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We introduce MolMiner, a fragment-based, geometry-aware, and order-agnostic autoregressive model for molecular design. MolMiner supports conditional generation of molecules over twelve properties, enabling flexible control across…
We present the first public release of plasmonX, a novel open-source code for simulating the plasmonic response of complex nanostructures. The code supports both fully atomistic and implicit descriptions of nanomaterials. In particular, it…
Most molecular diagram parsers recover chemical structure from raster images (e.g., PNGs). However, many PDFs include commands giving explicit locations and shapes for characters, lines, and polygons. We present a new parser that uses these…
This work purports to help understand the InterStellar Extinction Curve in and near the visible range. In this range, crystalline materials are known to be transparent, so amorphous dust is needed. Molecular modeling experiments are used to…
Atomistic simulations have become a powerful tool in materials research due to the extremely fine spatial and temporal resolution provided by such techniques. In order to understand the fundamental principles which govern material behavior…
Nanofluidic systems exploit nanometre-scale confinement in channels and pores to regulate ionic transport, enabling functionalities such as osmotic energy harvesting and neuromorphic ionic memory. Studying such confined transport requires…
Astronomical researchers often think of analysis and visualization as separate tasks. In the case of high-dimensional data sets, though, interactive exploratory data visualization can give far more insight than an approach where data…
With new catalogues arriving such as the Gaia DR1, containing more than a billion objects, new methods of handling and visualizing these data volumes are needed. In visualization, one problem is that the number of datapoints can become so…
This paper introduces OpenGaussian, a method based on 3D Gaussian Splatting (3DGS) capable of 3D point-level open vocabulary understanding. Our primary motivation stems from observing that existing 3DGS-based open vocabulary methods mainly…
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…
The Heusler compounds have provided a playground of material candidates for various technological applications based on their highly diverse and tunable properties, controlled by chemical composition and crystal structure. However, physical…
The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix ($C_{ij}$) obtained from any ab-initio density-functional theory (DFT) code. The current version of…
FEpX is a modeling framework for computing the elastoplastic deformations of polycrystalline solids. Using the framework, one can simulate the mechanical behavior of aggregates of crystals, referred to as virtual polycrystals, over large…
Correlated electron molecular orbital (CEMO) materials host emergent electronic states built from molecular orbitals localized over clusters of transition metal ions, yet have historically been discovered sporadically and generally been…
ASCRIBE-XR, a novel computational platform designed to facilitate the visualization and exploration of 3D volumetric data and mesh data in the context of synchrotron experiments, is described. Using Godot and PC-VR technologies, the…
A new web-server called The Molecule Calculator (MolCalc) is presented. The entry page is a molecular editor (JSmol) for interactive molecule building. The resulting structure can then be used to estimate molecular properties such as heats…
Software visualization seeks to represent software artifacts graphical-ly in two or three dimensions, with the goal of enhancing comprehension, anal-ysis, maintenance, and evolution of the source code. In this context, visualiza-tions…
This article reports prototype web apps that use commodity, open-source technologies for augmented and virtual reality to provide immersive, interactive human-computer interfaces for chemistry, structural biology and related disciplines.…
The geometry of atomic arrangement underpins the structural understanding of molecules in many fields. However, no general framework of mathematical/computational theory for the geometry of atomic arrangement exists. Here we present…
Computational analyses of, e.g., genomic, proteomic, or metabolomic data, commonly result in one or more sets of candidate genes, proteins, or enzymes. These sets are often the outcome of clustering algorithms. Subsequently, it has to be…