Related papers: BioVEC: A program for Biomolecule Visualization wi…
Virtual screening (VS) is an essential technique for understanding biomolecular interactions, particularly, drug design and discovery. The best-performing VS models depend vitally on three-dimensional (3D) structures, which are not…
We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment --- simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by 4 million…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Understanding chemical modifications on proteins opens up further possibilities for research on rare diseases. This work proposes visualization approaches using two-dimensional (2D) and three-dimensional (3D) visual representations to…
We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
The simulation of problems in kinetic plasma physics are often challenging due to strongly coupled phenomena across multiple scales. In this work, we propose a wavelet-based coarse-grained numerical scheme, based on the framework of…
The growth of computational astrophysics and complexity of multidimensional datasets evidences the need for new versatile visualization tools for both analysis and presentation of the data. In this work we show how to use the open source…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
The CellxGene project has enabled access to single-cell data in the scientific community, providing tools for browsed-based no-code analysis of more than 500 annotated datasets. However, single-cell data requires dimensional reduction to…
During the training phase of machine learning (ML) models, it is usually necessary to configure several hyperparameters. This process is computationally intensive and requires an extensive search to infer the best hyperparameter set for the…
Recent advances in deep neuroevolution have demonstrated that evolutionary algorithms, such as evolution strategies (ES) and genetic algorithms (GA), can scale to train deep neural networks to solve difficult reinforcement learning (RL)…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
This paper presents a new technique for the virtual reality (VR) visu-alization of complex volume images obtained from computer tomography (CT) and Magnetic Resonance Imaging (MRI) by combining three-dimensional (3D) mesh processing and…
Whole-slide multiplex imaging of brain tissue generates massive information-dense images that are challenging to analyze and require custom software. We present an alternative query-driven programming-free strategy using a multiplex visual…
The ALICE Collaboration at CERN developed a 3D visualisation tool capable of displaying a representation of collected collision data (particle trajectories, clusters and calorimeter towers) called the Event Display. The Event Display is…
Biofouling$\unicode{x2013}$communities of organisms that grow on hard surfaces immersed in water$\unicode{x2013}$provides a pathway for the spread of invasive marine species and diseases. To address this risk, international vessels are…
The CAVE-type virtual reality (VR) system was introduced for scientific visualization of large scale data in the plasma simulation community about a decade ago. Since then, we have been developing a VR visualization software, VFIVE, for…
In non-linear systems, where explicit analytic solutions usually can't be found, visualisation is a powerful approach which can give insights into the dynamical behaviour of models; it is also crucial for teaching this area of mathematics.…