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

Equation of state and initial temperature of quark gluon plasma at RHIC

In gold-gold collisions of the Relativistic Heavy Ion Collider (RHIC) a perfect fluid of quarks, sometimes called the strongly interacting quark gluon plasma (sQGP) is created for an extremely short time. The time evolution of this fluid can be described by hydrodynamical models. After expansion and cooling, the freeze-out happens and hadrons are created. Their distribution reveals information about the final state of the fluid. To investigate the time evolution one needs to analyze penetrating probes, such as direct photon observables. Transverse momentum distributions of low energy direct photons were mesured in 2010 by PHENIX, while azimuthal asymmetry in 2011. These measurements can be compared to hydrodynamics to determine the equation of state and the initial temperature of sQGP. In this paper we analyze an 1+3 dimensional solution of relativistic hydrodynamics. We calculate momentum distribution, azimuthal asymmetry and momentum correlations of direct photons. Based on earlier fits to hadronic spectra, we compare photon calculations to measurements to determine the equation of state and the initial temperature of sQGP. We find that the initial temperature in the center of the fireball is 507+-12 MeV, while for the sound speed we get a speed of sound of 0.36+-0.02. We also estimate a systematic error of these results. We find that the measured azimuthal asymmetry is also not incompatible with this model, and predict a photon source that is significantly larger in the out direction than in the side direction.Comment: 12 pages, 4 figures. This work was supported by the OTKA grant NK-73143 and NK-101438 and M. Csanad's Bolyai scholarshi

Transverse momentum distributions and their forward- backward correlations in the percolating colour string approach

The forward-backward correlations in the $p_T$ distributions, which present a clear signature of non-linear effects in particle production, are studied in the model of percolating colour strings. Quantitative predictions are given for these correlations at SPS, RHIC and LHC energies. Interaction of strings also naturally explains the flattening of $p_T$ distributions and increase of $$ with energy and atomic number for nuclear collisionsComment: 6 pages in LaTex, 3 figures in Postscrip

Influence of airway‐occluding instruments on airway pressure during jet ventilation for rigid bronchoscopy

We measured changes in airway pressure (Paw) caused by microsurgical instruments introduced into a rigid bronchoscope during high frequency jet ventilation (HFJV). With approval of the institutional Ethics Committee, 10 adults undergoing elective tracheobronchial endoscopy and endosonography during general anaesthesia were investigated. Inflation of an endosonography probe balloon in the left main stem bronchus caused airway obstruction. Pressure measurements proximal and distal to the obstruction were compared after three degrees of obstruction (0%, 50% and 90%) and with two different driving pressure settings. Airway obstruction increased the mean (sd) peak inspiratory pressure (PIP) from 7.5 (2.6) to 9.5 (3.5) mm Hg for 2 atm (P=0.0008) and from 9.7 (3.7) to 13.0 (5.1) mm Hg for 3 atm (P=0.0001). Airway obstruction did not alter peripheral PIP (7.2 (4.1) to 7.1 (3.7) mm Hg for 2 atm and 8.8 (4.3) to 9.4 (5.2) mm for 3 atm), but resulted in an end‐expiratory pressure (EEP) beyond the narrowing being significantly greater than in the unobstructed airway (2.5 (3.4) to 5.5 (3.7) mm Hg for 2 atm; P=0.0005) and 3.2 (3.6) to 8.0 (4.3) mm for 3 atm; P<0.0001). Severe airway narrowing increases inspiratory pressure proximal and expiratory pressure distal to the obstruction in relation to the applied driving pressure. Since the distal EEP never exceeded PIP, even near‐total airway obstruction should not cause severe lung distension or barotrauma in subjects with normal lungs. Br J Anaesth 2000; 85: 463-

Forming Disoriented Chiral Condensates through Fluctuations

Using the influence functional formalism, classical equations of motion for the O(N) model are derived in the presence of a heat bath, in both the symmetric phase as well as the phase of spontaneously broken symmetry. The heat bath leads to dissipation and fluctuation terms in the classical equations of motion, which are explicitly computed to lowest order in perturbation theory. In the broken phase these terms are found to be large for the sigma field, even at zero temperature, due to the decay process sigma -> pi pi, while they are small for the pi fields at temperatures below T_c = 160 MeV. It is shown that in large volumes the presence of dissipation and fluctuations suppresses the formation of disoriented chiral condensates (DCC's). In small volumes, however, fluctuations become sufficiently large to induce the formation of DCC's even if chiral symmetry has not been restored in the initial stage of the system's evolution.Comment: 34 pages, 11 figures, ReVTeX, eps-, aps-, psfig-style files require

Modeling Eclipses in the Classical Nova V Persei: The Role of the Accretion Disk Rim

Multicolor (BVRI) light curves of the eclipsing classical nova V Per are presented, and a total of twelve new eclipse timings are measured for the system. When combined with previous eclipse timings from the literature, these timings yield a revised ephemeris for the times of mid-eclipse given by HJD = 2,447,442.8260(1) + 0.107123474(3) E. The eclipse profiles are analyzed with a parameter-fitting model that assumes four sources of luminosity: a white dwarf primary star, a main-sequence secondary star, a flared accretion disk with a rim, and a bright spot at the intersection of the mass-transfer stream and the disk periphery. A matrix of model solutions are computed, covering an extensive range of plausible parameter values. The solution matrix is then explored to determine the optimum values for the fitting parameters and their associated errors. For models that treat the accretion disk as a flat structure without a rim, optimum fits require that the disk have a flat temperature profile. Although models with a truncated inner disk (R_in >> R_wd) result in a steeper temperature profile, steady-state models with a temperature profile characterized by T(r) \propto r^{-3/4} are found only for models with a significant disk rim. A comparison of the observed brightness and color at mid-eclipse with the photometric properties of the best-fitting model suggests that V Per lies at a distance of ~ 1 kpc.Comment: Accepted for publication in The Astrophysical Journal. Thirty-nine pages, including 9 figures. V2 - updated to include additional references and related discussion to previous work overlooked in the original version, and to correct a typo in the ephemeris given in the abstract. V3 - Minor typos corrected. The paper is scheduled for the 20 June 2006 issue of the ApJ. V4 - An error in equation (9) has been corrected. The results presented in the paper were not affected, as all computations were made using the correct formulation of this equatio

Nonlinear evolution of the momentum dependent condensates in strong interaction: the ``pseudoscalar laser''

We discuss the relaxation of the scalar and pseudoscalar condensates after a rapid quench from an initial state with fluctuations. If we include not only the zero-mode but also higher modes of the condensates in the classical evolution, we observe parametric amplification of those ``hard'' modes. Thus, they couple nonlinearly to the ``soft'' modes. As a consequence, domains of coherent pi-field emerge long after the initial spinodal decomposition. The momentum-space distribution of pions emerging from the decay of that momentum-dependent condensate is discussed.Comment: 6 Pages, REVTEX, 8 Figures; one reference and one figure adde

Percolation of strings and the first RHIC data on multiplicity and tranverse momentum distributions

The dependence of the multiplicity on the number of collisions and the transverse momentum distribution for central and peripheral Au-Au collisions are studied in the model of percolation of strings relative to the experimental conditions at RHIC. The comparison with the first RHIC data shows a good agreement.Comment: RevTeX, 11 pages, 4 eps figures included using epsfi

The Proteomic Code: a molecular recognition code for proteins

<p>Abstract</p> <p>Background</p> <p>The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic Code is part of the redundant Genetic Code.</p> <p>Review</p> <p>The 25-year-old history of this concept is reviewed from the first independent suggestions by Biro and Mekler, through the works of Blalock, Root-Bernstein, Siemion, Miller and others, followed by the discovery of a Common Periodic Table of Codons and Nucleic Acids in 2003 and culminating in the recent conceptualization of partial complementary coding of interacting amino acids as well as the theory of the nucleic acid-assisted protein folding.</p> <p>Methods and conclusions</p> <p>A novel cloning method for the design and production of specific, high-affinity-reacting proteins (SHARP) is presented. This method is based on the concept of proteomic codes and is suitable for large-scale, industrial production of specifically interacting peptides.</p

Chaotic Symmetry Breaking and Dissipative Two-Field Dynamics

The dynamical symmetry breaking in a two-field model is studied by numerically solving the coupled effective field equations. These are dissipative equations of motion that can exhibit strong chaotic dynamics. By choosing very general model parameters leading to symmetry breaking along one of the field directions, the symmetry broken vacua make the role of transitory strange attractors and the field trajectories in phase space are strongly chaotic. Chaos is quantified by means of the determination of the fractal dimension, which gives an invariant measure for chaotic behavior. Discussions concerning chaos and dissipation in the model and possible applications to related problems are given.Comment: 18 pages, 2 .eps figures (uses epsf), Revtex. A much larger version, more comments, refs. and results. Version in press Physical Review