CN109117497A - The time-optimized method of digital microcurrent-controlled biochip CAD layout - Google Patents
The time-optimized method of digital microcurrent-controlled biochip CAD layout Download PDFInfo
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Abstract
The invention discloses a kind of time-optimized methods of digital microcurrent-controlled biochip CAD layout, comprise the following steps: establishing precedence constraint, resource constraint, the model for being overlapped four constraint, confines fluid constraint condition；Establish the object module that chain biochemical reaction completes total time on digital microcurrent-controlled biochip；Based on Markovian decision, according to the optimal solution of the object module of deadline described in the model solution of four constraint condition；According to the optimal solution, the realization process of biochemical reaction on digital microcurrent-controlled biochip is controlled.The present invention can be near minimum by the time of the biochemical reaction in digital microcurrent-controlled biochip, also has the advantages that inexpensive, in high precision and efficient.
Description
Technical field
The present invention relates to digital microcurrent-controlled biochip field of computer aided design, more specifically to a kind of number
The time-optimized method of word microflow controlled biochip CAD layout.
Background technique
The physical Design of microflow controlled biochip is introduced first.As shown in Figure 1, microflow controlled biochip is mainly by electrode plate
It constitutes, carries out the operation such as moving, mix, react and store by electrowetting electrode drive drop, store bioid in drop
Related reagent sample, all drops required for testing are learned to be clipped among two layers of indium-tin oxide electrode plate.Here there are two types of
Not reconfigurable resource is fluorescence detector and optical distribution port respectively, and whether fluorescence detector is used to detect each operation
It is normally carried out, as a kind of special resource, its position was just fixed and in entire physical Design in the fabrication stage
In can not all move, optical distribution port be used to generate drop.
With the progress of science, also more sophisticated, traditional microflow controlled biochip design can not expire biochemical test
Sufficient demand, but by the help of CAD, the problem is not only solved, but also there is low cost, high-precision
With efficient advantage.The CAD of microflow controlled biochip is mainly by mission planning, place and route three parts
Composition, includes two optimization aims of time and size, CAD simulates miniflow by establishing a 3D model
The a series of experiments process of biochip is controlled, as shown in Fig. 2, time t is z using the physical plane of biochip as x-y plane
Axis, each module the inside contain drop, and drop carries out relevant operation in module, such as moves, mixes, reacts and deposit
Storage etc., the length of module represents space size required for the operation with width, highly represents the time required for the operation.Miniflow
Control biochip carries out biochemical reaction under certain experiment constraint condition, and it is quickly complete how to control microflow controlled biochip
A research direction in microflow controlled biochip at all biochemical reactions, then this technical problem there is presently no
It is well solved.
Summary of the invention
The technical problem to be solved in the present invention is that for the above-mentioned in the micro- of CAD layout of the prior art
In micro-continuous-flow biochip, the technological deficiency that all biochemical reactions are effectively solved not yet how is rapidly completed, mentions
For a kind of time-optimized method of digital microcurrent-controlled biochip CAD layout.
The technical solution adopted by the present invention to solve the technical problems is: constructing a kind of digital microcurrent-controlled biochip calculating
The time-optimized method of machine Computer Aided Design layout, comprises the following steps:
S1, the model for establishing following four constraint condition:
1) precedence constraints: the priority of chemical reaction defines pair during digital microcurrent-controlled biochip design
Sequence is executed in different operation；
2) resource constraint: ensure that entire series biochemical reaction using each type of chemical agent, does not surpass
Cross the upper limit of its resource constraint；
3) it is overlapped constraint condition: ensuring that range of biochemical reaction will not be held in point at the same time in the same position
Row；
4) confines fluid condition: the minimum spacing between digital microcurrent-controlled biochip drop is defined；
S2, the object module that chain biochemical reaction completes total time on digital microcurrent-controlled biochip is established:
Wherein, { o1,o2,…,onRepresent all operation sets tested, n >=2, t (oi) represent each operation oiHold
The row time；
S3, it is based on Markovian decision, according to the target of deadline described in the model solution of four constraint condition
The optimal solution of model；
S4, according to the optimal solution, control the realization process of biochemical reaction on digital microcurrent-controlled biochip.
Preferably, the time-optimized method being laid out in digital microcurrent-controlled biochip CAD of the invention
In, the modeling of the precedence constraints specifically includes:
Digraph is established according to the relation of interdependence between reactant for a series of chain biochemical reaction
The constraint relationship between biochemical reaction is defined, is denoted as G={ O, P }, the O in G is schemed, two parameter definitions of O are as follows:
O={ o1,o2,…,on}: indicate a series of biochemical reaction；
P={ p1,p2,…,pm}: indicate the precedence constraints between two chemical reactions, m >=n.
Preferably, the time-optimized method being laid out in digital microcurrent-controlled biochip CAD of the invention
In, the modeling of resource constraint specifically includes:
The medicament a dosage of definition chemical reaction is ma, medicament a total amount is Ma, the model of resource constraint are as follows:
Preferably, the time-optimized method being laid out in digital microcurrent-controlled biochip CAD of the invention
In, the modeling for being overlapped constraint condition specifically includes:
Define a Cx,y∈ { 0,1 }: indicating whether chemical reagent can reside in point (x, y), if Cx,y=1, indicating should
Point can place chemical reagent, be regarded as a free cells lattice；If Cx,y=0, indicate that the point is occupied, Bu Nengzai
In the presence of from current different chemical reagent；
It is overlapped the model of constraint condition are as follows:
∑x,yCx,y(L)≤1,All reagent L.
Preferably, the time-optimized method being laid out in digital microcurrent-controlled biochip CAD of the invention
In, the modeling of confines fluid condition specifically includes:
Digital microcurrent-controlled biochip is subjected to blocking, i.e., by digital microcurrent-controlled biochip according to set industrial ruler
Very little standard is divided into several cells, and the lower left corner of each cell is the starting point of cell, the coordinate difference of each cell
It is calculated with the relative position of itself and starting point cell, is denoted as (x, y), on digital microcurrent-controlled biochip, chemical agent is with list
First lattice are that unit move, retains, reacts, to guarantee to meet confines fluid condition.
Preferably, the time-optimized method being laid out in digital microcurrent-controlled biochip CAD of the invention
In, minimum spacing described in the confines fluid condition in step S1 is a cell on chip.
Preferably, the time-optimized method being laid out in digital microcurrent-controlled biochip CAD of the invention
In, step S3 is specifically included:
Establish topological relation figure G={ O, P }；Wherein, topological relation figure generates oriented according to the dependence of chemical reaction
Side, each of figure node are a chemical reaction；
Then it is scanned for from topological relation figure G according to the priority of digraph, judges whether there is and do not carry out also
With the chemical reaction of completion；If so, then therefrom choosing default node carries out Markovian decision, and more according to the result of decision
Then new G is rejudged with the presence or absence of the node not used in G, until there is no the nodes not used in G；
Obtain final G as optimal solution.
The time-optimized method for implementing digital microcurrent-controlled biochip CAD layout of the invention, can incite somebody to action
The time of biochemical reaction in digital microcurrent-controlled biochip is near minimum, also has low cost, high-precision and high efficiency
The advantages of.
Detailed description of the invention
Present invention will be further explained below with reference to the attached drawings and examples, in attached drawing:
Fig. 1 is the physical Design of digital microcurrent-controlled biochip；
Fig. 2 is the 3D model of digital microcurrent-controlled biochip CAD；
Fig. 3 is the time-optimized method flow diagram of digital microcurrent-controlled biochip CAD layout；
Fig. 4 is the topological relation figure example of operation；
Fig. 5 is resource constraint example；
Fig. 6 is a simplified example about Markovian decision algorithm；
Fig. 7 is Markovian decision algorithm iterative process；
Fig. 8 is the flow chart that optimal solution is solved based on Markovian decision.
Specific embodiment
For a clearer understanding of the technical characteristics, objects and effects of the present invention, now control attached drawing is described in detail
A specific embodiment of the invention.
With reference to Fig. 3, the time-optimized side being laid out for digital microcurrent-controlled biochip CAD of the invention
Method flow chart, this method specifically include:
S1, precedence constraint, resource constraint, the model for not being overlapped constraint, confines fluid condition are established:
Microflow controlled biochip each standard analog experiment have oneself parameter setting, in input file given
The upper dimension bound and time upper limit of the experiment, such as parameter setting Fixed:10 10 360, then it represents that the upper dimension bound of the experiment
For 10*10, time upper limit 360, each reagent or operation are carrying out the experiment also given occupied size
During series reaction, no more than the boundary of the size, total reaction time can not be more than the time for all operations
The upper limit.
When carrying out CAD, it is also necessary to consider following four constraint condition:
(1) precedence constraint.The priority of chemical reaction define during digital microcurrent-controlled biochip design for
Different operation executes sequence.During the CAD of chip, precedence constraint defines the execution of all operations
Sequence.Digraph definition is established according to the relation of interdependence between reactant for a series of chain biochemical reaction
The constraint relationship between biochemical reaction is denoted as G={ O, P }, schemes the O in G, and two parameter definitions of P are as follows:
O={ o1,o2,…,on}: indicate a series of biochemical reaction；
P={ p1,p2,…,pm}: indicate the precedence constraints between two chemical reactions, m >=n.
As shown in figure 4, the execution sequence of operation can be indicated by a time-based topological diagram, each node generation
One, table buffering or an operation, t axis represent when each node is executing.DsB represents buffering, and buffering has to pass through preparation
Time can just come into operation and enter and operate in next step, and DsR represents reaction reagent, and Mix represents hybrid manipulation, and Dlt represents dilution
Operation, most node must could all execute after the forerunner of oneself has executed, and existing simultaneously a part of node does not have
Forerunner still has time.In Fig. 3, the product of Mix2 and Mix3 are only obtained, it is mixed that Dlt2, DsB1 and DsB2 could be executed
The product and DsR of conjunction are diluted operation, and the product that DsB3 and DsB4 are mixed is diluted with DsB4 and the DsB5 product mixed
Operation, can just obtain final product Opt.
(2) resource constraint.Ensure that entire series biochemical reaction using each type of chemical agent, is no more than it
The upper limit of resource constraint.Resource is divided into not reconfigurable resource and reconfigurable resource, and not reconfigurable resource includes optics inspection
Survey device and optical distribution port.Reconfigurable resource includes that all bufferings, reagent and operation product, resource constraint define institute
The reconfigurable resource having is when the same time is by multiple operate with, no more than the upper limit of the resource owning amount.Resource is about
The modeling of beam condition specifically includes:
The medicament a dosage of definition chemical reaction is ma, medicament a total amount is Ma, the model of resource constraint are as follows:
As shown in figure 5, a simple 2D figure is employed herein to explain, resource i only has two parts in t moment, but at this time
Operation 1, operation 2 and operation 3 are required to using resource i, then two kinds of operations only therein can be completed.
(3) it is not overlapped constraint.Be not overlapped constraint ensure synchronization there are no two or more operation same
Position carries out.The modeling of overlapping constraint condition specifically includes:
Define a Cx,y∈ { 0,1 }: indicating whether chemical reagent can reside in point (x, y), if Cx,y=1, indicating should
Point can place chemical reagent, be regarded as a free cells lattice；If Cx,y=0, indicate that the point is occupied, Bu Nengzai
In the presence of from current different chemical reagent；
It is overlapped the model of constraint condition are as follows:
∑x,yCx,y(L)≤1,All reagent L.
(4) confines fluid.Confines fluid defines between the minimum in the same module between two nonreactive drops
Away from the minimum spacing is a cell on chip.The modeling of confines fluid condition specifically includes:
Digital microcurrent-controlled biochip is subjected to blocking, i.e., by digital microcurrent-controlled biochip according to set industrial ruler
Very little standard is divided into several cells, and the lower left corner of each cell is the starting point of cell, the coordinate difference of each cell
It is calculated with the relative position of itself and starting point cell, is denoted as (x, y), on digital microcurrent-controlled biochip, chemical agent is with list
First lattice are that unit move, retains, reacts, to guarantee to meet confines fluid condition.
All operations all must comply with constraints above condition.
S2, the object module that chain biochemical reaction completes total time on digital microcurrent-controlled biochip is established:
Wherein, { o1,o2,…,onRepresent all operation sets tested, n >=2, t (oi) represent each operation oiHold
The row time；
S3, it is based on Markovian decision, according to the target of deadline described in the model solution of four constraint condition
The optimal solution of model；
In probability theory and statistics, Markovian decision process (English: Markov Decision Processes, contracting
It is written as MDPs) a mathematics framework model is provided, for random in face of part, in the state of can partially being controlled by policymaker,
How decision is carried out.Markovian decision process is five-tuple { S, A, a Pa(s,s′),Ra(s, s '), δ ∈ (0,1) }, wherein
(1) S={ s0,s1,…,snIt is a state set；
(2) A is a behavior aggregate, AsIndicate the acceptable movement in state s；
(3)Ra(s, s ') indicates the probability that state s is converted to state s ' by acting a；
(4)Ra(s, s ') indicates that the reward value that state s is converted to state s ' by acting a, the value are calculated by reward function R
It obtains；
(5) δ is discount factor, it is used to indicate influence of the condition conversion in future to rewarding now.
Markovian decision process has a feature to be exactly between its every two state is all conditional sampling each other, under
One state s ' depends on current state s.Condition conversion each time can all have a reward value to calculate by reward function R
Come, the key problem of Markovian decision process is exactly to find out the maximum scheme of cumulative award value, and π (s) is used to store the program
Middle state s and movement.
Formula 1 illustrates the workflow of Markovian decision process, and π (s) indicates the cumulative award value since state s most
Big scheme, v (s) are cumulative award values, and the movement chosen and state are all determined by π (s).Markovian decision process passes through
The mode of iteration obtains scheme π (s), and in iterative process each time, when state is in s, policymaker can choose all
Available movement, state s can be converted to next state s ', Markovian decision process at random after a certain movement response
The reward value of all condition conversions can be calculated.Meanwhile state converts the probability that can all have oneself each time, in iterative process
In, reward value meeting continuous decrement finally returns to cumulative award value.After all calculated result all returns, markov is determined
Plan process will choose the maximum scheme of cumulative award value.It is the definition of π (s) He v (s) below:
Fig. 6 illustrates the example of a Markovian decision process, shares 4 states, 5 movements and corresponding on the way
Probability and reward value, it is assumed that s0For original state, the available movement a of it only one0, s0It can be by acting a0It is converted to
State s1With state s2, it is converted to state s1Reward value be 0.6*2, be converted to state s2Reward value be 0.4*3.They
Reward value is 1.2, but the former big return of probability is small, and the probability of the latter is small to have high repayment.Then Markovian decision process
Into next iteration, from state s1Or state s2Start.It is not difficult to find out that end-state can be reached there are four types of scheme altogether in figure
s3, calculating compare four kinds of schemes obtain preferred plan be (s0,a0,s2,a2,s3), as shown in Figure 7.
With reference to Fig. 8, the flow chart of optimal solution is solved based on Markovian decision.
Data are first directed to, the data of importing include constraint condition, the reactant for the chemical reaction for needing to occur, generation
Object, reaction time and total amount, the chip overall size of completing chip space, every kind of chemicals that reaction needs；
Then topological relation figure G={ O, P } is established；Topological relation figure generates oriented according to the dependence of chemical reaction
Side, each of figure node are a chemical reaction；
Then it is scanned for from topological relation figure G according to the priority of digraph, judges whether there is and do not carry out also
With the chemical reaction of completion；If so, then therefrom choosing default node carries out Markovian decision, and more according to the result of decision
Then new G is rejudged with the presence or absence of the node not used in G, until there is no the nodes not used in G；
Obtain final G as optimal solution.
S4, according to the optimal solution, control the realization process of biochemical reaction on digital microcurrent-controlled biochip.
The present invention is based on markov decision process, propose a kind of digital microcurrent-controlled biochip CAD
The time-optimized algorithm of layout.The input of location problem is expressed as figure G={ O, P } by we, and G contains all associations of experiment
View, O={ o1,o2,…,on(n >=2) represent the operation set of the experiment, P={ p1,p2,…,pm(n >=2) represent all operations
Between precedence constraints, here be react total time objective function:
s.t.
Wherein n represents operation sum, t (oi) represent each operation oiThe execution time, the medicament a dosage of chemical reaction
For ma, medicament a total amount is Ma, Cx,y∈ { 0,1 } indicates whether chemical reagent can reside in point (x, y), and each operation is worked as
At a module, module projects to x-y plane and has reformed into a rectangle, and the equal position of each rectangle is true by four coordinates
It is fixed.
The embodiment of the present invention is described with above attached drawing, but the invention is not limited to above-mentioned specific
Embodiment, the above mentioned embodiment is only schematical, rather than restrictive, those skilled in the art
Under the inspiration of the present invention, without breaking away from the scope protected by the purposes and claims of the present invention, it can also make very much
Form, all of these belong to the protection of the present invention.
Claims (7)
1. a kind of time-optimized method of digital microcurrent-controlled biochip CAD layout, which is characterized in that include
Following steps:
S1, the model for establishing following four constraint condition:
1) precedence constraints: the priority of chemical reaction define during digital microcurrent-controlled biochip design for not
Biconditional operation executes sequence；
2) resource constraint: ensure that entire series biochemical reaction using each type of chemical agent, is no more than it
The upper limit of resource constraint；
3) it is overlapped constraint condition: ensuring that range of biochemical reaction will not be executed in point at the same time in the same position；
4) confines fluid condition: the minimum spacing between digital microcurrent-controlled biochip drop is defined；
S2, the object module that chain biochemical reaction completes total time on digital microcurrent-controlled biochip is established:
Wherein, { o1,o2,…,onRepresent all operation sets tested, n >=2, t (oi) represent each operation oiExecution when
Between；
S3, it is based on Markovian decision, according to the object module of deadline described in the model solution of four constraint condition
Optimal solution；
S4, according to the optimal solution, control the realization process of biochemical reaction on digital microcurrent-controlled biochip.
2. the time-optimized method of digital microcurrent-controlled biochip CAD layout according to claim 1,
It is characterized in that, the modeling of the precedence constraints specifically includes:
Digraph definition is established according to the relation of interdependence between reactant for a series of chain biochemical reaction
The constraint relationship between biochemical reaction is denoted as G={ O, P }, schemes the O in G, and two parameter definitions of P are as follows:
O={ o1,o2,…,on}: indicate a series of biochemical reaction；
P={ p1,p2,…,pm}: indicate the precedence constraints between two chemical reactions, m >=n.
3. the time-optimized method of digital microcurrent-controlled biochip CAD layout according to claim 1,
It is characterized in that, the modeling of resource constraint specifically includes:
The medicament a dosage of definition chemical reaction is ma, medicament a total amount is Ma, the model of resource constraint are as follows:
4. the time-optimized method of digital microcurrent-controlled biochip CAD layout according to claim 1,
It is characterized in that, the modeling of overlapping constraint condition specifically includes:
Define a Cx,y∈ { 0,1 }: indicating whether chemical reagent can reside in point (x, y), if Cx,y=1, indicate that the point can
To place chemical reagent, it is regarded as a free cells lattice；If Cx,y=0, it indicates that the point is occupied, cannot exist again
From current different chemical reagent；
It is overlapped the model of constraint condition are as follows:
∑x,yCx,y(L)≤1,All reagent L.
5. the time-optimized method of digital microcurrent-controlled biochip CAD layout according to claim 1,
It is characterized in that, the modeling of confines fluid condition specifically includes:
Digital microcurrent-controlled biochip is subjected to blocking, i.e., by digital microcurrent-controlled biochip according to set industrial size mark
Standard is divided into several cells, and the lower left corner of each cell is the starting point of cell, and the coordinate of each cell is respectively with it
It is calculated with the relative position of starting point cell, is denoted as (x, y), on digital microcurrent-controlled biochip, chemical agent is with cell
Move for unit, retain, react, to guarantee to meet confines fluid condition.
6. the time-optimized method of digital microcurrent-controlled biochip CAD layout according to claim 1,
It is characterized in that, step S3 is specifically included:
Establish topological relation figure G={ O, P }；Wherein, topological relation figure generates directed edge according to the dependence of chemical reaction,
Each of figure node is a chemical reaction；
Then scanned for from topological relation figure G according to the priority of digraph, judge whether there is do not carry out also with it is complete
At chemical reaction；If so, then therefrom choosing default node carries out Markovian decision, and G is updated according to the result of decision,
Then it rejudges with the presence or absence of the node not used in G, until there is no the nodes not used in G；
Obtain final G as optimal solution.
7. the time-optimized method of digital microcurrent-controlled biochip CAD layout according to claim 1,
It is characterized in that, minimum spacing described in confines fluid condition in step S1 is a cell on chip.
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| US20110136179A1 (en) * | 2009-10-30 | 2011-06-09 | National Cheng Kung University | Microfluidic biochip |
| CN106934173A (en) * | 2017-03-24 | 2017-07-07 | 哈尔滨工业大学 | Based on the digital microcurrent-controlled chip on-line testing method that TABU search is combined with Artificial Potential Field Method |
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| Publication number | Priority date | Publication date | Assignee | Title |
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| CN112836397A (en) * | 2021-03-30 | 2021-05-25 | 福州大学 | Advanced comprehensive design method for minimizing storage under continuous microfluidic biochip |
| CN112836397B (en) * | 2021-03-30 | 2023-02-21 | 福州大学 | Advanced comprehensive design method for minimizing storage under continuous microfluidic biochip |
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