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PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
Modern online mass spectrometry generates multi-terabyte data streams critical for understanding Earth's environmental systems. However, extracting actionable chemical insights from these repositories is impeded by a computational…
In clinical applications, the utility of segmentation models is often based on the accuracy of derived downstream metrics such as organ size, rather than by the pixel-level accuracy of the segmentation masks themselves. Thus, uncertainty…
LES/PDF approaches can be used for simulating challenging turbulent combustion configurations with strong turbulence chemistry interactions. Transported PDF methods are computationally expensive compared to flamelet-like turbulent…
The self-assembly of anisotropic patchy particles with triangular shape was studied by experiments and computer simulations. The colloidal particles were synthesized in a two-step seeded emulsion polymerization process, and consist of a…
Understanding the complex self-assembly of biomacromolecules is a major outstanding question. Microtubules are one example of a biopolymer that possesses characteristics quite distinct from standard synthetic polymers that are derived from…
The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication…
ParticLS (\emph{Partic}le \emph{L}evel \emph{S}ets) is a software library that implements the discrete element method (DEM) and meshfree methods. ParticLS tracks the interaction between individual particles whose geometries are defined by…
Machine learning-based interatomic potentials and force fields depend critically on accurate atomic structures, yet such data are scarce due to the limited availability of experimentally resolved crystals. Although atomic-resolution…
Colloidal particles dispersed in liquid crystals can form new materials with tunable elastic and electro-optic properties. In a periodic `blue phase' host, particles should template into colloidal crystals with potential uses in photonics,…
A 3D fluid-structure interaction solver based on an improved weakly-compressible moving particle simulation (WC-MPS) method and a geometrically nonlinear shell structural model is developed and applied to hydro-elastic free-surface flows.…
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
The construction industry represents a major sector in terms of resource consumption. Recycled construction material has high reuse potential, but quality monitoring of the aggregates is typically still performed with manual methods.…
Extensive experimental studies have shown that numerous ordered phases can be formed via the self-assembly of T-shaped liquid crystalline molecules (TLCMs) composed of a rigid backbone, two flexible end chains and a flexible side chain.…
Predicting the rheological behavior of associative polymers bridging colloidal particles into transient networks is fundamentally challenging because the coupled spatiotemporal scales prevent efficient molecular-fidelity modeling. We…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
The three-dimensional (3D) microstructures of polycrystalline materials exert a critical influence on their mechanical and physical properties. Realistic, controllable construction of these microstructures is a key step toward elucidating…
We propose a new mechanism to create self-assembled porous media with highly tunable geometrical properties and permeabilities: We first allow a particle-stabilized emulsion to form from a mixture of two fluids and colloidal particles.…
Designing and fabricating self-assembled open colloidal crystals have become one major direction in soft matter community because of many promising applications associated with open colloidal crystals. However, most of the self-assembled…
We present a novel Relativistic Semi-Implicit Method (RelSIM) for particle-in-cell (PIC) simulations of astrophysical plasmas, implemented in a code framework ready for production runs. While explicit PIC methods have gained widespread…