Conformational Dynamics of Supramolecular Protein Assemblies in the EMDB

The Electron Microscopy Data Bank (EMDB) is a rapidly growing repository for the dissemination of structural data from single-particle reconstructions of supramolecular protein assemblies including motors, chaperones, cytoskeletal assemblies, and viral capsids. While the static structure of these assemblies provides essential insight into their biological function, their conformational dynamics and mechanics provide additional important information regarding the mechanism of their biological function. Here, we present an unsupervised computational framework to analyze and store for public access the conformational dynamics of supramolecular protein assemblies deposited in the EMDB. Conformational dynamics are analyzed using normal mode analysis in the finite element framework, which is used to compute equilibrium thermal fluctuations, cross-correlations in molecular motions, and strain energy distributions for 452 of the 681 entries stored in the EMDB at present. Results for the viral capsid of hepatitis B, ribosome-bound termination factor RF2, and GroEL are presented in detail and validated with all-atom based models. The conformational dynamics of protein assemblies in the EMDB may be useful in the interpretation of their biological function, as well as in the classification and refinement of EM-based structures.Comment: Associated online data bank available at: http://lcbb.mit.edu/~em-nmdb

D-π-D chromophores based on dithieno[3,2-b:2′,3'-d]thiophene (DTT) : potential application in the fabrication of solar cell

In this work, four stable dithieno[3,2-b:2′,3'-d]thiophene-based π-extended molecules were designed and synthesized via a Pd-catalysed Sonogashira coupling reaction. The structures of these symmetrical compounds, including dithieno[3,2-b:2′,3'-d]thiophene (DTT) as the π-center and various donor (D) groups, were determined on the basis of NMR spectral data, elemental analysis, and X-ray crystallography. The photo-physical properties of the DTT-based derivatives 2 were fully investigated in both solution and solid state. The notable optical features of their solid-state powders showed significant red-shift in comparison with the luminescence of their dilute dichloromethane solutions. These results combined with the theoretical calculations indicate that they are promising candidates for the several applications in electronic and optoelectronic devices, as well as organic dyes for solar cells

Discovery of low-metallicity stars in the central parsec of the Milky Way

We present a metallicity analysis of 83 late-type giants within the central 1 pc of the Milky Way. K-band spectroscopy of these stars were obtained with the medium-spectral resolution integral-field spectrograph NIFS on Gemini North using laser-guide star adaptive optics. Using spectral template fitting with the MARCS synthetic spectral grid, we find that there is large variation in metallicity, with stars ranging from [M/H] $<$ -1.0 to above solar metallicity. About 6\% of the stars have [M/H] $<$ -0.5. This result is in contrast to previous observations, with smaller samples, that show stars at the Galactic center have approximately solar metallicity with only small variations. Our current measurement uncertainties are dominated by systematics in the model, especially at [M/H] $>$ 0, where there are stellar lines not represented in the model. However, the conclusion that there are low metallicity stars, as well as large variations in metallicity is robust. The metallicity may be an indicator of the origin of these stars. The low-metallicity population is consistent with that of globular clusters in the Milky Way, but their small fraction likely means that globular cluster infall is not the dominant mechanism for forming the Milky Way nuclear star cluster. The majority of stars are at or above solar metallicity, which suggests they were formed closer to the Galactic center or from the disk. In addition, our results indicate that it will be important for star formation history analyses using red giants at the Galactic center to consider the effect of varying metallicity.Comment: 11 pages, 10 figures, ApJ Accepte

Properties of the Remnant Clockwise Disk of Young Stars in the Galactic Center

We present new kinematic measurements and modeling of a sample of 116 young stars in the central parsec of the Galaxy in order to investigate the properties of the young stellar disk. The measurements were derived from a combination of speckle and laser guide star adaptive optics imaging and integral field spectroscopy from the Keck telescopes. Compared to earlier disk studies, the most important kinematic measurement improvement is in the precision of the accelerations in the plane of the sky, which have a factor of six smaller uncertainties (~10 uas/yr/yr). We have also added the first radial velocity measurements for 8 young stars, increasing the sample at the largest radii (6"-12") by 25%. We derive the ensemble properties of the observed stars using Monte-Carlo simulations of mock data. There is one highly significant kinematic feature (~20 sigma), corresponding to the well-known clockwise disk, and no significant feature is detected at the location of the previously claimed counterclockwise disk. The true disk fraction is estimated to be ~20%, a factor of ~2.5 lower than previous claims, suggesting that we may be observing the remnant of what used to be a more densely populated stellar disk. The similarity in the kinematic properties of the B stars and the O/WR stars suggests a common star formation event. The intrinsic eccentricity distribution of the disk stars is unimodal, with an average value of = 0.27 +/- 0.07, which we show can be achieved through dynamical relaxation in an initially circular disk with a moderately top-heavy mass function.Comment: 65 pages, 22 figures, 8 tables, submitted to Ap

Recent Results and Perspectives for Precision Astrometry and Photometry with Adaptive Optics

Large ground-based telescopes equipped with adaptive optics (AO) systems have ushered in a new era of high-resolution infrared photometry and astrometry. Relative astrometric accuracies of <0.2 mas have already been demonstrated from infrared images with spatial resolutions of 55-95 mas resolution over 10-20'' fields of view. Relative photometric accuracies of 3% and absolute photometric accuracies of 5%-20% are also possible. I will review improvements and current limitations in astrometry and photometry with adaptive optics of crowded stellar fields. These capabilities enable experiments such as measuring orbits for brown dwarfs and exoplanets, studying our Galaxy's supermassive black hole and its environment, and identifying individual stars in young star clusters, which can be used test the universality of the initial mass function.Comment: SPIE Conference Proceedin

Decision support system for the long-term city metabolism planning problem

A Decision Support System (DSS) tool for the assessment of intervention strategies (Alternatives) in an Urban Water System (UWS) with an integral simulation model called “WaterMet²” is presented. The DSS permits the user to identify one or more optimal Alternatives over a fixed long-term planning horizon using performance metrics mapped to the TRUST sustainability criteria (Alegre et al., 2012). The DSS exposes lists of in-built intervention options and system performance metrics for the user to compose new Alternatives. The quantitative metrics are calculated by the WaterMet² model and further qualitative or user-defined metrics may be specified by the user or by external tools feeding into the DSS. A Multi-Criteria Decision Analysis (MCDA) approach is employed within the DSS to compare the defined Alternatives and to rank them with respect to a pre-specified weighting scheme for different Scenarios. Two rich, interactive Graphical User Interfaces, one desktop and one web-based, are employed to assist with guiding the end user through the stages of defining the problem, evaluating and ranking Alternatives. This mechanism provides a useful tool for decision makers to compare different strategies for the planning of UWS with respect to multiple Scenarios. The efficacy of the DSS is demonstrated on a northern European case study inspired by a real-life urban water system for a mixture of quantitative and qualitative criteria. The results demonstrate how the DSS, integrated with an UWS modelling approach, can be used to assist planners in meeting their long-term, strategic level sustainability objectives

A Spitzer Study of the Mass Loss Histories of Three Bipolar Pre-Planetary Nebulae

We present the results of far-infrared imaging of extended regions around three bipolar pre-planetary nebulae, AFGL 2688, OH 231.8+4.2, and IRAS 16342$-$3814, at 70 and 160 $\mu$m with the MIPS instrument on the Spitzer Space Telescope. After a careful subtraction of the point spread function of the central star from these images, we place constraints on the existence of extended shells and thus on the mass outflow rates as a function of radial distance from these stars. We find no apparent extended emission in AFGL 2688 and OH 231.8+4.2 beyond 100 arcseconds from the central source. In the case of AFGL 2688, this result is inconsistent with a previous report of two extended dust shells made on the basis of ISO observations. We derive an upper limit of $2.1\times10^{-7}$ M$_\odot$ yr$^{-1}$ and $1.0\times10^{-7}$ M$_\odot$ yr$^{-1}$ for the dust mass loss rate of AFGL 2688 and OH 231.8, respectively, at 200 arcseconds from each source. In contrast to these two sources, IRAS 16342$-$3814 does show extended emission at both wavelengths, which can be interpreted as a very large dust shell with a radius of $\sim$ 400 arcseconds and a thickness of $\sim$ 100 arcseconds, corresponding to 4 pc and 1 pc, respectively, at a distance of 2 kpc. However, this enhanced emission may also be galactic cirrus; better azimuthal coverage is necessary for confirmation of a shell. If the extended emission is a shell, it can be modeled as enhanced mass outflow at a dust mass outflow rate of $1.5\times10^{-6}$ M$_\odot$ yr$^{-1}$ superimposed on a steady outflow with a dust mass outflow rate of $1.5\times10^{-7}$ M$_\odot$ yr$^{-1}$. It is likely that this shell has swept up a substantial mass of interstellar gas during its expansion, so these estimates are upper limits to the stellar mass loss rate.Comment: 31 pages, 12 figures, accepted to A