30,051 research outputs found
Finite Boolean Algebras for Solid Geometry using Julia's Sparse Arrays
The goal of this paper is to introduce a new method in computer-aided
geometry of solid modeling. We put forth a novel algebraic technique to
evaluate any variadic expression between polyhedral d-solids (d = 2, 3) with
regularized operators of union, intersection, and difference, i.e., any CSG
tree. The result is obtained in three steps: first, by computing an independent
set of generators for the d-space partition induced by the input; then, by
reducing the solid expression to an equivalent logical formula between Boolean
terms made by zeros and ones; and, finally, by evaluating this expression using
bitwise operators. This method is implemented in Julia using sparse arrays. The
computational evaluation of every possible solid expression, usually denoted as
CSG (Constructive Solid Geometry), is reduced to an equivalent logical
expression of a finite set algebra over the cells of a space partition, and
solved by native bitwise operators.Comment: revised version submitted to Computer-Aided Geometric Desig
Nuclear Disks of Gas and Dust in Early Type Galaxies and the Hunt for Massive Black Holes: Hubble Space Telescope Observations of NGC 6251
We discuss Hubble Space Telescope optical images and spectra of NGC 6251, a
giant E2 galaxy and powerful radio source at a distance of 106 Mpc (for H_0 =
70 km/s/Mpc). The galaxy is known to host a very well defined dust disk (O'Neil
et al. 1994); the exceptional resolution of our V and I images allows a
detailed study of the disk structure. Furthermore, narrow band images centered
on the Halpha+[NII] emission lines, reveal the presence of ionized gas in the
inner 0.3 arcsec of the disk. We used the HST/Faint Object Spectrograph with
the 0.09 arcsec aperture to study the velocity structure of the disk. Dynamical
models were constructed for two extreme (in terms of central concentration)
analytical representations of the stellar surface brightness profile, from
which the mass density and corresponding rotational velocity are derived
assuming a constant mass-to-light ratio (M/L)_V ~ 8.5 M_solar/L_solar. For both
representations of the stellar component, the models show that the gas is in
Keplerian motion around a central mass ~ 4 - 8 X 10^8 solar masses, and that
the contribution of radial flows to the velocity field is negligible.Comment: 45 pages, submitted to Ap
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Archiving and disseminating integrative structure models.
Limitations in the applicability, accuracy, and precision of individual structure characterization methods can sometimes be overcome via an integrative modeling approach that relies on information from all available sources, including all available experimental data and prior models. The open-source Integrative Modeling Platform (IMP) is one piece of software that implements all computational aspects of integrative modeling. To maximize the impact of integrative structures, the coordinates should be made publicly available, as is already the case for structures based on X-ray crystallography, NMR spectroscopy, and electron microscopy. Moreover, the associated experimental data and modeling protocols should also be archived, such that the original results can easily be reproduced. Finally, it is essential that the integrative structures are validated as part of their publication and deposition. A number of research groups have already developed software to implement integrative modeling and have generated a number of structures, prompting the formation of an Integrative/Hybrid Methods Task Force. Following the recommendations of this task force, the existing PDBx/mmCIF data representation used for atomic PDB structures has been extended to address the requirements for archiving integrative structural models. This IHM-dictionary adds a flexible model representation, including coarse graining, models in multiple states and/or related by time or other order, and multiple input experimental information sources. A prototype archiving system called PDB-Dev ( https://pdb-dev.wwpdb.org ) has also been created to archive integrative structural models, together with a Python library to facilitate handling of integrative models in PDBx/mmCIF format
Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools.
This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations
Current Status of Simulations
As the title suggests, the purpose of this chapter is to review the current
status of numerical simulations of black hole accretion disks. This chapter
focuses exclusively on global simulations of the accretion process within a few
tens of gravitational radii of the black hole. Most of the simulations
discussed are performed using general relativistic magnetohydrodynamic (MHD)
schemes, although some mention is made of Newtonian radiation MHD simulations
and smoothed particle hydrodynamics. The goal is to convey some of the exciting
work that has been going on in the past few years and provide some speculation
on future directions.Comment: 15 pages, 14 figures, to appear in the proceedings of the ISSI-Bern
workshop on "The Physics of Accretion onto Black Holes" (8-12 October 2012
Wind from the black-hole accretion disk driving a molecular outflow in an active galaxy
Powerful winds driven by active galactic nuclei (AGN) are often invoked to
play a fundamental role in the evolution of both supermassive black holes
(SMBHs) and their host galaxies, quenching star formation and explaining the
tight SMBH-galaxy relations. Recent observations of large-scale molecular
outflows in ultra-luminous infrared galaxies (ULIRGs) have provided the
evidence to support these studies, as they directly trace the gas out of which
stars form. Theoretical models suggest an origin of these outflows as
energy-conserving flows driven by fast AGN accretion disk winds. Previous
claims of a connection between large-scale molecular outflows and AGN activity
in ULIRGs were incomplete because they were lacking the detection of the
putative inner wind. Conversely, studies of powerful AGN accretion disk winds
to date have focused only on X-ray observations of local Seyferts and a few
higher redshift quasars. Here we show the clear detection of a powerful AGN
accretion disk wind with a mildly relativistic velocity of 0.25c in the X-ray
spectrum of IRAS F11119+3257, a nearby (z = 0.189) optically classified type 1
ULIRG hosting a powerful molecular outflow. The AGN is responsible for ~80% of
the emission, with a quasar-like luminosity of L_AGN = 1.5x10^46 erg/s. The
energetics of these winds are consistent with the energy-conserving mechanism,
which is the basis of the quasar mode feedback in AGN lacking powerful radio
jets.Comment: Revised file including the letter, methods and supplementary
information. Published in the March 26th 2015 issue of Natur
The Computer Graphics Scene in the United States
We briefly survey the major thrusts of computer graphics activities, examining trends and topics rather than offering a comprehensive survey of all that is happening. The directions of professional activities, hardware, software, and algorithms are outlined. Within hardware we examine workstations, personal graphics systems, high performance systems, and low level VLSI chips; within software, standards and interactive system design; within algorithms, visible surface rendering and shading, three-dimensional modeling techniques, and animation.
Note: This paper was presented at Eurographics\u2784 in Copenhagen, Denmark
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