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This article describes a volumetric approach for procedural shape modeling and a new Procedural Shape Modeling Language (PSML) that facilitates the specification of these models. PSML provides programmers the ability to describe shapes in…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
Dynamic programming (DP) is a fundamental and powerful algorithmic paradigm taught in most undergraduate (and many graduate) algorithms classes. DP problems are challenging for many computer science students because they require identifying…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Polymer composite performance depends significantly on the polymer matrix, additives, processing conditions, and measurement setups. Traditional physics-based optimization methods for these parameters can be slow, labor-intensive, and…
Particle-in-Cell (PIC) methods are widely used computational tools for fluid and kinetic plasma modeling. While both the fluid and kinetic PIC approaches have been successfully used to target either kinetic or fluid simulations, little was…
Molecular representation learning is fundamental for many drug related applications. Most existing molecular pre-training models are limited in using single molecular modality, either SMILES or graph representation. To effectively leverage…
In recent years, a wide variety of automated machine learning (AutoML) methods have been proposed to search and generate end-to-end learning pipelines. While these techniques facilitate the creation of models for real-world applications,…
This communication is both a pedagogical note for understanding polyatomic modelling in kinetic theory and a ''cheat sheet'' for a series of corresponding concepts and formulas. We explain, detail and relate three possible approaches for…
Machine learned interaction potentials (MLIPs) have become a critical component of large-scale, high-quality simulations for a range of chemical and biochemical systems. Yet, despite their in-distribution accuracy, molecular dynamics…
This article introduces an approach to facilitate cooperative exploration and mapping of large-scale, near-ground, underground, or indoor spaces via a novel integration framework for locally-dense agent map data. The effort targets limited…
In this paper, we present BIMS (Biomedical Information Management System). BIMS is a software architecture designed to provide a flexible computational framework to manage the information needs of a wide range of biomedical research…
Polymer informatics tools have been recently gaining ground to efficiently and effectively develop, design, and discover new polymers that meet specific application needs. So far, however, these data-driven efforts have largely focused on…
Simulation tools are playing an increasingly important role in materials science and engineering and beyond their well established importance in research and development, these tools have a significant pedagogical potential. We describe a…
This paper presents a 2D/3D Free Surface Lattice Boltzmann Method simulation package called LBfoam for the simulation of foaming processes. The model incorporates the essential physics of foaming phenomena: gas diffusion into nucleated…
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
Research in cell biology is steadily contributing new knowledge about many different aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function.…
Since Lorenz's seminal work on a simplified weather model, the numerical analysis of nonlinear dynamical systems has become one of the main subjects of research in physics. Despite of that, there remains a need for accessible, efficient,…
Artificial intelligence-based methods are becoming increasingly effective at screening libraries of polymers down to a selection that is manageable for experimental inquiry. The vast majority of presently adopted approaches for polymer…