Simulation of F-actin filaments of several microns

Dengming Ming, Yifei Kong, Yinghao Wu, Jianpeng Ma

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Here we report the results of applying substructure synthesis method to the simulation of F-actin filaments of several microns in length. The elastic deformational modes of long F-actin filaments were generated from the vibrational modes of the 13-subunit repeat of F-actin using a hierarchical synthesis scheme. The computationally synthesized deformational modes, in the very low-frequency regime, are in good agreement with theoretical solutions for long homogeneous elastic rods, which confirmed the usefulness of substructure synthesis method. Other low-frequency modes carry rich local deformational features that are unique to F-actins. All these modes thus provide a theoretical basis set for a description of spontaneously occurring thermal deformations, such as undulations, of the filaments. The results demonstrate that substructure synthesis method, as a method for computational modal analysis, is capable of scaling up the microscopic dynamic information, obtained from atomistic simulations, to a wide range of macroscopic length scale. Moreover, the combination of substructure synthesis method and hierarchical synthesis scheme provides an effective way in dealing with complex systems of periodic repeats that are abundant in cells.

Original languageEnglish (US)
Pages (from-to)27-35
Number of pages9
JournalBiophysical Journal
Volume85
Issue number1
StatePublished - Jul 1 2003
Externally publishedYes

Fingerprint

Actin Cytoskeleton
Actins
Hot Temperature

ASJC Scopus subject areas

  • Biophysics

Cite this

Ming, D., Kong, Y., Wu, Y., & Ma, J. (2003). Simulation of F-actin filaments of several microns. Biophysical Journal, 85(1), 27-35.

Simulation of F-actin filaments of several microns. / Ming, Dengming; Kong, Yifei; Wu, Yinghao; Ma, Jianpeng.

In: Biophysical Journal, Vol. 85, No. 1, 01.07.2003, p. 27-35.

Research output: Contribution to journalArticle

Ming, D, Kong, Y, Wu, Y & Ma, J 2003, 'Simulation of F-actin filaments of several microns', Biophysical Journal, vol. 85, no. 1, pp. 27-35.
Ming, Dengming ; Kong, Yifei ; Wu, Yinghao ; Ma, Jianpeng. / Simulation of F-actin filaments of several microns. In: Biophysical Journal. 2003 ; Vol. 85, No. 1. pp. 27-35.
@article{6bb653e452564f7ba98046800f253b19,
title = "Simulation of F-actin filaments of several microns",
abstract = "Here we report the results of applying substructure synthesis method to the simulation of F-actin filaments of several microns in length. The elastic deformational modes of long F-actin filaments were generated from the vibrational modes of the 13-subunit repeat of F-actin using a hierarchical synthesis scheme. The computationally synthesized deformational modes, in the very low-frequency regime, are in good agreement with theoretical solutions for long homogeneous elastic rods, which confirmed the usefulness of substructure synthesis method. Other low-frequency modes carry rich local deformational features that are unique to F-actins. All these modes thus provide a theoretical basis set for a description of spontaneously occurring thermal deformations, such as undulations, of the filaments. The results demonstrate that substructure synthesis method, as a method for computational modal analysis, is capable of scaling up the microscopic dynamic information, obtained from atomistic simulations, to a wide range of macroscopic length scale. Moreover, the combination of substructure synthesis method and hierarchical synthesis scheme provides an effective way in dealing with complex systems of periodic repeats that are abundant in cells.",
author = "Dengming Ming and Yifei Kong and Yinghao Wu and Jianpeng Ma",
year = "2003",
month = "7",
day = "1",
language = "English (US)",
volume = "85",
pages = "27--35",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "1",

}

TY - JOUR

T1 - Simulation of F-actin filaments of several microns

AU - Ming, Dengming

AU - Kong, Yifei

AU - Wu, Yinghao

AU - Ma, Jianpeng

PY - 2003/7/1

Y1 - 2003/7/1

N2 - Here we report the results of applying substructure synthesis method to the simulation of F-actin filaments of several microns in length. The elastic deformational modes of long F-actin filaments were generated from the vibrational modes of the 13-subunit repeat of F-actin using a hierarchical synthesis scheme. The computationally synthesized deformational modes, in the very low-frequency regime, are in good agreement with theoretical solutions for long homogeneous elastic rods, which confirmed the usefulness of substructure synthesis method. Other low-frequency modes carry rich local deformational features that are unique to F-actins. All these modes thus provide a theoretical basis set for a description of spontaneously occurring thermal deformations, such as undulations, of the filaments. The results demonstrate that substructure synthesis method, as a method for computational modal analysis, is capable of scaling up the microscopic dynamic information, obtained from atomistic simulations, to a wide range of macroscopic length scale. Moreover, the combination of substructure synthesis method and hierarchical synthesis scheme provides an effective way in dealing with complex systems of periodic repeats that are abundant in cells.

AB - Here we report the results of applying substructure synthesis method to the simulation of F-actin filaments of several microns in length. The elastic deformational modes of long F-actin filaments were generated from the vibrational modes of the 13-subunit repeat of F-actin using a hierarchical synthesis scheme. The computationally synthesized deformational modes, in the very low-frequency regime, are in good agreement with theoretical solutions for long homogeneous elastic rods, which confirmed the usefulness of substructure synthesis method. Other low-frequency modes carry rich local deformational features that are unique to F-actins. All these modes thus provide a theoretical basis set for a description of spontaneously occurring thermal deformations, such as undulations, of the filaments. The results demonstrate that substructure synthesis method, as a method for computational modal analysis, is capable of scaling up the microscopic dynamic information, obtained from atomistic simulations, to a wide range of macroscopic length scale. Moreover, the combination of substructure synthesis method and hierarchical synthesis scheme provides an effective way in dealing with complex systems of periodic repeats that are abundant in cells.

UR - http://www.scopus.com/inward/record.url?scp=0037636333&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0037636333&partnerID=8YFLogxK

M3 - Article

C2 - 12829461

AN - SCOPUS:0037636333

VL - 85

SP - 27

EP - 35

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 1

ER -