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Visualization plays a relevant role for discovering patterns in big sets of data. In fact, the most common way to help a human with a pattern interpretation is through a graphic. In 2D/3D virtual environments for procedural training the…
Graph Neural Networks (GNNs) have achieved significant success across various applications. However, their complex structures and inner workings can be challenging for non-AI experts to understand. To address this issue, this study presents…
Merge trees are a type of topological descriptors that record the connectivity among the sublevel sets of scalar fields. They are among the most widely used topological tools in visualization. In this paper, we are interested in sketching a…
Generic coarse-grained models are designed such that they are (i) simple and (ii) computationally efficient. They do not aim at representing particular materials, but classes of materials, hence they can offer insight into universal…
We present a light and fast, public available, ray-tracer {\tt Splotch} software tool which supports the effective visualization of cosmological simulations data. We describe the algorithm it relies on, which is designed in order to deal…
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…
Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top…
In recent years, the use of expressive surface visualizations in the representation of vascular structures has gained significant attention. These visualizations provide a comprehensive understanding of complex anatomical structures and are…
Leveraging hypergraph structures to model advanced processes has gained much attention over the last few years in many areas, ranging from protein-interaction in computational biology to image retrieval using machine learning. Hypergraph…
Here practical aspects of conducting research via computer simulations are discussed. The following issues are addressed: software engineering, object-oriented software development, programming style, macros, make files, scripts, libraries,…
The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…
Atomistic simulations have become a powerful tool in materials research due to the extremely fine spatial and temporal resolution provided by such techniques. In order to understand the fundamental principles which govern material behavior…
Molecule design is a fundamental problem in molecular science and has critical applications in a variety of areas, such as drug discovery, material science, etc. However, due to the large searching space, it is impossible for human experts…
The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes…
In the last years, Distributed Visualization over Personal Computer (PC) clusters has become important for research and industrial communities. They have made large-scale visualizations practical and more accessible. In this work we survey…
We describe glsim, a C++ library designed to provide routines to perform basic housekeeping tasks common to a very wide range of simulation programs, such as reading simulation parameters or reading and writing self-describing binary files…
Ultrasound is one of the most frequently used imaging modality in medicine. The high spatial resolution, its interactive nature and non-invasiveness makes it the first choice in many examinations. Image interpretation is one of ultrasound's…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Many forms of programmable matter have been proposed for various tasks. We use an abstract model of self-organizing particle systems for programmable matter which could be used for a variety of applications, including smart paint and…
Researchers in the humanities are among the many who are now exploring the world of big data. They have begun to use programming languages like Python or R and their corresponding libraries to manipulate large data sets and discover brand…