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This paper proposes the application of some well known two-dimensional geometrical shape descriptors for the visualisation of the structure of architectural open spaces. The paper demonstrates the use of visibility measures such as distance…
One need only compare the number of three-dimensional molecular illustrations in the first (1990) and third (2004) editions of Voet & Voet's "Biochemistry" in order to appreciate this field's profound communicative value in modern…
Graph neural networks have recently become a standard method for analysing chemical compounds. In the field of molecular property prediction, the emphasis is now put on designing new model architectures, and the importance of atom…
The problem of mathematical modeling in geography is one of the most important strategies in order to establish the evolution and the prevision of geographical phenomena. Models must have a simplified structure, to reflect essential…
This document attempts to clarify potential confusion regarding electrostatics calculations, specifically in the context of biomolecular structure and specifically as regards the units typically used to contour/visualize isopotential…
We report an implementation of a program for visualizing complex-valued molecular orbitals. The orbital phase information is encoded on each of the vertices of triangle meshes using the standard color wheel. Using this program, we…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
We present a method for producing documentary-style content using real-time scientific visualization. We produce molecumentaries, i.e., molecular documentaries featuring structural models from molecular biology. We employ scalable methods…
This chapter describes how astronomical imaging survey data have become a vital part of modern astronomy, how these data are archived and then served to the astronomical community through on-line data access portals. The Virtual…
Quantum computers promise to efficiently solve important problems classical computers never will. However, in order to capitalize on these prospects, a fully automated quantum software stack needs to be developed. This involves a multitude…
Cosmological N-Body simulations have become an essential tool for studying formation of large scale structure. These simulations are computationally challenging even though the available computing power gets better every year. A number of…
Glycans are tree-like polymers made up of sugar monomer building blocks. They are found on the surface of all living cells, and distinct glycan trees act as identity markers for distinct cell types. Proteins called GTase enzymes assemble…
The aim of this paper is to develop an approach to visualizations that benefits from distributed computing. Three schemes of process distribution are considered: parallel, pipeline, and expanding pipeline computations. Expanding pipeline…
A standing challenge in undergraduate Computer Science curricula is the teaching and learning of computer programming. Through this paper which is an essay about programming, we aim to contribute to the plethora of existing pedagogies,…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Geometric algebra (GA) is a mathematical tool for geometric computing, providing a framework that allows a unified and compact approach to geometric relations which in other mathematical systems are typically described using different more…
Computational models are an essential tool for the design, characterization, and discovery of novel materials. Hard computational tasks in materials science stretch the limits of existing high-performance supercomputing centers, consuming…
Molecular representation learning (MRL) is a powerful tool for bridging the gap between machine learning and chemical sciences, as it converts molecules into numerical representations while preserving their chemical features. These encoded…
Synthetic polymers are versatile and widely used materials. Similar to small organic molecules, a large chemical space of such materials is hypothetically accessible. Computational property prediction and virtual screening can accelerate…
An analogy between combinatorial chemistry and Monte Carlo computer simulation is pursued. Examples of how to design libraries for both materials discovery and protein molecular evolution are given. For materials discovery, the concept of…