161 research outputs found
Structure and Dynamics of the Sun's Open Magnetic Field
The solar magnetic field is the primary agent that drives solar activity and
couples the Sun to the Heliosphere. Although the details of this coupling
depend on the quantitative properties of the field, many important aspects of
the corona - solar wind connection can be understood by considering only the
general topological properties of those regions on the Sun where the field
extends from the photosphere out to interplanetary space, the so-called open
field regions that are usually observed as coronal holes. From the simple
assumptions that underlie the standard quasi-steady corona-wind theoretical
models, and that are likely to hold for the Sun, as well, we derive two
conjectures on the possible structure and dynamics of coronal holes: (1)
Coronal holes are unique in that every unipolar region on the photosphere can
contain at most one coronal hole. (2) Coronal holes of nested polarity regions
must themselves be nested. Magnetic reconnection plays the central role in
enforcing these constraints on the field topology. From these conjectures we
derive additional properties for the topology of open field regions, and
propose several observational predictions for both the slowly varying and
transient corona/solar wind.Comment: 26 pages, 6 figure
Dynamics of solar coronal loops II. Catastrophic cooling and high-speed downflows
This work addresses the problem of plasma condensation and ``catastrophic
cooling'' in solar coronal loops. We have carried out numerical calculations of
coronal loops and find several classes of time-dependent solutions (static,
periodic, irregular), depending on the spatial distribution of a temporally
constant energy deposition in the loop. Dynamic loops exhibit recurrent plasma
condensations, accompanied by high-speed downflows and transient brightenings
of transition region lines, in good agreement with features observed with
TRACE. Furthermore, these results also offer an explanation for the recent EIT
observations of De Groof et al. (2004) of moving bright blobs in large coronal
loops. In contrast to earlier models, we suggest that the process of
catastrophic cooling is not initiated by a drastic decrease of the total loop
heating but rather results from a loss of equilibrium at the loop apex as a
natural consequence of heating concentrated at the footpoints of the loop, but
constant in time.Comment: 13 pages, 15 figure
Physics of Solar Prominences: II - Magnetic Structure and Dynamics
Observations and models of solar prominences are reviewed. We focus on
non-eruptive prominences, and describe recent progress in four areas of
prominence research: (1) magnetic structure deduced from observations and
models, (2) the dynamics of prominence plasmas (formation and flows), (3)
Magneto-hydrodynamic (MHD) waves in prominences and (4) the formation and
large-scale patterns of the filament channels in which prominences are located.
Finally, several outstanding issues in prominence research are discussed, along
with observations and models required to resolve them.Comment: 75 pages, 31 pictures, review pape
On Solving the Coronal Heating Problem
This article assesses the current state of understanding of coronal heating,
outlines the key elements of a comprehensive strategy for solving the problem,
and warns of obstacles that must be overcome along the way.Comment: Accepted by Solar Physics; Published by Solar Physic
Homologous Flares and Magnetic Field Topology in Active Region NOAA 10501 on 20 November 2003
We present and interpret observations of two morphologically homologous
flares that occurred in active region (AR) NOAA 10501 on 20 November 2003. Both
flares displayed four homologous H-alpha ribbons and were both accompanied by
coronal mass ejections (CMEs). The central flare ribbons were located at the
site of an emerging bipole in the center of the active region. The negative
polarity of this bipole fragmented in two main pieces, one rotating around the
positive polarity by ~ 110 deg within 32 hours. We model the coronal magnetic
field and compute its topology, using as boundary condition the magnetogram
closest in time to each flare. In particular, we calculate the location of
quasiseparatrix layers (QSLs) in order to understand the connectivity between
the flare ribbons. Though several polarities were present in AR 10501, the
global magnetic field topology corresponds to a quadrupolar magnetic field
distribution without magnetic null points. For both flares, the photospheric
traces of QSLs are similar and match well the locations of the four H-alpha
ribbons. This globally unchanged topology and the continuous shearing by the
rotating bipole are two key factors responsible for the flare homology.
However, our analyses also indicate that different magnetic connectivity
domains of the quadrupolar configuration become unstable during each flare, so
that magnetic reconnection proceeds differently in both events.Comment: 24 pages, 10 figures, Solar Physics (accepted
Recurrence quantification analysis as a tool for the characterization of molecular dynamics simulations
A molecular dynamics simulation of a Lennard-Jones fluid, and a trajectory of
the B1 immunoglobulin G-binding domain of streptococcal protein G (B1-IgG)
simulated in water are analyzed by recurrence quantification, which is
noteworthy for its independence from stationarity constraints, as well as its
ability to detect transients, and both linear and nonlinear state changes. The
results demonstrate the sensitivity of the technique for the discrimination of
phase sensitive dynamics. Physical interpretation of the recurrence measures is
also discussed.Comment: 7 pages, 8 figures, revtex; revised for review for Phys. Rev. E
(clarifications and expansion of discussion)-- addition of the 8 postscript
figures previously omitted, but unchanged from version
Origins of the Ambient Solar Wind: Implications for Space Weather
The Sun's outer atmosphere is heated to temperatures of millions of degrees,
and solar plasma flows out into interplanetary space at supersonic speeds. This
paper reviews our current understanding of these interrelated problems: coronal
heating and the acceleration of the ambient solar wind. We also discuss where
the community stands in its ability to forecast how variations in the solar
wind (i.e., fast and slow wind streams) impact the Earth. Although the last few
decades have seen significant progress in observations and modeling, we still
do not have a complete understanding of the relevant physical processes, nor do
we have a quantitatively precise census of which coronal structures contribute
to specific types of solar wind. Fast streams are known to be connected to the
central regions of large coronal holes. Slow streams, however, appear to come
from a wide range of sources, including streamers, pseudostreamers, coronal
loops, active regions, and coronal hole boundaries. Complicating our
understanding even more is the fact that processes such as turbulence,
stream-stream interactions, and Coulomb collisions can make it difficult to
unambiguously map a parcel measured at 1 AU back down to its coronal source. We
also review recent progress -- in theoretical modeling, observational data
analysis, and forecasting techniques that sit at the interface between data and
theory -- that gives us hope that the above problems are indeed solvable.Comment: Accepted for publication in Space Science Reviews. Special issue
connected with a 2016 ISSI workshop on "The Scientific Foundations of Space
Weather." 44 pages, 9 figure
Variational Approach to Molecular Kinetics
The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and state-to-state transition rates. Here, we present a variational approach for computing these dominant eigenvalues and eigenvectors. This approach is analogous the variational approach used for computing stationary states in quantum mechanics. A corresponding method of linear variation is formulated. It is shown that the matrices needed for the linear variation method are correlation matrices that can be estimated from simple MD simulations for a given basis set. The method proposed here is thus to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics
A two-step mechanism for epigenetic specification of centromere identity and function
The basic determinant of chromosome inheritance, the centromere, is specified in many eukaryotes by an epigenetic mark. Using gene targeting in human cells and fission yeast, chromatin containing the centromere-specific histone H3 variant CENP-A is demonstrated to be the epigenetic mark that acts through a two-step mechanism to identify, maintain and propagate centromere function indefinitely. Initially, centromere position is replicated and maintained by chromatin assembled with the centromere-targeting domain (CATD) of CENP-A substituted into H3. Subsequently, nucleation of kinetochore assembly onto CATD-containing chromatin is shown to require either the amino- or carboxy-terminal tail of CENP-A for recruitment of inner kinetochore proteins, including stabilizing CENP-B binding to human centromeres or direct recruitment of CENP-C, respectively.National Institutes of Health grant: (GM 074150); Ludwig Institute for Cancer Research; European Molecular Biology Organization (EMBO) long-term fellowship
Calculation of the Free Energy and Cooperativity of Protein Folding
Calculation of the free energy of protein folding and delineation of its pre-organization are of foremost importance for understanding, predicting and designing biological macromolecules. Here, we introduce an energy smoothing variant of parallel tempering replica exchange Monte Carlo (REMS) that allows for efficient configurational sampling of flexible solutes under the conditions of molecular hydration. Its usage to calculate the thermal stability of a model globular protein, Trp cage TC5b, achieves excellent agreement with experimental measurements. We find that the stability of TC5b is attained through the coupled formation of local and non-local interactions. Remarkably, many of these structures persist at high temperature, concomitant with the origin of native-like configurations and mesostates in an otherwise macroscopically disordered unfolded state. Graph manifold learning reveals that the conversion of these mesostates to the native state is structurally heterogeneous, and that the cooperativity of their formation is encoded largely by the unfolded state ensemble. In all, these studies establish the extent of thermodynamic and structural pre-organization of folding of this model globular protein, and achieve the calculation of macromolecular stability ab initio, as required for ab initio structure prediction, genome annotation, and drug design
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