Add force spectroscopy and research posts.

diff --git a/posts/Force_spectroscopy.mdwn b/posts/Force_spectroscopy.mdwn
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+++ b/posts/Force_spectroscopy.mdwn
@@ -0,0 +1,41 @@
+[Force spectroscopy][fs] is the process of extracting information
+about the unfolding (or unbinding) characteristics of a protein (or
+ligand-receptor pair) by measuring force vs. extension curves while
+gradually ripping the protein (or pair) apart.  Consider this cartoon
+representation of the procedure
+
+[[!img afm_protein_pulling_cartoon.jpg class="scaled"
+  alt="Protein unfolding cartoon"
+  title="Protein unfolding cartoon"]]
+
+The AFM tip is pulling a protein chain away from the substrate,
+causing one of the protein domains to uncoil.
+
+The procedure yields 'force curves' like this
+
+[[!img force_curve_regions.png class="scaled"
+  alt="Protein unfolding force curve"
+  title="Protein unfolding force curve"]]
+
+To interpret the force curve, let us examine it piece-by-piece as the
+AFM tip gradually pulls away from the substrate.
+
+1. The linear 'contact' region demonstrates the Hooke's law behavior
+   of the AFM cantilever, with force ∝ displacement.
+2. The high force 'bulge' linking the contact region to the sawtooth
+   comes from the AFM tip pulling free of the surface and associated
+   protein 'mat' (the cartoon being excessively pretty, and our sample
+   having too high a protein concentration :p).
+3. The characteristic 'sawtooth' comes from several identical domains
+   unfolding one after the other.
+4. After the last of the protein domains unfolds the protein snaps off
+   of the AFM tip (or the substrate), and the deflection of the
+   now-free cantilever ceases to depend on distance.
+
+[[!img force_curve_regions_cantilever.png class="scaled"
+  alt="Force curve cantilever positions"
+  title="Force curve cantilever positions"]]
+
+[fs]: http://en.wikipedia.org/wiki/Force_spectroscopy
+
+[[!tag tags/theory]]

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diff --git a/posts/Force_spectroscopy/force_curve_regions_cantilever.png b/posts/Force_spectroscopy/force_curve_regions_cantilever.png
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diff --git a/posts/Gentoo_overlay.mdwn b/posts/Gentoo_overlay.mdwn
index b0d9d3e69bbbabd1a5335b8e93fc5f115d59c091..a3a5c3a2826d56cc5ede59b1f0ee642e08be2d28 100644 (file)
--- a/posts/Gentoo_overlay.mdwn
+++ b/posts/Gentoo_overlay.mdwn
@@ -23,7 +23,7 @@ personal `layman.xml`).  The overlay is a fairly strange mix:
   ([Gentoo 76017](http://bugs.gentoo.org/76017),
         also in the [Sunrise overlay][])
 - sci-physics/hooke
-  (my branch of the [[Hooke]] force spectroscopy analyzer)
+  (my branch of the [[Hooke]] [[force spectroscopy]] analyzer)
 - sci-physics/sawsim
   (my [[sawsim]] force spectroscopy simulator)
 

diff --git a/posts/Hooke.mdwn b/posts/Hooke.mdwn
index 38d5d5280957e23b741ec64a40396c99d081fc72..97af0c5837cbad752609469ab6d9d5ac9e0b70ec 100644 (file)
--- a/posts/Hooke.mdwn
+++ b/posts/Hooke.mdwn
@@ -1,11 +1,11 @@
 [[!template id=hgrepo repo=hooke]]
 
-[Hooke][] is a force spectroscopy data analysis package.  For example,
-Hooke can extract unfolding forces from your experimental data.  You
-can then fit the unfolding forces to models using my [[sawsim]]
-simulator.  Of course, some experiments (e.g. force clamp) need no
-Monte Carlo analysis, so for those, Hooke alone provides a complete
-analysis package.
+[Hooke][] is a [[force spectroscopy]] data analysis package.  For
+example, Hooke can extract unfolding forces from your experimental
+data.  You can then fit the unfolding forces to models using my
+[[sawsim]] simulator.  Of course, some experiments (e.g. force clamp)
+need no Monte Carlo analysis, so for those, Hooke alone provides a
+complete analysis package.
 
 Getting started
 ===============

diff --git a/posts/Research.mdwn b/posts/Research.mdwn
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+++ b/posts/Research.mdwn
@@ -0,0 +1,20 @@
+My current work for [Prof. Yang][GY] involves unfolding proteins using
+an Atomic Force Microscope (AFM) at different temperatures to estimate
+the roughness of their free energy landscape. For a brief overview of
+force spectroscopy, see my [[two second
+summary|Force_spectroscopy]]. For more detail, you can look at some of
+my [[papers|tags/papers]].
+
+I've written some [[experimental control software|unfold_protein]], a
+Monte Carlo simulation program ([[sawsim]]) for analyzing the
+unfolding sawtooth curves, as well as software for calibrating AFM
+cantilevers via the thermal tune method ([[calibcant]]), scaling the
+unfolding data, selecting good curves, and fitting those curves with
+wormlike chains ([[Hooke]]).
+
+Along the way I've had to learn way too much about the internal
+workings of our [[MultiMode]] AFM.
+
+I've also posted my notes for our [[Debian cluster|Abax]].
+
+[GY]: http://www.physics.drexel.edu/~gyang/

diff --git a/posts/sawsim.mdwn b/posts/sawsim.mdwn
index fdb2b61a89419de75b87c3da8c35d19835301cc5..15882ae19b96ef38d0138f0e07cf1402ecabbeef 100644 (file)
--- a/posts/sawsim.mdwn
+++ b/posts/sawsim.mdwn
@@ -4,7 +4,7 @@ Introduction
 ============
 
 My [[thesis]] project investigates protein unfolding via the
-experimental technique of [force spectroscopy][fs].  In force
+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][].
 
@@ -27,7 +27,6 @@ actually going on behind the scenes.  Sawsim is my ([published][]!)
 tool for simulating force spectroscopy experiments and matching the
 simulations to experimental results.
 
-[fs]: http://en.wikipedia.org/wiki/Force_spectroscopy
 [AFM]: http://en.wikipedia.org/wiki/Atomic_force_microscopy
 [published]: http://dx.doi.org/10.1016/j.ijbiomac.2009.12.001