264 research outputs found

    Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers

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    To function as gene regulatory elements in response to environmental signals, riboswitches must adopt specific secondary structures on appropriate time scales. We employ kinetic Monte Carlo simulation to model the time-dependent folding during transcription of TPP riboswitch expression platforms. According to our simulations, riboswitch transcriptional terminators, which must adopt a specific hairpin configuration by the time they have been transcribed, fold with higher efficiency than Shine-Dalgarno sequesterers, whose proper structure is required only at the time of ribosomal binding. Our findings suggest both that riboswitch transcriptional terminator sequences have been naturally selected for high folding efficiency, and that sequesterers can maintain their function even in the presence of significant misfolding.Comment: 12 pages, 6 figure

    Enumeration of octagonal tilings

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    Random tilings are interesting as idealizations of atomistic models of quasicrystals and for their connection to problems in combinatorics and algorithms. Of particular interest is the tiling entropy density, which measures the relation of the number of distinct tilings to the number of constituent tiles. Tilings by squares and 45 degree rhombi receive special attention as presumably the simplest model that has not yet been solved exactly in the thermodynamic limit. However, an exact enumeration formula can be evaluated for tilings in finite regions with fixed boundaries. We implement this algorithm in an efficient manner, enabling the investigation of larger regions of parameter space than previously were possible. Our new results appear to yield monotone increasing and decreasing lower and upper bounds on the fixed boundary entropy density that converge toward S = 0.36021(3)

    Viscous fingering patterns in ferrofluids

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    Viscous fingering occurs in the flow of two immiscible, viscous fluids between the plates of a Hele-Shaw cell. Due to pressure gradients or gravity, the initially planar interface separating the two fluids undergoes a Saffman-Taylor instability and develops finger-like structures. When one of the fluids is a ferrofluid and a perpendicular magnetic field is applied, the labyrinthine instability supplements the usual viscous fingering instability, resulting in visually striking, complex patterns. We consider this problem in a rectangular flow geometry using a perturbative mode-coupling analysis. We deduce two general results: viscosity contrast between the fluids drives interface asymmetry, with no contribution from magnetic forces; magnetic repulsion within the ferrofluid generates finger tip-splitting, which is absent in the rectangular geometry for ordinary fluids.Comment: 29 pages, 5 figures, Late

    A Free Energy Model of Boron Carbide

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    The assessed phase diagram of the boron-carbon system contains a single non-stoichiometric boron-carbide phase of rhombohedral symmetry with a broad, thermodynamically improbable, low temperature composition range. We combine first principles total energy calculations with phenomenological thermodynamic modeling to propose a revised low temperature phase diagram that contains two boron-carbide phases of differing symmetries and compositions. One structure has composition B4C and consists of B11C icosahedra and C-B-C chains, with the placement of carbon on the icosahedron breaking rhombohedral symmetry. This phase is destabilized above 600K by the configurational entropy of alternate carbon substitutions. The other structure, of ideal composition B13C2, has a broad composition range at high temperature, with rhombohedral symmetry throughout, as observed experimentally.Comment: 15 pages, 3 figures, submitted to J. Stat. Phys. August 9th, 201