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The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing…
Computational study of molecules and materials from first principles is a cornerstone of physics, chemistry, and materials science, but limited by the cost of accurate and precise simulations. In settings involving many simulations, machine…
In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization. The wave function analysis module can calculate and generate 3D cubes for various types of molecular…
Glycans are the most complex biological sequence, with monosaccharides forming extended, non-linear sequences. As post-translational modifications, they modulate protein structure, function, and interactions. Due to their diversity and…
In the context of a classroom lesson, concepts must be visualized and organized in many ways depending on the needs of the teacher and students. Traditional presentation media such as the blackboard or electronic whiteboard allow for static…
Quantum computing, an innovative computing system carrying prominent processing rate, is meant to be the solutions to problems in many fields. Among these realms, the most intuitive application is to help chemical researchers correctly…
Writing complex computer programs to study scientific problems requires careful planning and an in-depth knowledge of programming languages and tools. In this chapter the importance of using the right tool for the right problem is…
The construction of business process models has become an important requisite in the analysis and optimization of processes. The success of the analysis and optimization efforts heavily depends on the quality of the models. Therefore, a…
Biochars have been attracting renewed attention as economical and environmentally friendly carbon sequestration materials with a diverse range of applications. However, experimental developments may be limited by the lack of molecular-level…
Software cost estimation based on multivariate data from completed projects requires the building of efficient models. These models essentially describe relations in the data, either on the basis of correlations between variables or of…
The software tool GRworkbench is an ongoing project in visual, numerical General Relativity at The Australian National University. Recently, GRworkbench has been significantly extended to facilitate numerical experimentation in…
The ability to represent scientific data and concepts visually is becoming increasingly important due to the unprecedented exponential growth of computational power during the present digital age. The data sets and simulations scientists in…
Despite the popularity of the Graphics Processing Unit (GPU) for general purpose computing, one should not forget about the practicality of the GPU for fast scientific visualisation. As astronomers have increasing access to three…
Advances in data collection in radiation therapy have led to an abundance of opportunities for applying data mining and machine learning techniques to promote new data-driven insights. In light of these advances, supporting collaboration…
Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing…
This paper presents a toolkit for spreadsheet visualization based on logical areas, semantic classes and data modules. Logical areas, semantic classes and data modules are abstract representations of spreadsheet programs that are meant to…
Probabilistic graphical models combine the graph theory and probability theory to give a multivariate statistical modeling. They provide a unified description of uncertainty using probability and complexity using the graphical model.…
In this review, we highlight recent developments in the application of machine learning for molecular modeling and simulation. After giving a brief overview of the foundations, components, and workflow of a typical supervised learning…
Interactive molecular graphics applications facilitate analysis of three dimensional protein structures. Naturally, non-interactive 2-D snapshots of the protein structures do not convey the same level of geometric detail. Several 2-D…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…