diff --git a/examples/papers/README.md b/examples/benchmark/README.md
similarity index 61%
rename from examples/papers/README.md
rename to examples/benchmark/README.md
index 8f91bc9..889e9eb 100644
--- a/examples/papers/README.md
+++ b/examples/benchmark/README.md
@@ -1,20 +1,19 @@
 This directory contains an executable python script:
   * figure_analysis.py
+
 and one library file for each paper, currently:
   * zhang2007.py
   * zhang2009.py
   * zhang2010.py
+  * zhang2010cooperative.py
   * genot2011.py
+  * qian2011.py
   * kotani2017.py
+  * zhang2009_rates.py
+  * dabby2013_rates.py
+
   ...
-soon:
-  * yin2008.py
-  * zhang2010cooperative.py
-  * qian2011.py
-  * groves2015.py
-  * srinivas2017.py
-  * seelig2006.py
 
-In order to (re)produce results, you might want to adapt
-settings in the library files.
+In order to (re)produce results, you might want to adapt settings in the
+library files.
 
diff --git a/examples/papers/dabby2013_rates.py b/examples/benchmark/dabby2013_rates.py
similarity index 100%
rename from examples/papers/dabby2013_rates.py
rename to examples/benchmark/dabby2013_rates.py
diff --git a/examples/papers/figure_analysis.py b/examples/benchmark/figure_analysis.py
similarity index 100%
rename from examples/papers/figure_analysis.py
rename to examples/benchmark/figure_analysis.py
diff --git a/examples/papers/genot2011.py b/examples/benchmark/genot2011.py
similarity index 100%
rename from examples/papers/genot2011.py
rename to examples/benchmark/genot2011.py
diff --git a/examples/papers/kotani2017.py b/examples/benchmark/kotani2017.py
similarity index 100%
rename from examples/papers/kotani2017.py
rename to examples/benchmark/kotani2017.py
diff --git a/examples/papers/qian2011.py b/examples/benchmark/qian2011.py
similarity index 100%
rename from examples/papers/qian2011.py
rename to examples/benchmark/qian2011.py
diff --git a/examples/papers/zhang2007.py b/examples/benchmark/zhang2007.py
similarity index 100%
rename from examples/papers/zhang2007.py
rename to examples/benchmark/zhang2007.py
diff --git a/examples/papers/zhang2009.py b/examples/benchmark/zhang2009.py
similarity index 100%
rename from examples/papers/zhang2009.py
rename to examples/benchmark/zhang2009.py
diff --git a/examples/papers/zhang2009_rates.py b/examples/benchmark/zhang2009_rates.py
similarity index 100%
rename from examples/papers/zhang2009_rates.py
rename to examples/benchmark/zhang2009_rates.py
diff --git a/examples/papers/zhang2010.py b/examples/benchmark/zhang2010.py
similarity index 100%
rename from examples/papers/zhang2010.py
rename to examples/benchmark/zhang2010.py
diff --git a/examples/literature/kotani_hughes_fig2.pil b/examples/literature/kotani_hughes_fig2.pil
deleted file mode 100644
index 3dc16ae..0000000
--- a/examples/literature/kotani_hughes_fig2.pil
+++ /dev/null
@@ -1,27 +0,0 @@
-# Shohei Kotani and William L. Hughes (2017)
-# Multi-Arm Junctions for Dynamic DNA Nanotechnology
-# 
-# Figure 2A: Single-layer catalytic system with three-arm junction substrates.
-
-length a = long
-length b = long
-length c = long
-length d1s = long
-length d2 = long
-
-length T2 = short
-length t1 = short # name = 1 in Figure 
-length t2 = short # name = 2 in Figure
-length t3 = short # name = 3 in Figure
-
-S1 = d1s T2 b( a( t2( + ) ) c*( t1* + ) )
-S2 = t1( c( a( + t2* ) b*( d2 t3 + ) ) )
-C1 = t1 c a
-
-P1 = t2* a*( c*( t1*( + ) ) )
-I1 = d1s T2 b( a t2 + c )
-I2 = d1s T2 b( a( t2( + ) ) b*( d2 t3 + ) c*( t1* + ) )
-
-P2 = d1s T2 b( a( t2( + ) ) ) d2 t3
-P3 = b( c*( t1* + ) )
-