1. Research Summary and Findings

The primary aim of this Spark project was to create an augmented reality (AR) platform tailored for chemistry and structural biology education. This platform operates through web pages, ensuring accessibility and ease of use without requiring complex software or hardware. It allows educators and students to visualize, manipulate, and engage with 3D molecular models as if they were physical objects, all via an AR interface that leverages computer graphics and computations.

This goal has been successfully achieved, culminating in the establishment of a comprehensive website named MoleculARweb, which is further discussed below.

Update: For my peer-reviewed articles and blog posts related to MoleculARweb (which has undergone significant evolution since project completion), please refer to:

All Articles on Web Augmented and Virtual Reality Tools for Education (as of July 2022)

A centralized page for accessing all articles: [lucianosphere.medium.com](https://lucianosphere.medium.com)

The project also included a long-term evaluation of the AR activities' impact on teaching and learning, utilizing online surveys and automated analytics. The site has attracted thousands of visitors, including many repeat users, yielding substantial statistics on various aspects as described below. However, survey responses have been slow to accumulate since we opted not to make participation mandatory to encourage broader usage. We have supplemented online survey data with in-class assessments from collaborating educators worldwide, who utilized the website with their students and provided feedback. The website will remain operational, allowing us to gather more usage data over time and engage additional teachers for classroom testing.

In the following sections, I will outline the key developments and results, noting deviations from the original plan, and detail the contributions of various individuals involved, organized by each Goal as outlined in the submitted grant proposal. For clarity, the title of each Goal corresponds directly to the original proposal, with additional comments underlined. Detailed information regarding Goals 1 and 2 can be found in our preprint, while Goal 3 will be detailed in a forthcoming peer-reviewed publication.

Goal 1: Development of Core Web Pages Creating the AR Environment

MoleculARweb is now fully operational, featuring over 20 AR activities focused on chemistry and biology, accessible at [molecularweb.epfl.ch](https://molecularweb.epfl.ch). The activities are organized into modules: (i) atomic and molecular orbitals and shapes, (ii) hydrogen bonding and acid-base equilibria, (iii) atomic structures of biological macromolecules, (iv) large biological assemblies, and (v) a virtual modeling kit. This aligns closely with the original plan, with no notable deviations.

Activities (i) to (iv) utilize fiducial AR markers and barcodes, which have been optimized for back-to-back use to enhance user interaction with virtual objects. Each activity employs two markers, facilitating independent handling of virtual items with both hands. Activity (v) employs a different programming approach, utilizing a cubic marker that enhances manipulation capabilities, albeit displaying only one molecule at a time. We have recently developed a second cube marker to allow for the simultaneous handling of two molecules, though this feature has not yet been implemented on the website. Our goal is to adapt these two cubes for activities (i) to (iv) in the future. While there was a slight delay in the development of the two-cube system compared to the initial timeline, we remain within the agreed schedule for the engineer, who is finalizing this work.

The creation of chemical education content and preliminary web applications was led by the main applicant, in collaboration with software engineer Cortes Rodriguez. All subsequent coding, optimization, technical developments, server setup, and project management were conducted by the engineer under the applicant's supervision. We extend our gratitude to Mr. Paul Martin Schalbetter from EPFL's SV IT service for assisting with the purchase and setup of the computer hosting the MoleculARweb server.

Additionally, we integrated a novel method to achieve AR on web pages without any markers. This marker-free mode, which emerged during the grant submission process, is limited to less interactive scenarios and operates solely on smartphones, providing a user-friendly alternative to marker-based applications.

Goal 2: Implementation of Molecular Mechanics in the Virtual Modeling Kit

Activity (v) is a web application that enables users to load any molecule using coordinates from a PDB file. In AR, users see the cube overlay in real time. The app allows users to adjust an artificial temperature, leading to atomic movements. We designed a simple rigid body-based force field to maintain bond lengths and angles but not torsion angles, resulting in realistic movements akin to those exerted on a plastic model. We are now advancing this to a two-cube system and incorporating non-covalent mechanics for molecular interactions. Although we had hoped to have non-covalent mechanics ready by this point, it has been delayed until we can run both cube markers simultaneously.

The underlying physics were conceptualized and tested by the main applicant, while the software engineer restructured the code for optimization and ease of future extensions, implementing it into the website.

Goal 3: Testing and Adoption at Various Educational Levels

Many AR or VR-based educational tools for chemistry claim significant pedagogical utility but are challenging to deploy, often limiting testing to small groups. In contrast, our platform is an open-access website that requires no special hardware, facilitating its use globally among educators and students. Access statistics confirmed this, with over 15,000 visits recorded by the time of this report.

Additionally, tailored surveys for teachers and students indicated that about 80% could successfully use the activities, with half reporting ease of use on their first attempt. Feedback from both groups suggested that the activities were highly engaging and positively affected student comprehension of the subjects taught. The tool's relevance was highlighted during the COVID-19 pandemic, with many students utilizing the website from home.

This phase of the project is ongoing, and initial results have been submitted for peer review (the paper will be included as an Output in mySNF upon acceptance for publication).

A notable deviation from our original plan was the intention to visit schools and teacher training programs to introduce the website to educators and students, which was rendered impossible due to the pandemic. However, the website's user-friendly nature proved beneficial for online learning and at-home study, allowing us to gather considerable feedback through online usage and informal communications.

2. Research Output

Update as of this publication:

Publications: - Preprint available at: [ChemRxiv](https://chemrxiv.org/articles/preprint/MoleculARweb_A_Website_for_Chemistry_and_Structural_Biology_Education_Through_Interactive_Augmented_Reality_out_of_the_Box_in_Commodity_Devices/13012463) - A manuscript is under peer review in a journal. - The preliminary version of the website was discussed in the latest Methods in Molecular Biology: [Link](https://link.springer.com/protocol/10.1007/978-1-0716-0892-0_20).

Talks: * L. A. Abriata. "MoleculARweb: A Website for Chemistry and Structural Biology Education Through Interactive Augmented Reality out of the Box in Commodity Devices." XI Workshop in Complexity of Water, Other Liquids and Education, Brazil (Online) Dec. 2020. * F. Cortes Rodriguez. "UI Design for WebXR." Global XR Bootcamp, USA (Online) Nov 2020.

Social Media: Notable tweets reflecting interest in the website, particularly from educators: - [EPFL Tweet](https://twitter.com/EPFL_en/status/1334879745734045699) - [My Tweet](https://twitter.com/labriataphd/status/1312140523382005760)

Example comments: - "Thanks! Much needed tools." - "Incredible tool for education. Simple materials, great visuals, all open-source, and in multiple languages." - "Check it out! Great tool for experimenting with molecules in augmented reality using your browser."

Example YouTube Channel: Molecules in Web Augmented Reality ================================================ All about molecules, explained through augmented reality activities usable at home, school, or university: [YouTube Link](http://www.youtube.com)