Direct Numerical Simulation of Single-Molecule DNA by Cable Dynamics

Zhu, Qiang; Zeng, Jun; Triantafyllou, Michael S.; Yue, Dick K. P.

doi:10.1109/jmems.2006.880238

Cited by 5 publications

(5 citation statements)

References 34 publications

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“…The translational drag coefficients are only weakly dependent upon L for L >> d and therefore the formulation above provides a reasonable approximation for drag. A similar approximation is described in Zhu et al (49). As with the electrostatic force, these drag relations contribute to the external forces and moments (F body and Q body ) in the governing equations (Eqs.…”

Section: Review Of Rod Model (3132)mentioning

confidence: 86%

A Multiscale Dynamic Model of DNA Supercoil Relaxation by Topoisomerase IB

Lillian

Taranova

Wereszczynski

et al. 2011

Biophysical Journal

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In this study, we report what we believe to be the first multiscale simulation of the dynamic relaxation of DNA supercoils by human topoisomerase IB (topo IB). We leverage our previous molecular dynamics calculations of the free energy landscape describing the interaction between a short DNA fragment and topo IB. Herein, this landscape is used to prescribe boundary conditions for a computational, elastodynamic continuum rod model of a long length of supercoiled DNA. The rod model, which accounts for the nonlinear bending, twisting, and electrostatic interaction of the (negatively charged) DNA backbone, is extended to include the hydrodynamic drag induced by the surrounding physiological buffer. Simulations for a 200-bp-long DNA supercoil in complex with topo IB reveal a relaxation timescale of ∼0.1-1.0 μs. The relaxation follows a sequence of cascading reductions in the supercoil linking number (Lk), twist (Tw), and writhe (Wr) that follow companion cascading reductions in the supercoil elastic and electrostatic energies. The novel (to our knowledge) multiscale modeling method may enable simulations of the entire experimental setup that measures DNA supercoiling and relaxation via single molecule magnetic trapping.

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Section: Review Of Rod Model (3132)mentioning

confidence: 86%

A Multiscale Dynamic Model of DNA Supercoil Relaxation by Topoisomerase IB

Lillian

Taranova

Wereszczynski

et al. 2011

Biophysical Journal

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“…To calculate the transient behavior of a polymer using the WLC description, a direct numerical simulation cable-dynamics model has been developed (50). Essentially a WLC model in time domain, this model depicts the biopolymer as an elastic cable that can be bent and twisted with finite curvature everywhere.…”

Section: Appendix: Tension-strain Relation Of the Spmentioning

confidence: 99%

A Hybrid Model for Erythrocyte Membrane: A Single Unit of Protein Network Coupled with Lipid Bilayer

Zhu

Vera

Asaro

et al. 2007

Biophysical Journal

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To investigate the nanomechanics of the erythrocyte membrane we developed a hybrid model that couples the actin-spectrin network to the lipid bilayer. This model features a Fourier space Brownian dynamics model of the bilayer, a Brownian dynamics model of the actin protofilament, and a modified wormlike-chain model of the spectrin (including a cable-dynamics model to predict the oscillation in tension). This model enables us to predict the nanomechanics of single or multiple units of the protein network, the lipid bilayer, and the effect of their interactions. The present work is focused on the attitude of the actin protofilament at the equilibrium states coupled with the elevations of the lipid bilayer through their primary linkage at the suspension complex in deformations. Two different actin-spectrin junctions are considered at the junctional complex. With a point-attachment junction, large pitch angles and bifurcation of yaw angles are predicted. Thermal fluctuations at bifurcation may lead to mode-switching, which may affect the network and the physiological performance of the membrane. In contrast, with a wrap-around junction, pitch angles remain small, and the occurrence of bifurcation is greatly reduced. These simulations suggest the importance of three-dimensional molecular junctions and the lipid bilayer/protein network coupling on cell membrane mechanics.

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“…One approach to the multiscale modeling of RBC mechanics in blood flow, due to Peng et al ., defines three length scales (Figure ): (1) whole cell scale; (2) junctional‐complex (JC) scale; and (3) spectrin (Sp) protein scale. The protein‐scale submodel used a worm‐like chain description that was parameterized using measured properties of intraprotein linkages and causally confirmed experimentally observed folding/unfolding dynamics. The JC scale submodel describes the actin proto‐filament attachments to the RBC lipid bilayer and the Sp network.…”

Section: Multiscale Models Of the Cardiovascular Systemmentioning

confidence: 95%

“…Establishing ‘determination of effect’ of RBC membrane microstructural details on tank‐treading dynamics of RBC in shear flow. ‘Simulation’ refers to the multiscale model and ‘single‐layer model’ refers to a single‐scale model. The multiscale model simulation with zero membrane viscosity ( v b = v s = 0) retrieves the single‐scale model result.…”

Section: Multiscale Models Of the Cardiovascular Systemmentioning

confidence: 99%

Multiscale modeling methods in biomechanics

Bhattacharya

Viceconti

2017

WIREs Mechanisms of Disease

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More and more frequently, computational biomechanics deals with problems where the portion of physical reality to be modeled spans over such a large range of spatial and temporal dimensions, that it is impossible to represent it as a single space–time continuum. We are forced to consider multiple space–time continua, each representing the phenomenon of interest at a characteristic space–time scale. Multiscale models describe a complex process across multiple scales, and account for how quantities transform as we move from one scale to another. This review offers a set of definitions for this emerging field, and provides a brief summary of the most recent developments on multiscale modeling in biomechanics. Of all possible perspectives, we chose that of the modeling intent, which vastly affect the nature and the structure of each research activity. To the purpose we organized all papers reviewed in three categories: ‘causal confirmation,’ where multiscale models are used as materializations of the causation theories; ‘predictive accuracy,’ where multiscale modeling is aimed to improve the predictive accuracy; and ‘determination of effect,’ where multiscale modeling is used to model how a change at one scale manifests in an effect at another radically different space–time scale. Consistent with how the volume of computational biomechanics research is distributed across application targets, we extensively reviewed papers targeting the musculoskeletal and the cardiovascular systems, and covered only a few exemplary papers targeting other organ systems. The review shows a research subdomain still in its infancy, where causal confirmation papers remain the most common. WIREs Syst Biol Med 2017, 9:e1375. doi: 10.1002/wsbm.1375For further resources related to this article, please visit the WIREs website.

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Direct Numerical Simulation of Single-Molecule DNA by Cable Dynamics

Cited by 5 publications

References 34 publications

A Multiscale Dynamic Model of DNA Supercoil Relaxation by Topoisomerase IB

A Multiscale Dynamic Model of DNA Supercoil Relaxation by Topoisomerase IB

A Hybrid Model for Erythrocyte Membrane: A Single Unit of Protein Network Coupled with Lipid Bilayer

Multiscale modeling methods in biomechanics

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