The GSFC scientific data storage problem

Scientific data storage problems of telemetry tape

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

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

Stability domains of actin genes and genomic evolution

In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains of actin genes for various organisms in the animal, plant and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e. before introns insertion. Common stability boundaries are found in evolutionary distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general boundaries correspond with introns positions of vertebrates and other animals actins, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae and animals have introns in positions separated by one nucleotide only, which identifies a hot-spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamic driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for introns insertion in plants and animals.Comment: 9 Pages, 7 figures. Phys. Rev. E in pres

Griffiths singularities in unbinding of strongly disordered polymers

Griffiths singularities occurring in the unbinding of strongly disordered heteropolymers are studied. A model with two randomly distributed binding energies -1 and -v, is introduced and studied analytically by analyzing the Lee-Yang zeros of the partition sum. It is demonstrated that in the limit v -> infinity the model exhibits a Griffiths type singularity at a temperature T_G =O(1) corresponding to melting of long homogeneous domains of the low binding energy. For finite v >> 1 the model is expected to exhibit an additional, unbinding, transition at a high temperature T_M=O(v)

Osmotic pressure induced coupling between cooperativity and stability of a helix-coil transition

Most helix-coil transition theories can be characterized by a set of three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to the helical state formation; and geometric, indicating how many repeating units are affected by the formation of one helical state. Depending on their effect on the helix-coil transition, solvents or co-solutes can be classified with respect to their action on these parameters. Solvent interactions that alter the entropic cost of helix formation by their osmotic action can affect both the stability (transition temperature) and the cooperativity (transition interval) of the helix-coil transition. A consistent inclusion of osmotic pressure effects in a description of helix-coil transition for poly(L-glutamic acid) in solution with polyethylene glycol can offer an explanation of the experimentally observed linear dependence of transition temperature on osmotic pressure as well as the concurrent changes in the cooperativity of the transition.Comment: 5 pages, 3 figures. To be submitted to Phys.Rev.Let

Why is the DNA Denaturation Transition First Order?

We study a model for the denaturation transition of DNA in which the molecules are considered as composed of a sequence of alternating bound segments and denaturated loops. We take into account the excluded-volume interactions between denaturated loops and the rest of the chain by exploiting recent results on scaling properties of polymer networks of arbitrary topology. The phase transition is found to be first order in d=2 dimensions and above, in agreement with experiments and at variance with previous theoretical results, in which only excluded-volume interactions within denaturated loops were taken into account. Our results agree with recent numerical simulations.Comment: Revised version. To appear in Phys. Rev. Let

Denaturation of Heterogeneous DNA

The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second order melting transition in the simplest (Peyrard-Bishop) model. However, sequence heterogeneity is dramatically amplified upon adopting a more realistic treatment of the backbone stiffness. The model yields features of ``multi-step melting'' similar to those observed in experiments.Comment: 4 pages, LaTeX, text and figures also available at http://matisse.ucsd.edu/~hw

Master equation approach to DNA-breathing in heteropolymer DNA

After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent single-stranded bubbles. Their unzipping and zipping dynamics can be monitored by single molecule fluorescence or NMR methods. We here establish a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence. The transfer coefficients are based on the Poland-Scheraga free energy model. We derive the autocorrelation function for the bubble dynamics and the associated relaxation time spectrum. In particular, we show how one can obtain the probability densities of individual bubble lifetimes and of the waiting times between successive bubble events from the master equation. A comparison to results of a stochastic Gillespie simulation shows excellent agreement.Comment: 12 pages, 8 figure