The deformation of biological macroparticles such as DNA and proteins in a flow has been a subject of great important in the last decade due to the interest in single molecule analysis. In this paper, a multiscale numerical method was used to analyze deformation of biological macroparticles in uniform flows. To bridge the gap between huge scale differences between the protein dynamics (in Pico scales) and the underlying hydrodynamics (from nano to micro scales), a hybrid coarse-grained model is coupled with the continuum Navier-Stokes solver. Based on the Go¯-type modeling, biological dynamics is governed by the Langevin equation for which the biological macroparticles are represented by a collection of micro-sized spherical beads that are tethered by harmonic potentials. The velocity vector is coupled through the friction factors, which are amino acid dependent, in the stochastic Langevin equation. With this model, simulation results show that flow may stretch biological macroparticles to partially unravel stationary conformations that depend on the flow rate and on the terminus which is anchored. These features potentially offer richer diagnostic results to investigate biological macroparticles configuration process, as compared to force clamp results using AFM.
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2008 Second International Conference on Integration and Commercialization of Micro and Nanosystems
June 3–5, 2008
Clear Water Bay, Kowloon, Hong Kong
Conference Sponsors:
- Nanotechnology Institute
ISBN:
0-7918-4294-0
PROCEEDINGS PAPER
Multiscale Modeling of Protein Stretching in Nanofluidic Flows
Zhi Yang,
Zhi Yang
University of Alabama - Huntsville, Huntsville, AL
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C. P. Chen,
C. P. Chen
University of Alabama - Huntsville, Huntsville, AL
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Z. J. Chen,
Z. J. Chen
CFD Research Corporation, Huntsville, AL
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C. C. Chieng
C. C. Chieng
National Tsing-Hua University, Hsinchu, Taiwan
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Zhi Yang
University of Alabama - Huntsville, Huntsville, AL
C. P. Chen
University of Alabama - Huntsville, Huntsville, AL
Z. J. Chen
CFD Research Corporation, Huntsville, AL
C. C. Chieng
National Tsing-Hua University, Hsinchu, Taiwan
Paper No:
MicroNano2008-70027, pp. 467-472; 6 pages
Published Online:
June 12, 2009
Citation
Yang, Z, Chen, CP, Chen, ZJ, & Chieng, CC. "Multiscale Modeling of Protein Stretching in Nanofluidic Flows." Proceedings of the 2008 Second International Conference on Integration and Commercialization of Micro and Nanosystems. 2008 Second International Conference on Integration and Commercialization of Micro and Nanosystems. Clear Water Bay, Kowloon, Hong Kong. June 3–5, 2008. pp. 467-472. ASME. https://doi.org/10.1115/MicroNano2008-70027
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