Molecular simulations and visualization: introduction and overview

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building

Immersive analytics for oncology patient cohorts

This thesis proposes a novel interactive immersive analytics tool and methods to interrogate the cancer patient cohort in an immersive virtual environment, namely Virtual Reality to Observe Oncology data Models (VROOM). The overall objective is to develop an immersive analytics platform, which includes a data analytics pipeline from raw gene expression data to immersive visualisation on virtual and augmented reality platforms utilising a game engine. Unity3D has been used to implement the visualisation. Work in this thesis could provide oncologists and clinicians with an interactive visualisation and visual analytics platform that helps them to drive their analysis in treatment efficacy and achieve the goal of evidence-based personalised medicine. The thesis integrates the latest discovery and development in cancer patients’ prognoses, immersive technologies, machine learning, decision support system and interactive visualisation to form an immersive analytics platform of complex genomic data. For this thesis, the experimental paradigm that will be followed is in understanding transcriptomics in cancer samples. This thesis specifically investigates gene expression data to determine the biological similarity revealed by the patient's tumour samples' transcriptomic profiles revealing the active genes in different patients. In summary, the thesis contributes to i) a novel immersive analytics platform for patient cohort data interrogation in similarity space where the similarity space is based on the patient's biological and genomic similarity; ii) an effective immersive environment optimisation design based on the usability study of exocentric and egocentric visualisation, audio and sound design optimisation; iii) an integration of trusted and familiar 2D biomedical visual analytics methods into the immersive environment; iv) novel use of the game theory as the decision-making system engine to help the analytics process, and application of the optimal transport theory in missing data imputation to ensure the preservation of data distribution; and v) case studies to showcase the real-world application of the visualisation and its effectiveness

A Vision for Science Gateways: Bridging the Gap and Broadening the Outreach

The future for science gateways warrants exploration as we consider the possibilities that extend well beyond science and high performance computing into new interfaces, applications and user communities. In this paper, we look retrospectively at the successes of representative gateways thus far. This serves to highlight existing gaps gateways need to overcome in areas such as accessibility, usability and interoperability, and in the need for broader outreach by drawing insights from technology adoption research. We explore two particularly promising opportunities for gateways - computational social sciences and virtual reality – and make the case for the gateway community to be more intentional in engaging with users to encourage adoption and implementation, especially in the area of educational usage. We conclude with a call for focused attention on legal hurdles in order to realize the full future potential of science gateways. This paper serves as a roadmap for a vision of science gateways in the next ten years

The proliferation of virtual laboratories in educational fields

Since its emergence in the 1960s, the use of virtual reality (VR) has grown progressively. This wide dissemination of VR has allowed its application in an increasing number of disciplines, including education. It is well known that virtual laboratories (VLs), which base their use in VR technology, are very useful tools in both university and professional training. In this article, the main advantages and disadvantages of the use of modern VLs in teaching are analyzed. In addition, the design and development process that must be followed to appropriately create these VLs is described in detail, as well as a small-scale study of the perception that university teachers have about the use of VR in education. Lastly, the reasons why the implementation of VR is not currently as broad as it would be expected, given its proven potential in different fields, are discussed

An Architecture Approach for 3D Render Distribution using Mobile Devices in Real Time

Nowadays, video games such as Massively Multiplayer Online Game (MMOG) have become cultural mediators. Mobile games contribute to a large number of downloads and potential benefits in the applications market. Although processing power of mobile devices increases the bandwidth transmission, a poor network connectivity may bottleneck Gaming as a Service (GaaS). In order to enhance performance in digital ecosystem, processing tasks are distributed among thin client devices and robust servers. This research is based on the method ‘divide and rule’, that is, volumetric surfaces are subdivided using a tree-KD of sequence of scenes in a game, so reducing the surface into small sets of points. Reconstruction efficiency is improved, because the search of data is performed in local and small regions. Processes are modeled through a finite set of states that are built using Hidden Markov Models with domains configured by heuristics. Six test that control the states of each heuristic, including the number of intervals are carried out to validate the proposed model. This validation concludes that the proposed model optimizes response frames per second, in a sequence of interactions

Teaching Sciences in Virtual Worlds with Mastery Learning: A Case of Study in Elementary School

Virtual worlds are 3D environments that provide a feeling of immersion and a high degree of interaction, collaboration, communication between users. Its applicability can be focused on the educational scope, in which theories can be integrated as the basis to didactic activities carried out in the 3D environment, being its area of interdisciplinary comprehension. In this context, this article presents the use of a Virtual World built to assist in the teaching of Science for students of the middle school, whose articulation of the activities performed in the course are based on the precepts of the educational theory Mastery Learning. Tests were carried out in the subject of science, being divided into two periods with different groups for comparative purposes and realized evaluations during the period of the experiments. Kruskal-Wallis and Wilcoxon-Mann-Whitney non-parametric test were applied to the results of the assessments to ascertain the performance of each group. It was verified in the general analyzis that the participants who used the Virtual World had a growing performance, with high medians and adequate distribution of the results, being predominant of a smaller variability and amplitude. Thus, was possible to conclude that the results obtained with the approach were positive, which led to the validation of this research and presented a clear contribution to the academic environment

Investigating Real-time Touchless Hand Interaction and Machine Learning Agents in Immersive Learning Environments

The recent surge in the adoption of new technologies and innovations in connectivity, interaction technology, and artificial realities can fundamentally change the digital world. eXtended Reality (XR), with its potential to bridge the virtual and real environments, creates new possibilities to develop more engaging and productive learning experiences. Evidence is emerging that thissophisticated technology offers new ways to improve the learning process for better student interaction and engagement. Recently, immersive technology has garnered much attention as an interactive technology that facilitates direct interaction with virtual objects in the real world. Furthermore, these virtual objects can be surrogates for real-world teaching resources, allowing for virtual labs. Thus XR could enable learning experiences that would not bepossible in impoverished educational systems worldwide. Interestingly, concepts such as virtual hand interaction and techniques such as machine learning are still not widely investigated in immersive learning. Hand interaction technologies in virtual environments can support the kinesthetic learning pedagogical approach, and the need for its touchless interaction nature hasincreased exceptionally in the post-COVID world. By implementing and evaluating real-time hand interaction technology for kinesthetic learning and machine learning agents for self-guided learning, this research has addressed these underutilized technologies to demonstrate the efficiency of immersive learning. This thesis has explored different hand-tracking APIs and devices to integrate real-time hand interaction techniques. These hand interaction techniques and integrated machine learning agents using reinforcement learning are evaluated with different display devices to test compatibility. The proposed approach aims to provide self-guided, more productive, and interactive learning experiences. Further, this research has investigated ethics, privacy, and security issues in XR and covered the future of immersive learning in the Metaverse.<br/