scholarly journals Peppy: A Virtual Reality Environment for Exploring the Principles of Polypeptide Structure

2019 ◽  
Author(s):  
David G Doak ◽  
Gareth S Denyer ◽  
Juliet A Gerrard ◽  
Joel P Mackay ◽  
Jane R Allison
Keyword(s):  
Virtual Reality ◽  
Protein Structure ◽  
Molecular Modelling ◽  
Video Game ◽  
Electrostatic Interactions ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Undergraduate Teaching ◽  
Two Dimensional ◽  
Polypeptide Structure

ABSTRACTA key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two-dimensional (2D) images on paper, physical molecular modelling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic, 3D nature of proteins. We have built a virtual reality application, Peppy, aimed at facilitating teaching of the principles of protein secondary structure. Rather than attempt to model molecules with the same fidelity to the underlying physical chemistry as existing, research-oriented molecular modelling approaches, we took the more straightforward approach of harnessing the Unity video game physics engine. Indeed, the simplicity and limitations of our model are a strength in a teaching context, provoking questions and thus deeper understanding. Peppy allows exploration of the relative effects of hydrogen bonding (and electrostatic interactions more generally), backbone ϕ/ψ angles, basic chemical structure and steric effects on polypeptide structure in an accessible format that is novel, dynamic and fun to use. As well as describing the implementation and use of Peppy, we discuss the outcomes of deploying Peppy in undergraduate biochemistry courses.STATEMENTProtein structure is inherently dynamic and three-dimensional, but traditional teaching tools are static and/or two-dimensional. We have developed a virtual reality teaching tool, Peppy, that facilitates undergraduate teaching of the principles of protein structure. We outline how Peppy works in terms of how it is used and what goes on ‘under the hood’. We then illustrate its use in undergraduate teaching, where its playful nature stimulated exploration and, thus, deeper understanding.

scholarly journals Physiological State and Learning Ability of Students in Normal and Virtual Reality Conditions: Complexity-Based Analysis (Preprint)

2020 ◽  
Author(s):  
Mohammad H Babini ◽  
Vladimir V Kulish ◽  
Hamidreza Namazi
Keyword(s):  
Virtual Reality ◽  
Fractal Theory ◽  
Physiological State ◽  
Three Dimensional ◽  
Physiological Signals ◽  
Learning Ability ◽  
Two Dimensional ◽  
Reality Condition ◽  
Computer Mediated ◽  
Dimensional Condition

BACKGROUND Education and learning are the most important goals of all universities. For this purpose, lecturers use various tools to grab the attention of students and improve their learning ability. Virtual reality refers to the subjective sensory experience of being immersed in a computer-mediated world, and has recently been implemented in learning environments. OBJECTIVE The aim of this study was to analyze the effect of a virtual reality condition on students’ learning ability and physiological state. METHODS Students were shown 6 sets of videos (3 videos in a two-dimensional condition and 3 videos in a three-dimensional condition), and their learning ability was analyzed based on a subsequent questionnaire. In addition, we analyzed the reaction of the brain and facial muscles of the students during both the two-dimensional and three-dimensional viewing conditions and used fractal theory to investigate their attention to the videos. RESULTS The learning ability of students was increased in the three-dimensional condition compared to that in the two-dimensional condition. In addition, analysis of physiological signals showed that students paid more attention to the three-dimensional videos. CONCLUSIONS A virtual reality condition has a greater effect on enhancing the learning ability of students. The analytical approach of this study can be further extended to evaluate other physiological signals of subjects in a virtual reality condition.

scholarly journals BigTop: A Three-Dimensional Virtual Reality tool for GWAS Visualization

2019 ◽  
Author(s):  
Samuel T. Westreich ◽  
Maria Nattestad ◽  
Christopher Meyer
Keyword(s):  
Virtual Reality ◽  
Association Studies ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Gene Location ◽  
P Value ◽  
Genome Wide Association Studies ◽  
Two Dimensional ◽  
Three Dimensional Representation ◽  
Manhattan Plot

AbstractBackgroundGenome-wide association studies (GWAS) are typically visualized using a two-dimensional Manhattan plot, displaying chromosomal location of SNPs along the x-axis and the negative log-10 of their p-value on the y-axis. This traditional plot provides a broad overview of the results, but offers little opportunity for interaction or expansion of specific regions, and is unable to show additional dimensions of the dataset.ResultsWe created BigTop, a visualization framework in virtual reality (VR), designed to render a Manhattan plot in three dimensions, wrapping the graph around the user in a simulated cylindrical room. BigTop uses the z-axis to display minor allele frequency of each SNP, allowing for the identification of allelic variants of genes. BigTop also offers additional interactivity, allowing users to select any individual SNP and receive expanded information, including SNP name, exact values, and gene location, if applicable. BigTop is built in JavaScript using the React and A-Frame frameworks, and can be rendered using commercially available VR headsets or in a two-dimensional web browser such as Google Chrome. Data is read into BigTop in JSON format, and can be provided as either JSON or a tab-separated text file.ConclusionsUsing additional dimensions and interactivity options offered through VR, we provide a new, interactive, three-dimensional representation of the traditional Manhattan plot for displaying and exploring GWAS data.

scholarly journals A Virtual Reality System for Improved Image-based Planning of Complex Cardiac Procedures

2021 ◽  
Author(s):  
Shujie Deng ◽  
Gavin Wheeler ◽  
Nicolas Toussaint ◽  
Lindsay Munroe ◽  
Suryava Bhattacharya ◽  
...  
Keyword(s):  
Congenital Heart Disease ◽  
Virtual Reality ◽  
Heart Disease ◽  
Congenital Heart ◽  
Three Dimensional ◽  
Patient Specific ◽  
Two Dimensional ◽  
Virtual Reality System ◽  
Dimensional Echocardiography ◽  
Three Dimensional Echocardiography

The intricate nature of congenital heart disease requires understanding of complex, patient-specific three-dimensional dynamic anatomy of the heart, from imaging data such as three-dimensional echocardiography for successful outcomes from surgical and interventional procedures. Conventional clinical systems use flat screens and therefore display remains two-dimensional, which undermines the full understanding of the three-dimensional dynamic data. Additionally, control of three-dimensional visualisation with two-dimensional tools is often difficult, so used only by imaging specialists. In this paper we describe a virtual reality system for immersive surgery planning using dynamic three-dimensional echocardiography, which enables fast prototyping for visualisation such as volume rendering, multi-planar reformatting, flow visualisation, and advanced interaction such as three-dimensional cropping, windowing, measurement, haptic feedback, automatic image orientation, and multi-user interactions. The available features were evaluated by imaging and non-imaging clinicians, showing that the virtual reality system can help improve understanding and communication of the three-dimensional echocardiography imaging and potentially benefit congenital heart disease treatment.

scholarly journals Protein Secondary Structure Prediction

2019 ◽  
Vol 8 (9) ◽  
pp. 1370-1373
Keyword(s):  
Amino Acids ◽  
Comparative Analysis ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Two Dimensional ◽  
Ionic Bond

Proteins are made up of basic units called amino acids which are held together by bonds namely hydrogen and ionic bond. The way in which the amino acids are sequenced has been categorized into two dimensional and three dimensional structures. The main advantage of predicting secondary structure is to produce tertiary structure likelihoods that are in great demand for continuous detection of proteins. This paper reviews the different methods adopted for predicting the protein secondary structure and provides a comparative analysis of accuracies obtained from various input datasets [1].

scholarly journals Pemanfaatan Augmented Reality Sebagai Media Pembelajaran Pengenalan Buah-Buahan

2019 ◽  
Vol 3 (1) ◽  
pp. 54
Author(s):  
Anang Pramono ◽  
Martin Dwiky Setiawan
Keyword(s):  
Virtual Reality ◽  
Augmented Reality ◽  
Mobile Phones ◽  
Mobile Device ◽  
Real World ◽  
Three Dimensional ◽  
Motivation To Learn ◽  
Two Dimensional ◽  
Virtual Objects ◽  
Real Environment

The concept of education for children is important. The aspects that must be considered are methods and learning media. In this research innovative and alternative learning media are made to understand fruits for children with Augmented Reality (AR). Augmented Reality (AR) in principle is a technology that is able to combine two-dimensional or three-dimensional virtual objects into a real environment and then project it. This learning media combines picture cards and virtual reality. Markers contained on picture cards will be captured by the mobile device camera, processed and will 3D animated pieces appear on the mobile screen in realtime. By using the concept of combining real world, real images on cards and virtual, applications can stimulate imagination and sense of desire in children and motivation to learn more and more. 3D fruit estimation created using the 3D Blender application and the Augmented Rea process lity is made using Unity and the Vuforia SDK library. The application of fruit recognition has been applied to several child respondents and has been tested on several types and brands of Android-based mobile phones. Based on research trials, 86% of 30 respondents stated that the application which was developed very effectively as a medium for the introduction of fruits.

How can the Oculus Rift enrich the interactive storytelling experience?

2021 ◽  
Author(s):  
◽  
Mohsin Ali
Keyword(s):  
Virtual Reality ◽  
Video Game ◽  
Three Dimensional ◽  
Head Tracking ◽  
Testing Session ◽  
Game Engine ◽  
User Testing ◽  
Interactive Storytelling ◽  
Oculus Rift ◽  
The Past

<p>The technology of today, such as the Oculus Rift, can provide immersion in ways that were unachievable in the past. The Oculus Rift is a virtual reality headset that allows the user to see the three-dimensional world without the use of a traditional monitor. Unlike television, computer and mobile screens, a virtual reality headset digitally transports the user into the environment. Functionality such as depth tracking and rotational head tracking provides immersion unlike anything experienced to date.   My interest is to investigate interactive storytelling in combination with the Oculus Rift, to determine if virtual reality headsets can enrich storytelling experiences. This will be achieved by developing an application where interactive storytelling is compatible with the Oculus Rift, and testing that application with participants. Finally, a conclusion will be drawn from the data collected by participants.   Alongside the written thesis, a digital application will be produced in Unreal Engine 4 (Video game engine). The application will be an Oculus Rift driven experience, meaning that users can only experience it through an Oculus Rift. The application will have an interactive plot, which allows the user to influence the storyline. The design will be iterative and will be refined after each user testing session. The application hopes to strengthen the theories and concepts found in the written section of the thesis.</p>

scholarly journals Peppy

2020 ◽  
Vol 2 (1) ◽  
pp. 49-50
Author(s):  
David Doak ◽  
Gareth Denyer ◽  
Juliet Gerrard ◽  
Joel Mackay ◽  
Jane Allison
Keyword(s):  
Virtual Reality ◽  
Secondary Structure ◽  
Degrees Of Freedom ◽  
Model Building ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Peptide Backbone ◽  
Molecular Forces ◽  
And Function ◽  
The University

Science students are traditionally taught protein structure and function through textbook pictures and/or physical model building. This is not effective for most students because conceiving large, complex three-dimensional chemicals structure and dynamic molecular interactions requires a very high degree of abstract thought, imagination and extrapolation. It is intuitively reasonable to believe that a virtual reality approach would aid appreciation of nanoscale molecular structure, function and dynamics. I will describe the Virtual Reality (VR) tool, “Peppy” (1), that we have developed for exploring the molecular forces which drive protein secondary structure. Peppy allows students to build, visualise and manipulate polypeptides within the six degrees of freedom that characterises the VR environment. Peppy not only recreates traditional secondary structures dependent on hydrogen- bonding in a generic peptide backbone, it also permits students to insert any and all of the 20 amino acids and to examine the effect of the shapes and electrostatic forces of these on secondary structure. The highly extrapolative environment created by Peppy is extended with features that encourage student engagement, such as a selfie camera, interactive Ramachandran plot, and even features to emphasise the dynamics of a vibrant macromolecular structure. Being able to physically and directly grab and manipulate the atoms and angles with the virtual hand enhances the connection of students with the molecules and results in an exploration experience unmatched by traditional 3D visualisation software. I will also describe the testing and iterative improvement of Peppy during deployment to large undergraduate classes at the University of Sydney, which boasts the Immersive Learning Lab, with 26 VR (Oculus Rift) headsets. Remarkably, even students with no prior VR experience are able to interact with Peppy in an engaged and meaningful way within just 10 minutes and, after less than an hour many are able to build highly complex multi-peptide structures such as β-barrels or experiment with long peptides containing a variety of side chains and disulphide bonds. The experience resonates with the students well after the session, as evidenced by their reflections and follow-up questions regarding the physics of the simulation and ideas for extension of the software.

Avatars

2010 ◽  
pp. 33-48
Author(s):  
Angela Adrian
Keyword(s):  
Virtual Reality ◽  
Social Interaction ◽  
Virtual Worlds ◽  
Video Game ◽  
Three Dimensional ◽  
Well Being ◽  
The Internet ◽  
Dimensional Image ◽  
On Line ◽  
Hindu Deity

Virtual worlds may be the future of e-commerce. The game designers who fashioned these flourishing virtual worlds have invented a much more appealing way to use the internet: through an avatar. This usage of the term was coined in 1985 by Chip Morningstar, a user of the first avatar environment created by LucasFilm called Habitat. Habitat lacked many of the features we have in today’s games such as quests and puzzles. It was more similar to a social MUD in which the interactivity between avatars was the ultimate goal. According to Encarta: “Avatar [Sanskrit]: 1. incarnation of Hindu deity: an incarnation of a Hindu deity in human or animal form, especially one of the incarnations of Vishnu such as Rama and Krishna. 2. embodiment of something: somebody who embodies, personifies, or is the manifestation of an idea or concept. 3. image of person in virtual reality: a movable three-dimensional image that can be used to represent somebody in cyberspace, for example, an Internet user.” Unlike previous video game alter-egos, these avatars can be completely customized and are designed mainly for social interaction (Lastowka and Hunter, 2004). The average player dedicates hundreds of hours (and hundreds of dollars, in some cases). To cultivate his avatar. A survey suggested that approximately 20 percent of Norrath’s citizens deem it their place of residence; they just commute to Earth and back. To a large and growing number of people, virtual worlds are an important source of material and emotional well-being. (Yee). Ordinary people, who are bored and frustrated by regular web commerce, participate vigorously and passionately in avatar-based on-line markets.

scholarly journals Contextual-Cueing beyond the Initial Field of View—A Virtual Reality Experiment

2020 ◽  
Vol 10 (7) ◽  
pp. 446
Author(s):  
Nico Marek ◽  
Stefan Pollmann
Keyword(s):  
Virtual Reality ◽  
Incidental Learning ◽  
Three Dimensional ◽  
Search Time ◽  
Specific Aspect ◽  
Head Movements ◽  
Field Of View ◽  
Contextual Cueing ◽  
Two Dimensional ◽  
Initial Field

In visual search, participants can incidentally learn spatial target-distractor configurations, leading to shorter search times for repeated compared to novel configurations. Usually, this is tested within the limited visual field provided by a computer monitor. While contextual cueing is typically investigated on two-dimensional screens, we present for the first time an implementation of a classic contextual cueing task (search for a T-shape among L-shapes) in a three-dimensional virtual environment. This enabled us to test if the typical finding of incidental learning of repeated search configurations, manifested by shorter search times, would hold in a three-dimensional virtual reality (VR) environment. One specific aspect that was tested by combining virtual reality and contextual cueing was if contextual cueing would hold for targets outside the initial field of view (FOV), requiring head movements to be found. In keeping with two-dimensional search studies, reduced search times were observed after the first epoch and remained stable in the remaining experiment. Importantly, comparable search time reductions were observed for targets both within and outside of the initial FOV. The results show that a repeated distractors-only configuration in the initial FOV can guide search for target locations requiring a head movement to be seen.

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