1,903 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
The Phase Structure of Supersymmetric Sp(2N_c) Gauge Theories with an Adjoint
We study the phase structure of N = 1 supersymmetric Sp(2N_c) gauge theories
with 2N_f fundamentals, an adjoint, and vanishing superpotential. Using
a-maximization, we derive analytic expressions for the values of N_f below
which the first several gauge-invariant operators in the chiral ring violate
the unitarity bound and become free fields. In doing so we are able to
explicitly check previous conjectures about the behavior of this theory made by
Luty, Schmaltz, and Terning. We then compare this to an analysis of the first
two 'deconfined' dual descriptions based on the gauge groups Sp(2N_f+2) x
SO(2N_c+5) and Sp(2N_f+2) x SO(4N_f+4) x Sp(2N_c+2), finding precise agreement.
In particular, we find no evidence for non-obvious accidental symmetries or the
appearance of a mixed phase in which one of the dual gauge groups becomes free.Comment: 18 pages, 2 figures; v2: added references to match JHEP versio
Propfan Test Assessment (PTA)
The objectives of the Propfan Test Assessment (PTA) Program were to validate in flight the structural integrity of large-scale propfan blades and to measure noise characteristics of the propfan in both near and far fields. All program objectives were met or exceeded, on schedule and under budget. A Gulfstream Aerospace Corporation GII aircraft was modified to provide a testbed for the 2.74m (9 ft) diameter Hamilton Standard SR-7 propfan which was driven by a 4475 kw (600 shp) turboshaft engine mounted on the left-hand wing of the aircraft. Flight research tests were performed for 20 combinations of speed and altitude within a flight envelope that extended to Mach numbers of 0.85 and altitudes of 12,192m (40,000 ft). Propfan blade stress, near-field noise on aircraft surfaces, and cabin noise were recorded. Primary variables were propfan power and tip speed, and the nacelle tilt angle. Extensive low altitude far-field noise tests were made to measure flyover and sideline noise and the lateral attenuation of noise. In coopertion with the FAA, tests were also made of flyover noise for the aircraft at 6100m (20,000 ft) and 10,668m (35,000 ft). A final series of tests were flown to evaluate an advanced cabin wall noise treatment that was produced under a separate program by NASA-Langley Research Center
A simple model for DNA denaturation
Following Poland and Scheraga, we consider a simplified model for the
denaturation transition of DNA. The two strands are modeled as interacting
polymer chains. The attractive interactions, which mimic the pairing between
the four bases, are reduced to a single short range binding term. Furthermore,
base-pair misalignments are forbidden, implying that this binding term exists
only for corresponding (same curvilinear abscissae) monomers of the two chains.
We take into account the excluded volume repulsion between monomers of the two
chains, but neglect intra-chain repulsion. We find that the excluded volume
term generates an effective repulsive interaction between the chains, which
decays as . Due to this long-range repulsion between the chains, the
denaturation transition is first order in any dimension, in agreement with
previous studies.Comment: 10 page
Helix or Coil? Fate of a Melting Heteropolymer
We determine the probability that a partially melted heteropolymer at the
melting temperature will either melt completely or return to a helix state.
This system is equivalent to the splitting probability for a diffusing particle
on a finite interval that moves according to the Sinai model. When the initial
fraction of melted polymer is f, the melting probability fluctuates between
different realizations of monomer sequences on the polymer. For a fixed value
of f, the melting probability distribution changes from unimodal to a bimodal
as the strength of the disorder is increased.Comment: 4 pages, 5 figure
Higgs Boson Decays to Neutralinos in Low-Scale Gauge Mediation
We study the decays of a standard model-like MSSM Higgs boson to pairs of
neutralinos, each of which subsequently decays promptly to a photon and a
gravitino. Such decays can arise in supersymmetric scenarios where
supersymmetry breaking is mediated to us by gauge interactions with a
relatively light gauge messenger sector (M_{mess} < 100 TeV). This process
gives rise to a collider signal consisting of a pair of photons and missing
energy. In the present work we investigate the bounds on this scenario within
the minimal supersymmetric standard model from existing collider data. We also
study the prospects for discovering the Higgs boson through this decay mode
with upcoming data from the Tevatron and the LHC.Comment: 18 pages, 5 figures, added references and discussion of neutralino
couplings, same as journal versio
Roles of stiffness and excluded volume in DNA denaturation
The nature and the universal properties of DNA thermal denaturation are
investigated by Monte Carlo simulations. For suitable lattice models we
determine the exponent c describing the decay of the probability distribution
of denaturated loops of length l, . If excluded volume effects
are fully taken into account, c= 2.10(4) is consistent with a first order
transition. The stiffness of the double stranded chain has the effect of
sharpening the transition, if it is continuous, but not of changing its order
and the value of the exponent c, which is also robust with respect to inclusion
of specific base-pair sequence heterogeneities.Comment: RevTeX 4 Pages and 4 PostScript figures included. Final version as
publishe
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
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
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
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