There are 1 repository under soft-matter topic.
The ESPResSo package
LAMMPS inputs and data files
Publication quality path tracing in real time.
The Morpho language 🦋. Morpho is a small embeddable language for scientific computing applications.
The Active Matter Evaluation Package (AMEP) - a Python library for the analysis of particle-based and continuum simulation data of soft and active matter systems
Pychastic is a stochastic differential equations integrator written entirely in python.
Neural functional theory for inhomogeneous fluids - Tutorial
Python code that can be used to analyze molecular dynamics simulations of proteins/polymers solvated in water. The first and second hydration shells are calculated, the molecular volume, the partial molar volume, and the number of waters associated with each side chain are calculated. This is specifically for PNIPAM but can be modified fairly easily to suit other polymers/protiens. The MDAnalysis library is used for parsing trajectories. Voronio polygons are created using the pyvoro wrapper of Voro++.
Computational statistical mechanics of field-responsive polymer chains
Iterative training to explore glassy landscapes
Python GUI for the quick processing, analysis and plotting of differential dynamic microscopy data
Code developed for a research project at the University of British Columbia focusing on a simple model of active particles, supervised by Jörg Rottler.
Data from recent publications
A deep learning approach for particle detection from super-resolution microscopy.
Code to run simulations and produce figures for Bradley et al. 2021, "Droplet trapping in bendotaxis caused by contact angle hysteresis"
All Python package to compute small angle X-ray scattering (SAXS) profiles in one-bead-per-residue approximation with numpy
2D simulation of confluent cell collectives based on a coarse-grained bead-spring model
Bending Stiffness of Actin Filaments
Create a consistent, documented pipline and folder structure for self-consistent MD charge optimization.
Code developed for a research project at Umeå universitet focusing on sheared packings of ellipsoids, supervised by Peter Olsson.
Wiki of a research project at the University of British Columbia focusing on a simple model of active particles, supervised by Jörg Rottler.
Notes of a research project at Umeå universitet focusing on sheared packings of ellipsoids, supervised by Peter Olsson.