Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie

OPTIMIZATION OF wasteWOIMA’s MODULAR POWER PLANT INSTALLATION USING 3D SIMULATION AND VIRTUAL REALITY

The primary objective of this research is to optimize module installation procedure for Woima’s modular WTE power plant by making a Three-Dimensional (3D) simulation of the power plant and inspecting the model using Virtual Reality (VR). This thesis ad-dresses the research question on how to use 3D simulation to reduce time and cost dur-ing the construction. Therefore, this thesis suggests an installation procedure where each module fits into the other as it were a lego puzzle. This proposed building procedure is previewed as 3D simulation that could then be used to optimize the construction of wasteWOIMA’s modular power plant. This research work employs the use of primary data, CAD blueprints, sourced from the case company, while secondary data was sourced from books, online repository, aca-demic and scientific journals. To uphold the credibility of this research, it utilized both experimental and case study research strategies to conceptualize the simulation of the power plant which can be previewed on Virtual Reality (VR) glasses. VR model inspec-tion provides an immersive and real-life scale experience. The entire 3D simulation was done using SketchUp software, a 3D modelling and simulation tool. A VR session was also carried out during the research to help identify areas of possible improvement with safety, cost and quality, using HTC Vive VR glasses and Symmetry Alpha software. The outcome of this research shows that 3D simulation, especially when combined with VR models inspection, can help to optimize models to prevent errors during actual con-struction work, hence, saving cost and reducing lead time

CFD Modelling of matte droplets coalescence in Flash smelting settler

Computer simulations are popular due to difficulty in setup of conventional experimental methods at high temperature processes. Computational Fluid dynamics is an important tool to study settling mechanism in Outotec's flash smelting settler. Commercial Ansys Fluent model was used to study settling previously by researchers, but no study was done to model coalescence. The thesis aims in studying the suitability of the Ansys fluent built in code to model coalescence for flash smelting settler. The success of the model helps to understand copper loss mechanisms and find ways to increase copper recovery. Firstly, collision theory and coalescence mechanism is reviewed thoroughly. Secondly, Ansys fluent built in models for modeling coalescence are listed and compared to select best mathematical model. The primary criteria for selection was ability to model collisions, coalescence, particle tracking and better visualization capacities. The selected discrete phase model is parametrized to model coalescence during settling of matte droplets through slag phase. It is noted that DPM could be used to simulate settling and coalescence of matte droplets. DPM can be used to get the idea of the process/coalescence phenomenon in a short period. The simulation showed droplets change trajectory after collisions/coalescence. Simulation also revealed coalescence dramatically affects settling time. Settling time is not only affected by increase in droplet diameter but also due to change in droplet trajectory after coalescences. However, Parametrized DPM model uses parcels injection technique that makes it difficult to track droplets individually for accurate comparison. In future user defined function should be written to identify and track droplets individually for accurate analysis of individual droplets

Advanced Computer Graphics Aided Molecular Visualization and Manipulation Softwares: The Hierarchy of Research Methodologies

In the present day, the huge obstacles, and the major technical problems encountered by the teaching and research faculties, academicians, industrial specialists, laboratory demonstrators and instructors, fellow students and researchers, etc. are to adopt integrative approaches of demonstrating (learning) chemistry and chemical education, and the realistic ways of delivering (grasping) scientific materials articulately with graceful and effortless manner. Towards minimizing these challenges, various audio-visual tools and technologies, advanced computer aided molecular graphics, freely available electronic gadgets assisted chemistry and chemical education apps, human unreadable data reading and accessing softwares, etc. are being incorporated worldwide as the most indispensable physical and electronic means for successful professionalisms. This short article is essentially a collective report underscoring extraordinary approaches, incredible efforts, and innovative skills of the computer based chemical and molecular graphics towards illuminating intrinsic parts of the chemistry and chemical education, and revealing various aspects of the cutting -edge research. As their representatives, herein, the different type computer coding languages based graphical tools such as Molden, GaussView, Jmol, and Visual Molecular Dynamics (VMD) are referred, and elucidated their potential applications and remarkable attempts in the advancement of diverse areas of chemistry and chemical education. Beside this, the most essential graphical features, unique rendering abilities with magnificent views, splendid visualizing skills, awesome data accessing functionalities, etc. of each of them, and their invaluable roles for studying complex molecules, biomolecules, crystals, and the entire material assemblies as well as for investigating global and local molecular physicochemical properties are presented concisely with the special stresses on their relatively better and comparatively more applicable distinctive attributes explicitl

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

VR-CHEM Developing a virtual reality interface for molecular modelling

VR-CHEM is a prototype for a virtual reality molecular modelling program with a modern 3D user interface. In this thesis, the author discusses the research behind the development of the prototype, provides a detailed description of the program and its features, and reports on the user tests. The research includes reviewing previous programs of a similar category that have appeared in studies in the literature. Some of these are related to chemistry and molecular modelling while others focus on 3D input techniques. Consequently, the prototype contributes by exploring the design of the user interface and how it can affect productivity in this category of programs. The prototype is subjected to a pilot user test to evaluate what further developments are required. Based on this, the thesis proposes that 3D interfaces, while capable of several unique tasks, are yet to overcome some significant drawbacks such as limitations in accuracy and precision. It also suggests that virtual reality can aid in spatial understanding but virtual hands and controllers are far inferior to real hands for even basic tasks due to a lack of tactile feedback

Visualizing silicon chemistry

The research presented in this thesis may be divided into three areas: transition metal catalysis, graphical user interfaces, and the derivation and application of effective core potentials;Transition metal catalysis. The titanium catalyzed hydrosilation reaction has been examined in detail to determine a possible minimum energy reaction path. Two reactions and three catalysts were considered. In addition to a model system consisting of the reaction of silane with ethylene, the simplest known experimental reaction involving trichlorosilane and ethylene was also examined. In addition to a model catalyst of TiH2, the experimental catalysts TiCl2, and Ti(C5H5) 2 were considered. In all reactions studied the catalyst had a dramatic effect on the reaction system changing the overall reaction barrier from over 50 kcal/mol without the catalyst to a barrierless process with the catalyst. In addition to the overall reaction energies, several low energy intermediate structures were predicted which might be experimentally observable;Graphical user interfaces. A description is given of a new graphical user interface for the GAMESS program. This interface includes many features useful for interpreting complex wavefunctions and reaction systems. These include the ability to animate reaction paths and normal modes of vibration, as well as the ability to view molecular orbitals, total electron densities, molecular electrostatic potentials, and density differences;Effective core potentials. The derivation of an enhanced method for the computation of integrals involving effective core potentials is presented and has been implemented in the electronic structure code GAMESS. This method has helped produce a large reduction in the computational cost of ECPs. It has also enabled the implementation of analytical second derivatives. The new method is also applied to the determination of the minimum energy structures of Si8C12, Ge8C12 and Sn8C12 which are main group analogs of the Ti8 C12 compounds (known as metcars). Relative energies, geometries, and vibrational frequencies are reported for several novel structures

Computational Steering in the Problem Solving Environment WBCSim

Computational steering allows scientists to interactively control a numerical experiment and adjust parameters of the computation on-the-fly and explore “what if ” analysis. Computational steering effectively reduces computational time, makes research more efficient, and opens up new product design opportunities. There are several problem solving environments (PSEs) featuring computational steering. However, there is hardly any work explaining how to enable computational steering for PSEs embedded with legacy simulation codes. This paper describes a practical approach to implement computational steering for such PSEs by using WBCSim as an example. WBCSim is a Web based simulation system designed to increase the productivity of wood scientists conducting research on wood-based composites manufacturing processes. WBCSim serves as a prototypical example for the design, construction, and evaluation of small-scale PSEs. Various changes have been made to support computational steering across the three layers—client, server, developer—comprising the WBCSim system. A detailed description of the WBCSim system architecture is presented, along with a typical scenario of computational steering usage

The development of local solar irradiance for outdoor computer graphics rendering

Atmospheric effects are approximated by solving the light transfer equation, LTE, of a given viewing path. The resulting accumulated spectral energy (its visible band) arriving at the observer’s eyes, defines the colour of the object currently on the line of sight. Due to the convenience of using a single rendering equation to solve the LTE for daylight sky and distant objects (aerial perspective), recent methods had opt for a similar kind of approach. Alas, the burden that the real-time calculation brings to the foil had forced these methods to make simplifications that were not in line with the actual world observation. Consequently, the results of these methods are laden with visual-errors. The two most common simplifications made were: i) assuming the atmosphere as a full-scattering medium only and ii) assuming a single density atmosphere profile. This research explored the possibility of replacing the real-time calculation involved in solving the LTE with an analytical-based approach. Hence, the two simplifications made by the previous real-time methods can be avoided. The model was implemented on top of a flight simulator prototype system since the requirements of such system match the objectives of this study. Results were verified against the actual images of the daylight skies. Comparison was also made with the previous methods’ results to showcase the proposed model strengths and advantages over its peers