Rotational Brownian dynamics of semiflexible broken rods

Iniesta, A.; López, Manuela; Torre, José Garcı́a de la

doi:10.1007/bf00865208

Cited by 5 publications

(3 citation statements)

References 26 publications

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“…Equation 8 can be transferred to the laboratory system, giving two equations3 An sin 2 = 2Crxy An cos 2 = C(ryy rxx) (10) where we have assumed that the solvent does not contribute to the birefringence. The intrinsic birefringence is defined as An…”

Section: Theory and Methodsmentioning

confidence: 99%

Flow birefringence of flexible polymer chains in steady shear flow: a Brownian dynamics simulation

Knudsen¹,

Elgsaeter²,

Cascales³

et al. 1993

Macromolecules

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The steady-shear flow birefringence of flexible polymers modeled as Gaussian chains has been studied using Brownian dynamics simulation. The influence of flow rate and chain length on the two important parameters in flow birefringence measurements, the extinction angle and the birefringence An, has been investigated, and the power laws obtained have been compared with theoretical predictions. Hydrodynamic interaction (HI) has been included by means of the Rotne-Prager^Yamakawa tensor, and the simulation results have been compared with the no-HI case. For low shear rates inclusion of HI reduces the influence of flow on An and tan 2 , while for high flow rates the chain behaves as in the no-HI case due to the large separation between beads and thereby elimination of flow interaction. For the shear compliance J, we obtain the value 0.29, which is higher than the theoretical value with preaveraged HI (0.20) and lower than that of the free-draining case (0.40), suggesting that preaveraged HI puts a too high weight on the HI contribution.The stress optical coefficient C has also been studied and found to be independent of chain length, shear rate, and HI.

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Section: Theory and Methodsmentioning

confidence: 99%

Flow birefringence of flexible polymer chains in steady shear flow: a Brownian dynamics simulation

Knudsen¹,

Elgsaeter²,

Cascales³

et al. 1993

Macromolecules

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“…Hydrodynamic interaction between arms is not responsible for the difference, as its influence on Znw is about 10% (Wegener 1982a). Brownian Dynamics simulation have been used to clarify this discrepancy (Iniesta et al 1991;Garcia de la Torre et al, in preparation). Figure 9 shows the decay of C a (t) for broken rods of varying flexibility (Ca (t) for the broken rod is equivalent to C b (t) for the trumbbell; now the pertinent vector is that going from the joint to the end of the arm).…”

Section: The Broken Rodmentioning

confidence: 99%

Hydrodynamics of segmentally flexible macromolecules

1994

Eur Biophys J

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Segmentally flexible macromolecules are composed of a few rigid subunits linked by joints which are more or less flexible. The dynamics in solution of this type of macromolecule present special aspects that are reviewed here. Three alternative approaches are described. One is the rigid-body treatment, which is shown to be valid for overall dynamic properties such as translational diffusion and intrinsic viscosity. Another approach is the Harvey-Wegener treatment, which is particularly suited for rotational diffusion. The simplest version of this treatment, which ignores hydrodynamic interaction (HI) effects, is found to be quite accurate when compared to a more rigorous version including HI. A third approach is the Brownian dynamics simulation that, albeit at some computational cost, might describe rigorously cases of arbitrary complexity. This technique has been used to test the approximations in the rigid-body and Harvey-Wegener treatments, thus allowing a better understanding of their validity. Brownian trajectories of simplified models such as the trumbbell and the broken rod have been simulated. The comparison of the decay rates of some correlation functions with the predictions of the two treatments leads to a general conclusion: the Harvey-Wegener treatment determines the initial rate, while the long-time behavior is dominated by the rigid-body relaxation time. As an example of application to a specific biological macromolecule, we present a simulation of an immunoglobulin molecule, showing how Brownian Dynamics can be used to predict rotational and internal dynamics. Another typical example is myosin. Literature data of hydrodynamic properties of whole myosin and the myosin rod are compared with predictions from the Harvey-Wegener and rigid-body treatments. The present situation of the problem on myosin flexibility is analyzed, and some indications are given for future experimental and simulation work.

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“…58,[60][61][62][63][64] We use a simulation procedure based on Ermak and McCammon's algorithm, 65 with a modification proposed by Iniesta and García de la Torre. 58,[60][61][62][63][64] We use a simulation procedure based on Ermak and McCammon's algorithm, 65 with a modification proposed by Iniesta and García de la Torre.…”

Section: B Brownian Dynamics Simulationmentioning

confidence: 99%

Transient electric birefringence of wormlike macromolecules in electric fields of arbitrary strength: A computer simulation study

Pérez‐Sánchez¹,

Torre²,

Baños³

2005

The Journal of Chemical Physics

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We have studied the birefringence decay of linear models of macromolecules for two different types of flexibility, the broken-rod chain and the wormlike chain, using a computer simulation of a transient electric birefringence experiment. We have paid particular attention to the influence of the intensity of the orienting field, including two orienting mechanisms, the induced dipole, and the permanent dipole. We have compared wormlike and broken-rod models of the same radius of gyration, finding that they present a different decay curve under the influence of the same intensity of the field. We have seen that these differences are due to the faster relaxation times (smaller in the wormlike chain model) and amplitudes, because, regardless of the type of flexibility, the overall size of a molecule (measured by the radius of gyration) essentially determines the longest relaxation time. We have also analyzed how the relaxation process is affected by the degree of flexibility, the orientation mechanisms, and the intensity of the field. Studying a different aspect, we have paid attention to the deformation of a molecule in a transient electric birefringence experiment as a source of information. In this work we have developed equations to characterize this deformation in terms of one of the components of the gyration tensor, if a dynamic light scattering experiment under the influence of an electric field could be performed. To develop this work we have simulated the Brownian dynamics of the different models, relaxing after the removal of an orienting external electric field of arbitrary strength. A comparison with other methods such a the rigid body treatment or the correlation analysis of Brownian trajectories has also been included. We have seen that differences between the two Brownian dynamics methods are small and that the rigid-body treatment is only an acceptable approximation to obtain the longest relaxation time.

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Rotational Brownian dynamics of semiflexible broken rods

Cited by 5 publications

References 26 publications

Flow birefringence of flexible polymer chains in steady shear flow: a Brownian dynamics simulation

Flow birefringence of flexible polymer chains in steady shear flow: a Brownian dynamics simulation

Hydrodynamics of segmentally flexible macromolecules

Transient electric birefringence of wormlike macromolecules in electric fields of arbitrary strength: A computer simulation study

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