Related papers: BioVEC: A program for Biomolecule Visualization wi…
We introduce Bin2Vec, a new framework that helps compare software programs in a clear and explainable way. Instead of focusing only on one type of information, Bin2Vec combines what a program looks like (its built-in functions, imports, and…
Computational micromagnetics requires numerical solution of partial differential equations to resolve complex interactions in magnetic nanomaterials. The Virtual Micromagnetics project described here provides virtual machine simulation…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Molecular dynamics is crucial for understanding molecular systems but its applicability is often limited by the vast timescales of rare events like protein folding. Enhanced sampling techniques overcome this by accelerating the simulation…
Insect vision supports complex behaviors including associative learning, navigation, and object detection, and has long motivated computational models for understanding biological visual processing. However, many contemporary models…
Deep generative models have been praised for their ability to learn smooth latent representation of images, text, and audio, which can then be used to generate new, plausible data. However, current generative models are unable to work with…
Large-scale numerical simulations of planetary interiors require dedicated visualization algorithms that are able to efficiently extract a large amount of information in an interactive and user-friendly way. Here we present a software…
Phylogenetics is a fundamental component of evolutionary analysis frameworks in biology and linguistics. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has highlighted the necessity for phylogenetic software to…
It is challenging for humans to enable visual knowledge discovery in data with more than 2-3 dimensions with a naked eye. This chapter explores the efficiency of discovering predictive machine learning models interactively using new…
Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to…
Characterizing the photolysis processes undergone by transient volatile organic compounds in the troposphere requires the knowledge of their photoabsorption cross-section - quantities often challenging to determine experimentally,…
Generating a detailed near-field perceptual model of the environment is an important and challenging problem in both self-driving vehicles and autonomous mobile robotics. A Bird Eye View (BEV) map, providing a panoptic representation, is a…
Advances in imaging methods such as electron microscopy, tomography and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for…
We describe a system for visualization and editing of data in a computational chemistry environment. The system is a collaborative tool allowing researchers using virtual reality and/or desktop computer displays to work together on results…
Visualization, from simple line plots to complex high-dimensional visual analysis systems, has established itself throughout numerous domains to explore, analyze, and evaluate data. Applying such visualizations in the context of simulation…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…
We introduce RuleVis, a web-based application for defining and editing "correct-by-construction" executable rules that model biochemical functionality, which can be used to simulate the behavior of protein-protein interaction networks and…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Vision-language models, such as CLIP, have achieved significant success in aligning visual and textual representations, becoming essential components of many multi-modal large language models (MLLMs) like LLaVA and OpenFlamingo. However,…
The use of floating bipolar electrodes in copper electro-winning cells represents an emerging technology that promises economic and operational impacts. This thesis presents EWCellCAD, a computational tool designed for the simulation and…