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Theory of mRNA degradation
(2012)
One of the central themes of biology is to understand how individual cells achieve a high fidelity in gene expression. Each cell needs to ensure accurate protein levels for its proper functioning and its capability to proliferate. Therefore, complex regulatory mechanisms have evolved in order to render the expression of each gene dependent on the expression level of (all) other genes. Regulation can occur at different stages within the framework of the central dogma of molecular biology. One very effective and relatively direct mechanism concerns the regulation of the stability of mRNAs. All organisms have evolved diverse and powerful mechanisms to achieve this. In order to better comprehend the regulation in living cells, biochemists have studied specific degradation mechanisms in detail. In addition to that, modern high-throughput techniques allow to obtain quantitative data on a global scale by parallel analysis of the decay patterns of many different mRNAs from different genes. In previous studies, the interpretation of these mRNA decay experiments relied on a simple theoretical description based on an exponential decay. However, this does not account for the complexity of the responsible mechanisms and, as a consequence, the exponential decay is often not in agreement with the experimental decay patterns. We have developed an improved and more general theory of mRNA degradation which provides a general framework of mRNA expression and allows describing specific degradation mechanisms. We have made an attempt to provide detailed models for the regulation in different organisms. In the yeast S. cerevisiae, different degradation pathways are known to compete and furthermore most of them rely on the biochemical modification of mRNA molecules. In bacteria such as E. coli, degradation proceeds primarily endonucleolytically, i.e. it is governed by the initial cleavage within the coding region. In addition, it is often coupled to the level of maturity and the size of the polysome of an mRNA. Both for S. cerevisiae and E. coli, our descriptions lead to a considerable improvement of the interpretation of experimental data. The general outcome is that the degradation of mRNA must be described by an age-dependent degradation rate, which can be interpreted as a consequence of molecular aging of mRNAs. Within our theory, we find adequate ways to address this much debated topic from a theoretical perspective. The improvements of the understanding of mRNA degradation can be readily applied to further comprehend the mRNA expression under different internal or environmental conditions such as after the induction of transcription or stress application. Also, the role of mRNA decay can be assessed in the context of translation and protein synthesis. The ultimate goal in understanding gene regulation mediated by mRNA stability will be to identify the relevance and biological function of different mechanisms. Once more quantitative data will become available, our description allows to elaborate the role of each mechanism by devising a suitable model.
In this work, we show how Gibbs or thermal states appear dynamically in closed quantum many-body systems, building on the program of dynamical typicality. We introduce a novel perturbation theorem for physically relevant weak system-bath couplings that is applicable even in the thermodynamic limit. We identify conditions under which thermalization happens and discuss the underlying physics. Based on these results, we also present a fully general quantum algorithm for preparing Gibbs states on a quantum computer with a certified runtime and error bound. This complements quantum Metropolis algorithms, which are expected to be efficient but have no known runtime estimates and only work for local Hamiltonians.
Context. The true mass-loss rates from massive stars are important for many branches of astrophysics. For the correct modeling of the resonance lines, which are among the key diagnostics of stellar mass-loss, the stellar wind clumping has been found to be very important. To incorporate clumping into a radiative transfer calculation, three-dimensional (3D) models are required. Various properties of the clumps may have a strong impact on the resonance line formation and, therefore, on the determination of empirical mass-loss rates.
Aims. We incorporate the 3D nature of the stellar wind clumping into radiative transfer calculations and investigate how different model parameters influence the resonance line formation.
Methods. We develop a full 3D Monte Carlo radiative transfer code for inhomogeneous expanding stellar winds. The number density of clumps follows the mass conservation. For the first time, we use realistic 3D models that describe the dense as well as the tenuous wind components to model the formation of resonance lines in a clumped stellar wind. At the same time, we account for non-monotonic velocity fields.
Results. The 3D density and velocity wind inhomogeneities show that there is a very strong impact on the resonance line formation. The different parameters describing the clumping and the velocity field results in different line strengths and profiles. We present a set of representative models for various sets of model parameters and investigate how the resonance lines are affected. Our 3D models show that the line opacity is lower for a larger clump separation and shallower velocity gradients within the clumps.
Conclusions. Our model demonstrates that to obtain empirically correct mass-loss rates from the UV resonance lines, the wind clumping and its 3D nature must be taken into account.
Time-dependent escape of cosmic rays from supernova remnants, and their interaction with dense media
(2012)
Context. Supernova remnants (SNRs) are thought to be the main source of Galactic cosmic rays (CRs) up to the "knee" in CR spectrum. During the evolution of a SNR, the bulk of the CRs are confined inside the SNR shell. The highest-energy particles leave the system continuously, while the remaining adiabatically cooled particles are released when the SNR has expanded sufficiently and decelerated so that the magnetic field at the shock is no longer able to confine them. Particles escaping from the parent system may interact with nearby molecular clouds, producing.-rays in the process via pion decay. The soft gamma-ray spectra observed for a number of SNRs interacting with molecular clouds, however, challenge current theories of non-linear particle acceleration that predict harder spectra.
Aims. We study how the spectrum of escaped particles depends on the time-dependent acceleration history in both Type Ia and core-collapse SNRs, as well as on different assumptions about the diffusion coefficient in the vicinity of the SNR.
Methods. We solve the CR transport equation in a test-particle approach combined with numerical simulations of SNR evolution.
Results. We extend our method for calculating the CR acceleration in SNRs to trace the escaped particles in a large volume around SNRs. We calculate the evolution of the spectra of CRs that have escaped from a SNR into a molecular cloud or dense shell for two diffusion models. We find a strong confinement of CRs in a close region around the SNR, and a strong dilution effect for CRs that were able to propagate out as far as a few SNR radii.
We employ the ultrafast response of a 15.4 nm thin SrRuO3 layer grown epitaxially on a SrTiO3 substrate to perform time-domain sampling of an x-ray pulse emitted from a synchrotron storage ring. Excitation of the sample with an ultrashort laser pulse triggers coherent expansion and compression waves in the thin layer, which turn the diffraction efficiency on and off at a fixed Bragg angle during 5 ps. This is significantly shorter than the duration of the synchrotron x-ray pulse of 100 ps. Cross-correlation measurements of the ultrafast sample response and the synchrotron x-ray pulse allow to reconstruct the x-ray pulse shape.
A Bose-Hubbard model on a dynamical lattice was introduced in previous work as a spin system analogue of emergent geometry and gravity. Graphs with regions of high connectivity in the lattice were identified as candidate analogues of spacetime geometries that contain trapped surfaces. We carry out a detailed study of these systems and show explicitly that the highly connected subgraphs trap matter. We do this by solving the model in the limit of no back-reaction of the matter on the lattice, and for states with certain symmetries that are natural for our problem. We find that in this case the problem reduces to a one-dimensional Hubbard model on a lattice with variable vertex degree and multiple edges between the same two vertices. In addition, we obtain a (discrete) differential equation for the evolution of the probability density of particles which is closed in the classical regime. This is a wave equation in which the vertex degree is related to the local speed of propagation of probability. This allows an interpretation of the probability density of particles similar to that in analogue gravity systems: matter inside this analogue system sees a curved spacetime. We verify our analytic results by numerical simulations. Finally, we analyze the dependence of localization on a gradual, rather than abrupt, falloff of the vertex degree on the boundary of the highly connected region and find that matter is localized in and around that region.
Ferroelectrets have been fabricated from low-density polyethylene (LDPE) films by means of a template-based lamination. The temperature dependence of the piezoelectric d(33) coefficient has been investigated. It was found that low-density polyethylene ferroelectrets have rather low thermal stability with the piezoelectric coefficient decaying almost to zero already at 100 degrees C. This behavior is attributed to the poor electret properties of the polyethylene films used for the fabrication of the ferroelectrets. In order to improve the charge trapping and the thermal stability of electret charge and piezoelectricity, LDPE ferroelectrets were treated with orthophosphoric acid. The treatment resulted in considerable improvements of the charge stability in LDPE films and in ferroelectret systems made from them. For example, the charge and piezoelectric-coefficient decay curves shifted to higher temperatures by 60 K and 40 K, respectively. It is shown that the decay of the piezoelectric coefficient in LDPE ferroelectrets is governed by the relaxation of less stable positive charges. The treatment also leads to noticeable changes in the chemical composition of the LDPE surface. Infrared spectroscopy reveals absorption bands attributed to phosphorus-containing structures, while scanning electron microscopy shows new island-like structures, 50-200 nm in diameter, on the modified surface.
A membrane of a dielectric elastomer coated with compliant electrodes may form wrinkles as the applied voltage is ramped up. We present a combination of experiment and theory to investigate the transition to wrinkles using a clamped membrane subject to a constant force and a voltage ramp. Two types of transitions are identified. In type-I transition, the voltage-stretch curve is N-shaped, and flat and wrinkled regions coexist in separate areas of the membrane. The type-I transition progresses by nucleation of small wrinkled regions, followed by the growth of the wrinkled regions at the expense of the flat regions, until the entire membrane is wrinkled. By contrast, in type-II transition, the voltage-stretch curve is monotonic, and the entire flat membrane becomes wrinkled with no nucleation barrier. The two types of transitions are analogous to the first and the second order phase transitions. While the type-I transition is accompanied by a jump in the vertical displacement, type-II transition is accompanied by a continuous change in the vertical displacement. Such transitions may enable applications in muscle-like actuation and energy harvesting, where large deformation and large energy of conversion are desired.
Correlation functions of a driven two-level system embedded in a photonic crystal are analyzed. The spectral density of the photonic bands near a gap makes this system non-Markovian. The equations of motion for two-time correlations are derived by two different methods, the quantum regression theorem and the fluctuation dissipation theorem, and found to be the same.
We study the dispersion interaction of the van der Waals and Casimir-Polder (vdW-CP) type between a neutral atom and the surface of a conductor by allowing for nonlocal electrodynamics, i.e. electron diffusion. We consider two models: (i) bulk diffusion, and (ii) diffusion in a surface charge layer. In both cases, we find that the transition to a semiconductor as a function of the conductivity is continuous, unlike the case of a local model. The relevant parameter is the electric screening length and depends on the carrier diffusion constant. We find that for distances comparable to the screening length, vdW-CP data can distinguish between bulk and surface diffusion, hence it can be a sensitive probe for surface states.
Velocity and displacement correlation functions for fractional generalized Langevin equations
(2012)
We study analytically a generalized fractional Langevin equation. General formulas for calculation of variances and the mean square displacement are derived. Cases with a three parameter Mittag-Leffler frictional memory kernel are considered. Exact results in terms of the Mittag-Leffler type functions for the relaxation functions, average velocity and average particle displacement are obtained. The mean square displacement and variances are investigated analytically. Asymptotic behaviors of the particle in the short and long time limit are found. The model considered in this paper may be used for modeling anomalous diffusive processes in complex media including phenomena similar to single file diffusion or possible generalizations thereof. We show the importance of the initial conditions on the anomalous diffusive behavior of the particle.
The VERITAS array of Cherenkov telescopes has carried out a deep observational program on the nearby dwarf spheroidal galaxy Segue 1. We report on the results of nearly 48 hours of good quality selected data, taken between January 2010 and May 2011. No significant gamma-ray emission is detected at the nominal position of Segue 1, and upper limits on the integrated flux are derived. According to recent studies, Segue 1 is the most dark matter-dominated dwarf spheroidal galaxy currently known. We derive stringent bounds on various annihilating and decaying dark matter particle models. The upper limits on the velocity-weighted annihilation cross-section are <sigma upsilon >(95%) (CL) less than or similar to 10(-23) cm(3) s(-1), improving our limits from previous observations of dwarf spheroidal galaxies by at least a factor of 2 for dark matter particle masses m(chi) greater than or similar to 300 GeV. The lower limits on the decay lifetime are at the level of tau(95%) (CL) greater than or similar to 10(24) s. Finally, we address the interpretation of the cosmic ray lepton anomalies measured by ATIC and PAMELA in terms of dark matter annihilation, and show that the VERITAS observations of Segue 1 disfavor such a scenario.
VERITAS has been monitoring the very-high-energy (VHE; > 100 GeV) gamma-ray activity of the radio galaxy M87 since 2007. During 2008, flaring activity on a timescale of a few days was observed with a peak flux of (0.70 +/- 0.16) x 10(-11) cm(-2) s(-1) at energies above 350 GeV. In 2010 April, VERITAS detected a flare from M 87 with peak flux of (2.71 +/- 0.68) x 10(-11) cm(-2) s(-1) for E > 350 GeV. The source was observed for six consecutive nights during the flare, resulting in a total of 21 hr of good-quality data. The most rapid flux variation occurred on the trailing edge of the flare with an exponential flux decay time of 0.90(-0.15)(+0.22) days. The shortest detected exponential rise time is three times as long, at 2.87(+1.65)(-0.99) days. The quality of the data sample is such that spectral analysis can be performed for three periods: rising flux, peak flux, and falling flux. The spectra obtained are consistent with power-law forms. The spectral index at the peak of the flare is equal to 2.19 +/- 0.07. There is some indication that the spectrum is softer in the falling phase of the flare than the peak phase, with a confidence level corresponding to 3.6 standard deviations. We discuss the implications of these results for the acceleration and cooling rates of VHE electrons in M 87 and the constraints they provide on the physical size of the emitting region.
We report on VERITAS very high energy (VHE; E >= 100 GeV) observations of six blazars selected from the Fermi Large Area Telescope First Source Catalog (1FGL). The gamma-ray emission from 1FGL sources was extrapolated up to the VHE band, taking gamma-ray absorption by the extragalactic background light into account. This allowed the selection of six bright, hard-spectrum blazars that were good candidate TeV emitters. Spectroscopic redshift measurements were attempted with the Keck Telescope for the targets without Sloan Digital Sky Survey spectroscopic data. No VHE emission is detected during the observations of the six sources described here. Corresponding TeV upper limits are presented, along with contemporaneous Fermi observations and non-concurrent Swift UVOT and X-Ray Telescope data. The blazar broadband spectral energy distributions (SEDs) are assembled and modeled with a single-zone synchrotron self-Compton model. The SED built for each of the six blazars shows a synchrotron peak bordering between the intermediate-and high-spectrum-peak classifications, with four of the six resulting in particle-dominated emission regions.
We report on very high energy (E > 100 GeV) gamma-ray observations of V407 Cygni, a symbiotic binary that underwent a nova outburst producing 0.1-10 GeV gamma rays during 2010 March 10-26. Observations were made with the Very Energetic Radiation Imaging Telescope Array System during 2010 March 19-26 at relatively large zenith angles due to the position of V407 Cyg. An improved reconstruction technique for large zenith angle observations is presented and used to analyze the data. We do not detect V407 Cygni and place a differential upper limit on the flux at 1.6 TeV of 2.3 x 10(-12) erg cm(-2) s(-1) (at the 95% confidence level). When considered jointly with data from Fermi-LAT, this result places limits on the acceleration of very high energy particles in the nova.
We report on sub-wavelength structuring of photosensitive azo-containing polymer films induced by a surface plasmon interference intensity pattern. The two surface plasmon waves generated at neighboring nano-slits in the metal layer during irradiation interfere constructively, resulting in an intensity pattern with a periodicity three times smaller than the wavelength of the incoming light. The near field pattern interacts with the photosensitive polymer film placed above it, leading to a topography change which follows the intensity pattern exactly, resulting in the formation of surface relief gratings of a size below the diffraction limit. We analyze numerically and experimentally how the depth of the nano-slit alters the interference pattern of surface plasmons and find that the sub-wavelength patterning of the polymer surface could be optimized by modifying the geometry and the size of the nano-slit.
The precise knowledge of one of two complementary experimental outcomes prevents us from obtaining complete information about the other one. This formulation of Niels Bohr's principle of complementarity when applied to the paradigm of wave-particle dualism-that is, to Young's double-slit experiment-implies that the information about the slit through which a quantum particle has passed erases interference. In the present paper we report a double-slit experiment using two photons created by spontaneous parametric down-conversion where we observe interference in the signal photon despite the fact that we have located it in one of the slits due to its entanglement with the idler photon. This surprising aspect of complementarity comes to light by our special choice of the TEM01 pump mode. According to quantum field theory the signal photon is then in a coherent superposition of two distinct wave vectors giving rise to interference fringes analogous to two mechanical slits.
In dieser Arbeit werden die Effekte der Synchronisation nichtlinearer, akustischer Oszillatoren am Beispiel zweier Orgelpfeifen untersucht. Aus vorhandenen, experimentellen Messdaten werden die typischen Merkmale der Synchronisation extrahiert und dargestellt. Es folgt eine detaillierte Analyse der Übergangsbereiche in das Synchronisationsplateau, der Phänomene während der Synchronisation, als auch das Austreten aus der Synchronisationsregion beider Orgelpfeifen, bei verschiedenen Kopplungsstärken. Die experimentellen Befunde werfen Fragestellungen nach der Kopplungsfunktion auf. Dazu wird die Tonentstehung in einer Orgelpfeife untersucht. Mit Hilfe von numerischen Simulationen der Tonentstehung wird der Frage nachgegangen, welche fluiddynamischen und aero-akustischen Ursachen die Tonentstehung in der Orgelpfeife hat und inwiefern sich die Mechanismen auf das Modell eines selbsterregten akustischen Oszillators abbilden lässt. Mit der Methode des Coarse Graining wird ein Modellansatz formuliert.