Simulation and Visualization for DNA
Computing in Microreactors
Danny van Noort1,Yuan Hong2,
Joseph Ibershoff2,and Jerzy W.Jaromczyk2
1Biointelligence Lab.,School of Computer Science and Engineering, Seoul National University,San56-1,Sinlim-dong,Gwanak-gu,
Seoul151-742,Korea
danny@bi.snu.ac.kr
2Department of Computer Science,University of Kentucky,
Lexington,KY40506,USA
jurek@cs.uky.edu
Abstract.A simulation program is a useful tool to predict the hy-
bridization error propagated through a microfluidic system.This pa-
per shows the hybridization event between solution strands and capture
probes.The program provides a Graphical User Interface that allows the
user to insert parameters as well as to observe results showing critical
values and additional visualization of the simulation process.The pro-
gram and its interface have been developed in Java,making it platform
independent and web-based.
1Introduction
DNA computering is very promising because it is closely connected to the biolog-ical world and can therefore have applications in biotechnology,such as medical diagnostics and drug lead-compound optimization.Research on operations with biomolecules can give a better insight into biological systems,while information processing and construction at molecular level can give rise to new computing paradigms and insights into nanobiotechnology.
Microfluidic networks can be incorporated as an information carrier in a DNA computing scheme.The advantages of microfluidics are the small volumes(in the pico-liter range)of DNA solution needed and the speed of reactions.When using fluidic valves and micro pumps,theflow can be(re-)directed[1].The channels are like the wires in an electronic circuit,transporting the information from one operator to another,tofluidicflip-fllogical operators.
The objective of this ongoing research is to develop a simulation environment to perform DNA-computing in a network of microreactors and to measure the effects of propagating errors.In this paper we will show the results of negative selection in one selection module,or microreactor.The objective of the simu-lation is to determine the parameters for optimal uptake of ssDNA from the solution and minimize the propagation of an erroneous strand.The simulator will be modular,so that objects and parameters of the process can be easily L.Wang,K.Chen,and Y.S.Ong(Eds.):ICNC2005,LNCS3611,pp.1206–1217,2005.
c Springer-Verlag Berlin Heidelberg2005
Simulation and Visualization for DNA Computing in Microreactors 1207updated or changed.Furthermore,it is developed in Java to make it platform independent and web-based.Beyond i
ac reactorts primary role to predict the hybridiza-tion error thus enhancing the laboratory infrastructure,the program can serve as a teaching aid and learning guide for DNA.
In this work the flows are considered here is no mixing of flows.2Selection Procedure
The basic operation is the selection from a sequence space {S i }of a single stranded DNA (ssDNA),i.e.a word,consisting of
15nt (nucleotide)sections representing bits,as defined in computer science (Fig.1).A 15nt complementary capture probe (CP;complementary bit)is immobilized to the surface of beads (with a diameter in the range of 5-10µm).Hybridization between these two is a selection,a YES or a logic operation.
It is clear from the above that logic operators can be defined with these selection procedures.A NOT operation corresponds to a negative selection which discards S k from the sequence space {S i }[2],while the retention of a certain member S k corresponds to a positive selection [3].Two selectors in sequence will Fig.1.Examples of possible words of n-bits.Each bit can consist of 15nucleotides.Furthermore,each bit is unique and should not hybridize to other bits nor to itself.Fig.2.An AND operation can be
made by having two selectors in se-
quence (left ),while an OR operation
is made by two selectors in parallel.
(right )Fig.3.A microreactor filled with beads.The reactor and the diagonal bead delivery channel has a depth of 15µm,while the horizontal flow chan-nel has a depth of 5µm and effectively
functions as a bead barrier.
1208  D.van Noort et al.
perform an AND operation,while two selectors in parallel will perform an OR operation(Figure2).
The advantage of positive selection is that there is a minimal amount of unwanted DNA,while the advantage of negative selection is the simplicity of operation and control,however with higher error rate.In the latter case it is possible to re-run the solution over the(regenerated)CP’s as to optimize the purity of the DNA template solution.However,in this simulation we want to minimize this error.
The microreactor is completely packed with these beads and the solution with ssDNA wordsflows in between the beads(Figure3).
3Factors Deciding the Rate of Hybridization
Hybridization depends on the following factors:
1.The size of the reactor.The larger the reactor the more beads can be held.
This means more CP and a larger uptake.However,the larger the reactor the longer the diffusion time and thus the reaction time.
2.The size of the beads.The larger the beads the more CP’s there are per
bead.However,the packing of beads is an issue as well.This determines the amount of beads that can
be held in the reactor.Smaller beads have a higher packing density.This factor determines the uptake of ssDNA.Here,we presume that the packing is not lose packing,but rather stacked with the dimension of their enveloping cube.
3.The concentration and volume of ssDNA.The higher the concentration of
ssDNA the faster and higher the uptake.The laws of chemical reactions dic-tate this.However,there is a problem connected to this.A certain volume is injected in the channels.Over time there is a diffusion taking place at the interface between the ssDNA and the carrier buffer.In this case timing is important.But with a suitable carrier buffFluorinert,Hampton Research,USA)this problem can be eliminated,since there will be no dif-fusion.In this case just the volume is important.A larger volume of ssDNA takes more time toflow through a reactor,while it will saturate the CP’s faster when at the same concentration.The best results will be gained by a small volume and high concentration of ssDNA.
4.The concentration of CP.The concentration of the CP’s depends on the
immobilization capacity of the bead.Each size or sort bead has a different capacity of binding,specified by the manufacturer.Typically the CP’s have
a biotin end that binds irreversibly to the streptavidin functionalized beads.
5.Flow velocity.The speed that the ssDNA passes the beads dictates the time
the ssDNA remains in the reactor.The reaction between the CP and ssDNA occurs in a certain time.The faster the velocity,the faster the DNA computer but the shorter the interaction time between the CP and ssDNA.
6.Environmental conditions(pH,salt concentration,temperature).Besides the
sequence of the DNA,environmental conditions determine the hybridization rate.The pH,salt concentration and temperature determine the melting
Simulation and Visualization for DNA Computing in Microreactors1209 temperature.The melting temperature(T m)is that T where half of the concentration of double stranded DNA is dissociated.The environmental conditions are important as they control the reaction rate as well. However,in the here presented program we will only consider the reactor size,flow volume and velocity,and the concentration of the DNA strands as input parameters.To include the environmental conditions requires a more complex model,which will not be considered here.This will presented elsewhere.
4Method
The simulation of a single selection icroreactor)is based on com-partmentalization.The module is divided in compartments of volume V.The smaller the compartments,the closer the model will be to a continuous model. The DNA solution is presumed toflow in a plug,so no diffusion is assumed.The plug is then divided in compartments with the same volume V as in the mod-ules(Figure4).Time and total volume decide the accuracy of the selection.The uptake of the ssDNA is calculated in a static fashion,which in principle means that theflow is stopped and started with time intervals depending on theflow velocity and the size of the compartment.
The objective of negative selection is to uptake all the ssDNA not wanted.In every compartment the uptake of ssDNA was calculated and that information was passed on to the next,in the direction of theflow.Furthermore,the error rate was calculated in case of negative selection.
One should be aware that if the binding capacity of the beads in a microreac-tor is insufficient to remove the vast majority of incorrect candidates,then they willflow through to the next selection module,contributing to the overall error rate.
Fig.4.A schematic of theflow of a plug with ssDNA though a compartmentalized microreactorfilled with beads.The sequence of thefigures is from left to right and top to bottom.In this example the volume of the plug corresponds to two compartments.
1210  D.van Noort et al.
Tofind appropriate DNA concentrations andflow rates for the solution con-taining the bit library,the adsorption rate of the ssDNA molecule to beads with the CP’s was calculated.Since the number of mol
ecules involved is sufficiently large(∼1010),it is possible to use deterministic and continuous,rather than stochastic,equations.It is assumed that annealing of two ssDNA molecules fol-lows second-order reaction kinetics:
[W]+[C]k−→[W C](1) where[W]is the concentration of the ssDNA in solution{S i}and[C]is the concentration of the CP.From eq.1we can derive the following about the de-crease of the concentration of{S i}and concentration of the he binding
capacity.
W i+1=εW i(W i−C i)
εW i−C i
(2)
C i+1=C i(W i−C i)
εW i−C i
(3)
ε=e kt(W i−C i)(4) where i is the compartment,k is the second-order rate constant and t is the duration of the incubation.
5The Program
The program that carries the simulation has a typical structure of the Model-View-Controller design pattern[5].The screenshot of the interface of the sim-ulation program is shown in Figure5and it illustrates that the window is divided into three major components.Thefirst part is responsible for controls and input parameters.The middle area displays the schematic animation of the flow through the microreactor.The third part contains text and graphs of the simulation results.
The program has a total of eight input parameters that can be set:
1.Reactor volume.This is the total free space available forflow of ssDNA
it does not include the volume consumed by beads).This cor-responds to the“the size of the reactor”(item(1)in the“factors deciding the rate of hybridization”section of this paper).
2.ssDNA volume.This is the volume of ssDNA solution that willflow through
the reactor.Note that in this model the ratio of these two volumes is all that is important,not the values themselves.This corresponds to the volume factor described in“the concentration and volume of ssDNA”(item(3)in the“factors deciding the rate of hybridization”section of this paper).
3.Reactorflow time.This is the total time it will take solution toflow to the
end of the reactor after it enters the front of the reactor;in other words,this is theflow time for n compartments of solution,not for the entire plug.This corresponds to“flow velocity”(item(5)in the“factors deciding the rate of hybridization”section of this paper).

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