaluating the absolute free energy of large molecules is presented. Quantum-mechanical contributions to the intramolecular torsions are included via the torsional path integral Monte Carlo (TPIMC) technique. Importance sampling schemes based on uncoupled free rotors and harmonic oscillators facilitate the use of the TPIMC technique for the direct evaluation of quantum partition functions. Absolute free energies are calculated for the molecules ethane, n-butane, n-octane, and enkephalin, and quantum contributions are found to be significant. Comparison of the TPIMC technique with the harmonic oscillator approximation and a variational technique is performed for the ethane molecule. For all molecules, the quantum contributions to free energy are found to be significant but slightly smaller than the quantum contributions to internal energy

Quantum free energies of the conformers of glycine on an ab initio potential energy surface

The torsional path integral Monte Carlo (TPIMC) technique is used to study the five lowest-energy conformers of glycine. The theoretical method provides an anharmonic and quantum-mechanical description of conformational free energy and is used for the first time with an ab initio potential energy surface. The 3-dimensional torsional potential energy surface of glycine was obtained at the MP2/6-311++G** level of theory and is optimized with respect to the non-torsional degrees of freedom. Calculated conformer populations compare well with those reported in recent matrix-isolation infrared spectroscopy experiments. An additional conformer, not yet observed, is predicted to be heavily populated in the thermal equilibria probed by experiment, and a new explanation for its elusiveness is provided. Quantum effects, such as zero point energy, are found to substantially alter conformer populations, and an algorithm for estimating the role of non-torsional vibrations in the conformational thermodynamics of a molecule is introduced

Torsional path integral Monte Carlo method for the quantum simulation of large molecules

A molecular application is introduced for calculating quantum statistical mechanical expectation values of large molecules at nonzero temperatures. The Torsional Path Integral Monte Carlo (TPIMC) technique applies an uncoupled winding number formalism to the torsional degrees of freedom in molecular systems. The internal energy of the molecules ethane, n-butane, n-octane, and enkephalin are calculated at standard temperature using the TPIMC technique and compared to the expectation values obtained using the harmonic oscillator approximation and a variational technique. All studied molecules exhibited significant quantum mechanical contributions to their internal energy expectation values according to the TPIMC technique. The harmonic oscillator approximation approach to calculating the internal energy performs well for the molecules presented in this study but is limited by its neglect of both anharmonicity effects and the potential coupling of intramolecular torsion

Torsional anharmonicity in the conformational thermodynamics of flexible molecules

We present an algorithm for calculating the conformational thermodynamics of large, flexible molecules that combines ab initio electronic structure theory calculations with a torsional path integral Monte Carlo (TPIMC) simulation. The new algorithm overcomes the previous limitations of the TPIMC method by including the thermodynamic contributions of non-torsional vibrational modes and by affordably incorporating the ab initio calculation of conformer electronic energies, and it improves the conventional ab initio treatment of conformational thermodynamics by accounting for the anharmonicity of the torsional modes. Using previously published ab initio results and new TPIMC calculations, we apply the algorithm to the conformers of the adrenaline molecule

Collision-induced conformational changes in glycine

We present quantum dynamical calculations on the conformational changes of glycine in collisions with the He, Ne, and Ar rare-gas atoms. For two conformer interconversion processes (III-->I and IV-->I), we find that the probability of interconversion is dependent on several factors, including the energy of the collision, the angle at which the colliding atom approaches the glycine molecule, and the strength of the glycine-atom interaction. Furthermore, we show that attractive interactions between the colliding atom and the glycine molecule catalyze conformer interconversion at low collision energies. In previous infrared spectroscopy studies of glycine trapped in rare-gas matrices and helium clusters, conformer III has been consistently observed, but conformer IV has yet to be conclusively detected. Because of the calculated thermodynamic stability of conformer IV, its elusiveness has been attributed to the IV-->I conformer interconversion process. However, our calculations present little indication that IV-->I interconversion occurs more readily than III-->I interconversion. Although we cannot determine whether conformer IV interconverts during experimental Ne- and Ar-matrix depositions, our evidence suggests that the conformer should be present in helium droplets. Anharmonic vibrational frequency calculations illustrate that previous efforts to detect conformer IV may have been hindered by the overlap of its IR-absorption bands with those of other conformers. We propose that the redshifted symmetric –CH2 stretch of conformer IV provides a means for its conclusive experimental detection

Cooperative program for design, fabrication, and testing of graphite/epoxy composite helicopter shafting

The fabrication of UH-1 helicopter tail rotor drive shafts from graphite/epoxy composite materials is discussed. Procedures for eliminating wrinkles caused by lack of precure compaction are described. The development of the adhesive bond between aluminum end couplings and the composite tube is analyzed. Performance tests to validate the superiority of the composite materials are reported

Memory Access Optimizations for High-Performance Computing

This paper discusses the importance of memory access optimizations which are shown to be highly effective on the MasPar architecture. The study is based on two MasPar machines, a 16K-processor MP-1 and a 4K-processor MP-2. A software pipelining technique overlaps memory accesses with computation and/or communication. Another optimization, called the register window technique reduces the number of loads in a loop. These techniques are evaluated using three parallel matrix multiplication algorithms on both the MasPar machines. The matrix multiplication study shows that for a highly computation intensive problem, reducing the interprocessor communication can become a secondary issue compared to memory access optimization. Also, it is shown that memory access optimizations can play a more important role than the choice of a superior parallel algorithm. Keywords: load/store architecture, memory accesses, matrix multiplication, parallel programming

Evaluation and Demonstration of BMPs for Cattle on Grazing Lands for the Lone Star Healthy Streams Program

According to the 2008 Texas Water Quality Inventory and 303(d) List, recreation is impaired in 274 waterbody segments and oyster harvest is impaired in another 21 due to bacteria. One of the primary strategies for reducing bacteria in many of these waterbodies is to provide technical and financial assistance to implement best management practices (BMPs) to reduce bacteria runoff from cattle on grazing lands. In order to inspire behavior change, evaluations and demonstrations of BMP effectiveness are needed to encourage voluntary implementation of BMPs and participation in federal and state technical and financial assistance programs designed to reduce bacterial runoff ultimately improve water quality. The goal of this project was to reduce bacterial contamination caused by grazing livestock in Texas waterbodies through evaluation and demonstration of BMP effectiveness in reducing bacteria runoff from grazing lands. This BMP effectiveness data then served as the scientific-basis for the Lone Star Healthy Streams education program (grazing cattle component). Lone Star Healthy Streams programs and other outreach and technology transfer were utilized to increase voluntary implementation of BMPs and participation in federal and state technical and financial assistance programs by providing landowners with feasible options for addressing sources of bacteria through education programs based on the evaluation and demonstration of BMP effectiveness

Improving Students Vocabulary In Writing Descriptive Text By Using Word Search Game In SMP

This research was conducted to find out how good the students' vocabulary in writing descriptive text was. This Classroom Action Reseach was conducted in SMP Negeri 2 Meliau to give solusion toward the students problem in writing descriptive text. The teaching learning process were carried out by using “word search game” as the media to help the students to overcome their problem. It was conducted in two cycles with the consideration that by using word search game, the students could improve their vocabulary mastery in writing descriptive text. The research finding showed that the students' mean score of the test in the first cycle was 62.38 which was categorized “average to good”. While, in the second cycle, the students' mean score increased up to 80, which was categorized “good to excellent. It shows us that using word search game could really help the students in improving their vocabulary mastery