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

The academic value of internships: benefits across disciplines and student backgrounds

While student benefits from internship experience have been frequently documented in research, the emphasis has been on internship effects on employment and career indicators. This work is concerned with effects on academic outcomes and focuses on the robustness of such effects across academic disciplines as well as for different achievement levels of students, student gender, and ethnicity. We present findings from a longitudinal sample (n > 15,000) that covers an extensive range of subjects and disciplines for large Undergraduate cohorts. Main effects and interactions for student background characteristics were investigated showing stable academic benefits for advantaged and disadvantaged students. Further, using ordinal logistic multi-level modelling, we explored the impact on the probability of attaining a higher degree classification for different student scenarios, thus illustrating the practical significance of these internship effects. Effects are less likely to stem from maturation or self-selection. Findings are therefore discussed against a background of motivational approaches suitable to integrate both direct and indirect paths from internship experience to academic outcomes to career indicators

Coherency in space of lake and river temperature and water quality records

Environmental time series observed over 100’s of monitoring locations usually possess some spatial structure in terms of common patterns throughout time, commonly described as temporal coherence. This paper will apply, develop and compare two methods for clustering time series on the basis of their patterns over time. The first approach treats the time series as functional data and applies hierarchical clustering while the second uses a state-space model based clustering approach. Both methods are developed to incorporate spatial correlation and stopping criteria are investigated to identify an appropriate number of clusters. The methods are applied to Total Organic Carbon data from river sites across Scotland

Landau Ginzburg Theory and Nuclear Matter at Finite Temperature

Based on recent studies of the temperature dependence of the energy and specific heat of liquid nuclear matter, a phase transition is suggested at a temperature $\sim .8$ MeV. We apply Landau Ginzburg theory to this transition and determine the behaviour of the energy and specific heat close to the critical temperature in the condensed phase.Comment: 10 pages, Revte

Synchronized voltage contrast display analysis system

An apparatus and method for comparing internal voltage potentials of first and second operating electronic components such as large scale integrated circuits (LSI's) in which voltage differentials are visually identified via an appropriate display means are described. More particularly, in a first embodiment of the invention a first and second scanning electron microscope (SEM) are configured to scan a first and second operating electronic component respectively. The scan pattern of the second SEM is synchronized to that of the first SEM so that both simultaneously scan corresponding portions of the two operating electronic components. Video signals from each SEM corresponding to secondary electron signals generated as a result of a primary electron beam intersecting each operating electronic component in accordance with a predetermined scan pattern are provided to a video mixer and color encoder