微流控系统计算机辅助设计软件开发
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摘要
微流控芯片技术,是当前微机电系统发展的热点领域之一。微流控芯片在生化分析、临床疾病诊断和环境检测等领域得到广泛应用,但其设计还主要依靠经验和多次反复设计,迫切需要研究微流控系统的设计方法和CAD工具。本文主要研究微流控系统计算机辅助设计方法,开发了一款具有系统仿真功能的微流控系统计算机辅助设计软件。本文还对微流控芯片结构参数优化问题进行研究,研究了芯片参数与DNA拉伸效果之间的关系;实现了对DNA分离微流控芯片结构参数的优化;开发了基于多核运算平台的并行算法,减少计算时间。
Microfluidic is only a supplementary of the nano-technology revolution at first.After experiencing propagandized wantonly and desolate,it has finally realized the commercialization production. Microfluidic was initially called "lab-on-a-chip" in USA. With the breakthrough progress of material science,micro and nanofabrication technology and microelectronics,Microfluidic has been developed quickly.
The design method of Microfluidic dropped far behind the manufacturing technology.Hitherto there is no Microfluidic CAD tool suitable for all Microfluidic system.Because of lacking Microfluidic CAD tool , developers can only use the software which only suitable for one Microfluidic system,or the commercial CAD tools like CoventorWare,CFD-ACE+ and COMSOL Multiphysics.Then manufacture the prototype directly and determined by experiment,then remodify the parameter according to the result.This method is Time-consuming.
This paper analyses the traditional design method of the Microfluidic,proposes a new CAD design method.using the CAD tool to make the numerical simulation and parameter optimization of the Microfluidic system.Then manufacture the prototype according to the optimization result,this method can reduce the iteration number and shorten the development period.A new software system is presented in this paper.
Recently,the parameter optimization of the Microfluidic system has gradually become research focus.Developers try to improve the performance of the Microfluidic by parameter optimization of the Microfluidic system.In this paper we analyze the parameter optimization of the DNA separation Microfluidic system.Using the CAD tools to simulate the Microfluidic system,and analyze the connection between parameters and the effects of the DNA stretching.then realize the parameter optimization of the DNA separation Microfluidic system.
After the appearance of the computer,people never stop the attempt to improve its calculation speed.Parallel computing is an effective method.In this paper,we analyze the parallel computing,proposed a parallel algorithm based on Multi-Core CPU System,reduce the computing time of the parameter optimization of the DNA separation Microfluidic system.
It is of great importance for scientists and researchers to use The CAD software presented in this paper to increase the efficiency.The optimization method and parallel algorithm can be used to study other Microfluidic systems.
Microfluidic is only a supplementary of the nano-technology revolution at first.After experiencing propagandized wantonly and desolate,it has finally realized the commercialization production. Microfluidic was initially called "lab-on-a-chip" in USA. With the breakthrough progress of material science,micro and nanofabrication technology and microelectronics,Microfluidic has been developed quickly.
The design method of Microfluidic dropped far behind the manufacturing technology.Hitherto there is no Microfluidic CAD tool suitable for all Microfluidic system.Because of lacking Microfluidic CAD tool , developers can only use the software which only suitable for one Microfluidic system,or the commercial CAD tools like CoventorWare,CFD-ACE+ and COMSOL Multiphysics.Then manufacture the prototype directly and determined by experiment,then remodify the parameter according to the result.This method is Time-consuming.
This paper analyses the traditional design method of the Microfluidic,proposes a new CAD design method.using the CAD tool to make the numerical simulation and parameter optimization of the Microfluidic system.Then manufacture the prototype according to the optimization result,this method can reduce the iteration number and shorten the development period.A new software system is presented in this paper.
Recently,the parameter optimization of the Microfluidic system has gradually become research focus.Developers try to improve the performance of the Microfluidic by parameter optimization of the Microfluidic system.In this paper we analyze the parameter optimization of the DNA separation Microfluidic system.Using the CAD tools to simulate the Microfluidic system,and analyze the connection between parameters and the effects of the DNA stretching.then realize the parameter optimization of the DNA separation Microfluidic system.
After the appearance of the computer,people never stop the attempt to improve its calculation speed.Parallel computing is an effective method.In this paper,we analyze the parallel computing,proposed a parallel algorithm based on Multi-Core CPU System,reduce the computing time of the parameter optimization of the DNA separation Microfluidic system.
It is of great importance for scientists and researchers to use The CAD software presented in this paper to increase the efficiency.The optimization method and parallel algorithm can be used to study other Microfluidic systems.
引文
[1]方肇伦.微流控分析芯片的制作和应用[M].北京:化学工业出版社,2005.
[2]林炳承,秦建华.微流控芯片实验室[M].北京:科学出版社,2006.
[3] Staats,Sau Lan Tang.Customized microfluidic device design, ordering, and manufacturing:US,10164022[P].2002-06-06.
[4] LEE Michael,WORTHINGTON Gajus.A MICROFLUIDIC DESIGN AUTOMATION METHOD AND SYSTEM:US,PCT/US2001/020639[P].2002-03-01.
[5] R.H Miyake, Ltd.Microfluidic Design Program:JP,04026273.5[P].2004-05-11.
[6] White.J.CAD challenges in BioMEMS design[C].San Diego:Annual ACM IEEE Design Automation Conference ,2004.
[7] White.J.Developing Design Tools for Biological and Biomedical Applications of Micro- and Nano-technology[C] . Jersey City : International Conference on Hardware Software Codesign ,2005.
[8] Mukherjee. T . Design automation issues for biofluidic microchips[C] . International Conference on Computer Aided Design ,2005.
[9] Fei.S , Chakrabarty.K . System-level design automation tools for digital microfluidic biochips[C].Jersey City:International Conference on Hardware Software Codesign ,2005.
[10] Aditya S , Bedekar . Design Software for Application-Specific Microfluidic Devices[J].Clinical Chemistry,2007,53(11):2023-2026.
[11] Shuang Yang,Jikun Liu,Don L.DeVoe.Optimization of sample transfer in two-dimensional microfluidic separation systems[J].Lab on a Chip,2008(8):1145-1152.
[12]田丽,刘晓为,王蔚,胡自洁.电泳微芯片进样口与微沟道形状的优化设计[J].传感器与微系统,2008,27(10):82-85.
[13]徐溢,吕君江,陆嘉莉,等.电泳芯片结构和芯片电泳分离操作参数的模拟、优化和实验验证[J].分析化学,2006,34(4):437-442.
[14] Fei.S , Chakrabarty.K . Architectural-level synthesis of digital microfluidics-based biochips[C].International Conference on Computer Aided Design,2004.
[15] Tao. X ,Chakrabarty.K.Automated Design of Digital Microfluidic Lab-on-Chip under Pin-Count Constraints[C].Portland:International Symposium on Physical Design ,2008.
[16] ZENG.J,Chakrabarty.K.Design Automation for Microfluidics-Based Biochips[J].Emerging Technologies in Computing Systems,2005,1(3):186-223.
[17] Atalay.Y T,Verboven.P,Vermeir.S.Design optimization of an enzymatic assay in an electrokinetically-driven microfluidic device[J].Microfluidics and Nanofluidics,2008(5):837-849.
[18] FOUILLET Y,JARY D,CHABROL C.Digital microfluidic design and optimization of classic and new fluidic functions for lab on a chip systems[J].Microfluidics and Nanofluidics,2008(4):159-165.
[19] Fei.S,Chakrabarty.K.High-Level Synthesis of Digital Microfluidic Biochips[J].Emerging Technologies in Computing Systems,2008,3(4):16.1-16.32.
[20] Yi Wang,Aditya.S B,Krishnamoorthy.S.System-level modeling and simulation of biochemical assays in lab-on-a-chip devices[J].Microfluidics and Nanofluidics,2006(3):307-322.
[21]杨敬松,左春柽,连静,崔广才.基于数字微流控生物芯片的液滴调度算法[J].吉林大学学报,2008,37(6):1380-1386.
[22] Tianhao Zhang,Krishnendu Chakrabarty,Richard B. Fair.Microelectrofluidic Systems Modeling and Simulation[M].Boca Raton:CRC PRESS,2002.
[23] Streek M,et al.Mechanisms of DNA separation in entropic trap arrays: a Brownian dynamics simulation[J].Biotechnol,2004,11(2):79-89.
[24] Streek M,et al.Two-state migration of DNA in a structured microchannel[J].Phys. Rev. E,2005(71):
[25] Tessier F,et al.Electrophoretic Separation of Long Polyelectrolytes in Submolecular-Size Constrictions: A Monte Carlo Study[J].Macromolecules,2002(35):4791-4800.
[26] Panwar A S,Kumar S.Time Scales in Polymer Electrophoresis through Narrow Constrictions: A Brownian Dynamics Study[J].Macromolecules,2006(39):1279-1289.
[27] Kim J M,Doyle P S.A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields[J] . Journal of Chemical Physics ,2006(125):074906.
[28] Ermak D L,McCammon J A.Brownian dynamics with hydrodynamic interactions[J].Journal of Chemical Physics,1978(69):1352-1360.
[29] Fixman M.Simulation of Polymer Dynamics .1. General Theory[J].Journal of Chemical Physics,1978(69):1527-1537.
[30] Fixman M . Simulation of Polymer Dynamics .2. Relaxation Rates and Dynamic Viscosity[J].Journal of Chemical Physics,1978(69):1538-1545.
[31] Liu T W . Flexible Polymer-Chain Dynamics and Rheological Properties in Steady Flows[J].Journal of Chemical Physics,1989(90):5826-5842.
[32] Zylka W,Ottinger H C.A Comparison between Simulations and Various Approximations for Hookean Dumbbells with Hydrodynamic Interaction[J].Journal of Chemical Physics,1989(90):474-480.
[33] Grassia P S,et al.Computer simulations of Brownian motion of complex systems[J].FluidMech,1995(282):373-403.
[34] Grassia P,Hinch E J.Computer simulations of polymer chain relaxation via Brownian motion[J].Fluid Mech,1996(308):255-288.
[35] Doyle P S,et al.Dynamic simulation of freely draining flexible polymers in steady linear flows[J].Fluid Mech,1997(334):251-291.
[36] Allison S A.Bending and Twisting Dynamics of Short Linear Dnas - Analysis of the Triplet Anisotropy Decay of a 209-Base Pair Fragment by Brownian Simulation[J].Journal of Chemical Physics,1989(90):3843-3854.
[37] Mazur S,Allison S A.Brownian dynamics simulation of DNA fragments in strong electric fields[J].Journal of Physical Chemistry B,1997(101):2244-2250.
[38] Allison S A . Brownian Dynamics Simulation of Wormlike Chains - Fluorescence Depolarization and Depolarized Light-Scattering[J].Macromolecules,1986(19):118-124.
[39] Chirico G,Langowski J.Brownian dynamics simulations of supercoiled DNA with bent sequences[J].Biophysical Journal,1996(71):955-971.
[40] Chirico G,Langowski J.Calculating Hydrodynamic Properties of DNA through a 2Nd-Order Brownian Dynamics Algorithm[J].Macromolecules,1992(25):769-775.
[41] Jian H M,et al.Combined wormlike-chain and bead model for dynamic simulations of long linear DNA[J].Journal of Chemical Physics,1997(136):168-179.
[42] Heath P J,et al..Comparison of analytical theory with Brownian dynamics simulations for small linear and circular DNAs[J].Macromolecules,1996(29):3583-3596.
[43] Huang J,et al.Dynamics of site juxtaposition in supercoiled DNA[J].Proceedings of the National Academy of Sciences of the United States of America,2001(98):968-973.
[44] Huang J,et al.Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion[J].Biophysical Journal,2003(85):804-817.
[45] Wang J,Gao H.A generalized bead-rod model for Brownian dynamics simulations of wormlike chains under strng confinement[J].Journal of Chemical Physics,2005(123):084906.
[46] Jian H M,et al.Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition[J].Journal of Molecular Biology,1998(284):287-296.
[47] Huang J.Macroscopic Modeling and Dynamic Simulations of Supercoiled DNA with Bound Proteins[D].New York :New York University,2003.
[48] Huang J,Schlick T.Macroscopic modeling and simulations of supercoiled DNA with bound proteins[J].Journal of Chemical Physics,2002(117):8573-8586.
[49]文伟力.聚合物微流控芯片的制作、检测及仿真研究[D].长春:吉林大学,2007.
[50]冀封.微流控多尺度现象研究[D].长春:吉林大学,2008.
[51]曹倩倩.新型微收缩组合结构中DNA拉伸动力学研究[D].长春:吉林大学,2007.
[52]邹会旭.基于有限元法的电渗流仿真研究[D].长春:吉林大学,2007.
[53]陈盈.微流控芯片中核小体构象的布朗动力学模拟[D].长春:吉林大学,2006.
[54]孙向东.DNA在微流道中的耗散粒子动力学模拟[D].长春:吉林大学,2007.
[55]郑颢.微流控芯片中的Monte Carlo法应用研究[D].长春:吉林大学,2007.
[56]李璐.纳米颗粒制备及微流的分子动力学模拟研究[D].长春:吉林大学,2008.
[57]朱梦义.介电润湿驱动的数字微流体仿真研究[D].长春:吉林大学,2007.
[58]李红卫.微流控芯片系统级建模研究[D].西安:西北工业大学,2008.
[59] S.Fortune,J.Wyllie.Parallelism in Random Access Machines[J].ACM Symp,1978.114-118.
[60] D.E.Vullrt.LogP:Towards a Realistic Model of Parallel Computation[J].ACM Symp,1993.1-12.
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[2]林炳承,秦建华.微流控芯片实验室[M].北京:科学出版社,2006.
[3] Staats,Sau Lan Tang.Customized microfluidic device design, ordering, and manufacturing:US,10164022[P].2002-06-06.
[4] LEE Michael,WORTHINGTON Gajus.A MICROFLUIDIC DESIGN AUTOMATION METHOD AND SYSTEM:US,PCT/US2001/020639[P].2002-03-01.
[5] R.H Miyake, Ltd.Microfluidic Design Program:JP,04026273.5[P].2004-05-11.
[6] White.J.CAD challenges in BioMEMS design[C].San Diego:Annual ACM IEEE Design Automation Conference ,2004.
[7] White.J.Developing Design Tools for Biological and Biomedical Applications of Micro- and Nano-technology[C] . Jersey City : International Conference on Hardware Software Codesign ,2005.
[8] Mukherjee. T . Design automation issues for biofluidic microchips[C] . International Conference on Computer Aided Design ,2005.
[9] Fei.S , Chakrabarty.K . System-level design automation tools for digital microfluidic biochips[C].Jersey City:International Conference on Hardware Software Codesign ,2005.
[10] Aditya S , Bedekar . Design Software for Application-Specific Microfluidic Devices[J].Clinical Chemistry,2007,53(11):2023-2026.
[11] Shuang Yang,Jikun Liu,Don L.DeVoe.Optimization of sample transfer in two-dimensional microfluidic separation systems[J].Lab on a Chip,2008(8):1145-1152.
[12]田丽,刘晓为,王蔚,胡自洁.电泳微芯片进样口与微沟道形状的优化设计[J].传感器与微系统,2008,27(10):82-85.
[13]徐溢,吕君江,陆嘉莉,等.电泳芯片结构和芯片电泳分离操作参数的模拟、优化和实验验证[J].分析化学,2006,34(4):437-442.
[14] Fei.S , Chakrabarty.K . Architectural-level synthesis of digital microfluidics-based biochips[C].International Conference on Computer Aided Design,2004.
[15] Tao. X ,Chakrabarty.K.Automated Design of Digital Microfluidic Lab-on-Chip under Pin-Count Constraints[C].Portland:International Symposium on Physical Design ,2008.
[16] ZENG.J,Chakrabarty.K.Design Automation for Microfluidics-Based Biochips[J].Emerging Technologies in Computing Systems,2005,1(3):186-223.
[17] Atalay.Y T,Verboven.P,Vermeir.S.Design optimization of an enzymatic assay in an electrokinetically-driven microfluidic device[J].Microfluidics and Nanofluidics,2008(5):837-849.
[18] FOUILLET Y,JARY D,CHABROL C.Digital microfluidic design and optimization of classic and new fluidic functions for lab on a chip systems[J].Microfluidics and Nanofluidics,2008(4):159-165.
[19] Fei.S,Chakrabarty.K.High-Level Synthesis of Digital Microfluidic Biochips[J].Emerging Technologies in Computing Systems,2008,3(4):16.1-16.32.
[20] Yi Wang,Aditya.S B,Krishnamoorthy.S.System-level modeling and simulation of biochemical assays in lab-on-a-chip devices[J].Microfluidics and Nanofluidics,2006(3):307-322.
[21]杨敬松,左春柽,连静,崔广才.基于数字微流控生物芯片的液滴调度算法[J].吉林大学学报,2008,37(6):1380-1386.
[22] Tianhao Zhang,Krishnendu Chakrabarty,Richard B. Fair.Microelectrofluidic Systems Modeling and Simulation[M].Boca Raton:CRC PRESS,2002.
[23] Streek M,et al.Mechanisms of DNA separation in entropic trap arrays: a Brownian dynamics simulation[J].Biotechnol,2004,11(2):79-89.
[24] Streek M,et al.Two-state migration of DNA in a structured microchannel[J].Phys. Rev. E,2005(71):
[25] Tessier F,et al.Electrophoretic Separation of Long Polyelectrolytes in Submolecular-Size Constrictions: A Monte Carlo Study[J].Macromolecules,2002(35):4791-4800.
[26] Panwar A S,Kumar S.Time Scales in Polymer Electrophoresis through Narrow Constrictions: A Brownian Dynamics Study[J].Macromolecules,2006(39):1279-1289.
[27] Kim J M,Doyle P S.A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields[J] . Journal of Chemical Physics ,2006(125):074906.
[28] Ermak D L,McCammon J A.Brownian dynamics with hydrodynamic interactions[J].Journal of Chemical Physics,1978(69):1352-1360.
[29] Fixman M.Simulation of Polymer Dynamics .1. General Theory[J].Journal of Chemical Physics,1978(69):1527-1537.
[30] Fixman M . Simulation of Polymer Dynamics .2. Relaxation Rates and Dynamic Viscosity[J].Journal of Chemical Physics,1978(69):1538-1545.
[31] Liu T W . Flexible Polymer-Chain Dynamics and Rheological Properties in Steady Flows[J].Journal of Chemical Physics,1989(90):5826-5842.
[32] Zylka W,Ottinger H C.A Comparison between Simulations and Various Approximations for Hookean Dumbbells with Hydrodynamic Interaction[J].Journal of Chemical Physics,1989(90):474-480.
[33] Grassia P S,et al.Computer simulations of Brownian motion of complex systems[J].FluidMech,1995(282):373-403.
[34] Grassia P,Hinch E J.Computer simulations of polymer chain relaxation via Brownian motion[J].Fluid Mech,1996(308):255-288.
[35] Doyle P S,et al.Dynamic simulation of freely draining flexible polymers in steady linear flows[J].Fluid Mech,1997(334):251-291.
[36] Allison S A.Bending and Twisting Dynamics of Short Linear Dnas - Analysis of the Triplet Anisotropy Decay of a 209-Base Pair Fragment by Brownian Simulation[J].Journal of Chemical Physics,1989(90):3843-3854.
[37] Mazur S,Allison S A.Brownian dynamics simulation of DNA fragments in strong electric fields[J].Journal of Physical Chemistry B,1997(101):2244-2250.
[38] Allison S A . Brownian Dynamics Simulation of Wormlike Chains - Fluorescence Depolarization and Depolarized Light-Scattering[J].Macromolecules,1986(19):118-124.
[39] Chirico G,Langowski J.Brownian dynamics simulations of supercoiled DNA with bent sequences[J].Biophysical Journal,1996(71):955-971.
[40] Chirico G,Langowski J.Calculating Hydrodynamic Properties of DNA through a 2Nd-Order Brownian Dynamics Algorithm[J].Macromolecules,1992(25):769-775.
[41] Jian H M,et al.Combined wormlike-chain and bead model for dynamic simulations of long linear DNA[J].Journal of Chemical Physics,1997(136):168-179.
[42] Heath P J,et al..Comparison of analytical theory with Brownian dynamics simulations for small linear and circular DNAs[J].Macromolecules,1996(29):3583-3596.
[43] Huang J,et al.Dynamics of site juxtaposition in supercoiled DNA[J].Proceedings of the National Academy of Sciences of the United States of America,2001(98):968-973.
[44] Huang J,et al.Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion[J].Biophysical Journal,2003(85):804-817.
[45] Wang J,Gao H.A generalized bead-rod model for Brownian dynamics simulations of wormlike chains under strng confinement[J].Journal of Chemical Physics,2005(123):084906.
[46] Jian H M,et al.Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition[J].Journal of Molecular Biology,1998(284):287-296.
[47] Huang J.Macroscopic Modeling and Dynamic Simulations of Supercoiled DNA with Bound Proteins[D].New York :New York University,2003.
[48] Huang J,Schlick T.Macroscopic modeling and simulations of supercoiled DNA with bound proteins[J].Journal of Chemical Physics,2002(117):8573-8586.
[49]文伟力.聚合物微流控芯片的制作、检测及仿真研究[D].长春:吉林大学,2007.
[50]冀封.微流控多尺度现象研究[D].长春:吉林大学,2008.
[51]曹倩倩.新型微收缩组合结构中DNA拉伸动力学研究[D].长春:吉林大学,2007.
[52]邹会旭.基于有限元法的电渗流仿真研究[D].长春:吉林大学,2007.
[53]陈盈.微流控芯片中核小体构象的布朗动力学模拟[D].长春:吉林大学,2006.
[54]孙向东.DNA在微流道中的耗散粒子动力学模拟[D].长春:吉林大学,2007.
[55]郑颢.微流控芯片中的Monte Carlo法应用研究[D].长春:吉林大学,2007.
[56]李璐.纳米颗粒制备及微流的分子动力学模拟研究[D].长春:吉林大学,2008.
[57]朱梦义.介电润湿驱动的数字微流体仿真研究[D].长春:吉林大学,2007.
[58]李红卫.微流控芯片系统级建模研究[D].西安:西北工业大学,2008.
[59] S.Fortune,J.Wyllie.Parallelism in Random Access Machines[J].ACM Symp,1978.114-118.
[60] D.E.Vullrt.LogP:Towards a Realistic Model of Parallel Computation[J].ACM Symp,1993.1-12.
[61] Valiant L G.A bridge model for parallel computation[J].Comm.of the ACM,1990,33(8):103-111.
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