Related papers: PeppyChains: Simplifying the assembly of 3D-printe…
pPython seeks to provide a parallel capability that provides good speed-up without sacrificing the ease of programming in Python by implementing partitioned global array semantics (PGAS) on top of a simple file-based messaging library…
Summary: PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to…
Above a critical concentration a wide variety of peptides and proteins self-assemble into amyloid fibrils which entangle to form percolating networks called hydrogels. Such hydrogels have important applications as biomaterials and in…
Micropatterning techniques have become an important tool for the study of cell behavior in controlled microenvironments. As a consequence, several approaches for the creation of micropatterns have been developed in recent years. However,…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Archaeological pottery documentation traditionally requires a time-consuming manual process of converting pencil sketches into publication-ready inked drawings. I present PyPotteryInk, an open-source automated pipeline that transforms…
Improving the detailed understanding of the underlying properties and functions of biomolecules has recently attracted growing interest, enabled by the possibility of real-space imaging of single, intact macromolecules using Scanning…
The purpose of this review is to analyze the physics at play in particle resuspension in order to bring insights into the rich complexity of this common but challenging concern. Following the more-is-different vision, this is performed by…
Recent advances in protein language models have catalyzed significant progress in peptide sequence representation. Despite extensive exploration in this field, pre-trained models tailored for peptide-specific needs remain largely…
Summary: Medical researchers obtain knowledge about the prevention and treatment of disability and disease using physical measurements and image data. To assist in this endeavor, feature extraction packages are available that are designed…
This paper describes a novel approach for on demand volumetric texture synthesis based on a deep learning framework that allows for the generation of high quality 3D data at interactive rates. Based on a few example images of textures, a…
Doubly periodic (DP) weaves and polycatenanes are complex entangled structures embedded in the Euclidean thickened plane, invariant under translations in two independent directions. Their topological properties are fully encoded within a…
As a machine-learned potential, the neuroevolution potential (NEP) method features exceptional computational efficiency and has been successfully applied in materials science. Constructing high-quality training datasets is crucial for…
The integration of artificial intelligence (AI) into pathology is advancing precision medicine by improving diagnosis, treatment planning, and patient outcomes. Digitised whole-slide images (WSIs) capture rich spatial and morphological…
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale…
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…
A single-step, single-material 4D printing method is developed for programmable structures featuring spatially patterned strain trapping for one-way actuation. This approach enables fabrication on desktop fused filament fabrication 3D…
Patchy colloids are promising candidates for building blocks in directed self-assembly. To be successful the surface patterns need to both be simple enough to be synthesized, while feature-rich enough to cause the colloids to self-assemble…
We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software to design custom Coarse-Grained (CG) models, as well as pre-defined models of polyelectrolytes, peptides and globular proteins in the Extensible…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…