Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases

Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases, are expected to regulate the formation of structures encompassing coding sequences. Results: The sequence/folding energy (FE) relationship was studied by statistical, bioinformatic methods in 90 CDS containing 26,370 codons. I found that the FE (dG) associated with coding sequences is significant and negative (407 kcal/1000 bases, mean +/- S.E.M.) indicating that these sequences are able to form structures. However, the FE has only a small free component, less than 10% of the total. The contribution of the 1st and 3rd codon bases to the FE is larger than the contribution of the 2nd (central) bases. It is possible to achieve a ~ 4-fold change in FE by altering the wobble bases in synonymous codons. The sequence/FE relationship can be described with a simple algorithm, and the total FE can be predicted solely from the sequence composition of the nucleic acid. The contributions of different synonymous codons to the FE are additive and one codon cannot replace another. The accumulated contributions of synonymous codons of an amino acid to the total folding energy of an mRNA is strongly correlated to the relative amount of that amino acid in the translated protein. Conclusion: Synonymous codons are not interchangable with regard to their role in determining the mRNA FE and the relative amounts of amino acids in the translated protein, even if they are indistinguishable in respect of amino acid coding.Comment: 14 pages including 6 figures and 1 tabl

Folding Polyominoes into (Poly)Cubes

We study the problem of folding a polyomino $P$ into a polycube $Q$, allowing faces of $Q$ to be covered multiple times. First, we define a variety of folding models according to whether the folds (a) must be along grid lines of $P$ or can divide squares in half (diagonally and/or orthogonally), (b) must be mountain or can be both mountain and valley, (c) can remain flat (forming an angle of $180^\circ$), and (d) must lie on just the polycube surface or can have interior faces as well. Second, we give all the inclusion relations among all models that fold on the grid lines of $P$. Third, we characterize all polyominoes that can fold into a unit cube, in some models. Fourth, we give a linear-time dynamic programming algorithm to fold a tree-shaped polyomino into a constant-size polycube, in some models. Finally, we consider the triangular version of the problem, characterizing which polyiamonds fold into a regular tetrahedron.Comment: 30 pages, 19 figures, full version of extended abstract that appeared in CCCG 2015. (Change over previous version: Fixed a missing reference.

Chemical equilibration and thermal dilepton production from the quark gluon plasma at finite baryon density

The chemical equilibration of a highly unsaturated quark-gluon plasma has been studied at finite baryon density. It is found that in the presence of small amount of baryon density, the chemical equilibration for gluon becomes slower and the temperature decreases less steeply as compared to the baryon free plasma. As a result, the space time integrated yield of dilepton is enhanced if the initial temperature of the plasma is held fixed. Even at a fixed initial energy density, the suppression of the dilepton yields at higher baryo-chemical potential is compensated, to a large extent, by the slow cooling of the plasma.Comment: Latex, 19 pages, 8 postscript figures. To appear in Phys. Rev.

Jets and the shaping of the giant bipolar envelope of the planetary nebula KjPn 8

A hydrodynamic model involving cooling gas in the stagnation region of a collimated outflow is proposed for the formation of the giant parsec-scale bipolar envelope that surrounds the planetary nebula KjPn 8. Analytical calculations and numerical simulations are presented to evaluate the model. The envelope is considered to consist mainly of environmental gas swept-up by shocks driven by an episodic, collimated, bipolar outflow. In this model, which we call the ``free stagnation knot'' mechanism, the swept-up ambient gas located in the stagnation region of the bow-shock cools to produce a high density knot. This knot moves along with the bow-shock. When the central outflow ceases, pressurization of the interior of the envelope stops and its expansion slows down. The stagnation knot, however, has sufficient momentum to propagate freely further along the axis, producing a distinct nose at the end of the lobe. The model is found to successfully reproduce the peculiar shape and global kinematics of the giant bipolar envelope of KjPn 8.Comment: 20 pages + 8 figures (in 1 tar-file 0.67 Mb

Structural Characterization of Charcoal Exposed to High and Low pH: Implications for 14C Sample Preparation and Charcoal Preservation

Chemical and structural similarities between poorly preserved charcoal and its contaminants, as well as low radiocarbon concentrations in old samples, complicate 14C age determinations. Here, we characterize 4 fossil charcoal samples from the late Middle Paleolithic and early Upper Paleolithic strata of Kebara Cave, Israel, with respect to the structural and chemical changes that occur when they are subjected to the acid-base-acid (ABA) treatment. Differential thermal analysis and TEM show that acid treatment disrupts the structure, whereas alkali treatment results in the reformation of molecular aggregates. The major changes are ascribed to the formation of salt bridges at high pH and the disruption of the graphite-like crystallites at low pH. Weight losses during the treatments are consistently greater for older samples, implying that they are less well preserved. Based on the changes observed in vitro due to pH fluctuations, various methods for removing contamination, as well as a mechanism for preferential preservation of charcoal in nature, are proposed.Anthropolog

The Partition Function and Level Density for Yang-Mills-Higgs Quantum Mechanics

We calculate the partition function $Z(t)$ and the asymptotic integrated level density $N(E)$ for Yang-Mills-Higgs Quantum Mechanics for two and three dimensions ($n = 2, 3$). Due to the infinite volume of the phase space $\Gamma$ on energy shell for $n= 2$, it is not possible to disentangle completely the coupled oscillators ($x^2 y^2$-model) from the Higgs sector. The situation is different for $n = 3$ for which $\Gamma$ is finite. The transition from order to chaos in these systems is expressed by the corresponding transitions in $Z(t)$ and $N(E)$, analogous to the transitions in adjacent level spacing distribution from Poisson distribution to Wigner-Dyson distribution. We also discuss a related system with quartic coupled oscillators and two dimensional quartic free oscillators for which, contrary to YMHQM, both coupling constants are dimensionless.Comment: 10 pages, LaTeX; minor changes; version accepted for publication as a Letter in J. Phys.

Quantum kinetics and thermalization in an exactly solvable model

We study the dynamics of relaxation and thermalization in an exactly solvable model with the goal of understanding the effects of off-shell processes. The focus is to compare the exact evolution of the distribution function with different approximations to the relaxational dynamics: Boltzmann, non-Markovian and Markovian quantum kinetics. The time evolution of the distribution function is evaluated exactly using two methods: time evolution of an initially prepared density matrix and by solving the Heisenberg equations of motion. There are two different cases that are studied in detail: i) no stable particle states below threshold of the bath and a quasiparticle resonance above it and ii) a stable discrete exact `particle' state below threshold. For the case of quasiparticles in the continuum (resonances) the exact quasiparticle distribution asymptotically tends to a statistical equilibrium distribution that differs from a simple Bose-Einstein form as a result of off-shell processes. In the case ii), the distribution of particles does not thermalize with the bath. We study the kinetics of thermalization and relaxation by deriving a non-Markovian quantum kinetic equation which resums the perturbative series and includes off-shell effects. A Markovian approximation that includes off-shell contributions and the usual Boltzmann equation are obtained from the quantum kinetic equation in the limit of wide separation of time scales upon different coarse-graining assumptions. The relaxational dynamics predicted by the non-Markovian, Markovian and Boltzmann approximations are compared to the exact result of the model. The Boltzmann approach is seen to fail in the case of wide resonances and when threshold and renormalization effects are important.Comment: 49 pages, LaTex, 17 figures (16 eps figures

Model of Centauro and strangelet production in heavy ion collisions

We discuss the phenomenological model of Centauro event production in relativistic nucleus-nucleus collisions. This model makes quantitative predictions for kinematic observables, baryon number and mass of the Centauro fireball and its decay products. Centauros decay mainly to nucleons, strange hyperons and possibly strangelets. Simulations of Centauro events for the CASTOR detector in Pb-Pb collisions at LHC energies are performed. The signatures of these events are discussed in detail.Comment: 19 pages, LaTeX+revtex4, 14 eps-figures and 3 table

Comparative study on the uniform energy deposition achievable via optimized plasmonic nanoresonator distributions

Plasmonic nanoresonators of core-shell composition and nanorod shape were optimized to tune their absorption cross-section maximum to the central wavelength of a short pulse. Their distribution along a pulse-length scaled target was optimized to maximize the absorptance with the criterion of minimal absorption difference in between neighbouring layers. Successive approximation of layer distributions made it possible to ensure almost uniform deposited energy distribution up until the maximal overlap of two counter-propagating pulses. Based on the larger absorptance and smaller uncertainty in absorptance and energy distribution core-shell nanoresonators override the nanorods. However, optimization of both nanoresonator distributions has potential applications, where efficient and uniform energy deposition is crucial, including phase transitions and even fusion