William F. Humphrey

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PAWS (Parallel Application WorkSpace) is a software infrastructure for use in connecting separate parallel applications within a component-like model. A central PAWS Controller coordinates the linking of serial or parallel applications across a network to allow them to share parallel data structures such as multidimensional arrays. Applications use the PAWS(More)
The primary all-trans --> 13-cis photoisomerization of retinal in bacteriorhodopsin has been investigated by means of quantum chemical and combined classical/quantum mechanical simulations employing the density matrix evolution method. Ab initio calculations on an analog of a protonated Schiff base of retinal in vacuo reveal two excited states S1 and S2,(More)
The structure of bacteriorhodopsin based on electron microscopy (EM) studies, as provided in Henderson et al. (1990), is refined using molecular dynamics simulations. The work is based on a previously refined and simulated structure which had added the interhelical loops to the EM model of bR. The present study applies an all-atom description to this(More)
The Parallel Object-Oriented Methods and Applications (POOMA) Framework, written in ANSI/ISO C++, has demonstrated both great expressiveness and eecient code performance for large-scale scientiic applications on computing platforms ranging from workstations to massively parallel supercomputers. The POOMA Framework provides high-level abstractions for(More)
The early stages of the bacteriorhodopsin photocycle, including the J625, K ~ w , and L550 intermediates and the role of water molecules within the protein interior, are studied by means of molecular dynamics simulations. Our calculations examine two models for the excited state potential surface governing the observed all-trans-13-cis photoisomerization:(More)
Molecular dynamics simulations of wild-type bacteriorhodopsin (bR) and of its D85N, D85T, D212N, and Y57F mutants have been carried out to investigate possible differences in the photoproducts of these proteins. For each mutant, a series of 50 molecular dynamics simulations of the photoisomerization and subsequent relaxation process were completed. The(More)
13 leven-binding myeloma proteins (LBMP) of BALB/c origin were classified into two groups with different binding specificities; one group of 11 proteins bound beta2 leads to 1 fructosans, a second group of two proteins bound fructosans probably of beta2 leads to 6 linkage. Anti-idiotypic sera prepared to 10 of the proteins in the appropriate strains of mice(More)
The POOMA Framework is an object-oriented library and application suite implemented in C++ which enables the parallel simulation of the dynamics of interacting particles and elds. Using templates, POOMA provides a exible and intuitive syntax to express global eld and particle operations and creates applications with near hand-coded performance. POOMA is(More)
Idiotypes of inulin-binding myeloma proteins (InuBMP) were determined primarly by variable region light chains (VL) or by variable region heavy chains (VH) but needed both chains to be expressed. Recombinant molecules were used to show that individual idiotypes (IdI) of U61, E109, T957, and A4 InuBMP and cross-specific idiotypes (IdXB) of U61 were primarily(More)
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