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An in-silico study of the type II NADH: Quinone Oxidoreductase (ndh2). A new anti-malaria drug target

  • Authors: Baye, Bertha Cinthia
  • Date: 2022-10-14
  • Subjects: Malaria , Plasmodium , Molecular dynamics , Computer simulation , Quinone , Antimalarials , Molecules Models , Docking , Drugs Computer-aided design
  • Language: English
  • Type: Academic theses , Doctoral theses , text
  • Identifier: http://hdl.handle.net/10962/365633 , vital:65767 , DOI https://doi.org/10.21504/10962/365633
  • Description: Malaria is caused by Plasmodium parasites, spread to people through the bites of infected female Anopheles mosquitoes. This study focuses on all 5 (Plasmodium falciparum, Plasmodium knowlesi, Plasmodium malariae, Plasmodium ovale and Plasmodium vivax) parasites that cause malaria in humans. Africa is a developing continent, and it is the most affected with an estimation of 90% of more than 400 000 malaria-related deaths reported by the World Health Organization (WHO) report in 2020, in which 61% of that number are children under the ages of five. Malaria resistance was initially observed in early 1986 and with the progression of time anti-malarial drug resistance has only increased. As a result, there is a need to study the malarial proteins mechanism of action and identify alternative treatment strategies for this disease. Type II NADH: quinone oxidoreductase (NDH2) is a monotopic protein that catalyses the electron transfer from NADH to quinone via FAD without a proton-pumping activity, and functions as an initial enzyme, either in addition to or as an alternative to proton-pumping NADH dehydrogenase (complex I) in the respiratory chain of bacteria, archaea, and fungal and plant mitochondrial. The structures for the Plasmodium knowlesi, Plasmodium malariae, Plasmodium ovale and Plasmodium vivax were modelled from the crystal structure of Plasmodium falciparum (5JWA). Compounds from the South African natural compounds database (SANCDB) were docked against both the NDH2 crystal structure and modelled structures. By performing in silico screening the study aimed to find potential compounds that might interrupt the electron transfer to quinone therefore disturbing the enzyme‟s function and thereby possibly eliminating the plasmodium parasite. CHARMM-GUI was used to create the membrane (since this work is with membrane-bound proteins) and to orient the protein on the membrane using OPM server guidelines, the interface produced GROMACS topology files that were used in molecular dynamics simulations. Molecular dynamics simulations were performed in the Centre for high performance computing (CHPC) cluster under the CHEM0802 project and the trajectories produced were further analysed. In this work not only were hit compounds from SANCDB identified, but also differences in behaviour across species and in the presence or absence of the membrane were described. This highlights the need to include the correct protein environment when studying these systems. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
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  • Date Issued: 2022-10-14

Identification of novel compounds against Plasmodium falciparum Cytochrome bc1 Complex inhibiting the trans-membrane electron transfer pathway: an In Silico study

  • Authors: Chebon, Lorna Jemosop
  • Date: 2022-10-14
  • Subjects: Malaria , Plasmodium falciparum , Molecular dynamics , Antimalarials , Molecules Models , Docking , Cytochromes , Drug resistance , Computer simulation , Drugs Computer-aided design , System analysis
  • Language: English
  • Type: Academic theses , Doctoral theses , text
  • Identifier: http://hdl.handle.net/10962/365666 , vital:65774 , DOI https://doi.org/10.21504/10962/365666
  • Description: Malaria continues to be a burden globally with a myriad of challenges deterring eradication efforts. With most antimalarials facing drug resistance, such as atovaquone (ATQ), alternative compounds that can withstand resistance are warranted. The Plasmodium falciparum cytochrome b (PfCytb), a subunit of P. falciparum cytochrome bc1 complex, is a validated drug target. Structurally, cytochrome b, cytochrome c1, and iron sulphur protein (ISP) subunits form the catalytic domain of the protein complex having heme bL, heme bH and iron-sulphur [2FE-2S] cluster cofactors. These cofactos have redox centres to aid in the electron transfer (ET) process. These subunits promote ET mainly through the enzyme’s ubiquinol oxidation (Qo) and ubiquinone reduction (Qi) processes in the catalytic domain. ATQ drug has been used in the prevention and treatment of uncomplicated malaria by targeting PfCytb protein. Once the mitochondrial transmembrane ET pathway is inhibited, it causes a collapse in its membrane potential. Previously reported ATQ drug resistance has been associated with the point mutations Y268C, Y268N and Y268S. Thus, in finding alternatives to the ATQ drug, this research aimed to: i) employ in silico approaches incorporating protein into phospholipid bilayer for the first time to understand the parasites’ resistance mechanism; ii) determine any sequence and structural differences that could be explored in drug design studies; and iii) screen for PfCytb-iron sulphur protein (Cytb-ISP) hit compounds from South African natural compound database (SANCDB) and Medicines for Malaria Venture (MMV) that can withstand the identified mutations. Using computational tools, comparative sequence and structural analyses were performed on the cytochrome b protein, where the ultimate focus was on P. falciparum cytochrome b and its human homolog. Through multiple sequence alignment, motif discovery and phylogeny, differences between P. falciparum and H. sapiens cytochrome b were identified. Protein modelling of both P. falciparum and H. sapiens cytochrome b - iron sulphur protein (PfCytb-ISP and HsCytb-ISP) was performed. Results showed that at the sequence level, there were few amino acid residue differences because the protein is highly conserved. Important to note is the four-residue deletion in Plasmodium spp. absent in the human homolog. Motif analysis discovered five unique motifs in P. falciparum cytochrome b protein which were mapped onto the predicted protein model. These motifs were not in regions of functional importance; hence their function is still unknown. At a structural level, the four-residue deletion was observed to alter the Qo substrate binding pocket as reported in previous studies and confirmed in this study. This deletion resulted in a 0.83 Å structural displacement. Also, there are currently no in silico studies that have performed experiments with P. falciparum cytochrome b protein incorporated into a phospholipid bilayer. Using 350 ns molecular dynamics (MD) simulations of the holo and ATQ-bound systems, the study highlighted the resistance mechanism of the parasite protein where the loss of active site residue-residue interactions was identified, all linked to the three mutations. The identified compromised interactions are likely to destabilise the protein’s function, specifically in the Qo substrate binding site. This showed the possible effect of mutations on ATQ drug activity, where all three mutations were reported to share a similar resistance mechanism. Thereafter, this research work utilised in silico approaches where both Qo active site and interface pocket were targeted by screening the South African natural compounds database (SANCDB) and Medicines for Malaria Venture (MMV) compounds to identify novel selective hits. SANCDB compounds are known for their structural complexity that preserves the potency of the drug molecule. Both SANCDB and MMV compounds have not been explored as inhibitors against the PfCytb drug target. Molecular docking, molecular dynamics (MD) simulations, principal component, and dynamic residue network (DRN; global and local) analyses were utilised to identify and confirm the potential selective inhibitors. Docking results identified compounds that bound selectively onto PfCytb-ISP with a binding energy ≤ -8.7 kcal/mol-1. Further, this work validated a total of eight potential selective compounds to inhibit PfCytb-ISP protein (Qo active site) not only in the wild-type but also in the presence of the point mutations Y268C, Y268N and Y268S. The selective binding of these hit compounds could be linked to the differences reported at sequence/residue level in chapter 3. DRN and residue contact map analyses of the eight compounds in holo and ligand-bound systems revealed reduced residue interactions and decreased protein communication. This suggests that the eight compounds show the possibility of inhibiting the parasite and disrupting important residue-residue interactions. Additionally, 13 selective compounds were identified to bind at the protein’s heterodimer interface, where global and local analysis confirmed their effect on active site residues (distal location) as well as on the communication network. Based on the sequence differences between PfCytb and the human homolog, these findings suggest these selective compounds as potential allosteric modulators of the parasite enzyme, which may serve as possible replacements of the already resistant ATQ drug. Therefore, these findings pave the way for further in vitro studies to establish their anti-plasmodial inhibition levels. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
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  • Date Issued: 2022-10-14

Synthesis, In-Silico molecular modelling and biological studies of 1,4-Dihydroxyanthraquinone and its derivatives

  • Authors: Kisula, Lydia Mboje
  • Date: 2022-10-14
  • Subjects: Computer simulation , Molecules Models , Dihydroxyanthraquinone , Trypanosomiasis , Leishmaniasis , Docking
  • Language: English
  • Type: Academic theses , Doctoral theses , text
  • Identifier: http://hdl.handle.net/10962/365828 , vital:65793 , DOI https://doi.org/10.21504/10962/365828
  • Description: This current study of investigation reports on the synthesis of 1,4-dihydroxyanthraquinone and its derivatives on explorations of their medicinal potential. The study initially aimed to synthesize an analogue of a natural anthraquinone, 1,3,6-trihydroxy-7-((S)-1- hydroxyethyl)anthracene-9,10-dione 5 using Friedel-Crafts acylation of phthalic anhydride and a benzene derivative. Synthetic transformation of anacardic acid 63, obtained as a by- product of the cashew industry successfully afforded 4-ethoxyisobenzofuran-1,3-dione 89. However, when attempted to couple 4-ethoxyisobenzofuran-1,3-dione 89 with 2- hydroxyacetophenone 91 in a Friedel-Crafts acylation manner to form 2-acetyl-1,8- dihydroxyanthracene-9,10-dione 87 the reaction did not work efficiently. A simple derivative of benzene which is; benzene-1,4-diol 102 was reacted instead with 3-ethoxyphthalic acid 71 and isobenzofuran-1,3-dione 96 to form 1,4,5-trihydroxy anthraquinone 72 and 1,4- dihydroxyanthraquinone 42, respectively. A modified Marschalk reaction was then used to introduce the hydroxyl alkyl group to 1,4-dihydroxy anthraquinone 42, which allowed further elaboration of the hydroxyl-substituent in moderate to good yields (22-80%). A molecular docking study was performed using Schrödinger software to predict the binding affinity of the test compounds to the target protein trypanothione reductase (PDB ID: 6BU7). An in-vitro screening of 1,4-dihydroxyanthraquinone derivatives and some selected precursors for antitrypanosomal, antiplasmodial, antibacterial, and cytotoxicity activities produced encouraging results. Derivatives of anacardic acid and cardanol from CNSL were found to have moderate activity against trypanosomes with no activity against Plasmodium falciparum. Almost 63% of synthesized 1,4-dihydroxyanthraquinone derivatives displayed activity against trypanosomes. The in-vitro evaluation and the in silico molecular docking studies revealed that 1,4-dihydroxyanthraquinone derivatives can be potential drug-like candidates active against T.brucei parasites (IC50 = 0.70-1.20 μM). Only four 1,4- iv dihydroxyanthraquinone derivatives with thiosemicarbazone, chloride, pyrrole, and diethanolamine functionality displayed activity against Plasmodium falciparum (IC50 = 3.17- 14.36 μM). In-vitro evaluated of test compounds against antibacterial screen and cytotoxicity effects significantly showed that 2-hydroxy-6-pentadecylbenzoic acid 63a and 2-((2- chlorophenyl)(piperazin-1-yl) methyl)-1,4-dihydroxyanthracene-9,10-dione 78 have potency against Staphylococcus aureus and reduced the viability of the cells below 20% at an initial concentration of 50 μg/mL. Only 1,4-dihydroxyanthraquinone derivatives with thiosemicarbazone 76, piperazine 78, and diethanolamine 80 motifs were active against HeLa cells and reduced the viability of cells below 20% at a concentration of 50 μg/mL. In conclusion, this current reported study has generated useful knowlege on the applicability of the agro-waste CNSL as an agent active against trypanosomiasis but also as a low-cost starting material to synthesize hydroxy anthraquinones. The study has further given an overview to the understanding of the medicinal value 1,4-dihydroxyanthraquinone derivatives as promising candidates towards developing drugs suitable for treating neglected tropical diseases particularly trypanosomiasis. , Thesis (PhD) -- Faculty of Science, Chemistry, 2022
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  • Date Issued: 2022-10-14

Network simulation for professional audio networks

  • Authors: Otten, Fred
  • Date: 2015
  • Subjects: Sound engineers , Ethernet (Local area network system) , Computer networks , Computer simulation
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: vital:4713 , http://hdl.handle.net/10962/d1017935
  • Description: Audio Engineers are required to design and deploy large multi-channel sound systems which meet a set of requirements and use networking technologies such as Firewire and Ethernet AVB. Bandwidth utilisation and parameter groupings are among the factors which need to be considered in these designs. An implementation of an extensible, generic simulation framework would allow audio engineers to easily compare protocols and networking technologies and get near real time responses with regards to bandwidth utilisation. Our hypothesis is that an application-level capability can be developed which uses a network simulation framework to enable this process and enhances the audio engineer’s experience of designing and configuring a network. This thesis presents a new, extensible simulation framework which can be utilised to simulate professional audio networks. This framework is utilised to develop an application - AudioNetSim - based on the requirements of an audio engineer. The thesis describes the AudioNetSim models and implementations for Ethernet AVB, Firewire and the AES- 64 control protocol. AudioNetSim enables bandwidth usage determination for any network configuration and connection scenario and is used to compare Firewire and Ethernet AVB bandwidth utilisation. It also applies graph theory to the circular join problem and provides a solution to detect circular joins.
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  • Date Issued: 2015

Gasification characteristics of sugarcane bagasse

  • Authors: Anukam, Anthony Ike
  • Date: 2013
  • Subjects: Bagasse -- Bagasse industry , Sugarcane -- Biotechnology , Computer simulation
  • Language: English
  • Type: Thesis , Masters , MSc (Chemistry)
  • Identifier: vital:11343 , http://hdl.handle.net/10353/d1016170 , Bagasse -- Bagasse industry , Sugarcane -- Biotechnology , Computer simulation
  • Description: Sugarcane is a major crop in many countries. It is the most abundant lignocellulosic material in tropical countries such as South Africa. It is one of the plants with the highest bioconversion efficiency. The sugarcane crop is able to efficiently fix solar energy, yielding some 55 tons of dry matter per hectare of land annually. After harvest, the crop produces sugar juice and bagasse. Sugarcane bagasse is a residue that results from the crushing of sugarcane in the sugar industry. It is a renewable feedstock that can be used for power generation and manufacturing cellulosic ethanol. As biomass, sugarcane bagasse holds promise as a fuel source since it can produce more than enough electricity and heat energy to supply the needs of a common sugar factory. However, in the sugarcane industry the bagasse is currently burnt inefficiently in boilers that provide the heating for the industry. This project seeks to investigate the possibility of gasifying sugarcane bagasse as an efficient conversion technology. The investigation is necessary because fuel properties govern the gasifier design and ultimately, the gasification efficiency. Proximate and ultimate analysis of sugarcane bagasse was conducted after which the results were used to conduct a computer simulation of the mass and energy balance during gasification. The kinetic investigation undertaken through the TGA and DTG analyses revealed the activation energy and pre – exponential factor which were obtained by the model – free Kissinger method of kinetic analysis and were found to be 181.51 kJ/mol and 3.1 × 103/min respectively. The heating value of sugarcane bagasse was also measured and found to be 17.8 MJ/kg, which was used in the calculation of the conversion efficiency of the gasification process. Fuel properties, including moisture content and gasifier operating parameters were varied in order to determine optimum gasifier operating conditions that results in maximum conversion efficiency. The highest conversion efficiency was achieved at low moisture content after computer simulation of the gasification process. Moisture content also affected the volume of CO and H2 as the former decreases with increasing moisture content while the latter increases with increasing moisture content, accelerating the water – gas reaction. Scanning electron microscope fitted to an Energy dispersive X – ray spectroscopy was also used in order to view the shape and size distribution as well as determine the elemental composition of sugarcane bagasse. The results obtained established that the fuel properties and gasification conditions affect the conversion efficiency. During computer simulation, it was established that smaller particle size resulted in higher conversion efficiency. The smaller throat diameter also resulted in higher conversion efficiency. The throat angle of 25° also resulted in higher conversion efficiency. The temperature of input air was also found to be one of the major determining factors in terms of conversion efficiency. The dissertation presents the proximate and ultimate analysis results as well as the kinetic analysis results. The SEM/EDX analysis as well as the computer simulation results of the gasification process is also presented. The major contribution of this project was on the investigation of the gasification characteristics of sugarcane bagasse and the utilization of these in the design of a laboratory scale sugarcane bagasse gasifier with enhanced conversion efficiency through computer simulation.
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  • Date Issued: 2013

An investigation into the design and implementation of an internet-scale network simulator

  • Authors: Richter, John Peter Frank
  • Date: 2009
  • Subjects: Computer simulation , Computer network resources , Computer networks , Internet
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4597 , http://hdl.handle.net/10962/d1004840 , Computer simulation , Computer network resources , Computer networks , Internet
  • Description: Simulation is a complex task with many research applications - chiey as a research tool, to test and evaluate hypothetical scenarios. Though many simulations execute similar operations and utilise similar data, there are few simulation frameworks or toolkits that allow researchers to rapidly develop their concepts. Those that are available to researchers are limited in scope, or use old technology that is no longer useful to modern researchers. As a result of this, many researchers build their own simulations without a framework, wasting time and resources on a system that could already cater for the majority of their simulation's requirements. In this work, a system is proposed for the creation of a scalable, dynamic-resolution network simulation framework that provides scalable scope for researchers, using modern technologies and languages. This framework should allow researchers to rapidly develop a broad range of semantically-rich simulations, without the necessity of superor grid-computers or clusters. Design and implementation are discussed and alternative network simulations are compared to the proposed framework. A series of simulations, focusing on malware, is run on an implementation of this framework, and the results are compared to expectations for the outcomes of those simulations. In conclusion, a critical review of the simulator is made, considering any extensions or shortcomings that need to be addressed.
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  • Date Issued: 2009

Non-interactive modeling tools and support environment for procedural geometry generation

  • Authors: Morkel, Chantelle
  • Date: 2006
  • Subjects: Computer graphics -- Mathematical models , Three-dimensional display systems , Computer simulation
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4644 , http://hdl.handle.net/10962/d1006589 , Computer graphics -- Mathematical models , Three-dimensional display systems , Computer simulation
  • Description: This research examines procedural modeling in the eld of computer graphics. Procedural modeling automates the generation of objects by representing models as procedures that provide a description of the process required to create the model. The problem we solve with this research is the creation of a procedural modeling environment that consists of a procedural modeling language and a set of non-interactive modeling tools. A goal of this research is to provide comparisons between 3D manual modeling and procedural modeling, which focus on the modeling strategies, tools and model representations used by each modeling paradigm. A procedural modeling language is presented that has the same facilities and features of existing procedural modeling languages. In addition, features such as caching and a pseudorandom number generator is included, demonstrating the advantages of a procedural modeling paradigm. The non-interactive tools created within the procedural modeling framework are selection, extrusion, subdivision, curve shaping and stitching. In order to demonstrate the usefulness of the procedural modeling framework, human and furniture models are created using this procedural modeling environment. Various techniques are presented to generate these objects, and may be used to create a variety of other models. A detailed discussion of each technique is provided. Six experiments are conducted to test the support of the procedural modeling benets provided by this non- interactive modeling environment. The experiments test, namely parameterisation, re-usability, base-shape independence, model complexity, the generation of reproducible random numbers and caching. We prove that a number of distinct models can be generated from a single procedure through the use parameterisation. Modeling procedures and sub-procedures are re-usable and can be applied to different models. Procedures can be base-shape independent. The level of complexity of a model can be increased by repeatedly applying geometry to the model. The pseudo-random number generator is capable of generating reproducible random numbers. The caching facility reduces the time required to generate a model that uses repetitive geometry.
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  • Date Issued: 2006

The use of interactive computer simulations to engender conceptual changes about wave motion

  • Authors: Jacob, Sunny
  • Date: 2001
  • Subjects: Computer simulation
  • Language: English
  • Type: Thesis , Masters , MEd
  • Identifier: vital:1921 , http://hdl.handle.net/10962/d1007409
  • Description: Computers are expensive equipment which most schools in South Africa cannot afford to use as an instructional tool in the same way as they are being used in affluent schools in the countly and in the western world. In this study a computer was used as a demonstration tool to help learners to visualise the different aspects of wave motion with the aid of interactive computer simulations. The study investigated how learners alter their intuitive notions of wave motion after experiencing the common teaching techniques in township schools, and then by observing interactive computer simulations. Data was collected by means of field notes, observation, questionnaires and in-depth semi-structured interviews with the participation of twelve Grade 9 learners in a secondary school over a three-week period. A combination of qualitative and quantitative methods was used in the study and the data was analysed within an interpretive framework. A detailed analysis revealed that interactive computer simulations could bring about positive conceptual changes in learners, especially in the micro level aspects of wave motion. The inexperience of the learners in a discovery method of learning and a learner centred approach of teaching seemed to interfere with the teaching techniques. To a considerable extent, language problems also hindered the revelation of conceptualisation.In writing this report of the research study J agree wilh Squires and McDougall (1994: 12) that it is difficult to use a non-interactive medium (paper-based text) to report on the interactive medium of computer simulations, as written words cannot bring out all the essential aspects of interactive computer simulations.
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  • Date Issued: 2001

Designing and implementing a virtual reality interaction framework

  • Authors: Rorke, Michael
  • Date: 2000
  • Subjects: Virtual reality , Computer simulation , Human-computer interaction , Computer graphics
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4623 , http://hdl.handle.net/10962/d1006491 , Virtual reality , Computer simulation , Human-computer interaction , Computer graphics
  • Description: Virtual Reality offers the possibility for humans to interact in a more natural way with the computer and its applications. Currently, Virtual Reality is used mainly in the field of visualisation where 3D graphics allow users to more easily view complex sets of data or structures. The field of interaction in Virtual Reality has been largely neglected due mainly to problems with input devices and equipment costs. Recent research has aimed to overcome these interaction problems, thereby creating a usable interaction platform for Virtual Reality. This thesis presents a background into the field of interaction in Virtual Reality. It goes on to propose a generic framework for the implementation of common interaction techniques into a homogeneous application development environment. This framework adds a new layer to the standard Virtual Reality toolkit – the interaction abstraction layer, or interactor layer. This separation is in line with current HCI practices. The interactor layer is further divided into specific sections – input component, interaction component, system component, intermediaries, entities and widgets. Each of these performs a specific function, with clearly defined interfaces between the different components to promote easy objectoriented implementation of the framework. The validity of the framework is shown in comparison with accepted taxonomies in the area of Virtual Reality interaction. Thus demonstrating that the framework covers all the relevant factors involved in the field. Furthermore, the thesis describes an implementation of this framework. The implementation was completed using the Rhodes University CoRgi Virtual Reality toolkit. Several postgraduate students in the Rhodes University Computer Science Department utilised the framework implementation to develop a set of case studies. These case studies demonstrate the practical use of the framework to create useful Virtual Reality applications, as well as demonstrating the generic nature of the framework and its extensibility to be able to handle new interaction techniques. Finally, the generic nature of the framework is further demonstrated by moving it from the standard CoRgi Virtual Reality toolkit, to a distributed version of this toolkit. The distributed implementation of the framework utilises the Common Object Request Broker Architecture (CORBA) to implement the distribution of the objects in the system. Using this distributed implementation, we are able to ascertain that CORBA is useful in the field of distributed real-time Virtual Reality, even taking into account the extra overhead introduced by the additional abstraction layer. We conclude from this thesis that it is important to abstract the interaction layer from the other layers of a Virtual Reality toolkit in order to provide a consistent interface to developers. We have shown that our framework is implementable and useful in the field, making it easier for developers to include interaction in their Virtual Reality applications. Our framework is able to handle all the current aspects of interaction in Virtual Reality, as well as being general enough to implement future interaction techniques. The framework is also applicable to different Virtual Reality toolkits and development platforms, making it ideal for developing general, cross-platform interactive Virtual Reality applications.
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  • Date Issued: 2000

Virtual sculpting : an investigation of directly manipulated free-form deformation in a virtual environment

  • Authors: Gain, James Edward
  • Date: 1996
  • Subjects: Computer simulation , Computer graphics , Virtual reality
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4660 , http://hdl.handle.net/10962/d1006661 , Computer simulation , Computer graphics , Virtual reality
  • Description: This thesis presents a Virtual Sculpting system, which addresses the problem of Free-Form Solid Modelling. The disparate elements of a Polygon-Mesh representation, a Directly Manipulated Free-Form Deformation sculpting tool, and a Virtual Environment are drawn into a cohesive whole under the mantle of a clay-sculpting metaphor. This enables a user to mould and manipulate a synthetic solid interactively as if it were composed of malleable clay. The focus of this study is on the interactivity, intuitivity and versatility of such a system. To this end, a range of improvements is investigated which significantly enhances the efficiency and correctness of Directly Manipulated Free-Form Deformation, both separately and as a seamless component of the Virtual Sculpting system.
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  • Date Issued: 1996

Parallel implementation of a virtual reality system on a transputer architecture

  • Authors: Bangay, Shaun Douglas
  • Date: 1994 , 2012-10-11
  • Subjects: Virtual reality , Computer simulation , Transputers
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4668 , http://hdl.handle.net/10962/d1006687 , Virtual reality , Computer simulation , Transputers
  • Description: A Virtual Reality is a computer model of an environment, actual or imagined, presented to a user in as realistic a fashion as possible. Stereo goggles may be used to provide the user with a view of the modelled environment from within the environment, while a data-glove is used to interact with the environment. To simulate reality on a computer, the machine has to produce realistic images rapidly. Such a requirement usually necessitates expensive equipment. This thesis presents an implementation of a virtual reality system on a transputer architecture. The system is general, and is intended to provide support for the development of various virtual environments. The three main components of the system are the output device drivers, the input device drivers, and the virtual world kernel. This last component is responsible for the simulation of the virtual world. The rendering system is described in detail. Various methods for implementing the components of the graphics pipeline are discussed. These are then generalised to make use of the facilities provided by the transputer processor for parallel processing. A number of different decomposition techniques are implemented and compared. The emphasis in this section is on the speed at which the world can be rendered, and the interaction latency involved. In the best case, where almost linear speedup is obtained, a world containing over 250 polygons is rendered at 32 frames/second. The bandwidth of the transputer links is the major factor limiting speedup. A description is given of an input device driver which makes use of a powerglove. Techniques for overcoming the limitations of this device, and for interacting with the virtual world, are discussed. The virtual world kernel is designed to make extensive use of the parallel processing facilities provided by transputers. It is capable of providing support for mUltiple worlds concurrently, and for multiple users interacting with these worlds. Two applications are described that were successfully implemented using this system. The design of the system is compared with other recently developed virtual reality systems. Features that are common or advantageous in each of the systems are discussed. The system described in this thesis compares favourably, particularly in its use of parallel processors. , KMBT_223
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  • Date Issued: 1994
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