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Parts I and II of this paper describe the extension and testing of two sets of Boussinesq-type equations to include surf zone phenomena. Part I is restricted to 1D tests of shoaling, breaking, and runup, while Part II deals with two horizontal dimensions. The model uses two main extensions to the Boussinesq equations: a momentum-conserving eddy viscosity(More)
In this paper, we focus on the implementation and verification of an extended Boussinesq model for surf zone hydrodynamics in two horizontal dimensions. The time-domain numerical model is based on the fully nonlinear Boussinesq equations. As described in Part I of this two-part paper, the energy dissipation due to wave breaking is modeled by introducing an(More)
[1] A large, unpredicted, water level increase appeared along a substantial section of the western Louisiana and northern Texas (LATEX) coasts 12–24 hrs in advance of the landfall of Hurricane Ike (2008), with water levels in some areas reaching 3 m above mean sea level. During this time the cyclonic wind field was largely shore parallel throughout the(More)
CRISPR-Cas-mediated genome editing relies on guide RNAs that direct site-specific DNA cleavage facilitated by the Cas endonuclease. Here we report that chemical alterations to synthesized single guide RNAs (sgRNAs) enhance genome editing efficiency in human primary T cells and CD34(+) hematopoietic stem and progenitor cells. Co-delivering chemically(More)
Recent advances have demonstrated the use of RNA-based control devices to program sophisticated cellular functions; however, the efficiency with which these devices can be quantitatively tailored has limited their broader implementation in cellular networks. Here, we developed a high-efficiency, high-throughput and quantitative two-color(More)
Genetic devices that directly detect and respond to intracellular concentrations of proteins are important synthetic biology tools, supporting the design of biological systems that target, respond to or alter specific cellular states. Here, we develop ribozyme-based devices that respond to protein ligands in two eukaryotic hosts, yeast and mammalian cells,(More)
Methods for rapidly assessing sequence-structure-function landscapes and developing conditional gene-regulatory devices are critical to our ability to manipulate and interface with biology. We describe a framework for engineering RNA devices from preexisting aptamers that exhibit ligand-responsive ribozyme tertiary interactions. Our methodology utilizes(More)
Based on the fully nonlinear Boussinesq equations in Cartesian coordinates, the equations in generalized coordinates are derived to adapt computations to irregularly shaped shorelines, such as harbors, bays and tidal inlets, and to make computations more efficient in large near-shore regions. Contravariant components of velocity vectors are employed in the(More)
In this paper, we derive and test a set of extended Boussinesq equations with improved nonlinear performance. To do this, the concept of a reference elevation is further generalised to include a time-varying component that moves with the instantaneous free surface. It is found that, when compared to Stokes-type expansions of the second harmonic and fully(More)
a r t i c l e i n f o Using Boussinesq scaling for water waves while imposing no constraints on rotationality, we derive and test model equations for nonlinear water wave transformation over varying depth. These use polynomial basis functions to create velocity profiles which are inserted into the basic equations of motion keeping terms up to the desired(More)