Interacting with the biomolecular solvent accessible surface via a haptic feedback device

Background: From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results: A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion: By using the software, named HaptiMol ISAS (available from http://​www.​haptimol.​co.​uk), one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water accessibility of the biomolecular surface that cannot be so easily attained using conventional molecular graphics software

Resolved Spectroscopy of the Narrow-Line Region in NGC 1068: Kinematics of the Ionized Gas

We have determined the radial velocities of the [O III] emitting gas in the inner narrow-line region (NLR) of the Seyfert 2 galaxy NGC 1068, along a slit at position angle of 202 degrees, from STIS observations at a spatial resolution of 0.1 arcsec and a spectral resolving power of approximately 1000. We use these data to investigate the kinematics of the NLR within 6 arcsec (430 pc) of the nucleus. The emission-line knots show evidence for radial acceleration, to a projected angular distance of 1.7 arcsec in most cases, followed by deceleration that approaches the systemic velocity at a projected distance of about 4 arcsec. We find that a simple kinematic model of biconical radial outflow can match the general trend of observed radial velocities. In this model, the emitting material is evacuated along the bicone axis, and the axis is inclined 5 degrees out of the plane of the sky. The acceleration of the emission-line clouds provides support for dynamical models that invoke radiation and/or wind pressure. We suggest that the deceleration of the clouds is due to their collision with a patchy and anistropically distributed ambient medium.Comment: 18 pages, Latex, includes 3 figures in postscript, to appear in the Astrophysical Journal Letter

Determining the Nature of Late Gunn-Peterson Troughs with Galaxy Surveys

Recent observations have discovered long (up to ~110 Mpc/h), opaque Gunn-Peterson troughs in the z ~ 5.5 Lyman-alpha forest, which are challenging to explain with conventional models of the post-reionization intergalactic medium. Here we demonstrate that observations of the galaxy populations in the vicinity of the deepest troughs can distinguish two competing models for these features: deep voids where the ionizing background is weak due to fluctuations in the mean free path of ionizing photons would show a deficit of galaxies, while residual temperature variations from extended, inhomogeneous reionization would show an overdensity of galaxies. We use large (~550 Mpc/h) semi-numerical simulations of these competing explanations to predict the galaxy populations in the largest of the known troughs at z ~ 5.7. We quantify the strong correlation of Lyman-alpha effective optical depth and galaxy surface density in both models and estimate the degree to which realistic surveys can measure such a correlation. While a spectroscopic galaxy survey is ideal, we also show that a relatively inexpensive narrowband survey of Lyman-alpha-emitting galaxies is ~90% likely to distinguish between the competing models.Comment: 12 pages, 16 figures. Submitted to Ap

2004 MICHIGAN LAND VALUES

Land Economics/Use,

Lake sedimentological and ecological response to hyperthermals : Boltysh impact crater, Ukraine

Acknowledgements Initial drilling of the Boltysh meteorite crater was funded by Natural Environment Research Council (NERC) grant NE/D005043/1. The authors are extremely grateful to the valuable scientific contributions of S. Kelley and I. Gilmour. The constructive and critical reviews by M. Schuster and an anonymous reviewer greatly helped to improve this manuscript.Peer reviewedPostprin

Mining topological relations from the web

Topological relations between geographic regions are of interest in many applications. When the exact boundaries of regions are not available, such relations can be established by analysing natural language information from web documents. In particular we demonstrate how redundancy-based techniques can be used to acquire containment and adjacency relations, and how fuzzy spatial reasoning can be employed to maintain the consistency of the resulting knowledge base

Ultraviolet Divergences in Cosmological Correlations

A method is developed for dealing with ultraviolet divergences in calculations of cosmological correlations, which does not depend on dimensional regularization. An extended version of the WKB approximation is used to analyze the divergences in these calculations, and these divergences are controlled by the introduction of Pauli--Villars regulator fields. This approach is illustrated in the theory of a scalar field with arbitrary self-interactions in a fixed flat-space Robertson--Walker metric with arbitrary scale factor $a(t)$. Explicit formulas are given for the counterterms needed to cancel all dependence on the regulator properties, and an explicit prescription is given for calculating finite regulator-independent correlation functions. The possibility of infrared divergences in this theory is briefly considered.Comment: References added on various regularization methods. Improved discussion of further issues. 26 pages, 1 figur