Improvements to the APBS biomolecular solvation software suite

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining p$K_a$ values, and an improved web-based visualization tool for viewing electrostatics

A Taxonomy of Data Grids for Distributed Data Sharing, Management and Processing

Data Grids have been adopted as the platform for scientific communities that need to share, access, transport, process and manage large data collections distributed worldwide. They combine high-end computing technologies with high-performance networking and wide-area storage management techniques. In this paper, we discuss the key concepts behind Data Grids and compare them with other data sharing and distribution paradigms such as content delivery networks, peer-to-peer networks and distributed databases. We then provide comprehensive taxonomies that cover various aspects of architecture, data transportation, data replication and resource allocation and scheduling. Finally, we map the proposed taxonomy to various Data Grid systems not only to validate the taxonomy but also to identify areas for future exploration. Through this taxonomy, we aim to categorise existing systems to better understand their goals and their methodology. This would help evaluate their applicability for solving similar problems. This taxonomy also provides a "gap analysis" of this area through which researchers can potentially identify new issues for investigation. Finally, we hope that the proposed taxonomy and mapping also helps to provide an easy way for new practitioners to understand this complex area of research.Comment: 46 pages, 16 figures, Technical Repor

Computational polarimetric microwave imaging

We propose a polarimetric microwave imaging technique that exploits recent advances in computational imaging. We utilize a frequency-diverse cavity-backed metasurface, allowing us to demonstrate high-resolution polarimetric imaging using a single transceiver and frequency sweep over the operational microwave bandwidth. The frequency-diverse metasurface imager greatly simplifies the system architecture compared with active arrays and other conventional microwave imaging approaches. We further develop the theoretical framework for computational polarimetric imaging and validate the approach experimentally using a multi-modal leaky cavity. The scalar approximation for the interaction between the radiated waves and the target---often applied in microwave computational imaging schemes---is thus extended to retrieve the susceptibility tensors, and hence providing additional information about the targets. Computational polarimetry has relevance for existing systems in the field that extract polarimetric imagery, and particular for ground observation. A growing number of short-range microwave imaging applications can also notably benefit from computational polarimetry, particularly for imaging objects that are difficult to reconstruct when assuming scalar estimations.Comment: 17 pages, 15 figure

Grid-enabling problem solving environments: a case study of SCIRun and NetSolve

Journal ArticleCombining the functionality of NetSolve, a grid-based middleware solution, with SCIRun, a graphically-based problem solving environment (PSE), yields a platform for creating and executing grid-enabled applications. Using this integrated system, hardware and/or software resources not previously accessible to a user become available completely behind the scenes. Neither the SCIRun system nor the SCIRun user need to know any details about how these resources are located and utilized. A SCIRun module merely makes an RPC-style call to NetSolve via the NetSolve C language API to invoke a certain routine and to pass its data. Distributed computation and the details of remote communication are completely abstracted away from the SCIRun framework and its end user

UITS Research Technologies Cyberinfrastucture for IU Research and Academics

UITS Research Technologies develops, delivers, and supports advanced technology to improve the productivity of and enable new possibilities in research, scholarly endeavors, and creative activity at IU. Join Robert Ping, RT Manager of Education and Outreach, as he introduces the nine service areas available to all IU faculty, staff, and students: Science Gateways, Computation, Data Storage, Visualization, Analysis and Software delivery and support, Services for biomedical biological and health-related research, Campus birding: connecting to local and national cyberinfrastructure, Education and outreach, and Grant support and custom for-fee services. http://researchtech.iu.ed

Towards Real-time Remote Processing of Laparoscopic Video

Laparoscopic surgery is a minimally invasive technique where surgeons insert a small video camera into the patient\u27s body to visualize internal organs and use small tools to perform these procedures. However, the benefit of small incisions has a disadvantage of limited visualization of subsurface tissues. Image-guided surgery (IGS) uses pre-operative and intra-operative images to map subsurface structures and can reduce the limitations of laparoscopic surgery. One particular laparoscopic system is the daVinci-si robotic surgical vision system. The video streams generate approximately 360 megabytes of data per second, demonstrating a trend toward increased data sizes in medicine, primarily due to higher-resolution video cameras and imaging equipment. Real-time processing this large stream of data on a bedside PC, single or dual node setup, may be challenging and a high-performance computing (HPC) environment is not typically available at the point of care. To process this data on remote HPC clusters at the typical 30 frames per second rate (fps), it is required that each 11.9 MB (1080p) video frame be processed by a server and returned within the time this frame is displayed or 1/30th of a second. The ability to acquire, process, and visualize data in real time is essential for the performance of complex tasks as well as minimizing risk to the patient. We have implemented and compared performance of compression, segmentation and registration algorithms on Clemson\u27s Palmetto supercomputer using dual Nvidia graphics processing units (GPUs) per node and compute unified device architecture (CUDA) programming model. We developed three separate applications that run simultaneously: video acquisition, image processing, and video display. The image processing application allows several algorithms to run simultaneously on different cluster nodes and transfer images through message passing interface (MPI). Our segmentation and registration algorithms resulted in an acceleration factor of around 2 and 8 times respectively. To achieve a higher frame rate, we also resized images and reduced the overall processing time. As a result, using high-speed network to access computing clusters with GPUs to implement these algorithms in parallel will improve surgical procedures by providing real-time medical image processing and laparoscopic data