Analysis of Three-Dimensional Protein Images

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains labor intensive and relies on an expert's ability to derive and evaluate a protein scene model. In this paper, the problem of protein structure determination is formulated as an exercise in scene analysis. A computational methodology is presented in which a 3D image of a protein is segmented into a graph of critical points. Bayesian and certainty factor approaches are described and used to analyze critical point graphs and identify meaningful substructures, such as alpha-helices and beta-sheets. Results of applying the methodologies to protein images at low and medium resolution are reported. The research is related to approaches to representation, segmentation and classification in vision, as well as to top-down approaches to protein structure prediction.Comment: See http://www.jair.org/ for any accompanying file

On the electromagnetic form factors of the proton from generalized Skyrme models

We compare the prediction of Skyrme-like effective Lagrangians with data for electromagnetic form factors of proton and consider the possibility of fixing the parameters of these higher-order Lagrangians. Our results indicate that one or two-parameter models can lead to better agreement with the data but more accurate determination of the effective Lagragian faces theoretical uncertainties.Comment: 8 pages, 2 figures, revte

Astronomical spectrograph calibration with broad-spectrum frequency combs

Broadband femtosecond-laser frequency combs are filtered to spectrographically resolvable frequency-mode spacing, and the limitations of using cavities for spectral filtering are considered. Data and theory are used to show implications to spectrographic calibration of high-resolution, astronomical spectrometers

Theoretical models of planetary system formation: mass vs semi-major axis

Planet formation models have been developed during the last years in order to try to reproduce the observations of both the solar system, and the extrasolar planets. Some of these models have partially succeeded, focussing however on massive planets, and for the sake of simplicity excluding planets belonging to planetary systems. However, more and more planets are now found in planetary systems. This tendency, which is a result of both radial velocity, transit and direct imaging surveys, seems to be even more pronounced for low mass planets. These new observations require the improvement of planet formation models, including new physics, and considering the formation of systems. In a recent series of papers, we have presented some improvements in the physics of our models, focussing in particular on the internal structure of forming planets, and on the computation of the excitation state of planetesimals, and their resulting accretion rate. In this paper, we focus on the concurrent effect of the formation of more than one planet in the same protoplanetary disc, and show the effect, in terms of global architecture and composition of this multiplicity. We use a N-body calculation including collision detection to compute the orbital evolution of a planetary system. Moreover, we describe the effect of competition for accretion of gas and solids, as well as the effect of gravitational interactions between planets. We show that the masses and semi-major axis of planets are modified by both the effect of competition and gravitational interactions. We also present the effect of the assumed number of forming planets in the same system (a free parameter of the model), as well as the effect of the inclination and eccentricity damping.Comment: accepted in Astronomy and Astrophysic

Letter from Arthur Stover, also letters of recommendation from S. Fortier and Elwood Mead

Letter concerning a position in the engineering department at Utah Agricultural College, as well as recommendations

Measurement of excited-state transitions in cold calcium atoms by direct femtosecond frequency-comb spectroscopy

We apply direct frequency-comb spectroscopy, in combination with precision cw spectroscopy, to measure the ${\rm 4s4p} ^3P_1 \to {\rm 4s5s} ^3S_1$ transition frequency in cold calcium atoms. A 657 nm ultrastable cw laser was used to excite atoms on the narrow ($\gamma \sim 400$ Hz) ${\rm 4s^2} ^1S_0 \to {\rm 4s4p} ^3P_1$ clock transition, and the direct output of the frequency comb was used to excite those atoms from the ${\rm 4s4p} ^3P_1$ state to the ${\rm 4s5s} ^3S_1$ state. The resonance of this second stage was detected by observing a decrease in population of the ground state as a result of atoms being optically pumped to the metastable ${\rm 4s4p} ^3P_{0,2}$ states. The ${\rm 4s4p} ^3P_1 \to {\rm 4s5s} ^3S_1$ transition frequency is measured to be $\nu = 489 544 285 713(56)$ kHz; which is an improvement by almost four orders of magnitude over the previously measured value. In addition, we demonstrate spectroscopy on magnetically trapped atoms in the ${\rm 4s4p} ^3P_2$ state.Comment: 4 pages 5 figure

Kilohertz-resolution spectroscopy of cold atoms with an optical frequency comb

We have performed sub-Doppler spectroscopy on the narrow intercombination line of cold calcium atoms using the amplified output of a femtosecond laser frequency comb. Injection locking of a 657-nm diode laser with a femtosecond comb allows for two regimes of amplification, one in which many lines of the comb are amplified, and one where a single line is predominantly amplified. The output of the laser in both regimes was used to perform kilohertz-level spectroscopy. This experiment demonstrates the potential for high-resolution absolute-frequency spectroscopy over the entire spectrum of the frequency comb output using a single high-finesse optical reference cavity.Comment: 4 pages, 4 Figure

Efficient avian pollination of Strelitzia reginae outside of South Africa

AbstractIn its native South Africa, endemic birds pollinate the complex flowers of Strelitzia reginae (bird of paradise) through a highly complex method of pollination. The plant is cultivated worldwide in warm-temperated regions but systematic pollination of the ornithophilous species by local birds has not been reported, and, consequently, seed production is rare outside of South Africa. We found that a member of the New World warblers, Geothlypis trichas, efficiently carried out pollination of S. reginae in southern California, thereby supplementing its typical diet of insects with the energy-rich nectar of S. reginae. Only occasionally, seeds were found in plantings not visited by these birds. The pollinator service provided by the warbler increases seed production in an area outside of South Africa. This could lead to adaptive changes in the exotic species, advance species establishment and persistence and possibly promote invasive behavior in a non-native environment

An experience sampling study of physical activity and positive affect: investigating the role of situational motivation and perceived intensity across time

The nature of the association between physical activity and positive affect is complex, prompting experts to recommend continued examination of moderating variables. The main purpose of this 2-week field study was to examine the influence of situational motivational regulations from self-determination theory (SDT) on changes in positive affect from pre- to post- to 3-hours post-physical activity. Another purpose was to clarify the relationship between physical activity intensity [i.e., Ratings of Perceived Exertion (RPE)] and positive affect at the stated time points. This study employed an experience sampling design using electronic questionnaires. Sixty-six healthy and active, multiple-role women provided recurrent assessments of their physical activity, situational motivation, and positive affect in their everyday lives over a 14-day period. Specifically, measures were obtained at the three time points of interest (i.e., pre-, post-, 3-hours post-physical activity). The data were analyzed using multilevel modeling. Results showed that intrinsic motivation was related to post-physical activity positive affect while the influence of identified regulation appeared 3-hours post-physical activity. In addition, RPE, which was significantly predicted by levels of introjection, was more strongly associated with an increase in positive affect post-physical activity than three hours later. The theoretical implications of these findings vis-à vis SDT, namely in regards to a viable motivational sequence predicting the influence of physical activity on affective states, are discussed. The findings regarding the differential influences of RPE and motivational regulations carries applications for facilitating women’s well-being