2,242 research outputs found
Exons, introns and DNA thermodynamics
The genes of eukaryotes are characterized by protein coding fragments, the
exons, interrupted by introns, i.e. stretches of DNA which do not carry any
useful information for the protein synthesis. We have analyzed the melting
behavior of randomly selected human cDNA sequences obtained from the genomic
DNA by removing all introns. A clear correspondence is observed between exons
and melting domains. This finding may provide new insights in the physical
mechanisms underlying the evolution of genes.Comment: 4 pages, 8 figures - Final version as published. See also Phys. Rev.
Focus 15, story 1
Ephemeral active regions and coronal bright points: A solar maximum Mission 2 guest investigator study
A dominate association of coronal bright points (as seen in He wavelength 10830) was confirmed with the approach and subsequent disappearance of opposite polarity magnetic network. While coronal bright points do occur with ephemeral regions, this association is a factor of 2 to 4 less than with sites of disappearing magnetic flux. The intensity variations seen in He I wavelength 10830 are intermittent and often rapid, varying over the 3 minute time resolution of the data; their bright point counterparts in the C IV wavelength 1548 and 20 cm wavelength show similar, though not always coincident time variations. Ejecta are associated with about 1/3 of the dark points and are evident in the C IV and H alpha data. These results support the idea that the anti-correlation of X-ray bright points with the solar cycle can be explained by the correlation of these coronal emission structures with sites of cancelling flux, indicating that, in some cases, the process of magnetic flux removal results in the release of energy. That the intensity variations are rapid and variable suggests that this process works intermittently
Globular Structures of a Helix-Coil Copolymer: Self-Consistent Treatment
A self-consistent field theory was developed in the grand-canonical ensemble
formulation to study transitions in a helix-coil multiblock globule. Helical
and coil parts are treated as stiff rods and self-avoiding walks of variable
lengths correspondingly. The resulting field-theory takes, in addition to the
conventional Zimm-Bragg (B.H. Zimm, I.K. Bragg, J. Chem. Phys. 31, 526 (1959))
parameters, also three-dimensional interaction terms into account. The
appropriate differential equations which determine the self-consistent fields
were solved numerically with finite element method. Three different phase
states are found: open chain, amorphous globule and nematic liquid-crystalline
(LC) globule. The LC-globule formation is driven by the interplay between the
hydrophobic helical segments attraction and the anisotropic globule surface
energy of an entropic nature. The full phase diagram of the helix-coil
copolymer was calculated and thoroughly discussed. The suggested theory shows a
clear interplay between secondary and tertiary structures in globular
homopolypeptides.Comment: 26 pages, 30 figures, corrected some typo
A length-dynamic Tonks gas theory of histone isotherms
We find exact solutions to a new one-dimensional (1D) interacting particle
theory and apply the results to the adsorption and wrapping of polymers (such
as DNA) around protein particles (such as histones). Each adsorbed protein is
represented by a Tonks gas particle. The length of each particle is a degree of
freedom that represents the degree of DNA wrapping around each histone.
Thermodynamic quantities are computed as functions of wrapping energy, adsorbed
histone density, and bulk histone concentration (or chemical potential); their
experimental signatures are also discussed. Histone density is found to undergo
a two-stage adsorption process as a function of chemical potential, while the
mean coverage by high affinity proteins exhibits a maximum as a function of the
chemical potential. However, {\it fluctuations} in the coverage are
concurrently maximal. Histone-histone correlation functions are also computed
and exhibit rich two length scale behavior.Comment: 5 pp, 3 fig
Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
We explore in detail the structural, mechanical and thermodynamic properties
of a coarse-grained model of DNA similar to that introduced in Thomas E.
Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101
(2010). Effective interactions are used to represent chain connectivity,
excluded volume, base stacking and hydrogen bonding, naturally reproducing a
range of DNA behaviour. We quantify the relation to experiment of the
thermodynamics of single-stranded stacking, duplex hybridization and hairpin
formation, as well as structural properties such as the persistence length of
single strands and duplexes, and the torsional and stretching stiffness of
double helices. We also explore the model's representation of more complex
motifs involving dangling ends, bulged bases and internal loops, and the effect
of stacking and fraying on the thermodynamics of the duplex formation
transition.Comment: 25 pages, 16 figure
Microscopic formulation of the Zimm-Bragg model for the helix-coil transition
A microscopic spin model is proposed for the phenomenological Zimm-Bragg
model for the helix-coil transition in biopolymers. This model is shown to
provide the same thermophysical properties of the original Zimm-Bragg model and
it allows a very convenient framework to compute statistical quantities.
Physical origins of this spin model are made transparent by an exact mapping
into a one-dimensional Ising model with an external field. However, the
dependence on temperature of the reduced external field turns out to differ
from the standard one-dimensional Ising model and hence it gives rise to
different thermophysical properties, despite the exact mapping connecting them.
We discuss how this point has been frequently overlooked in the recent
literature.Comment: 11 pages, 2 figure
DNA bubble dynamics as a quantum Coulomb problem
We study the dynamics of denaturation bubbles in double-stranded DNA on the
basis of the Poland-Scheraga model. We demonstrate that the associated
Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting
temperature the bubble lifetime is associated with the continuum of scattering
states of the repulsive Coulomb potential, at the melting temperature the
Coulomb potential vanishes and the underlying first exit dynamics exhibits a
long time power law tail, above the melting temperature, corresponding to an
attractive Coulomb potential, the long time dynamics is controlled by the
lowest bound state. Correlations and finite size effects are discussed.Comment: 4 pages, 3 figures, revte
Entropically driven transition to a liquid-crystalline polymer globule
A self-consistent-field theory (SCFT) in the grand canonical ensemble
formulation is used to study transitions in a helix-coil multiblock copolymer
globule. The helices are modeled as stiff rods. In addition to the established
coil-globule transition we show for the first time that, even without explicit
rod-rod alignment interaction, the system undergoes a transition to a nematic
liquid-crystalline (LC) globular state. The LC-globule formation is driven by
the hydrophobic helical segment attraction and the anisotropy of the globule
surface energy. The full phase diagram of the copolymer was calculated. It
discriminates between an open chain, amorphous globule and LC-globule. This
model provides a relatively simple example of the interplay between secondary
and tertiary structures in homopolypeptides. Moreover, it gives a simple
explanation for the formation of helix bundles in certain globular proteins.Comment: 5 pages, 5 figures, submitted to Europhys. Let
An efficient algorithm for learning with semi-bandit feedback
We consider the problem of online combinatorial optimization under
semi-bandit feedback. The goal of the learner is to sequentially select its
actions from a combinatorial decision set so as to minimize its cumulative
loss. We propose a learning algorithm for this problem based on combining the
Follow-the-Perturbed-Leader (FPL) prediction method with a novel loss
estimation procedure called Geometric Resampling (GR). Contrary to previous
solutions, the resulting algorithm can be efficiently implemented for any
decision set where efficient offline combinatorial optimization is possible at
all. Assuming that the elements of the decision set can be described with
d-dimensional binary vectors with at most m non-zero entries, we show that the
expected regret of our algorithm after T rounds is O(m sqrt(dT log d)). As a
side result, we also improve the best known regret bounds for FPL in the full
information setting to O(m^(3/2) sqrt(T log d)), gaining a factor of sqrt(d/m)
over previous bounds for this algorithm.Comment: submitted to ALT 201
SUMER: Solar Ultraviolet Measurements of Emitted Radiation
The SUMER (solar ultraviolet measurements of emitted radiation) experiment is described. It will study flows, turbulent motions, waves, temperatures and densities of the plasma in the upper atmosphere of the Sun. Structures and events associated with solar magnetic activity will be observed on various spatial and temporal scales. This will contribute to the understanding of coronal heating processes and the solar wind expansion. The instrument will take images of the Sun in EUV (extreme ultra violet) light with high resolution in space, wavelength and time. The spatial resolution and spectral resolving power of the instrument are described. Spectral shifts can be determined with subpixel accuracy. The wavelength range extends from 500 to 1600 angstroms. The integration time can be as short as one second. Line profiles, shifts and broadenings are studied. Ratios of temperature and density sensitive EUV emission lines are established
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