Related papers: METAGUI 3: a graphical user interface for choosing…
The Minkowski operators (addition and substraction of sets in vectorial spaces) has been extensively used for Computer Graphics and Image Processing to represent complex shapes. Here we propose to apply those mathematical concepts to extend…
In modern day simulations of many-body systems much of the computational complexity is shifted to the identification of slowly changing molecular order parameters called collective variables (CV) or reaction coordinates. A vast array of…
Multivariate networks are commonly found in real-world data-driven applications. Uncovering and understanding the relations of interest in multivariate networks is not a trivial task. This paper presents a visual analytics workflow for…
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
Models and simulations of collective behaviours are often based on considering them as assumed by interactive particle systems. The focus is then on behavioural and interaction rules by using approaches based on artificial agents designed…
It is common practice for developers of user-facing software to transform a mock-up of a graphical user interface (GUI) into code. This process takes place both at an application's inception and in an evolutionary context as GUI changes…
Neural network (NN) model chemistries (MCs) promise to facilitate the accurate exploration of chemical space and simulation of large reactive systems. One important path to improving these models is to add layers of physical detail,…
Live time-lapse microscopy is essential for a wide range of biological applications. Software-based automation is the gold standard for the operation of hardware accessories necessary for image acquisition. Given that current software…
Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…
Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: computational workflows for the coarse-grained (CG) Martini force…
Soft matter materials and polymers are widely used in the controlled delivery of drugs. Simulation and modeling provide insight at the atomic scale enabling a level of control unavailable to experiments. We present a workflow protocol for…
Modeling of turbulent combustion system requires modeling the underlying chemistry and the turbulent flow. Solving both systems simultaneously is computationally prohibitive. Instead, given the difference in scales at which the two…
Molecular dynamics (MD) simulations are widely used to study large-scale molecular systems. HPC systems are ideal platforms to run these studies, however, reaching the necessary simulation timescale to detect rare processes is challenging,…
Mediated by today's visual displays, information space allows users to discover, access and interact with a wide range of digital and physical information. The information presented in this space may be digital, physical or a blend of both,…
The data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Soft particles such as microgels and core-shell particles can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. Here we develop a…
Molecular dynamics (MD) simulations and computer-aided drug design (CADD) have advanced substantially over the past two decades, thanks to continuous computer hardware and software improvements. Given these advancements, MD simulations are…