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Mechanics of biomolecules: A hierarc...

Columbia University.

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Mechanics of biomolecules: A hierarchical study.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Mechanics of biomolecules: A hierarchical study./
Author:	Tang, Yuye.
Description:	197 p.
Notes:	Source: Dissertation Abstracts International, Volume: 69-05, Section: B, page: 3079.
Contained By:	Dissertation Abstracts International69-05B.
Subject:	Applied Mechanics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3317622
ISBN:	9780549658429

Mechanics of biomolecules: A hierarchical study.
Tang, Yuye.

Mechanics of biomolecules: A hierarchical study. - 197 p.

Source: Dissertation Abstracts International, Volume: 69-05, Section: B, page: 3079.

Thesis (Ph.D.)--Columbia University, 2008.

Many fundamentally important biological processes rely on the mechanical response of biomolecules and their assemblies, which span a large range of length-scales and time-scales. We develop a novel hierarchical computational method for mechanobiology, the molecular dynamics decorated finite element method, MDeFEM, to address such emerging challenge with application to study the gating of Mechanosensitive (MS) channels. Multiple scales are bridged using the MDeFEM protocol in which the most important components of the channels will be modeled as continuum objects, yet their mechanical/physical properties, as well as their interactions are be derived from atomistic simulations; the conformational response of a macromolecule to external mechanical perturbations will be simulated using finite element (FEM) analyses.

ISBN: 9780549658429Subjects--Topical Terms:

1018410
Applied Mechanics.

Mechanics of biomolecules: A hierarchical study.
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008 100701s2008 ||||||||||||||||| ||eng d
020 $a 9780549658429
035 $a (UMI)AAI3317622
035 $a AAI3317622
040 $a UMI $c UMI
100 1 $a Tang, Yuye. $3 1019144
245 1 0 $a Mechanics of biomolecules: A hierarchical study.
300 $a 197 p.
500 $a Source: Dissertation Abstracts International, Volume: 69-05, Section: B, page: 3079.
502 $a Thesis (Ph.D.)--Columbia University, 2008.
520 $a Many fundamentally important biological processes rely on the mechanical response of biomolecules and their assemblies, which span a large range of length-scales and time-scales. We develop a novel hierarchical computational method for mechanobiology, the molecular dynamics decorated finite element method, MDeFEM, to address such emerging challenge with application to study the gating of Mechanosensitive (MS) channels. Multiple scales are bridged using the MDeFEM protocol in which the most important components of the channels will be modeled as continuum objects, yet their mechanical/physical properties, as well as their interactions are be derived from atomistic simulations; the conformational response of a macromolecule to external mechanical perturbations will be simulated using finite element (FEM) analyses.
520 $a To demonstrate the potential of the MDeFEM method, we explore the detailed gating mechanisms of the MscL in bacteria (such as E. coli) embedded in a palmitoyloleoylphosphatidylethanolamine (POPE) lipid bilayer. The gating pathways of E. coli-MscL channels under various basic deformation modes are simulated. Upon equibiaxial tension, the MDeFEM results agree well with both experiments and all-atom simulations in literature. Different levels of model sophistication and effects of structural motifs are explored in detail, where the importance of mechanical roles of transmembrane helices, cytoplasmic helices and loops are discussed. The conformation transitions under complex membrane deformations are predicted, including bending, torsion, co-operativity, patch clamp and indentation.
520 $a In addition, analytical closed-form continuum model and elastic network model are established to complement the MDeFEM approach and to capture some of the most essential features of gating, as well as provide useful limits. Their effectiveness is verified via the comparison with MDeFEM approach.
520 $a The MDeFEM framework is uniquely suited for simulating complex deformations at large length scales seen in biological systems, which is one of the grand challenges of computational science. Insights obtained from MS channels in this study will be highly relevant in understanding a host of other biomolecular systems. It is envisioned that such a hierarchical multiscale framework will find great value in the study of a variety of biological processes involving complex mechanical deformations such as muscle contraction and mechanotransduction.
590 $a School code: 0054.
650 4 $a Applied Mechanics. $3 1018410
650 4 $a Biophysics, General. $3 1019105
690 $a 0346
690 $a 0786
710 2 $a Columbia University. $3 571054
773 0 $t Dissertation Abstracts International $g 69-05B.
790 $a 0054
791 $a Ph.D.
792 $a 2008
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3317622