Molecular dynamics simulations of RNA: An in silico single molecule approach

RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require an understanding of structure and dynamics at the atomistic level, which can be significantly improved by combining computational simulation with experiment. This review provides a critical survey of the state of molecular dynamics (MD) simulations of RNA, including a discussion of important current limitations of the technique and examples of its successful application. Several types of simulations are discussed in detail, including those of structured RNA molecules and their interactions with the surrounding solvent and ions, catalytic RNAs, and RNA–small molecule and RNA–protein complexes. Increased cooperation between theorists and experimentalists will allow expanded judicious use of MD simulations to complement conceptually related single molecule experiments. Such cooperation will open the door to a fundamental understanding of the structure–function relationships in diverse and complex RNA molecules. © 2006 Wiley Periodicals, Inc. Biopolymers 85:169–184, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [email protected] Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55864/1/20620_ftp.pd

Osmophores, Floral Features, and Systematics of \u3ci\u3eStanhopea\u3c/i\u3e (Orchidaceae)

The floral fragrance glands (osmophores) of 18 species of Stanhopea and Sievekingia were examined through a series of developmental studies at light and electron microscope levels including late bud stages through postanthesis. Various characters were identified to be of potential systematic value and were recorded for each species. These characters included: texture of the osmophore surface, number of distinct cell layers comprising the osmophore, nature of lipid inclusions in osmophore cells, and presence or absence of plastoglobuli in osmophore amyloplasts. These characters were combined with traditional features of floral lip morphology for cladistic analysis. Sievekingia was the postulated outgroup. Stanhopea ecornuta showed the largest number of plesiomorphic characters. Stanhopea pulla, S. annulata, and S. candida were only slightly more derived. Stanhopea anfracta, S. gibbosa, S. martiana, S. oculata, S. radiosa, S. ruckeri, S. saccata, S. shuttleworthii, S. tigrina, S. vasquezii, and S. wardii form a monophyletic group that can be recognized by a labellum with an articulated epichile and a bicornuate mesochile (or hypochile). Stanhopea tricornis may be a hybrid between a species of Sievekingia and Stanhopea

Does gender matter? A cross-national investigation of primary class-room discipline.

© 2018 Informa UK Limited, trading as Taylor & Francis GroupFewer than 15% of primary school teachers in both Germany and the UK are male. With the on-going international debate about educational performance highlighting the widening gender achievement gap between girl and boy pupils, the demand for more male teachers has become prevalent in educational discourse. Concerns have frequently been raised about the underachievement of boys, with claims that the lack of male ‘role models’ in schools has an adverse effect on boys’ academic motivation and engagement. Although previous research has examined ‘teaching’ as institutional talk, men’s linguistic behaviour in the classroom remains largely ignored, especially in regard to enacting discipline. Using empirical spoken data collected from four primary school classrooms in both the UK and in Germany, this paper examines the linguistic discipline strategies of eight male and eight female teachers using Interactional Sociolinguistics to address the question, does teacher gender matter?Peer reviewedFinal Accepted Versio

The Soft X-Ray Properties of a Complete Sample of Optically Selected Quasars II. Final Results

We present the final results of a ROSAT PSPC program to study the soft X-ray emission properties of a complete sample of low $z$ quasars. The main results are: 1. There is no evidence for significant soft excess emission or excess foreground absorption by cold gas in 22 of the 23 quasars. 2. The mean 0.2-2 keV continuum of quasars agrees remarkably well with an extrapolation of the mean 1050-350A continuum recently determined by Zheng et al. (1996), indicating that there is no steep soft component below 0.2 keV. 3. The occurrence of warm absorbers in quasars is rather rare, in sharp contrast to lower luminosity AGN. 4. The strongest correlation found is between the spectral slope, alpha_x, and the Hb FWHM. This remarkably strong correlation may result from a dependence of alpha_x on L/L_Edd, as seen in Galactic black hole candidates. 5. There appears to exist a distinct class of ``X-ray weak'' quasars. These may be quasars where the direct X-ray source is obscured, and only scattered X-rays are observed. 6. Thin accretion disk models cannot reproduce the observed optical to soft X-ray spectral shape. An as yet unknown physical mechanism maintains a strong correlation between the optical and soft X-ray emission. 7. The well known difference in alpha_x between radio-loud and radio-quiet quasars may be due only to their different Hb FWHM. 8. The agreement of the 21 cm and X-ray columns implies that He in the diffuse H II component of the Galactic ISM is ionized to He II or He III (shortened abstract).Comment: 19 pages of text only, uses aas2pp4.sty file, to appear in ApJ vol. 447, 3/1/97, complete postscript version of 34 pages including 5 tables and 8 figures available at http://physics.technion.ac.il/~laor/rosat/paper.p

The Far-Infrared Spectral Energy Distributions of X-ray-selected Active Galaxies

[Abridged] We present ISO far-infrared (IR) observations of 21 hard X-ray selected AGN from the HEAO-1 A2 sample. We compare the far-IR to X-ray spectral energy distributions (SEDs) of this sample with various radio and optically selected AGN samples. The hard-X-ray selected sample shows a wider range of optical/UV shapes extending to redder near-IR colors. The bluer objects are Seyfert 1s, while the redder AGN are mostly intermediate or type 2 Seyferts. This is consistent with a modified unification model in which the amount of obscuring material increases with viewing angle and may be clumpy. Such a scenario, already suggested by differing optical/near-IR spectroscopic and X-ray AGN classifications, allows for different amounts of obscuration of the continuum emission in different wavebands and of the broad emission line region which results in a mixture of behaviors for AGN with similar optical emission line classifications. The resulting limits on the column density of obscuring material through which we are viewing the redder AGN are 100 times lower than for the standard optically thick torus models. The resulting decrease in optical depth of the obscuring material allows the AGN to heat more dust at larger radial distances. We show that an AGN-heated, flared, dusty disk with mass 10^9 solar and size of few hundred pc is able to generate optical-far-IR SEDs which reproduce the wide range of SEDs present in our sample with no need for an additional starburst component to generate the long-wavelength, cooler part of the IR continuum.Comment: 40 pages, 14 figures, accepted for publication in Astrophysical Journal, V. 590, June 10, 200

Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In

Structure and dynamics are both critical to RNA’s vital functions in biology. Numerous techniques can elucidate the structural dynamics of RNA, but computational approaches based on experimental data arguably hold the promise of providing the most detail. In this Account, we highlight areas wherein molecular dynamics (MD) and quantum mechanical (QM) techniques are applied to RNA, particularly in relation to complementary experimental studies

Thinking outside the channel : modeling nitrogen cycling in networked river ecosystems

Author Posting. © Ecological Society of America, 2011. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Frontiers in Ecology and the Environment 9 (2011): 229–238, doi:10.1890/080211.Agricultural and urban development alters nitrogen and other biogeochemical cycles in rivers worldwide. Because such biogeochemical processes cannot be measured empirically across whole river networks, simulation models are critical tools for understanding river-network biogeochemistry. However, limitations inherent in current models restrict our ability to simulate biogeochemical dynamics among diverse river networks. We illustrate these limitations using a river-network model to scale up in situ measures of nitrogen cycling in eight catchments spanning various geophysical and land-use conditions. Our model results provide evidence that catchment characteristics typically excluded from models may control river-network biogeochemistry. Based on our findings, we identify important components of a revised strategy for simulating biogeochemical dynamics in river networks, including approaches to modeling terrestrial–aquatic linkages, hydrologic exchanges between the channel, floodplain/riparian complex, and subsurface waters, and interactions between coupled biogeochemical cycles.This research was supported by NSF (DEB-0111410). Additional support was provided by NSF for BJP and SMT (DEB-0614301), for WMW (OCE-9726921 and DEB-0614282), for WHM and JDP (DEB-0620919), for SKH (DEB-0423627), and by the Gordon and Betty Moore Foundation for AMH, GCP, ESB, and JAS, and by an EPA Star Fellowship for AMH