soft matter journal club

Code developed for a research project at Umeå universitet focusing on sheared packings of ellipsoids, supervised by Peter Olsson.

Code developed for a research project at the University of British Columbia focusing on a simple model of active particles, supervised by Jörg Rottler.

Create a consistent, documented pipline and folder structure for self-consistent MD charge optimization.

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.

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 ea…

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

Iterative training to explore glassy landscapes

Python GUI for the quick processing, analysis and plotting of differential dynamic microscopy data

Python port of Generalized Rotne Prager Yamakawa hydrodynamic tensors.

A deep learning approach for particle detection from super-resolution microscopy.

Random And Maximal PACKing PACKage

Bending Stiffness of Actin Filaments - https://doi.org/10.5281/zenodo.12808969

Computational statistical mechanics of field-responsive polymer chains

2D simulation of confluent cell collectives based on a coarse-grained bead-spring model

Neural functional theory for inhomogeneous fluids: Fundamentals and applications

LAMMPS inputs and data files

Neural functional theory for inhomogeneous fluids - Tutorial