In this study, the behavior of the DNA chain stretched at the RB-PCR reactor is predicted by the 2D simulation. In practice, the DNA chain is replicated in a 3D RB-PCR reactor.
Sine our simulation is performed at the 2D computational domain, the behavior of the DNA chain is not fully observed. If we want to further realize the behavior of the DNA chain in the replication in actual situations, the results of this study are not enough.
Therefore, considering the DNA chain stretched at the 3D computational domain can be implemented to get the available results for DNA research in the future studies.
[1] Perkins, T. T., Smith, D. E., Larson, R. G. and Chu, S., 1995, Stretching of a single tethered polymer in a uniform flow. Science 268, 83-87.
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[3] Jo, K., Chen, Y. L., de Pablo, J. J. and Schwartz, D. C., 2009, Elongation and migration of single DNA molecules in microchannels using oscillatory shear flows.
The Royal Society of Chemistry 9, 2348-2355.
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L 22.4 µm 34.8 µm 44.0 µm
L/1.37 16.4 µm 25.4 µm 32.1 µm
< R2 >0 1.62 pm 2.53 pm 3.20 pm
n 48502 base 74710 base 94461 base
NS 9 9 9
m 2.67E-21 kg 4.11E-21 kg 5.19E-21 kg
RS 4.17E-7 m 5.26E-7 m 5.89E-7 m
H 3.09E-10 kg/s2 1.94E-10 kg/s2 1.54E-10 kg/s2
ξ 1.31E-10 kg/s 1.50E-10 kg/s 1.63E-10 kg/s
Case study Uniform flow RB-PCR
Working fluid Aqueous glycerin solution (3%) Pure water
ρ 1007.10 kg/m3 978.79 kg/m3
ν 9.52E-7 m2/s ν=f(T )
Tref 298.15 K 340.50 K
α 1.62E-7 m2/s
β 5.68E-4 1/K
Temperature(K) ν(m2/s)
283 1.31E-6
293 1.00E-6
303 8.01E-7
313 6.58E-7
323 5.54E-7
333 4.75E-7
343 4.13E-7
353 3.65E-7
363 3.26E-7
373 2.94E-7
383 2.68E-7
Bead-rod model:
(Proposed by Kuhn)
Bead-spring model:
(Proposed by Larson)
L
≈ ≈
<R2>0
≈
≈
≈ ≈ ≈ ≈
<R2>0
<R2>0
L
L Second scaling process
First scaling process
Figure 1: The mean-square end-to-end distance and fully extended length of a real DNA, bead-rod model and bead-spring model.
Obtain flow solutions including u, P and T using CFD-ACE+
End of simulation
Obtain Fidragand Fispringfor the bead-spring model and
determine rinusing Langevin Eq.
Determine the extension,
Implement semi-implicit Euler method : rin+1
Figure 2: Flowchart of the simulation of DNA stretching.
Laser Lens
OpticalTweezers
Fixed by optical tweezers DNA
Flow cell installed on a motor
Movement of flow cell z
x
y x
DNA
Uniform flow
(a)
(b)
Figure 3: (a)Schematic of Perkins et al.’s [1] experiment. (b) Horizontal plane.
Length
Width
Inlet Outlet
Symmetry
Length = 26, 36, 46 μm Width = 12 μm
Bead of the bead-spring model :
Figure 4: Computational domain and boundary conditions of the simulation of the uniform flow field.
(b)
(c)
Figure 5: The DNA chain of L=44.0 µm and flow pattern while inlet velocity is equal to 5.96E-6 m/s.
(a) t=0.0 s, (b) t=3.5 s and (c) t=7 s when the steady state is reached.
t
Inlet velocity = 2.20E-5 m/s Inlet velocity = 8.25E-5 m/s
(m)
Figure 6: Time history of extension of the DNA chain of L=44.0 µm at various inlet velocities.
t
Extension / t = 2.21E-5d d
Figure 7: Time history of extension of the DNA chains of various L at the inlet velocity 2.00E-5 m/s.
Inlet velocity
0 2E-05 4E-05 6E-05 8E-05
0 5E-06 1E-05 1.5E-05 2E-05 2.5E-05
22.4 m - Perkins 34.8 m - Perkins 44.0 m - Perkins 22.4 m - Present study 34.8 m - Present study 44.0 m - Present study (m)
(m/s)
µ µ µ µ µ µ
L
DFigure 8: Comparison of extension between the present study and Perkins et al.’s [1] experiment.
Inlet velocity
0 2E-05 4E-05 6E-05 8E-05
0 5 10 15 20
34.8 m 44.0 m
(m/s) (%)
µ µ
Difference percentage
Figure 9: Difference percentage of extension between the present study and Perkins et al.’s [1]
experiment.
Figure 10: Three steps of RB-PCR. In the denaturation, the double-strand DNA chain is divided into two single-strand DNA chains at T =367 K. Subsequently, the annealing is performed at T =328 K while
the forward and backward primers connect to the DNA chain. In the extension, the dNTP are mated with the DNA chain to produce a new double-strand DNA chain at T =345 K. The DNA chain is
amplified after one cycle of the RB-PCR.
Length
Width
Length = 300 μm Width = 300 μm
Bead of the bead-spring model :
Isothermal wall at T = 383 K
Adiabatic wall Adiabatic wall
Figure 11: Computational domain and boundary conditions of the simulation of the RB-PCR reactor.
x
0 0.0001 0.0002 0.0003
0 5E-05 0.0001 0.00015 0.0002 0.00025
4.2E-05 3.8E-05 3.4E-05 3.0E-05 2.6E-05 2.2E-05 1.8E-05 1.4E-05 1.0E-05 6.0E-06 2.0E-06
(m)
y
(m)Figure 12: Streamline and velocity magnitude contours of the RB-PCR reactor.
Zoom factor = x50
i
i Zoom factor = x220
Zoom factor = x220 (a)
(b)
(c)
B1
B1
B1
Figure 13: Behavior of the DNA chain of L=44 µm and flow pattern at various time. The left column revels the velocity contours of the fluid flow and the position of the DNA chain at the RB-PCR reactor.
The right column displays the behavior of the DNA chain. (a) t=0.0 s,(b) t=4.0 s, (c) t=7.8 s, (d) t=12.5 s and (e) t=17.0 s.
i
Zoom factor = x220 (d)
(e)
B1
B1
Zoom factor = x220
Figure 13: (Continued)
t
0 5 10 15
0 1E-06 2E-06 3E-06 4E-06 5E-06
(s)
Extension
(m)
t
0 5 10 15
0 0.05 0.1 0.15 0.2
(s)
Extension/L
(%)
Figure 14: Time history of the extension of the DNA chain at the RB-PCR reactor. (Inset) Time history of the fractional extension of the DNA chain.
t
0 5 10 15
0 20 40 60 80 100 120 140 160
(s) θ
θ DNA
x
B1 B5
Figure 15: Time history of the angle between the DNA chain and the horizontal direction. (Inset) Schematic diagram of the θ of the DNA chain.
t
0 5 10 15
0 1E-07 2E-07 3E-07 4E-07 5E-07 6E-07
7E-07 S2
S3 S4 S5 S6 S7 S8 S9
(s) (m)
2a
S
iFigure 16: Time history of the length of each spring.
t
0 5 10 15
0 20 40 60 80 100
F1 F2drag F3drag F4drag F5drag F6drag F7drag F8drag F9drag F10drag
(s)
F
idrag(aN)Figure 17: Time history of the hydrodynamic drag applied on each bead.
t
Figure 18: Time history of the velocity of each bead.
國科會補助專題研究計畫項下出席國際學術會議心得報告
計畫編號 NSC 99－2221－E－011－041－
計畫名稱 對流型聚合酵素連鎖反應器內之基因拉伸研究 (英文)Marine Tech Summit 2010
發表論文 題目
(中文)非預先描述固體在流體中之運動數值模擬
(英文) Numerical modeling of unprescribed solid motion in fluids
二、與會心得
本次會議參與人數眾多，約有兩百多位來自學界與產業界。顯見各界對海洋能源發 展之關心，台灣雖四面環海，但明顯的在海洋能源的開發與應用基本上是不足。而 海洋能源發展不僅是技術問題，其實還包括生態與經濟議題。因此各國目前開發海 洋能源不僅僅從技術上是否可以從海洋取得能源來探討而是包含對環境的影響及是 否能夠普及來研究。因此台灣若要發展海洋方面的能源工業，這些經驗都可用來借 鏡參考。
三、考察參觀活動(無是項活動者略) 無此項活動
四、建議
本次參加之會議參與者廣泛，且皆為各國最好的研究機構之人員。建議將來對海洋 能源或海洋工程有興趣之學者可以參與此項會議。
五、攜回資料名稱及內容
2010 國際海洋技術大會論文集一本 六、其他
主持人攝於 Marine Tech Summit 2010 會場前
主持人攝於演講前
Title: Numerical modeling of unprescribed solid motion in fluids
Dr. Ming-Jyh Chern*, Dedy Zulhidayat Noor and Tzyy-Leng Horng
Abstract
An immersed boundary method with both virtual force and virtual heat is developed to solve the Navier-Stokes and the energy transport equations to study convection problems caused by a moving rigid solid object in an enclosure. The key point of this novel numerical method is that the solid object, stationary or moving, is first treated as fluids governed by the Navier-Stokes equations for velocity and pressure, and by the energy transport equation at each time step. Subsequently, an additional virtual force term is then compensated to the right hand side of momentum equations at the solid object region to make it acting
mechanically like a solid rigid body immersed in fluid exactly. Likewise, an additional virtual heat source term is applied to the right hand side of energy equation at the solid object region to maintain the solid object at the prescribed temperature all the time.
The proposed method is validated by a group of benchmark forced and natural convection problems such as a uniform flow past a heated circular cylinder and a heated circular cylinder inside a square enclosure. We further demonstrate this method by studying a mixed convection problem involving a heated circular cylinder moving inside a square enclosure. The established method avoids the requested grid generation in the body-fitted method at each time step and shows great efficiency in the computation of thermal and flow fields caused by fluid-structure interactions.
Biography
Ming-Jyh Chern received his first and master degrees from Department of Naval Architecture Engineering., National Taiwan University. Subsequently, he was awarded a government scholarship for studying abroad. He went to University of Oxford to pursue his PhD. He was supervised by Prof. Eatock Taylor and Prof. Borthwick. During his study at University Oxford, he developed a pseudospectral model to simulate the interaction of steep waves with offshore structures. After he finished his PhD study, he returned to Taiwan and initiated research academic activity at National Taiwan University of Science and Technology to study free surface flows, industrial ventilation, biofluid dynamics, energy saving in buildings and advanced numerical methods for
computational fluid dynamics. His research results have been published in several international journals, such as Journal of Fluids Engineering, Journal of Biomechanics, International Journal of Heat and Mass Transfer and etc.
Full Name: Dr. Ming-Jyh CHERN Title: Associate Professor,
Department: Mechanical Engineering
Organization: National Taiwan University of Science and Technology, Country: Taiwan
E-mail: [email protected]
Thank you for your acceptance to be a speaker at MarineTech Summit (MTS-2010), which will be held during October 26-28, 2010 in Dalian, China. I am sending the formal confirmation letter to you. You are welcome to join us with the other outstanding scientists.
Hereby, the organizing committee of MTS-2010 is to confirm that Dr. Ming Jyh Chern is a speaker at MarineTech Summit (MTS-2010).
To enable smooth meeting, we need to collect electronic copy of your presentation to us. This ensures your file is well compatible with the projector & computer system. To do so, please send your presentation attached in PowerPoint by email to us by the deadline of Sept. 30, 2010. Meanwhile, please send your itinerary by email at: [email protected] before Sept. 30 so that the organizing committee can manage the itinerary.
If you have any other questions about the meeting, please feel free to contact me at Tel:
0086-411-84799609-813, Fax: 0086-411-84799629, or email at: [email protected]
Sincerely yours,
Dr. Xiaodan Mei
Executive Chair of MTS-2010 The Organizing Commission of MTS-2010
Contacts: Debra Zhao, Tel: 0086-411-84799609-813 Email: [email protected]
國科會補助計畫
計畫名稱: 對流型聚合酵素連鎖反應器內之基因拉伸研究 計畫主持人: 陳明志
計畫編號: 99-2221-E-011-041- 學門領域: 熱傳學、流體力學
無研發成果推廣資料
計畫主持人：陳明志 計畫編號：99-2221-E-011-041-
(無法以量化表達之成
請就研究內容與原計畫相符程度、達成預期目標情況、研究成果之學術或應用價