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 <https://www.proquest.com/docview/2832979813>`_
       (Ondrej Maxian's PhD thesis)
    
Contents:

.. toctree::
   :maxdepth: 1
   
   Installation 
   Examples
   PythonClasses



Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`