MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data

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Browsing MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data by Subject "Molecular simulation"

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    Atomic Accessibility Radii for Molecular Dynamics Analysis
    (The Eurographics Association, 2018) Lindow, Norbert; Baum, Daniel; Hege, Hans-Christian; Jan Byska and Michael Krone and Björn Sommer
    In molecular structure analysis and visualization, the molecule's atoms are often modeled as hard spheres parametrized by their positions and radii. While the atom positions result from experiments or molecular simulations, for the radii typically values are taken from literature. Most often, van der Waals (vdW) radii are used, for which diverse values exist. As a consequence, different visualization and analysis tools use different atomic radii, and the analyses are less objective than often believed. Furthermore, for the geometric accessibility analysis of molecular structures, vdW radii are not well suited. The reason is that during the molecular dynamics simulation, depending on the force field and the kinetic energy in the system, non-bonded atoms can come so close to each other that their vdW spheres intersect. In this paper, we introduce a new kind of atomic radius, called 'atomic accessibility radius', that better characterizes the accessibility of an atom in a given molecular trajectory. The new radii reflect the movement possibilities of atoms in the simulated physical system. They are computed by solving a linear program that maximizes the radii of the atoms under the constraint that non-bonded spheres do not intersect in the considered molecular trajectory. Using this data-driven approach, the actual accessibility of atoms can be visualized more precisely.
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    Molecular Binding in a Visuohaptic Environment: An Enhanced Approach in STEM Learning
    (The Eurographics Association, 2020) Yasmin, Shamima; Quick, Rhianna; Byška, Jan and Krone, Michael and Sommer, Björn
    Learning science, technology, engineering, and mathematics (STEM) can be dull in the absence of adequate incentives; students may lose interest in STEM subjects during their high school education. This could result in a decline in enrollment in STEM fields in postsecondary education and employment as well. However, learning can be reinforced in a multimodal environment. For example, a haptic virtual environment (VE) that incorporates both vision and touch can provide better affordance in learning. This multimodal VE may help students to better understand the underlying concepts of molecular formation while pursuing chemistry and related subjects at the secondary level. Visuohaptics may work as an incentive in learning complex molecular structures and become a source of edutainment and extra motivation for students. Thus, a multimodal VE enhances attentiveness and interest among students in pursuing STEM fields in secondary and postsecondary education.