colloids

PyStokes: phoresis and Stokesian hydrodynamics in Python. github.com/rajeshrinet/pystokes

Code to perform chemical MPCD simulations

A Matlab code for tracking colloidal fluorescent nanoparticles.

This code trains and implements a stochastic physics-informed neural ordinary differential equation (SPINODE) framework on a directed colloidal self-assembly test case.

BDHM (Brownian Dynamics with Hydrodynamics and Magnetic forces) combines magnetic dipole interactions and hydrodynamics on the point particle level with a heuristic repulsion model for the spatial expansion of the colloids to imitate the dynamics observed in [1] (see the md file) and to act as a proof of concept of the corresponding results.

Command-line tool for making charged, patchy Particles

Jupyter Notebook code that analyzes an image or a video compilation of images for colloidal systems. Analyzes pair and triplet correlations, as well as the pair and triplet free energies/potentials of mean force.

Integral-equation theory and Jupyter/Mathematica notebooks for pair correlation functions and structure factors of sheared colloidal suspensions.

a series of workflows to operate hoomd-blue; a library to proceed trajectories of particles in 2D and get their structural or dynamic properties

HOOMD-blue version 4.2.1 modified for Rheoinformatic colloid simulations

Polydisperse tunable sequential aggregation (PTSA) method for generating a fractal-like aggregate of spheres

Concept and design sketch for the third axis of a three-part system: what the microscope and Brownian-dynamics agents should work on, and the knowledge base both of them read. Design documents only — no code, and no knowledge base yet.

This code trains and implements a characterization framework based on deep learning for characterizing structural states of colloidal self-assembly systems.

An agent that turns a hand-drawn sketch into a defended Brownian-dynamics result. Dimensions first, predictions sealed, failures kept.

Brush-mediated angular constraints in colloidal depletion gels

Python codes for the Countoscope

A simple simulation of a group of particles in a box, with electromagnetic interactions.

Calculate the Morse Potential from experimental values to simulate specific colloidal depletion gels

Mutual Dipolar Model and Micro Mutual Dipolar Model

Java software for the analysis of image-based experiments of microprobes in suspension