Publication

Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using moleculARweb's Virtual Modeling Kits

Abstract

moleculARweb (https://molecularweb.epfl.ch) began as a website for education and outreach in chemistry and structural biology through augmented reality (AR) content that runs in the web browsers of regular devices like smartphones, tablets, and computers. Here we present two evolutions of moleculARweb's Virtual Modeling Kits (VMK), tools where users can build and view molecules, and explore their mechanics, in 3D AR by handling the molecules in full 3D with custom-printed cube markers (VMK 2.0) or by moving around a simulated scene with mouse or touch gestures (VMK 3.0). Upon simulation the molecules experience visually realistic torsions, clashes, and hydrogen-bonding interactions that the user can manually switch on and off to explore their effects. Moreover, by manually tuning a fictitious temperature the users can accelerate conformational transitions or 'freeze' specific conformations for careful inspection in 3D. Even some phase transitions and separations can be simulated. We showcase here these and other features of the new VMKs connecting them to possible specific applications to teaching and self-learning of concepts from general, organic, biological, and physical chemistry; and in assisting with small tasks in molecular modelling for research. Last, in a short discussion section we overview what future developments are needed for the 'dream tool' for the future of chemistry education and work.

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Related concepts (38)
Mixed reality
Mixed reality (MR) is a term used to describe the merging of a real-world environment and a computer-generated one. Physical and virtual objects may co-exist in mixed reality environments and interact in real time. Mixed reality that incorporates haptics has sometimes been referred to as Visuo-haptic mixed reality. In a physics context, the term "interreality system" refers to a virtual reality system coupled with its real-world counterpart.
Molecule
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and molecule is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.
Augmented reality
Augmented reality (AR) is an interactive experience that combines the real world and computer-generated content. The content can span multiple sensory modalities, including visual, auditory, haptic, somatosensory and olfactory. AR can be defined as a system that incorporates three basic features: a combination of real and virtual worlds, real-time interaction, and accurate 3D registration of virtual and real objects. The overlaid sensory information can be constructive (i.e. additive to the natural environment), or destructive (i.
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