864 research outputs found
Variable-free exploration of stochastic models: a gene regulatory network example
Finding coarse-grained, low-dimensional descriptions is an important task in
the analysis of complex, stochastic models of gene regulatory networks. This
task involves (a) identifying observables that best describe the state of these
complex systems and (b) characterizing the dynamics of the observables. In a
previous paper [13], we assumed that good observables were known a priori, and
presented an equation-free approach to approximate coarse-grained quantities
(i.e, effective drift and diffusion coefficients) that characterize the
long-time behavior of the observables. Here we use diffusion maps [9] to
extract appropriate observables ("reduction coordinates") in an automated
fashion; these involve the leading eigenvectors of a weighted Laplacian on a
graph constructed from network simulation data. We present lifting and
restriction procedures for translating between physical variables and these
data-based observables. These procedures allow us to perform equation-free
coarse-grained, computations characterizing the long-term dynamics through the
design and processing of short bursts of stochastic simulation initialized at
appropriate values of the data-based observables.Comment: 26 pages, 9 figure
A FLAMINGOS Deep Near Infrared Imaging Survey of the Rosette Complex I: Identification and Distribution of the Embedded Population
We present the results of a deep near-infrared imaging survey of the Rosette
Complex. We studied the distribution of young embedded sources using a
variation of the Nearest Neighbor Method applied to a carefully selected sample
of near-infrared excess (NIRX) stars which trace the latest episode of star
formation in the complex. Our analysis confirmed the existence of seven
clusters previously detected in the molecular cloud, and identified four more
clusters across the complex. We determined that 60% of the young stars in the
complex and 86% of the stars within the molecular cloud are contained in
clusters, implying that the majority of stars in the Rosette formed in embedded
clusters. We compare the sizes, infrared excess fractions and average
extinction towards individual clusters to investigate their early evolution and
expansion. We found that the average infrared excess fraction of clusters
increases as a function of distance from NGC 2244, implying a temporal sequence
of star formation across the complex. This sequence appears to be primordial,
possibly resulting from the formation and evolution of the molecular cloud and
not from the interaction with the HII region.Comment: Accepted by Astrophysical Journa
A Disk Shadow Around the Young Star ASR 41 in NGC 1333
We present images of the young stellar object ASR 41 in the NGC 1333 star
forming region at the wavelengths of H_alpha and [SII] and in the I, J, H, and
K-bands.
ASR 41 has the near-infrared morphology of an edge-on disk object, but
appears an order of magnitude larger than typical systems of this kind.
We also present detailed models of the scattering and radiative transfer in
systems consisting of a young star surrounded by a proto-planetary disk, and
the whole system being embedded in either an infalling envelope or a uniform
molecular cloud. The best fit to the observed morphology can be achieved with a
disk of approx. 200 AU diameter, immersed in a low density cloud. The low cloud
density is necessary to stay below the sub-mm flux upper limits and to preserve
the shadow cast by the disk via single scattering.
The results demonstrate that ASR 41 is probably not inherently different from
typical edge-on disk objects, and that its large apparent size is due to the
shadow of a much smaller disk being projected into the surrounding dusty
molecular material
Directed motion emerging from two coupled random processes: Translocation of a chain through a membrane nanopore driven by binding proteins
We investigate the translocation of a stiff polymer consisting of M monomers
through a nanopore in a membrane, in the presence of binding particles
(chaperones) that bind onto the polymer, and partially prevent backsliding of
the polymer through the pore. The process is characterized by the rates: k for
the polymer to make a diffusive jump through the pore, q for unbinding of a
chaperone, and the rate q kappa for binding (with a binding strength kappa);
except for the case of no binding kappa=0 the presence of the chaperones give
rise to an effective force that drives the translocation process. Based on a
(2+1) variate master equation, we study in detail the coupled dynamics of
diffusive translocation and (partial) rectification by the binding proteins. In
particular, we calculate the mean translocation time as a function of the
various physical parameters.Comment: 22 pages, 5 figures, IOP styl
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