3,360 research outputs found

    Temperature-sensitive protein–DNA dimerizers

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    Programmable DNA-binding polyamides coupled to short peptides have led to the creation of synthetic artificial transcription factors. A hairpin polyamide-YPWM tetrapeptide conjugate facilitates the binding of a natural transcription factor Exd to an adjacent DNA site. Such small molecules function as protein-DNA dimerizers that stabilize complexes at composite DNA binding sites. Here we investigate the role of the linker that connects the polyamide to the peptide. We find that a substantial degree of variability in the linker length is tolerated at lower temperatures. At physiological temperatures, the longest linker tested confers a "switch"-like property on the protein-DNA dimerizer, in that it abolishes the ability of the YPWM moiety to recruit the natural transcription factor to DNA. These observations provide design principles for future artificial transcription factors that can be externally regulated and can function in concert with the cellular regulatory circuitry

    Numerical investigation of an incompressible flow over a backward facing step using a unified fractional step, artificial compressibility and pressure projection (ESAC-PP) method

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    This study focuses on an incompressible and laminar flow problem behind a backward facing step by employing a recently developed Fractional-Step, Artificial Compressibility and Pressure-Projection (FSAC-PP) method. The FSAC-PP approach unifies Chorin’s fully-explicit Artificial Compressibility (AC) and semiimplicit Fractional-Step Pressure-Projection (FS-PP) methods within the framework of characteristic-based (CB) Godunov-type schemes for solving the incompressible Navier-Stokes equations. The FSAC-PP approach has been originally introduced for low and moderate Reynolds number flows in conjunction with microfluidic and wide range of multiphysics applications. In this work, we demonstrate the applicability of the novel FSAC-PP method to macro-scale separated flows at a moderate Reynolds number. The computational results obtained with the FSAC-PP approach have been compared to the AC method and experimental data to highlight its favorable accuracy and convergence properties for separated flows

    Predicting non-linear flow phenomena through different characteristics-based schemes

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    The present work investigates the bifurcation properties of the Navier–Stokes equations using characteristics-based schemes and Riemann solvers to test their suitability to predict non-linear flow phenomena encountered in aerospace applications. We make use of a single- and multi-directional characteristics-based scheme and Rusanov’s Riemann solver to treat the convective term through a Godunov-type method. We use the Artificial Compressibility (AC) method and a unified Fractional-Step, Artificial Compressibility with Pressure-Projection (FSAC-PP) method for all considered schemes in a channel with a sudden expansion which provides highly non-linear flow features at low Reynolds numbers that produces a non-symmetrical flow field. Using the AC method, our results show that the multi-directional characteristics-based scheme is capable of predicting these phenomena while the single-directional counterpart does not predict the correct flow field. Both schemes and also Riemann solver approaches produce accurate results when the FSAC-PP method is used, showing that the incompressible method plays a dominant role in determining the behaviour of the flow. This also means that it is not just the numerical interpolation scheme which is responsible for the overall accuracy. Furthermore, we show that the FSAC-PP method provides faster convergence and higher level of accuracy, making it a prime candidate for aerospace applications
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