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In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that…
This paper presents the design and implementation of a modular multi-document interface (MDI) framework for scientific visualization and simulation in the Java Virtual Machine (JVM) ecosystem. The framework emphasizes architectural…
Pedestrian dynamics models have provided valuable insights into pedestrian interactions, collision avoidance, and self-organized crowd behavior using mathematical, computational, AI-based, and heuristic approaches. However, existing models…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
CLPGUI is a graphical user interface for visualizing and interacting with constraint logic programs over finite domains. In CLPGUI, the user can control the execution of a CLP program through several views of constraints, of finite domain…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Recent advances in (scanning) transmission electron microscopy have enabled routine generation of large volumes of high-veracity structural data on 2D and 3D materials, naturally offering the challenge of using these as starting inputs for…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
Understanding the long-time dynamics of complex physical processes depends on our ability to recognize patterns. To simplify the description of these processes, we often introduce a set of reaction coordinates, customarily referred to as…
MuSim is a new user-friendly program designed to interface to many different particle simulation codes, regardless of their data formats or geometry descriptions. It presents the user with a compelling graphical user interface that includes…
A conventional study of fluid simulation involves different stages including conception, simulation, visualization, and analysis tasks. It is, therefore, necessary to switch between different software and interactive contexts which implies…
Monte Carlo simulations are widely used to simulate complex molecular systems, but standard approaches suffer from metastability. Lately, the use of non-local proposal updates in a collective-variable (CV) space has been proposed in several…
In the modern drug discovery process, medicinal chemists deal with the complexity of analysis of large ensembles of candidate molecules. Computational tools, such as dimensionality reduction (DR) and classification, are commonly used to…
Photonic condensates are complex systems exhibiting phase transitions due to the interaction with their molecular environment. Given the macroscopic number of molecules that form a reservoir of excitations, numerical simulations are…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…