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Computer graphics, often associated with films, games, and visual effects, has long been a powerful tool for addressing scientific challenges--from its origins in 3D visualization for medical imaging to its role in modern computational…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…

We introduce statistical techniques required to handle complex computer models with potential applications to astronomy. Computer experiments play a critical role in almost all fields of scientific research and engineering. These computer…

We report the development of a user-friendly nano-visualization software program which can acquaint high-school students with nanotechnology. The visual introduction to atoms and molecules, which are the building blocks of this technology,…

Software engineering education and training have obstacles caused by a lack of basic knowledge about a process of program execution. The article is devoted to the development of special tools that help to visualize the process. We analyze…

Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…

PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts. By harnessing state-of-the-art web technologies…

Graphical models can represent a multivariate distribution in a convenient and accessible form as a graph. Causal models can be viewed as a special class of graphical models that not only represent the distribution of the observed system…

Protein-ligand scoring is an important step in a structure-based drug design pipeline. Selecting a correct binding pose and predicting the binding affinity of a protein-ligand complex enables effective virtual screening. Machine learning…

Machine Learning tools are nowadays widely applied extensively to the prediction of the properties of molecular materials, using datasets extracted from high-throughput computational models. In several cases of scientific and technological…

Past approaches for statistical shape analysis of objects have focused mainly on objects within the same topological classes, e.g., scalar functions, Euclidean curves, or surfaces, etc. For objects that differ in more complex ways, the…

Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites within molecules, but obtaining an integrated global view…

Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…

Spreadsheets are the go-to tool for computerized calculation and modelling, but are hard to comprehend and adapt after reaching a certain complexity. In general, cognition of complex systems is facilitated by having a higher order mental…

The use of machine learning is becoming increasingly common in computational materials science. To build effective models of the chemistry of materials, useful machine-based representations of atoms and their compounds are required. We…

I have developed a code which allows images to be produced of a variety of interacting binaries for any system parameters. The resulting images are not only helpful in visualising the geometry of a given system but are also helpful in talks…

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating…

Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…

Microstructures, characterized by intricate structures at the microscopic scale, hold the promise of important disruptions in the field of mechanical engineering due to the superior mechanical properties they offer. One fundamental…