[[!template id=gitrepo repo=sawsim]]

Introduction
============

My [[thesis]] project investigates protein unfolding via the
experimental technique of [[force spectroscopy]].  In force
spectroscopy, we mechanically stretch chains of proteins, usually by
pulling one end of the chain away from a surface with an [AFM][].

For velocity clamp experiments (the simplest to carry out
experimentally), the experiments produce "sawtooth" force-displacement
curves.  As the protein stretches, the tension increases.  At some
point, a protein domain unfolds, increasing the total length of the
chain and relaxing the tension.  As we continue to stretch the
protein, we see a series of unfolding peaks.  The [[GPLed|GPL]]
program [[Hooke]] analyzes the sawtooth curves and extracts lists of
unfolding forces.

Lists of unfolding forces are not particularly interesting by
themselves.  The most common approach for extracting some physical
insights from the unfolding curves is to take a guess at an
explanatory model and check the predicted behavior of the model
against the measured behavior of the protein.  If the model does a
good job of explaining the protein behavior, it might be what's
actually going on behind the scenes.  Sawsim is my ([published][]!)
tool for simulating force spectroscopy experiments and matching the
simulations to experimental results.

The main benefits of sawsim are its ability to simulate systems with
arbitrary numbers of states (see the [[manual|sawsim.pdf]]) and to
easily compare the simulated data with experimental values.  The
following figure shows a long valley of reasonable fits to some
ubiquitin unfolding data.  See the IJBM paper (linked above) for more
details.

[[!img fit-space.png alt="Fit space Surface bump for photodiode sensitivity"
  title="Surface bump for photodiode sensitivity" ]]


Getting started
===============

Sawsim should run anywhere you have a C compiler and Python 2.5+.
I've tested it on Gentoo and Debian, and I've got an ebuild in my
[[Gentoo overlay]].  It should also run fine on Windows, etc., but I
don't have access to any Windows boxes with a C compiler, so I haven't
tested that ([[email me|contact]] if you have access to such a machine
and want to try installing Sawsim).

See the [[README]], [[manual|sawsim.pdf]], and [PyPI page][pypi] for
more details.

[AFM]: http://en.wikipedia.org/wiki/Atomic_force_microscopy
[published]: http://dx.doi.org/10.1016/j.ijbiomac.2009.12.001
[pypi]: http://pypi.python.org/pypi/pysawsim/

[[!tag tags/C]]
[[!tag tags/papers]]
[[!tag tags/programming]]
[[!tag tags/pypi]]
[[!tag tags/python]]
[[!tag tags/sawsim]]
[[!tag tags/theory]]