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The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small…
This paper introduces a novel method of analysis for SoC development building upon commonly used tools and techniques to approximate and automate the human process of investigation. Knowledge of the interactions between components within a…
A visualisation tool is presented to facilitate the study on large-scale communications networks. This tool provides a simple and effective way to summarise the topology of a complex network at a coarse level.
Interactive data visualization is a major part of modern exploratory data analysis, with web-based technologies enabling a rich ecosystem of both specialized and general tools. However, current visualization tools often lack support for…
Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which…
Mathematical modelling is a cornerstone of computational biology. While mechanistic models might describe the interactions of interest of a system, they are often difficult to study. On the other hand, abstract models might capture key…
As the twin movements of open science and open source bring an ever greater share of the scientific process into the digital realm, new opportunities arise for the meta-scientific study of science itself, including of data science and…
Scientists often explore and analyze large-scale scientific simulation data by leveraging two- and three-dimensional visualizations. The data and tasks can be complex and therefore best supported using myriad display technologies, from…
The goal of this paper is to deliver the overview of the current state of the art, to provide experience report on developing quantum software tools, and to outline the perspective for developing quantum programming tools supporting…
Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at…
The difficulty of simulating quantum systems, well-known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on…
Understanding the various properties of glycans with machine learning has shown some preliminary promise. However, previous methods mainly focused on modeling the backbone structure of glycans as graphs of monosaccharides (i.e., sugar…
Teaching and advocating data visualization are among the most important activities in the visualization community. With growing interest in data analysis from business and science professionals, data visualization courses attract students…
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic…
Geometric, topological and graph theory modeling and analysis of biomolecules are of essential importance in the conceptualization of molecular structure, function, dynamics, and transport. On the one hand, geometric modeling provides…
With the increasing interplay between experimental and computational approaches at multiple length scales, new research directions are emerging in materials science and computational mechanics. Such cooperative interactions find many…
The paper presents a software tool for analysis and interactive engagement in various logical reasoning tasks. A first feature of the program consists in providing an interface for working with logic-specific repositories of formal…
Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one…