arXiv subjects

Luciano A. Abriata

Publications and source records attributed to Luciano A. Abriata.

5 recordsLinked to original sources

arXiv2025

The MolecularWeb Universe: Web-Based, Immersive, Multiuser Molecular Graphics And Modeling, for Education and Work in Chemistry, Structural Biology, and Materials Sciences

Molecular visualization software has long supported research and education in chemical and structural sciences, but consumer devices constrained to 2D inputs and outputs pose two major challenges: they poorly convey 3D nature, and 3D manipulation is very difficult. eXtended Reality (XR, including AR and VR) offers new ways to see and interact with molecules in three dimensions. This chapter presents the "MolecularWeb" ecosystem (https://molecularweb.org), a set of web-based tools for immersive visualization, modeling, and simulations, already widely used in education and science communication and now expanding toward research applications. We cover moleculARweb, which provides AR educational activities via phones, tablets, and computers; MolecularWebXR, a multiuser WebXR platform accessible from both headsets and simpler devices, supporting immersive education, outreach, and scientific discussion; and PDB2AR, which enables users to generate custom content for MolecularWebXR and standalone AR/VR. Finally, we introduce a prototype and an upcoming version of HandMol, our latest WebXR software which allows concurrent multiuser immersive visualization and modeling of molecules with bare hands supported by real-time molecular mechanics, natural language input via a language model, and access through both high-end headsets or consumer devices like smartphones and laptops. Together, these tools demonstrate the present and near-future of accessible, interactive molecular science on the web.

physics.chem-ph↗

arXiv2023

MolecularWebXR: Multiuser discussions about chemistry and biology in immersive and inclusive VR

MolecularWebXR is our new website for education, science communication and scientific peer discussion in chemistry and biology built on WebXR. It democratizes multi-user, inclusive virtual reality (VR) experiences that are deeply immersive for users wearing high-end headsets, yet allow participation by users with consumer devices such as smartphones, possibly inserted into cardboard goggles for immersivity, or even computers or tablets. With no installs as it is all web-served, MolecularWebXR enables multiple users to simultaneously explore, communicate and discuss chemistry and biology concepts in immersive 3D environments, manipulating objects with their bare hands, either present in the same real space or scattered throughout the globe thanks to built-in audio features. A series of preset rooms cover educational material on chemistry and structural biology, and an empty room can be populated with material prepared ad hoc using moleculARweb's VMD-based PDB2AR tool. We verified ease of use and versatility by users aged 12-80 in entirely virtual sessions or mixed real-virtual sessions at science outreach events, student instruction, scientific collaborations, and conference lectures. MolecularWebXR is available for free use without registration at https://molecularwebxr.org, and a blog post version of this preprint with embedded videos is available at https://go.epfl.ch/molecularwebxr-blog-post.

cs.HC↗

arXiv2020

Online interactive fitting and simulation of protein circular dichroism spectra for use in education and for preliminary spectral analysis

Far-UV circular dichroism (CD) spectroscopy provides a rapid, sensitive, nondestructive tool to analyze protein conformation by monitoring secondary structure composition. Originally intended for educational purposes, a spreadsheet-based program that implements a rudimentary routine for fitting and simulating far-UV protein CD spectra became quite used in research papers too, as it allowed very quick deconvolution of spectra into secondary structure compositions and easy simulation of spectra expected for defined secondary structure contents. To make such software more readily available, I present here an online version that runs directly on web browsers allowing even faster analyses on any modern device and without the need of any spreadsheet or third programs. The new version further extends the original capabilities to fit and simulate alpha, beta and random coil contents now including also beta turns; it allows to quickly select the effective spectral window used for fitting and enables interactive exploration of the effects of changes in secondary structure composition on the resulting spectra. The web app allows ubiquitous implementation in biophysics courses for example right on student smartphones, and seamless, rapid tests in research settings before moving to more advanced analysis programs (a few proposed here too). The web app is freely available without registration at http://lucianoabriata.altervista.org/jsinscience/cd/cd3.html

q-bio.BM↗

arXiv2018

Towards Commodity, Web-Based Augmented Reality Applications for Research and Education in Chemistry and Structural Biology

This article reports prototype web apps that use commodity, open-source technologies for augmented and virtual reality to provide immersive, interactive human-computer interfaces for chemistry, structural biology and related disciplines. The examples, which run in any standard web browser and are accessible at https://lucianoabriata.altervista.org/jsinscience/arjs/armodeling/ together with demo videos, showcase applications that could go well beyond pedagogy, i.e. advancing actual utility in research settings: molecular visualization at atomistic and coarse-grained levels in interactive immersive 3D, coarse-grained modeling of molecular physics and chemistry, and on-the-fly calculation of experimental observables and overlay onto experimental data. From this playground, I depict perspectives on how these emerging technologies might couple in the future to neural network-based quantum mechanical calculations, advanced forms of human-computer interaction such as speech-based communication, and sockets for concurrent collaboration through the internet -all technologies that are today maturing in web browsers- to deliver the next generation of tools for truly interactive, immersive molecular modeling that can streamline human thought and intent with the numerical processing power of computers.

cs.HC↗

arXiv2018

Concurrent interactive visualization and handling of molecular structures over the Internet in web browsers

This preprint presents a web app (essentially a web page-based program) with which two or more users (peers) can view and handle 3D molecular structures in a concurrent, interactive way through their web browsers. This means they can share orientation and zoom level, commands and other operations in almost real time over the Internet through standard web pages. This web app, open source and built with the open source components JSmol for molecular visualization and Peer.js for WebRTC connection, provides a practical tool for online collaboration and teaching at a distance. More broadly, it illustrates the strong integrability of technologies for client-side web programming, and paves the way for similar apps for concurrent work in other disciplines. Web app is available at: http://lucianoabriata.altervista.org/jsinscience/concurrent-jsmol/concurrent-jsmol-visualization.html

cs.CY↗