Related papers: PeppyChains: Simplifying the assembly of 3D-printe…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…
Synthetic polymeric materials underpin fundamental technologies in the energy, electronics, consumer goods, and medical sectors, yet their development still suffers from prolonged design timelines. Although polymer informatics tools have…
Self-assembling peptides (SAPs) have shown to offer great promise in therapeutics and have the ability to undergo self-assembly and form ordered nanostructures. However SAP gels are often associated with inherent weak and transient…
Relatively short peptides, such as toxins and antimicrobial-peptides, are known to insert themselves into cell membranes. On the basis of simple bead-spring models for the membrane lipids, the peptide, and water, detailed processes of the…
In this paper, we introduce a method to rapidly create 3D geometries by folding 2D sheets via pull-up nets. Given a 3D structure, we unfold its mesh into a planar 2D sheet using heuristic algorithms and populate these with cutlines and…
Recent advances in Foundation Models for Materials Science are poised to revolutionize the discovery, manufacture, and design of novel materials with tailored properties and responses. Although great strides have been made, successes have…
In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has…
DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures.…
PySPH is an open-source, Python-based, framework for particle methods in general and Smoothed Particle Hydrodynamics (SPH) in particular. PySPH allows a user to define a complete SPH simulation using pure Python. High-performance code is…
Electronically-active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from $\pi$-conjugated oligopeptides composed of an aromatic core…
Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this…
Consumer-level multi-material 3D printing with conductive thermoplastics enables fabrication of interactive elements for bespoke tangible devices. However, large feature sizes, high resistance materials, and limitations of printable control…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
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…
Diffusion and flow matching models have recently emerged as promising approaches for peptide binder design. Despite their progress, these models still face two major challenges. First, categorical sampling of discrete residue types…
Movies of human induced pluripotent stem cell (hiPSC)-derived engineered cardiac tissue (microbundles) contain abundant information about structural and functional maturity. However, extracting these data in a reproducible and…
This study introduces Pedophysics, an open-source Python package designed to facilitate solutions for users who work in the field of soil assessment using near-surface geophysical electromagnetic techniques. At the core of this software is…
Developing and training deep learning models is expensive, so software engineers have begun to reuse pre-trained deep learning models (PTMs) and fine-tune them for downstream tasks. Despite the wide-spread use of PTMs, we know little about…
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…
We present design and implementation of a chain of particles that can be programmed to fold the chain into a given curve. The particles guide an external force to fold, therefore the particles are simple and amenable for miniaturization. A…