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A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields
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| Zeitschriftentitel: | The Journal of Chemical Physics |
|---|---|
| Personen und Körperschaften: | , |
| In: | The Journal of Chemical Physics, 125, 2006, 7 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
AIP Publishing
|
| Schlagwörter: |
| author_facet |
Kim, Ju Min Doyle, Patrick S. Kim, Ju Min Doyle, Patrick S. |
|---|---|
| author |
Kim, Ju Min Doyle, Patrick S. |
| spellingShingle |
Kim, Ju Min Doyle, Patrick S. The Journal of Chemical Physics A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields Physical and Theoretical Chemistry General Physics and Astronomy |
| author_sort |
kim, ju min |
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Kim, Ju Min Doyle, Patrick S. 0021-9606 1089-7690 AIP Publishing Physical and Theoretical Chemistry General Physics and Astronomy http://dx.doi.org/10.1063/1.2222374 <jats:p>The objective of this work is to develop a numerical method to simulate DNA electrophoresis in complicated geometries. The proposed numerical scheme is composed of three parts: (1) a bead-spring Brownian dynamics (BD) simulation, (2) an iterative solver-enhanced finite element method (FEM) for the electric field, and (3) the connection algorithm between FEM and BD. A target-induced searching algorithm is developed to quickly address the electric field in the complex geometry which is discretized into unstructured finite element meshes. We also develop a method to use the hard-sphere interaction algorithm proposed by Heyes and Melrose [J. Non-Newtonian Fluid Mech. 46, 1 (1993)] in FEM. To verify the accuracy of our numerical schemes, our method is applied to the problem of λ-DNA deformation around an isolated cylindrical obstacle for which the analytical solution of the electric field is available and experimental data exist. We compare our schemes with an analytical approach and there is a good agreement between the two. We expect that the present numerical method will be useful for the design of future microfluidic devices to stretch and∕or separate DNA.</jats:p> A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields The Journal of Chemical Physics |
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| title |
A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| title_unstemmed |
A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| title_full |
A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| title_fullStr |
A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| title_full_unstemmed |
A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| title_short |
A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| title_sort |
a brownian dynamics-finite element method for simulating dna electrophoresis in nonhomogeneous electric fields |
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Physical and Theoretical Chemistry General Physics and Astronomy |
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http://dx.doi.org/10.1063/1.2222374 |
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2006 |
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<jats:p>The objective of this work is to develop a numerical method to simulate DNA electrophoresis in complicated geometries. The proposed numerical scheme is composed of three parts: (1) a bead-spring Brownian dynamics (BD) simulation, (2) an iterative solver-enhanced finite element method (FEM) for the electric field, and (3) the connection algorithm between FEM and BD. A target-induced searching algorithm is developed to quickly address the electric field in the complex geometry which is discretized into unstructured finite element meshes. We also develop a method to use the hard-sphere interaction algorithm proposed by Heyes and Melrose [J. Non-Newtonian Fluid Mech. 46, 1 (1993)] in FEM. To verify the accuracy of our numerical schemes, our method is applied to the problem of λ-DNA deformation around an isolated cylindrical obstacle for which the analytical solution of the electric field is available and experimental data exist. We compare our schemes with an analytical approach and there is a good agreement between the two. We expect that the present numerical method will be useful for the design of future microfluidic devices to stretch and∕or separate DNA.</jats:p> |
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| author | Kim, Ju Min, Doyle, Patrick S. |
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| description | <jats:p>The objective of this work is to develop a numerical method to simulate DNA electrophoresis in complicated geometries. The proposed numerical scheme is composed of three parts: (1) a bead-spring Brownian dynamics (BD) simulation, (2) an iterative solver-enhanced finite element method (FEM) for the electric field, and (3) the connection algorithm between FEM and BD. A target-induced searching algorithm is developed to quickly address the electric field in the complex geometry which is discretized into unstructured finite element meshes. We also develop a method to use the hard-sphere interaction algorithm proposed by Heyes and Melrose [J. Non-Newtonian Fluid Mech. 46, 1 (1993)] in FEM. To verify the accuracy of our numerical schemes, our method is applied to the problem of λ-DNA deformation around an isolated cylindrical obstacle for which the analytical solution of the electric field is available and experimental data exist. We compare our schemes with an analytical approach and there is a good agreement between the two. We expect that the present numerical method will be useful for the design of future microfluidic devices to stretch and∕or separate DNA.</jats:p> |
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| spelling | Kim, Ju Min Doyle, Patrick S. 0021-9606 1089-7690 AIP Publishing Physical and Theoretical Chemistry General Physics and Astronomy http://dx.doi.org/10.1063/1.2222374 <jats:p>The objective of this work is to develop a numerical method to simulate DNA electrophoresis in complicated geometries. The proposed numerical scheme is composed of three parts: (1) a bead-spring Brownian dynamics (BD) simulation, (2) an iterative solver-enhanced finite element method (FEM) for the electric field, and (3) the connection algorithm between FEM and BD. A target-induced searching algorithm is developed to quickly address the electric field in the complex geometry which is discretized into unstructured finite element meshes. We also develop a method to use the hard-sphere interaction algorithm proposed by Heyes and Melrose [J. Non-Newtonian Fluid Mech. 46, 1 (1993)] in FEM. To verify the accuracy of our numerical schemes, our method is applied to the problem of λ-DNA deformation around an isolated cylindrical obstacle for which the analytical solution of the electric field is available and experimental data exist. We compare our schemes with an analytical approach and there is a good agreement between the two. We expect that the present numerical method will be useful for the design of future microfluidic devices to stretch and∕or separate DNA.</jats:p> A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields The Journal of Chemical Physics |
| spellingShingle | Kim, Ju Min, Doyle, Patrick S., The Journal of Chemical Physics, A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields, Physical and Theoretical Chemistry, General Physics and Astronomy |
| title | A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| title_full | A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| title_fullStr | A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| title_full_unstemmed | A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| title_short | A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| title_sort | a brownian dynamics-finite element method for simulating dna electrophoresis in nonhomogeneous electric fields |
| title_unstemmed | A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields |
| topic | Physical and Theoretical Chemistry, General Physics and Astronomy |
| url | http://dx.doi.org/10.1063/1.2222374 |