The small mass assumption applied to the multibody dynamics of motor proteins

Bowling, Alan; Palmer, Andre F.

doi:10.1016/j.jbiomech.2009.03.017

Cited by 10 publications

(3 citation statements)

References 19 publications

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“…The most detailed models require minute molecular dynamics simulations with explicit solvent (Liu et al, 2006;Koppole et al, 2006;Kawakubo et al, 2005), but the large amount of computations needed to simulate reasonable time spans, even in the nanosecond scale, renders this method impractical for performing many consecutive simulations. More lightweight approaches have been devised, such as rule-based models (Gruenert et al, 2010;, classical coarse-grained models (Parker et al, 2009;Taylor and Katsimitsoulia, 2010;Bowling and Palmer, 2009;Craig and Linke, 2009), and even very simple models based on reaction kinetics (Schilstra and Martin, 2006) and ratchet potentials (Ciudad et al, 2006;Jülicher et al, 1997). These lightweight approaches vary over their degree of detail, explanatory power, and rigorous foundation.…”

Section: Introductionmentioning

confidence: 99%

Automating the search of molecular motor templates by evolutionary methods

Fernández

Vico

2011

Biosystems

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Biological molecular motors are nanoscale devices capable of transforming chemical energy into mechanical work, which are being researched in many scientific disciplines. From a computational point of view, the characteristics and dynamics of these motors are studied at multiple time scales, ranging from very detailed and complex molecular dynamics simulations spanning a few microseconds, to extremely simple and coarse-grained theoretical models of their working cycles. However, this research is performed only in the (relatively few) instances known from molecular biology. In this work, results from elastic network analysis and behaviour-finding methods are applied to explore a subset of the configuration space of template molecular structures that are able to transform chemical energy into directed movement. While using methods based on elastic networks limits the scope of our results, it enables the implementation of computationally lightweight methods, in a way that evolutionary search techniques can be applied to discover novel molecular motor templates. The results show that molecular motion can be attained from a variety of structural configurations. Additionally, these methods enable a new computational way to test hypotheses about molecular motors.

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Section: Introductionmentioning

confidence: 99%

Automating the search of molecular motor templates by evolutionary methods

Fernández

Vico

2011

Biosystems

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“…This can be addressed by modeling all of them, as in molecular dynamic simulations. These large models can be simplified by grouping particles into rigid bodies. − Here, this is reasonable because the protein is rigid enough to act as a lever. , …”

Section: Introductionmentioning

confidence: 99%

“…Analytic methods isolate the dynamics of the larger time scales. These include modal analysis retaining only low frequency modes, the method of multiple scales (MMS) retaining only low order perturbations, − and the small mass assumption , which omits the mass terms. ,, The relationship between the MMS and the small mass assumption was discussed in a previous paper . The relationship between the small mass assumption and the proposed analytic approach is discussed herein.…”

Section: Introductionmentioning

confidence: 99%

Contact and Impact in the Multibody Dynamics of Motor Protein Locomotion

2009

Self Cite

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This paper presents the development of a rigid multibody dynamics approach to modeling, simulation, and analysis of motor proteins. A key element of this new model is that it retains the mass properties, in contrast to many commonly used models that do not. The mass properties are usually omitted because their inclusion yields a model with multiple time scales whose simulation requires a significant amount of time. However, the proposed model can be numerically integrated in a reasonable amount of time. Thus this approach represents a new method for treating multiple scale models. In addition, retaining the mass properties allows a detailed study of contact and impact between the protein and substrate, which is critical for protein processivity. The new model also provides insights into the characteristics of the protein and its environment, specifically, the effective damping experienced by the protein moving through its fluid environment may be quite small yielding under or critically damped motion. This conclusion runs contrary to the widely accepted notion that the protein's motion is strictly over damped. Herein, the differences between the motion predicted by the old and new modeling approaches are compared using a simplified model of Myosin V.

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A new switching strategy for addressing Euler parameters in dynamic modeling and simulation of rigid multibody systems

Haghshenas-Jaryani

Bowling

2012

Multibody Syst Dyn

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The small mass assumption applied to the multibody dynamics of motor proteins

Cited by 10 publications

References 19 publications

Automating the search of molecular motor templates by evolutionary methods

Automating the search of molecular motor templates by evolutionary methods

Contact and Impact in the Multibody Dynamics of Motor Protein Locomotion

A new switching strategy for addressing Euler parameters in dynamic modeling and simulation of rigid multibody systems

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