Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain beyond reach. We present several new algorithms and implementation techniques that significantly accelerate parallel MD simulations compared with current stateof-the-art codes. These include a novel parallel decomposition method and message-passing techniques that reduce communication requirements, as well as novel communication primitives that further reduce communication time. We have also developed numerical techniques that maintain high accuracy while using single precision computation in order to exploit processor-level vector instructions. These methods are embodied in a newly developed MD code called Desmond that achieves unprecedented simulation throughput and parallel scalability on commodity clusters. Our results suggest that Desmond's parallel performance substantially surpasses that of any previously described code. For example, on a standard benchmark, Desmond's performance on a conventional Opteron cluster with 2K processors slightly exceeded the reported performance of IBM's Blue Gene/L machine with 32K processors running its Blue Matter MD code.

Most existing visualization applications use 3D polygonal geometry as their basic rendering primitive. As users demand more complex datasets, the memory requirements for storing and retrieving large 3D models are becoming excessive. In addition, current 3D rendering hardware is facing a large memory bus bandwidth bottleneck at the processor to graphics pipeline interface. Rendering 1 million triangles with 24 bytes per triangle at 30Hz requires as much as 720 MB/sec memory bus bandwidth. This transfer rate is well beyond that of current low-cost graphics systems. A solution is to compress the static 3D geometry as an off-line pre-process. Then, only the compressed geometry needs to be stored in main memory and sent to the graphics pipeline for real-time decompression and rendering.This thesis presents several new techniques for lossy compression of 3D geometry that compress surfaces 2 to 3 times better than existing methods. We first introduce several meshifying algorithms which efficiently encode the original geometry as generalized triangle meshes. This encoding allows most mesh vertices to be reused when forming new triangles. The second contribution allows various parts of a geometric model to be compressed with different precision depending on the level of detail present. Together, our meshifying algorithms and the variable compression method achieve compression ratios of between 10 and 15 to one. Our experimental results show a dramatically lower memory bandwidth required for real-time visualization of complex datasets. would also like to thank MIT for being the most challenging and exciting place I have experienced so far.The word "meshify" was coined by Michael Deering. The scanned models were from Stanford Graphics Lab, Marching Cubes data from Vtk, and others from Viewpoint DataLabs.

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Generalizing the degenerate KAM theorem under the Rüssmann non-degeneracy and the isoenergetic KAM theorem, we employ a quasi-linear iterative scheme to study the persistence and frequency preservation of invariant tori on a smooth sub-manifold for a real analytic, nearly integrable Hamiltonian system. Under a nondegenerate condition of Rüssmann type on the sub-manifold, we shall show the following: a) the majority of the unperturbed tori on the sub-manifold will persist; b) the perturbed toral frequencies can be partially preserved according to the maximal degeneracy of the Hessian of the unperturbed system and be fully preserved if the Hessian is nondegenerate; c) the Hamiltonian admits normal forms near the perturbed tori of arbitrarily prescribed high order. Under a sub-isoenergetic nondegenerate condition on an energy surface, we shall show that the majority of unperturbed tori give rise to invariant tori of the perturbed system of the same energy which preserve the ratio of certain components of the respective frequencies.

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Objective  To determine the long‐term results and assess the quality of life in patients with continent urinary diversions after cystectomy. Patients and methods  Eighty‐six consecutive patients who received a continent urinary diversion from 1988 to 1994 at the Vancouver Hospital and Health Sciences Center were evaluated. The evaluation comprised a review of their hospital charts and clinic visits at 3 months and then yearly. Quality of life issues were assessed using a postal questionnaire pertaining to the patient’s urinary symptoms, activity level and overall well‐being while living with a continent urinary diversion. Two separate questionnaires were sent, addressing heterotopic or orthotopic diversions. Results  There was an acceptable rate of complications, with stone formation and urinary tract infection as the most common morbidities. Continence was rated as good in most patients, with no patient reportingcomplete incontinence. Undesirable urinary symptoms occurred less often than 20% of the time in most patients. Although there was a significant effect on sex life, the overall quality of life appeared to be very good, as 70% of the patients had no limitations to their activities. Conclusions  The techniques currently evolved for urinary diversion produce good long‐term results and quality of life. These diversions should be considered in a well selected patient population.

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