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Proxima is a molecular perception library designed with a double purpose: to be used with immersive molecular viewers (thus providing any required feature not supported by third party libraries) and to be integrated in workflow managers thus providing the functionalities needed for the first steps of molecular modeling studies. It thus stands at the boundary between visualization and computation. The purpose of the present article is to provide a general introduction to the first release of Proxima, describe its most significant features, and highlight its performance by means of some case studies. The current version of Proxima is available for evaluation purposes at https://bitbucket.org/sns-smartlab/proxima/src/master/.
Assuntos
Percepção , Modelos Moleculares , Fluxo de TrabalhoRESUMO
The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential-energy surface to two process-tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring-puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.
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An integrated environment for the analysis of chemical bonding based on immersive virtual reality is presented. Using a multiscreen stereoscopic projection system, researchers are cast into the world of atoms and molecules, where they can visualize at a human scale the electron charge rearrangement (computed via state-of-the-art quantum-chemical methods) occurring on bond formation throughout the molecular region. Thanks to specifically designed features, such a virtual laboratory couples the immediacy of an immersive experience with a powerful, recently developed method yielding quantitative, spatially detailed pictures of the several charge flows involved in the formation of a chemical bond. By means of two case studies on organometallic complexes, we show how familiar concepts in coordination chemistry, such as donation and back-donation charge flows, can be effectively identified and quantified to predict experimental observables. © 2018 Wiley Periodicals, Inc.
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Is it possible to convert highly specialized research in the field of computational spectroscopy into robust and user-friendly aids to experiments and industrial applications? What kind of tools should be created to increase the interactions between researchers with different backgrounds and push towards new frontiers in computational chemistry? The outstanding advances in computational spectroscopy and the wide availability of computational and analytical tools are paving the route toward the study of problems that were previously difficult or impossible to solve and enable the imagination of even more ambitious targets for fundamental and applied research. The combination of new computer- and data-centric technologies is transforming data analysis from an uncommon and retrospective practice into a proactive process of strategic decision and action. This paper starts from these premises and proposes a perspective for a new cyberinfrastructure aimed at integrating developments in theory, algorithms and software with new tools for workflow management, data mining and visualization. We make a case for this approach by means of a few examples that deal with unmanageable types of data in molecular modelling and results obtained using different unsupervised learning algorithms.
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The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this contribution through the presentation of the Caffeine software to the quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, is specifically tailored for molecular representation and data visualization with VR systems, such as VR theaters and helmets. Usefulness and advantages that can be gained by exploiting VR are here reported, considering few examples specifically selected to illustrate different level of theory and molecular representation.