scholarly journals InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics

2021 ◽  
Author(s):  
Stefan Seritan ◽  
Yuanheng Wang ◽  
Jason E. Ford ◽  
alessio Valentini ◽  
Tom Gold ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Virtual Reality ◽  
Chemical Reactivity ◽  
User Interaction ◽  
Molecular Geometry ◽  
Classroom Setting ◽  
Time Varying ◽  
Ab Initio Methods ◽  
Molecular Systems ◽  
Considerable Success

Interactive molecular dynamics in virtual reality (IMD-VR) simulations provide a digital molecular playground for students as an alternative or complement to traditional molecular modelling kits or 2D illustrations. Previous IMD-VR studies have used molecular mechanics to enable simulations of macromolecules such as proteins and nanostructures for the<br>classroom setting with considerable success. Here, we present the INTERACHEM molecular visualizer, intended for reactive IMD-VR simulation using semiempirical and ab initio methods.<br>INTERACHEM visualizes not only the molecular geometry, but also 1) isosurfaces such as molecular orbitals and electrostatic potentials, and 2) two-dimensional graphs of time-varying<br>simulation quantities such as kinetic/potential energy, internal coordinates, and user-applied force. Additionally, INTERACHEM employs speech recognition to facilitate user interaction and introduces a novel “atom happiness” visualization using emojis to indicate the energetic<br>feasibility of a particular bonding arrangement. We include a set of accompanying exercises that we have used to teach chemical reactivity in small molecular systems.

scholarly journals InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics

2021 ◽  
Author(s):  
Stefan Seritan ◽  
Yuanheng Wang ◽  
Jason E. Ford ◽  
alessio Valentini ◽  
Tom Gold ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Virtual Reality ◽  
Chemical Reactivity ◽  
User Interaction ◽  
Molecular Geometry ◽  
Classroom Setting ◽  
Time Varying ◽  
Ab Initio Methods ◽  
Molecular Systems ◽  
Considerable Success

Interactive molecular dynamics in virtual reality (IMD-VR) simulations provide a digital molecular playground for students as an alternative or complement to traditional molecular modelling kits or 2D illustrations. Previous IMD-VR studies have used molecular mechanics to enable simulations of macromolecules such as proteins and nanostructures for the<br>classroom setting with considerable success. Here, we present the INTERACHEM molecular visualizer, intended for reactive IMD-VR simulation using semiempirical and ab initio methods.<br>INTERACHEM visualizes not only the molecular geometry, but also 1) isosurfaces such as molecular orbitals and electrostatic potentials, and 2) two-dimensional graphs of time-varying<br>simulation quantities such as kinetic/potential energy, internal coordinates, and user-applied force. Additionally, INTERACHEM employs speech recognition to facilitate user interaction and introduces a novel “atom happiness” visualization using emojis to indicate the energetic<br>feasibility of a particular bonding arrangement. We include a set of accompanying exercises that we have used to teach chemical reactivity in small molecular systems.

scholarly journals Computational Methods for Ab Initio Molecular Dynamics

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Eric Paquet ◽  
Herna L. Viktor
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
First Principles ◽  
Density Functional ◽  
Path Integrals ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Systems ◽  
Hartree Fock ◽  
Computational Perspective

Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.

scholarly journals Visualizing molecular structures and shapes: a comparison of virtual reality, computer simulation, and traditional modeling

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Corina E. Brown ◽  
Ben Whaley ◽  
Richard M. Hyslop
Keyword(s):  
Virtual Reality ◽  
Chemistry Education ◽  
Research Question ◽  
Molecular Geometry ◽  
Molecular Structures ◽  
Future Research ◽  
Chemistry Students ◽  
Positive Attitudes ◽  
The Difference ◽  
Students Attitudes

AbstractThe purpose of this study was to compare the effectiveness of three methods used to assist in teaching molecular geometry to college chemistry students. A pre- and post-test quasi-experiment was used to collect data about students’ performance in a given chemistry exercise. One research question was intended to evaluate and compare the effectiveness of the three methods in assisting students to understand the topic and carry out the exercise correctly, and a second research question addressed students’ attitudes towards the use of Virtual Reality (VR) in chemistry education. Results show a positive attitude towards the use of VR as an assisting tool to aid in understanding chemistry concepts. While the difference among the three methods was not significant, the results show that the VR brought more enthusiasm and positive attitudes toward the topic of molecular geometry among the students. Educational implications and recommendations for future research are presented as well.

Development of a Low-Cost Augmented Reality Head-Mounted Display Prototype

2018 ◽  
pp. 1-28
Author(s):  
Thiago D'Angelo ◽  
Saul Emanuel Delabrida Silva ◽  
Ricardo A. R. Oliveira ◽  
Antonio A. F. Loureiro
Keyword(s):  
Virtual Reality ◽  
Augmented Reality ◽  
User Experience ◽  
Low Cost ◽  
User Interaction ◽  
Daily Activities ◽  
Head Mounted Display ◽  
Time Performance ◽  
Work Tasks ◽  
Head Mounted Displays

Virtual Reality and Augmented Reality Head-Mounted Displays (HMDs) have been emerging in the last years. These technologies sound like the new hot topic for the next years. Head-Mounted Displays have been developed for many different purposes. Users have the opportunity to enjoy these technologies for entertainment, work tasks, and many other daily activities. Despite the recent release of many AR and VR HMDs, two major problems are hindering the AR HMDs from reaching the mainstream market: the extremely high costs and the user experience issues. In order to minimize these problems, we have developed an AR HMD prototype based on a smartphone and on other low-cost materials. The prototype is capable of running Eye Tracking algorithms, which can be used to improve user interaction and user experience. To assess our AR HMD prototype, we choose a state-of-the-art method for eye center location found in the literature and evaluate its real-time performance in different development boards.

Adaptive Virtual Reality Shopping Malls

2008 ◽  
pp. 1551-1559
Author(s):  
George Lepouras ◽  
Costas Vassilakis
Keyword(s):  
Virtual Reality ◽  
User Experience ◽  
Success Factors ◽  
User Interaction ◽  
Shopping Mall ◽  
Shopping Malls ◽  
Critical Success ◽  
New Business ◽  
Electronic Shopping ◽  
Public Offering

Firms and organizations are increasingly exploiting electronic channels to reach their customers and create new business opportunities. To this end, electronic shops have been developed, either offering products from a single firm or encompassing multiple individual electronic stores, comprising thus electronic shopping malls. Besides development activities, electronic shopping has attracted the attention of researchers, who have studied various perspectives, including user attitude, critical success factors, security, technical aspects, and so forth (e.g., Fang & Salvendy, 2003; Wang, Makaroff, & Edwards, 2003). Two main concerns for e-commerce are personalization and enhancement of user experience. Personalization addresses the ability to offer content tailored to the preferences of each user (Anupam, Hull, & Kumar, 2001) or user group (Wang et al., 2003). Preferences may be explicitly declared by the user, or derived by the system through inspecting user interaction; if the system dynamically reacts to changes of visitor behavior, it is termed as adaptive. Personalization allows customers to focus on the items they are interested in, and enables electronic shops to make targeted suggestions and send promotions to customers (Lekakos & Giaglis, 2005). Enhancement of user experience is another major issue in e-commerce, given that 2D images and texts on the screen are not sufficient to provide information on product aspects such as physical dimensions, textures, and manipulation feedback (Park & Woohun, 2004). Major e-commerce categories that could benefit from giving a more accurate and/or complete view of the products include real estate brokers who could present detailed models of properties, furniture stores that could allow their customers to view how certain pieces would fit in the target place (Hughes, Brusilovsky, & Lewis, 2002), and clothing shops that could provide a virtual fitting room with customizable avatars (Compucloz Corporation, 2003). Multimedia presentations can also be used as a means for “information acceleration” for promoting “really new” products (Urban et al., 1997). Enhancement of user experience may finally compensate for the loss of the pleasure associated with a visit to a shopping mall (Laskaridis, Vassilakis, Lepouras, & Rouvas, 2001). Nowadays, the technological potential of Internet systems provides adequate means for building online multimedia applications that can help e-commerce sites attract e-shoppers. Applications can be built to adapt to the user’s profile and provide the user with a suitable set of information in the most efficient way. Virtual reality (VR) technologies are also now mature enough to be used for the wide public, offering vivid and highly interactive environments, allowing users to view synthetic worlds within which they can visualize and manipulate artifacts. This article aims to specify a system that exploits capabilities offered by adaptation and VR technologies to offer e-shoppers personalized and enhanced experiences, while addressing challenges related to the cost, complexity, and effort of building and maintaining such a system.

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