ISSN Print: 1543-1649
ISSN Online: 1940-4352
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International Journal for Multiscale Computational Engineering
STOCHASTIC MODELING OF MACROMOLECULAR MOTIONS THROUGH POST ARRAYS
Department of Mechanical and Materials Engineering, University of Denver, Denver, Colorado 80208, USA
The dynamic motions of macromolecules through a microfluidic postarray system are simulated using a three-dimensional stochastic finite element approach. The effects of molecular conformation on the time for a macromolecule to move across the system are investigated. The analyses are first performed on disklike geometries and then extended to a representative carbonic anhydrase (CA) macromolecule model consisting of elastically deformable beam networks. The model predicts that smaller molecules typically take less time to pass through the post array, and that for stiff materials the time inversely increases with the aspect ratio of molecules due to the conformational changes in collisions between the molecules and the obstacles. In addition, the dynamic responses of molecules are highly stochastic. The work has potential applications in designing functional microfluidic devices for separation and purification of macromolecules such as plasmid DNA.
Bakajin, O., Duke, T. A. J., Tegenfeldt, J., Chou, C. F., Chan, S. S., Austin, R. H., and Cox, E. C.,
Separation of 100-kilobase DNA molecules in 10 seconds.
Berhan, L., Yi, Y. B., Sastry, A. M., Munoz, E., Selvidge, M., and Baughman, R.,
Mechanical properties of nanotube sheets: Alterations in joint morphology and achievable moduli in manufacturable materials.
Berhan, L., Yi, Y. B., and Sastry, A. M.,
Effect of nanorope waviness on the effective moduli of nanotube sheets.
Cabodi, M., Turner, S. W. P., and Craighead, H. G.,
Entropic recoil separation of long DNA molecules.
Chou, C. F., Bakajin, O., Turner, S. W. P., Duke, T. A. J., Chan, S. S., Cox, E. C., Craighead, H. G., and Austin, R. H.,
Sorting by diffusion: An asymmetric obstacle course for continuous molecular separation.
Cole, K. D., Tellez, C. M., and Blakesley, R. W.,
Separation of different physical forms of plasmid DNA using a combination of low electric field strength and flow in porous media: Effect of different field gradients and porosity of the media.
Cole, K. D. and Tellez, C. M.,
Separation of large circular DNA by electrophoresis in agarose gels.
Fish, J. and Shek, K.,
Multiscale analysis of composite materials and structures.
Bridging the scales in nano engineering and science.
Fish, J. and Fan, R.,
Mathematical homogenization of nonperiodic heterogeneous media subjected to large deformation transient loading.
Fish, J. and Wu, W.,
A nonintrusive stochastic multiscale solver.
Foquet, M., Korlach, J., Zipfel, W., Webb, W. W., and Craghead, H. G.,
DNA fragment sizing by single molecule detection in submicrometer-sized closed fluidic channels.
Han, J. and Craighead, H. G.,
Separation of long DNA molecules in a microfabricated entropic trap array.
Huang, C. C., Lesburg, C. A., Kiefer, L. L., Fierke, C. A., and Christianson, D. W.,
Reversal of the hydrogen bond to zinc ligand histidine-119 dramatically diminishes catalysis and enhances metal equilibration kinetics in carbonic anhydrase II.
Huang, L. R., Tegenfeldt, J. O., and Kraeft, J. A.,
DNA prism for high-speed continuous fractionation of large DNA molecules.
Hur, J. S. and Shaqfeh, E. S. G.,
Dynamics of dilute and semidilute DNA solutions in the start-up of shear flow.
Jendrejack, R. M., Dimalanta, E. T., Schwartz, D. C., Graham, M. D., and de Pablo, J. J.,
DNA dynamics in a microchannel.
Kaji, N., Tezuka, Y., Takamura, Y., Ueda, M., Nishimoto, T., Nakanishi, H., Horiike, Y., and Baba, Y.,
Separation of long DNA molecules by quartz nanopillar chips under a direct current electric field.
Mirny, L. and Shakhnovich, E.,
Protein folding theory: From lattice to all-atom models.
Onuchic, J. N., Lutheyschulten, Z., and Wolynes, P. G.,
Theory of protein folding: The energy landscape perspective.
Prazeres, D. M. F. and Ferreira, G. N. M.,
Design of flow sheets for the recovery and purification of plasmids for gene therapy and DNA vaccination.
Rzehak, R., Kromen, W., Kawakatsu, T., and Zimmerman, W.,
Deformation of a tethered polymer in uniform flow.
Shea, J. E. and Brooks, C. L.,
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding.
Turner, S. W. P., Cabodi, M., and Craighead, H. G.,
Confinement-induced entropic recoil of single DNA molecules in a nanofluidic structure.
Yi, Y. B., Berhan, L., and Sastry, A. M.,
Statistical geometry of random fibrous networks, revisited: Waviness, dimensionality, and percolation.
Yi, Y. B. and Lengsfeld, C. S.,
Mechanical modeling of carbonic anhydrase motion in simple channels.
Yuan, Z. and Fish, J.,
Toward realization of computational homogenization in practice.
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