Evaluating Model Fidelity to Aid Model Selection

In simulation, fidelity has become a topic of interest in determining how well a simulation is able to represent its referent situation. In many cases, the true referent is the real-world scenario in which the system will exist. However, the fidelity of a simulation may be computed in comparison to other referents including other simulation models or tests. Several metrics have been proposed to evaluate a model based on qualitative or subjective parameters. These proposed metrics offer possible solutions for the quantification of model fidelity, however their inability to compare features relative importance greatly limits their applicability to models and introduces ambiguity in model evaluation. Frist, previously presented metrics are introduced and evaluated. A new metric is then proposed to address concerns presented in the existing metric evaluation. The proposed metric uses model accuracy to a referent case to both determine feature weights and total model fidelity. The proposed metric is then applied to a simulation case and the results are used to make model selection decisions given hypothetical application scenarios. The proposed relative metric aims to compare similar models’ level of fidelity with the end goal of aiding in model selection. By combining the proposed metric with model computational cost, decisions on feature fidelity and inclusion can be made to meet the needs of a given simulation’s application

*Interactive Earthquake Visualization with Open Data

Because earthquakes claim thousands of lives and billions of dollars yearly, there is a great need to recognize patterns in seismic data. While some tools for analysis exist, most geological software is expensive and open earthquake visualizations are limited. In this project, we provide accessible earthquake visualizations aimed to encourage geologists, and science enthusiasts in general, to explore open data using accessible, yet powerful, tools

All-optical retrieval of the global phase for two-dimensional Fourier-transform spectroscopy

A combination of spatial interference patterns and spectral interferometry are used to find the global phase for non-collinear two-dimensional Fourier-transform (2DFT) spectra. Results are compared with those using the spectrally resolved transient absorption (STRA) method to find the global phase when excitation is with co-linear polarization. Additionally cross-linear polarized 2DFT spectra are correctly phased using the all-optical technique, where the SRTA is not applicable.Comment: 6 pages, 7 figures, journal publicatio

Reaction Kinetics of the Alcoholysis of Substituted Benzoyl Chlorides

The reaction kinetics of the alcoholysis of substituted benzoyl chlorides was studied. The mechanism of the alcoholysis reaction, which is most generally accepted (1), shows that the overall reaction should be second-order and that the reaction should be first-order with respect to the acid chloride and first-order with respect to the alcohol. This rate study was carried out using a large excess of alcohol as the solvent, thus obtaining pseudo-first order rate constants, first-order with respect to the acid chloride only

Two-Dimensional Infrared Spectroscopy of Antiparallel β-Sheet Secondary Structure

We investigate the sensitivity of femtosecond Fourier transform two-dimensional infrared spectroscopy to protein secondary structure with a study of antiparallel β-sheets. The results show that 2D IR spectroscopy is more sensitive to structural differences between proteins than traditional infrared spectroscopy, providing an observable that allows comparison to quantitative models of protein vibrational spectroscopy. 2D IR correlation spectra of the amide I region of poly-L-lysine, concanavalin A, ribonuclease A, and lysozyme show cross-peaks between the IR-active transitions that are characteristic of amide I couplings for polypeptides in antiparallel hydrogen-bonding registry. For poly-L-lysine, the 2D IR spectrum contains the eight-peak structure expected for two dominant vibrations of an extended, ordered antiparallel β-sheet. In the proteins with antiparallel β-sheets, interference effects between the diagonal and cross-peaks arising from the sheets, combined with diagonally elongated resonances from additional amide transitions, lead to a characteristic “Z”-shaped pattern for the amide I region in the 2D IR spectrum. We discuss in detail how the number of strands in the sheet, the local configurational disorder in the sheet, the delocalization of the vibrational excitation, and the angle between transition dipole moments affect the position, splitting, amplitude, and line shape of the cross-peaks and diagonal peaks.

The manipulation of massive ro-vibronic superpositions using time-frequency-resolved coherent anti-Stokes Raman scattering (TFRCARS): from quantum control to quantum computing

Molecular ro-vibronic coherences, joint energy-time distributions of quantum amplitudes, are selectively prepared, manipulated, and imaged in Time-Frequency-Resolved Coherent Anti-Stokes Raman Scattering (TFRCARS) measurements using femtosecond laser pulses. The studies are implemented in iodine vapor, with its thermally occupied statistical ro-vibrational density serving as initial state. The evolution of the massive ro-vibronic superpositions, consisting of 1000 eigenstates, is followed through two-dimensional images. The first- and second-order coherences are captured using time-integrated frequency-resolved CARS, while the third-order coherence is captured using time-gated frequency-resolved CARS. The Fourier filtering provided by time integrated detection projects out single ro-vibronic transitions, while time-gated detection allows the projection of arbitrary ro-vibronic superpositions from the coherent third-order polarization. Beside the control and imaging of chemistry, the controlled manipulation of massive quantum coherences suggests the possibility of quantum computing. We argue that the universal logic gates necessary for arbitrary quantum computing - all single qubit operations and the two-qubit controlled-NOT (CNOT) gate - are available in time resolved four-wave mixing in a molecule. The molecular rotational manifold is naturally "wired" for carrying out all single qubit operations efficiently, and in parallel. We identify vibronic coherences as one example of a naturally available two-qubit CNOT gate, wherein the vibrational qubit controls the switching of the targeted electronic qubit.Comment: PDF format. 59 pages, including 22 figures. To appear in Chemical Physic

Elucidating the initial dynamics of electron photodetachment from atoms in liquids using variably-time-delayed resonant multiphoton ionization

We study the photodetachment of electrons from sodium anions in room temperature liquid tetrahydrofuran (THF) using a new type of three-pulse pump-probe spectroscopy. Our experiments use two variably-time-delayed pulses for excitation in what is essentially a resonant 1+1 two-photon ionization: By varying the arrival time of the second excitation pulse, we can directly observe how solvent motions stabilize and trap the excited electron prior to electron detachment. Moreover, by varying the arrival times of the ionization (excitation) and probe pulses, we also can determine the fate of the photoionized electrons and the distance they are ejected from their parent Na atoms. We find that as solvent reorganization proceeds, the second excitation pulse becomes less effective at achieving photoionization, and that the solvent motions that stabilize the excited electron following the first excitation pulse occur over a time of similar to450 fs. We also find that there is no spectroscopic evidence for significant solvent relaxation after detachment of the electron is complete. In combination with the results of previous experiments and molecular dynamics simulations, the data provide new insight into the role of the solvent in solution-phase electron detachment and charge-transfer-to-solvent reactions. (C) 2004 American Institute of Physics

Genotyping a second growth coast redwood forest : a high throughput methodology

The idea that excitonic (electronic) coherences are of fundamental importance to natural photosynthesis gained popularity when slowly dephasing quantum beats (QBs) were observed in the two-dimensional electronic spectra of the Fenna–Matthews–Olson (FMO) complex at 77 K. These were assigned to superpositions of excitonic states, a controversial interpretation, as the strong chromophore–environment interactions in the complex suggest fast dephasing. Although it has been pointed out that vibrational motion produces similar spectral signatures, a concrete assignment of these oscillatory signals to distinct physical processes is still lacking. Here we revisit the coherence dynamics of the FMO complex using polarization-controlled two-dimensional electronic spectroscopy, supported by theoretical modelling. We show that the long-lived QBs are exclusively vibrational in origin, whereas the dephasing of the electronic coherences is completed within 240 fs even at 77 K. We further find that specific vibrational coherences are produced via vibronically coupled excited states. The presence of such states suggests that vibronic coupling is relevant for photosynthetic energy transfer

I. The crystal structures of mono- and the two dimethylureas. II. The determination and use of crystallographic parameters

Part I: The crystal structures of mono-, and the two dimethylureas were determined by x-ray crystallographic methods. The positional and anisotropic temperature parameters of all heavy atoms were refined by the method of least-squares. All of the hydrogen atoms bonded to the amide nitrogen atoms were found in difference map sections computed in the planes of the molecules. Preferred orientations were found for the two methyl groups on N,N-dimethylurea, but the methyl groups in N-methylurea and N, N'-dimethylurea appear to be rotating. The preferred methyl orientations are neither the perfectly staggered nor eclipsed arrangements and appear to depend, in part, on the manner of packing of the molecules to form hydrogen bonded chains in the crystal. The average bond distances were found to be: C=0, 1.253 A; c1-N (carbonyl C), 1.336 A and C2-N (methyl group C), 1.447 A. The partial double bond character is calculated to be 40% for the C=O bond and 30% for the C1-N bonds. The methyl groups appear to make little change in the contributions of the resonance structures to the hybrid structure. The average out of plane distance for the heavy atoms is 0.02 A, the maximum being 0.05 A. The various types and configurations of cis- and trans-amide hydrogen bonds are reviewed and classified by the type of hydrogen bonded chain structure formed. Part II: Expressions employable for the calculation of structure factors and their derivatives for any orthorhombic space group are developed. Complementing this work is a general description of the least-squares method as used to determine a parameter set. Several methods for the conversion of a parameter set into more perceptible quantities, such as interatomic distances, bond angles, planarity of groups of atoms, magnitudes and direction cosines of the principal axes of the vibrational ellipsoids of each atom and the rigid body representation of the thermal displacements and vibrations, are reviewed