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