Current navigation mechanisms for the World Wide Web promote a depth-first search for information on pages in hyperspace. This search strategy frequently results in the unintentional and often undesirable behavior of ``web surfing'' --- a user starts off in search of some information, but is side-tracked by tangential links. We propose a set of mechanisms based on breadth-first traversal that are better suited for directed searching. We have implemented our ideas as a scratchpad by augmenting an existing browser. Such a system makes web navigation both faster and easier.

We present a unique polygonal simplification method grounded in rigorous perceptual science. Local simplification operations are driven directly by perceptual metrics, rather than the geometric metrics common to other algorithms. The effect of each operation on the final image is considered in terms of the contrast the operation will induce in the image and the spatial frequency of the resulting change. Equations derived from psychophysical studies determine whether the simplification operation will be perceptible; the operation is performed only if its effect is judged imperceptible. To increase the range of simplification permitted, we incorporate gaze-directed rendering. A commercial eye tracker monitors the direction of the user's gaze, allowing the image to be simplified more aggressively in the periphery than at the center of vision. Our perceptual model addresses many interesting topics in polygonal simplification, including gaze-directed rendering, silhouette preservation, and imperceptible simplification. We describe two user studies to evaluate our model, and address the shortcomings as well as the potential of our approach.

A method and system of comparing a query and a subject database using a distributed computing platform is disclosed. The databases are divided into data elements having a size within a specified range. All data elements and task definitions are sent to a master CPU of a master-slave distributed computing platform, wherein task definitions comprise at least one comparison parameter, at least one executable comparison element, and a query and a subject data element ID/descriptor. Data elements are sent alternately from query and subject data elements. A task definition is sent for each task from the master CPU to one of a plurality of slave CPUs when all parts of a task definition and data elements referenced by the task definition are available at the master CPU. Data elements are then sent to the slave CPUs for performance of the tasks. Task results for each task are returned to a CPU.

We have created a novel implementation of BLAST and Smith-Waterman for the Parabon Frontier distributed computing platform. We present design specifics, implementation details, performance results, and sensitivity comparison for very large database searches using the Prospector versions of BLASTN, BLASTP, BLASTX, TBLASTN, and TBLASTX, and the analogous versions of Smith-Waterman.

We report the thermodynamics and kinetics of an off-lattice Go model β-hairpin from immunoglobulin-binding protein confined to an inert spherical pore. Confinement enhances the stability of the hairpin due to the decrease in the entropy of the unfolded state. Compared to its value in the bulk, the rates of hairpin formation increase in the spherical pore. Surprisingly, the dependence of the rates on the pore radius, R_s, is non-monotonic. The rates reach a maximum at R_s/R^b_g,N ≅ 1.5, where R^b_g,N is the radius of gyration of the β-hairpin in the bulk. The denatured state ensemble (DSE) of the encapsulated β-hairpin is highly structured even at substantially elevated temperatures. Remarkably, profound effect of the confinement is evident even when β-hairpin occupies less than a tenth of the sphere volume, i.e., (R_s/R^b_g,N)³ ≈ 11! Our calculations show that the emergence of substantial structure in denatured state of proteins in inert pores is a consequence of confinement. In contrast, the structure of the bulk DSE depends dramatically on the extent of denaturation.