Alicia A. Johnson

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We present strategies to update thc mesh as the spatial domain changcs its shape in computtttions of llow problcms with moving boundaries and interfaces. These strate.qics arc used in conjunction with the stabilized spacc-time finite clement formulati<lns introduccd carlicr for computation of flow problems with free surfaces. two-liquid interfaces. moving(More)
A high performance computing research tool has been developed for 3D simulation of uid-particle interactions with the number of particles reaching 100. The tool is based on a stabilized space-time nite element formulation for moving boundaries and interfaces and parallel computing. Other components of this tool include: fast automatic mesh generation with(More)
We consider two-component block Gibbs sampling for a Bayesian hierarchical version of the normal theory general linear model. This model is practically relevant in the sense that it is general enough to have many applications and in that it is not straightforward to sample directly from the corresponding posterior distribution. There are two possible orders(More)
We have examined the fidelity of polymerization catalyzed by the human mitochondrial DNA polymerase using wild-type and exonuclease-deficient (E200A mutation) forms of recombinant, reconstituted holoenzyme. Each of the four nucleotides bind and incorporate with similar kinetics; the average dissociation constant for ground state binding is 0.8 microm, and(More)
It is common practice in Markov chain Monte Carlo to update the simulation one variable (or sub-block of variables) at a time, rather than conduct a single full-dimensional update. When it is possible to draw from each full-conditional distribution associated with the target this is just a Gibbs sampler. Often at least one of the Gibbs updates is replaced(More)
We present our numerical methods for the solution of large-scale incompressible ow applications with complex geometries. These methods include a stabilized nite element formulation of the Navier-Stokes equations, implementation of this formulation on parallel architectures such as the Thinking Machines CM-5 and the CRAY T3D, and automatic 3D mesh generation(More)