ProteinVista: A Fast Molecular Visualization System Using Microsoft Direct3D

To process enormous 3D data, we have designed a VLIW (Very Long Instruction Word) processor called FLOVA (Floating-Point VLIW Architecture) exploiting the ILP (Instruction-Level Parallelism) in 3D programs. This paper presents FGA (FLOVA Geometry Accelerator) that is the 3D graphics system and it almost removes the time required to process in the geometry stage. We have developed the 3D graphics library, FGA-GL, to supports the FGA system. The deferred primitive rendering algorithm of FGA-GL enables the geometry processing of the primitive data to be done concurrently with the host job such as primitive data management or game play. FGA improves the average performance of 3D graphics system by 2.5-3.0.

A 3D computer graphics (3DCG) library with energy-efficient cache architecture is implemented for mobile multimedia systems. The developed library is based on fixed-point arithmetic for low energy consumption. To achieve high performance, the library is optimized at both the assembly and the algorithm levels on 3 different advanced RISC machine (ARM) processors. In order to enhance energy-efficiency as well as performance, a series of simulations have been performed on application programs with various cache configurations. We find that a 2-way set associative cache consumes low energy with negligible performance degradation. In this cache system, the optimized library can achieve 66.1% performance improvement and 25.3% energy saving on average compared with the conventional 4-way set associative cache system. Software and hardware co-optimization achieves 67 K polygons/s with low energy consumption. We verified the graphics library with proposed cache architecture by implementing a mobile graphics LSI.

We describe the reconstruction of a medieval building as an example of how the use of 3D computer graphics can facilitate the reconstruction of an ancient site. We suggest that different stages of a virtual reconstruction imply the use of different rendering techniques, as the style of visualization has a significant impact on both the reconstruction process and the presentation to non-expert viewers.

To provide a virtual reality 3D user interface with comprehensive molecular modeling, we have developed a novel haptic rendering system with a fingertip haptic rendering device and a hand-tracking Leap Motion controller. The system handles virtual molecular objects with real hands motion captured by the Leap Motion controller in a virtual reality environment. The fingertip haptic rendering device attached on each finger and a wrist gives haptic display, when virtual hands manipulating virtual molecular objects. Based on preliminary software development studies using existing 3D graphics toolkit such as CHAI3D and Unity, the fingertip haptic rendering device works with a reasonable performance for a polygon surface model and a ribbon model, but not for an atomic model due to the low rendering performance. On the other hand, the device provides us a grasping feeling of a large molecule represented by an atomic model, when used with the particle simulation system running on graphics library, DirectX 12. The haptic rendering performances, among the three software systems are discussed.

Molecular visualization software has the common objective of manipulation and interpretation of data from numerical simulations. They visualize many complicated molecular structures with personal computer and workstation, to help analyze a large quantity of data produced by various computational methods. However, users are often discouraged from using these tools for visualization and analysis due to the difficult and complicated user interface. In this regard, we have developed an easy-to-use three-dimensional molecular visualization and analysis program named POSMOL. This has been developed on the Microsoft Windows platform for the easy and convenient user environment, as a compact program which reads outputs from various computational chemistry software without editing or changing data. The program animates vibration modes which are needed for locating minima and transition states in computational chemistry, draws two and three dimensional (2D and 3D) views of molecular orbitals (including their atomic orbital components and these partial sums) together with molecular systems, measur es various geometrical parameters, and edits molecules and molecular structures.

This study aims to determine the effect of learning media and learning styles on learning outcomes in the cognitive domain of students in basic physiology subjects. This study used a quasi-experimental method using a 2X2 factorial design. The findings indicate that: (1) the learning outcomes of students who use model learning media are higher than those of students who use image learning media (2) the learning outcomes of students who have a kinesthetic learning style are higher than the learning outcomes of students who have visual learning styles. (3) there is an influence of the interaction between learning media and learning styles on student cognitive learning outcomes in Basic Physiology courses. (4) cognitive learning outcomes of students who have a kinesthetic learning style who learn using model learning media are higher than realm learning outcomes. cognitive students who have a kinesthetic learning style who learn using image learning media. (5) cognitive learning outcomes of students who have visual learning styles who learn using learning media models are lower than those of students who have visual learning styles who learn using image learning media. (6) the cognitive learning outcomes of students who have a kinesthetic learning style who learn using model learning media are higher than the cognitive learning outcomes of students who have a visual learning style who learn using model learning media. (7) the cognitive learning outcomes of students who have a kinesthetic learning style who learn using image learning media are lower than the cognitive learning outcomes of students who have a visual learning style who learn using image learning media.

Artists explore the visual style of animated characters through 2D concept art, since it affords them a nearly unlimited degree of creative freedom. Realizing the desired visual style, however, within the 3D character animation pipeline is often impossible, since artists must work within the technical limitations of the pipeline toolset. In order to expand the range of possible visual styles for digital characters, our research aims to incorporate the expressiveness afforded by 2D concept painting into the computer animation pipeline as a core component of character authoring and animation. While prior 3D painting methods focus on static geometry or simple animations, we develop tools for the more difficult task of character animation. Our system shows how 3D stroke-based paintings can be deformed using standard rigging tools. We also propose a configuration-space keyframing algorithm for authoring stroke effects that depend on scene variables such as character pose or light position. During animation, our system supports stroke-based temporal keyframing for one-off effects. Our primary technical contribution is a novel interpolation scheme for configuration-space keyframing that ensures smooth, controllable results. We demonstrate several characters authored with our system that exhibit painted effects difficult to achieve with traditional animation tools.

We are delighted to present the proceedings of High Performance Graphics 2013. This is the fifth year of the conference, which has become the leading international conference on graphics hardware, systems, and algorithms. The conference brings together researchers, engineers, and architects to discuss the complex interactions of parallel hardware, novel programming models, efficient graphics algorithms, and innovative applications. High Performance Graphics (HPG) was founded in 2009 to synthesize and expand on two important and well-respected conferences in computer graphics: Graphics Hardware, an annual conference focusing on graphics hardware, architecture, and systems since 1986; and Interactive Ray Tracing, an innovative symposium begun in 2006 focusing on the emerging field of interactive ray tracing and global illumination. By combining and expanding these two communities, we bring to authors and attendees the best of both fields and a conference covering a broad range of interactive 3D graphics systems and algorithm research. This year's proceedings continue to reflect this tradition of synthesis. Ray tracing has again emerged as a popular topic, and HPG 2013 includes papers on new algorithms for efficiently constructing and traversing ray tracing acceleration structures as well as complementary papers detailing specialized hardware designs for ray tracing. The conference includes papers on classic graphics hardware topics, such as advanced rasterization and real-time shadowing, as well as increasingly important topics such as interactive voxelization and reconstruction. In all 44 papers were submitted to HPG 2013, of which 15 were accepted for an acceptance rate of about 34%.

During 1979, CERN began to evaluate how interactive computer graphics displays could aid the analysis of high-energy physics experiments at the new Super Proton Synchrotron collider. This work led to PIONS, a 3D graphics system, which features the ability to store and view hierarchical graphics structures in a directed-acyclic-graph database. It is possible to change the attributes of these structures by making selections on nongraphical information also stored in the database. PIONS is implemented as an object-oriented message-passing system based on Small Talk design principles. It supports multiple viewing transformations, logical input devices, and 2D and 3D primitives. The design allows full use to be made of display hardware that provides dynamic 3D picture transformation.

This paper presents the development of a 3-D computer graphics software for displaying wellbore trajectories. The software is designed for use with PC microcomputer operating under MICROSOFT WINDOWS™ environment. Examples of the software application are given in two important areas of directional drilling: 1) avoidance of wellbore collisions and 2) planning and drilling monitoring of relief wells. First, the paper presents the basic theory behind the computer graphics techniques used for developing the computer software. Second, it presents the display modes and important features provided by the system that includes 2-D and 3-D views of wellbore trajectories with ability of rotation, zoom-in and zoom-out, and display of uncertainty ellipses. These features are very helpful in planning and monitoring wellbore trajectories. Also, these capabilities allow the software to be used as a powerful training tool. The last part of the paper illustrates the application of this graphic system in planning and monitoring: 1) directional drilling in high density well areas such as offshore platforms in order to avoid wellbore collision; and 2) the relief well drilling to assist in the approaching procedure between relief and blowing wells and the use of ranging tools.

A visual simulation system of human evacuation in subway station was introduced in the paper. The algorithm of data fit was designed according to the analysis of fire simulation numerical value and evacuation simulation numerical value, and the problem of the visual output in real time was resolved by the algorithm. The system was reviewed from model configuration, function, the establishment of model environment, and the visual simulation development tools. Based on personal computer as a hardware platform, this visual simulation system has been used in the Beijing Jishuitan subway station.

This research was intended to measure the effectiveness in the students’ writing achievement by using note-written and marked-written grammar feedback on students’ writing with visual learning styles. Based on the result of the computation, that in the experimental group using note-written grammar feedback, mean score for visual learning style is 78.78, while in the control group the visual learning style is 69.25. It means that there is a difference means score between experimental group and control group. Based on the statistical computation, the F value of Corrected Model was .519. It > .05 with the level of confidence 95% (α = .05). It means that was not valid. Further, the F value of Intercept was .000. It < .05 with the level of confidence 95% (α = .05). It means the dependent variable was not influenced by the independent variable. On the other words, the intercept was significant. While the effect of note-written grammar feedback to posttest score is .388. It > .05 with the level of confidence 95% (α = .05). It means that there is no a significance of note-written grammar feedback in students’ writing. Furthermore, for the technique on learning style was .347> .05 with the level of confidence 95% (α = .05). It means that there was no a significance of written grammar feedback techniques and students’ learning style on the students’ writing.

Recently, massively-parallel computing libraries and devices are much widely used, in addition to the traditional 3D graphics systems. In this paper, we present a full 3D fixed-function graphics pipeline, based on the OpenCL, which is one of the most widely used massively-parallel computing library. The full 3D graphics features including WebGL, Web3D and others can be implemented on the massively-parallel computations, without underlying 3D graphics hardware support. Many previous works focused on another massively-parallel system of CUDA, which has a drawback of limited availability. In contrast, we designed and implemented a new architecture with OpenCL, which is now available on various computing devices, including most CPUs, GPUs, and at least theoretically, special-purpose embedded FPGAs. Our work provides full 3D graphics features on OpenCL-capable systems, without dedicated 3D graphics hardware, to finally make 3D graphics features ubiquitous. Technically, we used a top-down approach in its rendering, from the whole screen to precise pixels. At each stage, we tuned our OpenCL implementations and also their global and local parameter spaces. We present the details of our design and also the final result of our implementation, and show its correctness and efficiency.

The Computer Networking course commonly taught in mixed mode involving lecture and practical session whereas beside face-to-face theory session, students need to experience hands-on activities in order to appreciate the technology and contents. Nevertheless the abstraction in Computer Networking course such as the complexity in TCP/IP network layering, the connection and configuration of client and server’s framework, differences in static and dynamic IP address configuration had imposed a great challenge for students to understand and grab the main concept of computer networking technology. As such, an approach of using computer network simulation and visualization tool in teaching and learning Computer Networking course is seen beneficial for educators and students. In this research, computer network simulation software of CISCO Packet Tracer was utilized in Computer Networking (MTN3023) course. Students (N=55) were exposed to CISCO Packet Tracer on which they developed Wide Area Network (WAN) that consists of configuration activities of Personal Computer (PC), Servers and Switches according to CISCO standard. Subsequently, student’s feedback and their insight on the effectiveness of CISCO packet Tracer in learning computer networking were probed using questionnaire. All the feedbacks were investigating statistically using SPSS 16.0. From the analysis, the descriptive results shown that all students were agreed (N=32 : Strongly Agree; N=23 : Agree) that CISCO Packet Tracer had successfully help them to understand several key concepts of computer networking and at the same quash some abstractions they faced in the course. In a nutshell, CISCO Packet Tracer as a simulation and visualization tool had been proven to be an effective software in supporting the teaching and learning of computer networking course.

Parallel computer systems are among the most complex of man's creations, making satisfactory performance characterization difficult. Despite this complexity, there are strong, indeed, almost irresistible, incentives to quantify parallel system performance using a single metric. The fallacy lies in succumbing to such temptations. A complete performance characterization requires not only an analysis of the system's constituent levels, it also requires both static and dynamic characterizations. Static or average behavior analysis may mask transients that dramatically alter system performance. Although the human visual system is remarkedly adept at interpreting and identifying anomalies in false color data, the importance of dynamic, visual scientific data presentation has only recently been recognized Large, complex parallel system pose equally vexing performance interpretation problems. Data from hardware and software performance monitors must be presented in ways that emphasize important events while eluding irrelevant details. Design approaches and tools for performance visualization are the subject of this paper.