dna

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This software supports the following publications

• [1] Guiding the folding pathway of DNA origami. Katherine E. Dunn †, Frits Dannenberg †, Thomas E. Ouldridge, Marta Kwiatkowska, Andrew J. Turberfield and Jonathan Bath. † equal contribution. Nature, 2015. Link to Publisher

• [2] Modelling DNA Origami Self-Assembly at the Domain Level. Frits Dannenberg, Thomas E. Ouldridge, Katherine Dunn, Jonathan Bath, Marta Kwiatkowska, and Andrew J. Turberfield. The Journal of Chemical Physics, 2015. Link to Publisher

and was used to generate all model results in [1,2]. A selection of results supporting [1] are included. By releasing this code, other researchers can independently verify results. The model implemented in this software is described both in [1,2].

This software has dependencies on some common libraries, which need to be installed first. Instructions for installation and running are found below.

email: fdannenberg/live/nl

INSTALLATION

Unzip the folder. The software depends on the following libraries that you should install. Dir lib/ should contain

• commons-math3-3.0.jar or equivalent http://commons.apache.org/
• jgrapht-jdk1.6.jar or equivalent http://jgrapht.org/ do not confuse with jgraph
• junit-4.12.jar or equivalent http://junit.org/

In addition, the plotting scripts require R to run. http://www.r-project.org/

COMPILE

javac  -cp lib/jgrapht-jdk1.6.jar:lib/commons-math3-3.0.jar src/folding/*.java src/writers/*.java src/plotting/*.java -d bin; 

SETTINGS

THREADS=8 PATHS=20 RATE=0.4; DESIGN0="design23eAll"  DESIGN1="design23eAllEnergy" DESIGN2="methodsPaperAllPlots" DESIGN3="methodsPaperNoCooperativity";

THREADS 	# number of simulation threads
PATHS		# number of folding pathways simulated per thread
RATE 		# temp drop in celsius per minute (rate)

DESIGN0="design23eAll"			# runs 5 different designs
DESIGN1="design23eAllEnergy" 		# runs same designs with sequence-specific domain stability
DESIGN2="methodsPaperAllPlots"  	# methods paper plots and data
DESIGN3="methodsPaperNoCooperativity" 	# special SI table in the methods paper

RUN

java -cp bin:lib/jgrapht-jdk1.6.jar:lib/commons-math3-3.0.jar -Xmx4000m folding.Control $DESIGN0 "distance" $THREADS $PATHS $RATE;

Correct calls will output to the commandline something similar to the below, at which point the simulation starts to run. After the run, output is placed in the /output/ dir.

design23eAll
distance
8
20
0.4
/mnt/ECFCC295FCC25A0A/workspace/dna-release/output/
The model used here is distance model
Gamma is 1.5
Prefactor is 6.69546718045E-19
numOfSteps is 3900
Number of legal states is 74
neighbourCorrectionDH - neighbourCorrectionDS -0.0 - -0.0

PRE-GENERATED RESULTS

output-pregenerated/overview.txt contains a summary of output for the experiments described in [1].