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Simulation of biomolecular nanomechanical systems

Record Type:	Electronic resources : Monograph/item
Title/Author:	Simulation of biomolecular nanomechanical systems
Author:	Hagan, Michael Francis.
Description:	143 p.
Notes:	Chair: Arup K. Chakraborty.
Notes:	Source: Dissertation Abstracts International, Volume: 65-02, Section: B, page: 0882.
Contained By:	Dissertation Abstracts International65-02B.
Subject:	Engineering, Chemical.
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3121509
ISBN:	049668860X

Simulation of biomolecular nanomechanical systems
Hagan, Michael Francis.

Simulation of biomolecular nanomechanical systems [electronic resource] - 143 p.

Chair: Arup K. Chakraborty.

Thesis (Ph.D.)--University of California, Berkeley, 2003.

Recent experiments [Fritz et al. Science 2000, 288, 316; Wu et al. Proc. Natl. Acad. Sci. USA 2001, 98, 1560] show that the adsorption of biomolecules on one surface of a microcantilever generates surface stresses that cause the cantilever to deflect. If a second species binds to the adsorbed molecules, the stresses change, resulting in a different deflection. By choosing adsorbed probe molecules that recognize specific molecules, it may be possible to detect pathogens and biohazards. In order to exploit this phenomenon for the development of reliable micro-devices, however, it is necessary to understand the origin of the nanomechanical forces that lead to cantilever deflection upon molecular recognition, as well as the dependence of such deflections on the identity and concentration of the target molecule. We discuss modeling efforts that are aimed toward understanding the kinetics of the processes that generate these forces as well as the resulting dynamical and equilibrium deflections. The predicted equilibrium deflections are strongly dependent on surface properties, suggesting that adsorption must be carefully characterized and controlled.

ISBN: 049668860XSubjects--Topical Terms:

226989
Engineering, Chemical.

Simulation of biomolecular nanomechanical systems
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245 1 0 $a Simulation of biomolecular nanomechanical systems $h [electronic resource]
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500 $a Chair: Arup K. Chakraborty.
500 $a Source: Dissertation Abstracts International, Volume: 65-02, Section: B, page: 0882.
502 $a Thesis (Ph.D.)--University of California, Berkeley, 2003.
520 # $a Recent experiments [Fritz et al. Science 2000, 288, 316; Wu et al. Proc. Natl. Acad. Sci. USA 2001, 98, 1560] show that the adsorption of biomolecules on one surface of a microcantilever generates surface stresses that cause the cantilever to deflect. If a second species binds to the adsorbed molecules, the stresses change, resulting in a different deflection. By choosing adsorbed probe molecules that recognize specific molecules, it may be possible to detect pathogens and biohazards. In order to exploit this phenomenon for the development of reliable micro-devices, however, it is necessary to understand the origin of the nanomechanical forces that lead to cantilever deflection upon molecular recognition, as well as the dependence of such deflections on the identity and concentration of the target molecule. We discuss modeling efforts that are aimed toward understanding the kinetics of the processes that generate these forces as well as the resulting dynamical and equilibrium deflections. The predicted equilibrium deflections are strongly dependent on surface properties, suggesting that adsorption must be carefully characterized and controlled.
520 # $a We model the dynamics of the reaction that leads to the change in cantilever deflection, DNA hybridization/melting, from two viewpoints. First, we combine free energy calculations and molecular dynamics to elucidate a mechanism for DNA base-pair binding and unbinding in atomic detail. Specifically, transition path sampling is used to overcome computational limitations associated with conventional techniques to harvest many trajectories for the flipping of a terminal cytosine in a three base pair oligomer in explicit water. Comparison with free energy projections obtained with umbrella sampling reveals four coordinates that describe the reaction well.
520 # $a We then present both Master equation and rate equation formalisms that connect these microscopic segment-segment binding rates to overall binding rates of surface attached DNA oligomer with solubilized targets. We show that, for surface coverages at which the attached molecules interact, barriers to penetration into the surface layer limit the number of accessible nucleation sites. Depending on surface coverage, molecular length, and location of the binding region on the surface attached chains, this effect can reduce binding rates by one or two orders of magnitude from those in bulk, as seen in experiments.
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791 $a Ph.D.
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