Welcome to SPHARCLE’s documentation!

SPHARCLE stands for Slender Particle Hydrodynamics And Reacting Cytoskeletal Linking Elements.

The theory behind this software can be found in the concluding publication:

1. A simulation platform for slender, semiflexible, and inextensible fibers with Brownian hydrodynamics and steric repulsion, by O. Maxian and A. Donev, November 2024.

See also some other references:

2. An integral-based spectral method for inextensible slender fibers in Stokes flow, by O. Maxian, A. Mogilner, and A. Donev, January 2021.

3. Simulations of dynamically cross-linked actin networks: morphology, rheology, and hydrodynamic interactions, by O. Maxian, R. P. Peláez, A. Mogilner, and A. Donev, December 2021.

4. Interplay between Brownian motion and cross-linking controls bundling dynamics in actin networks, by O. Maxian, A. Donev, and A. Mogilner, April 2022.

5. The hydrodynamics of a twisting, bending, inextensible fiber in Stokes flow, by O. Maxian, B. Sprinkle, C.S. Peskin, and A. Donev, July 2022.

6. Bending fluctuations in semiflexible, inextensible, slender filaments in Stokes flow: towards a spectral discretization, by O. Maxian, B. Sprinkle, and A. Donev, April 2023.

7. Hydrodynamics of transiently cross-linked actin networks: theory, numerics, and emergent behaviors (Ondrej Maxian’s PhD thesis)

Contents:

• Installing the software
• Running the examples
• Source code (Python) documentation

Indices and tables

• Index

• Module Index

• Search Page