Volumetric Curved Planar Reformation for virtual endoscopy

Curved Planar Reformation (CPR) has proved to be a practical and widely used tool for the visualization of curved tubular structures within the human body. It has been useful in medical procedures involving the examination of blood vessels and the spine. However, it is more difficult to use it for large, tubular, structures such as the trachea and the colon because abnormalities may be smaller relative to the size of the structure and may not have such distinct density and shape characteristics. Our new approach improves on this situation by using volume rendering for hollow regions and standard CPR for the surrounding tissue. This effectively combines gray scale contextual information with detailed color information from the area of interest. The approach is successfully used with each of the standard CPR types and the resulting images are promising as an alternative to virtual endoscopy. Because the CPR and the volume rendering are tightly coupled, the projection method used has a significant effect on properties of the volume renderer, such as distortion and isometry. We describe and compare the different CPR projection methods and how they affect the volume rendering process. A version of the algorithm is also presented which makes use of importance driven techniques; this ensures the users attention is always focused on the area of interest and also improves the speed of the algorithm.     

A comparison of the perceptual benefits of linear perspective and physically-based illumination for display of dense 3D streamtubes

Large datasets typically contain coarse features comprised of finer sub-features. Even if the shapes of the small structures are evident in a 3D display, the aggregate shapes they suggest may not be easily inferred. From previous studies in shape perception, the evidence has not been clear whether physically-based illumination confers any advantage over local illumination for understanding scenes that arise in visualization of large data sets that contain features at two distinct scales. In this paper we show that physically-based illumination can improve the perception for some static scenes of complex 3D geometry from flow fields. We perform human-subjects experiments to quantify the effect of physically-based illumination on participant performance for two tasks: selecting the closer of two streamtubes from a field of tubes, and identifying the shape of the domain of a flow field over different densities of tubes. We find that physically-based illumination influences participant performance as strongly as perspective projection, suggesting that physically-based illumination is indeed a strong cue to the layout of complex scenes. We also find that increasing the density of tubes for the shape identification task improved participant performance under physically-based illumination but not under the traditional hardware-accelerated illumination model.     

VisComplete: automating suggestions for visualization pipelines

Building visualization and analysis pipelines is a large hurdle in the adoption of visualization and workflow systems by domain scientists. In this paper, we propose techniques to help users construct pipelines by consensus--automatically suggesting completions based on a database of previously created pipelines. In particular, we compute correspondences between existing pipeline subgraphs from the database, and use these to predict sets of likely pipeline additions to a given partial pipeline. By presenting these predictions in a carefully designed interface, users can create visualizations and other data products more efficiently because they can augment their normal work patterns with the suggested completions. We present an implementation of our technique in a publicly-available, open-source scientific workflow system and demonstrate efficiency gains in real-world situations.     

Scientific sketching for collaborative VR visualization design

We present four studies investigating tools and methodologies for artist-scientist-technologist collaboration in designing multivariate, virtual reality (VR) visualizations. Design study 1 identifies the promise of 3D drawing-style interfaces for VR design and also establishes limitations of these tools with respect to precision and support for animation. Design study 2 explores animating artist-created visualization designs with scientific 3D fluid flow data. While results captured an accurate sense of flow that was advantageous as compared to the results of study 1, the potential for visual exploration using the design tools tested was limited. Design study 3 reveals the importance of a new 3D interface that overcomes the precision limitation found in study 1 while remaining accessible to artist collaborators. Drawing upon previous results, design study 4 engages collaborative teams in a design process that begins with traditional paper sketching and moves to animated, interactive, VR prototypes "sketched" by designers in VR using interactive 3D tools. Conclusions from these four studies identify important characteristics of effective artist-accessible VR visualization design tools and lead to a proposed formalized methodology for successful collaborative design that we expect to be useful in guiding future collaborations. We call this proposed methodology Scientific Sketching.     

有限元的未来是多物理场耦合

随着计算机技术的迅速发展,在工程领域中,有限元分析(FEA)越来越多地用于仿真模拟,来求解真实的工程问题。这些年来,越来越多的工程师、应用数学家和物理学家已经证明这种采用求解偏微分方程(PDE)的方法可以求解许多物理现象,这些偏微     

Molecular modeling optimization of anticoagulant pyridine derivatives

Intravascular clotting remains a major health problem in the United States, the most prominent being deep vein thrombosis, pulmonary embolism and thromboembolic stroke. Previous reports on the use of pyridine derivatives in cardiovascular drug development encourage us to pursue new types of compounds based on a pyridine scaffold. Eleven pyridine derivatives (oximes, semicarbazones, N-oxides) previously synthesized in our laboratories were tested as anticoagulants on pooled normal plasma using the prothrombin time (PT) protocol. The best anticoagulant within the oxime series was compound AF4, within the oxime N-oxide series was compound AF4-N-oxide, and within the semicarbazone series, compound MD1-30Y. We also used a molecular modeling approach to guide our efforts, and found that there was good correlation between coagulation data and computational energy scores. Molecular docking was performed to target the active site of thrombin with the DOCK v5.2 package. The results of molecular modeling indicate that improvement in anticoagulant activities can be expected by functionalization at the three-position of the pyridine ring and by N-oxide formation. Results reported here prove the suitability of DOCK in the lead optimization process.     

Extending IP to Low-Power, Wireless Personal Area Networks

Extending IP to low-power, wireless personal area networks (LoWPANs) was once considered impractical because these networks are highly constrained and must operate unattended for multiyear lifetimes on modest batteries. Many vendors embraced proprietary protocols, assuming that IP was too resource-intensive to be scaled down to operate on the microcontrollers and low-power wireless links used in LoWPAN settings. However, 6LoWPAN radically alters the calculation by introducing an adaptation layer that enables efficient IPv6 communication over IEEE 802.15.4 LoWPAN links.     

A ship motion simulation system

In this article, efficient computational models for ship motions are presented. These models are used to simulate ship movements in real time. Compared with traditional approaches, our method possesses the ability to cope with different ship shapes, engines, and sea conditions without the loss of efficiency. Based on our models, we create a ship motion simulation system for both entertainment and educational applications. Our system assists users to learn the motions of a ship encountering waves, currents, and winds. Users can adjust engine powers, rudders, and other ship facilities via a graphical user interface to create their own ship models. They can also change the environment by altering wave frequencies, wave amplitudes, wave directions, currents, and winds. Therefore, numerous combinations of ships and the environment are generated and the learning becomes more amusing. In our system, a ship is treated as a rigid body floating on the sea surface. Its motions compose of 6 degrees of freedom: pitch, heave, roll, surge, sway, and yaw. These motions are divided into two categories. The first three movements are induced by sea waves, and the last three ones are caused by propellers, rudders, currents, and winds. Based on Newton’s laws and other basic physics motion models, we deduce algorithms to compute the magnitudes of the motions. Our methods can be carried out in real time and possess high fidelity. According to ship theory, the net effects of external forces on the ship hull depend on the ship shape. Therefore, the behaviors of the ship are influenced by its shape. To enhance our physics models, we classify ships into three basic types. They are flat ships, thin ships, and slender ships. Each type of ship is associated with some predefined parameters to specify their characteristics. Users can tune ship behaviors by varying the parameters even though they have only a little knowledge of ship theory.     

Sensory-motor enhancement in a virtual therapeutic environment

The sensory-motor skills of persons with neuromuscular disabilities have been shown to be enhanced by intensive and repetitive therapeutic interventions. This paper describes a form of low immersion virtual reality and a prototype, open source system that allow a user with significant physical disability to actively interact with computer-generated objects whose behaviors promote a game-like interaction. Unlike fully immersive and haptic virtual reality, this approach frees the user from head-mounted displays and gloves. It extracts the user’s real-time silhouette from the output of a remote video camera and uses that two-dimensional outline to interact with graphical objects on screen. In contrast to video games that have been modified with specialized interfaces, this virtual interaction system promotes the repetitive use of goal directed movements of the arms and body, which are essential to promote cortical reorganization, as well as discourage unwanted changes in muscle tissue that result in contracture. A prototype system demonstrates the potential of low immersion technology to motivate users and encourage participation in therapy. It also offers the potential of accommodating the sensory-motor skills of individuals with very significant impairment. The behaviors of the computer-generated graphics can be altered to allow use by those with very limited range of motion and/or motor control. These behaviors can be adjusted to provide a continuing challenge as the user’s skills improve. This prototype is described in terms of functional capabilities that include a silhouette extraction from a video image, and generation of graphical objects that interact with the silhouette. The work is extended with a discussion of a more sophisticated region of interest detection algorithm that can select specific parts of the body.     

Application of single-level,pointwise algebraic,and smoothed aggregation multigrid methods to direct numerical simulations of incompressible turbulent flows

Single- and multi-level iterative methods for sparse linear systems are applied to unsteady flow simulations via implementation into a direct numerical simulation solver for incompressible turbulent flows on unstructured meshes. The performance of these solution methods, implemented in the well-established SAMG and ML packages, are quantified in terms of computational speed and memory consumption, with a direct sparse LU solver (SuperLU) used as a reference. The classical test case of unsteady flow over a circular cylinder at low Reynolds numbers is considered, employing a series of increasingly fine anisotropic meshes. As expected, the memory consumption increases dramatically with the considered problem size for the direct solver. Surprisingly, however, the computation times remain reasonable. The speed and memory usage of pointwise algebraic and smoothed aggregation multigrid solvers are found to exhibit near-linear scaling. As an alternative to multi-level solvers, a single-level ILUT-preconditioned GMRES solver with low drop tolerance is also considered. This solver is found to perform sufficiently well only on small meshes. Even then, it is outperformed by pointwise algebraic multigrid on all counts. Finally, the effectiveness of pointwise algebraic multigrid is illustrated by considering a large three-dimensional direct numerical simulation case using a novel parallelization approach on a large distributed memory computing cluster.