Influence of hydrodynamic coupling on the electric linear dichroism of DNA fragments

Umazano, J. P.; Bertolotto, J. A.

doi:10.1063/1.3568270

Cited by 3 publications

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“…Especially, the location of the CoH is unknown before the motion of any tracking point (TP) is analyzed. Boomerang particles are also an interesting model system for active microswimmers [37], the electro-optical properties of DNA molecules [39][40][41][42] and the liquid crystal ordering [43].Our experimental and theoretical studies show that the diffusion of the boomerangs is rather different from that of spheres and ellipsoids. (1) The mean displacements (MD) for fixed initial angle are biased towards the CoH, and the mean square displacements (MSDs) exhibit a crossover from short to long time diffusion with different diffusion coefficients.…”

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“…The subtle difference between the CBF and DBF has significant influence on proper calculations of diffusion coefficients. Prior theoretical studies have provided analytical results regarding the orientation distributions of bent-rods under external fields [39][40][41][42]; it will be interesting to study how the boomerangs transport under gravitational or electrophoretic forces.…”

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Brownian Motion of Boomerang Colloidal Particles

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Brownian Motion of Boomerang Colloidal ParticlesWe investigate the Brownian motion of boomerang colloidal particles confined between two glass plates. Our experimental observations show that the mean displacements are biased towards the center of hydrodynamic stress (CoH), and that the mean-square displacements exhibit a crossover from short time faster to long time slower diffusion with the short-time diffusion coefficients dependent on the points used for tracking. A model based on Langevin theory elucidates that these behaviors are ascribed to a superposition of two diffusive modes: the ellipsoidal motion of the CoH and the rotational motion of the tracking point with respect to the CoH.Brownian motion as a general phenomenon of the diffusion processes has inspired extensive research [1][2][3][4][5][6][7][8][9][10][11][12] due to both its interesting physics and practical applications such as in microrheology [13][14][15][16], selfpropelled microswimmers [17] and particle and molecular separation [18][19][20]. Inspired by the diverse geometric shapes of biological macromolecules, Brenner and others have extended the hydrodynamic theory of Brownian motion to particles with irregular shapes [21][22][23][24][25][26]. A set of hydrodynamic centers are introduced, which include the center of hydrodynamic stress (CoH) where the coupling diffusion matrix becomes zero, the center of reaction where the coupling resistance matrix becomes symmetric and the center of diffusion where the coupling diffusion matrix becomes symmetric [22,24,27]. For screw-like or skewed particles, the translational and rotational motions are intrinsically coupled, therefore, the CoH does not exist and the centers of diffusion and reaction differ from each other. By contrast, for non-skewed particles, there always exists a unique point at which these three hydrodynamic centers coincide.Thus far, experimental studies of Brownian motion have been focused primarily on spherical particles; it was only recently that the Brownian motion of lowsymmetry particles was explored in experiments [5,[28][29][30][31][32][33][34]. Particle shapes are critical to various applications such as self-propelled microswimmers and particle/molecular separations [17,35]. By engineering particle shapes, microswimmers may be tailored to perform circular, spinning-top or other types of motion [35][36][37]. Understanding the hydrodynamics of chiral particles may lead to new avenues towards separation of particle or molecular enantiomers [38].In this letter we study the Brownian motion of boomerang-shaped colloidal particles under quasi twodimensional confinements. The boomerang particles with C 2v mirror symmetry represent an attractive system for studying the Brownian motion of low symmetry particles because their CoM and CoH do not coincide and both lie outside the body. Especially, the location of the CoH is unknown before the motion of any tracking point (TP) is analyzed. Boomerang particles are also an interesting model system for active microswimmers [37], the elec...

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Brownian Motion of Boomerang Colloidal Particles

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“…Nowadays, the influence of hydrodynamic coupling on the electro-optical effects (electric birefringence and dichroism) of DNA fragments has been studied through Brownian dynamic simulation [3][4][5] and theoretical methods. [6][7][8][9][10][11][12][13][14][15] Theoretical analytic results have been reported only for the limit of low electric field strength because the study of the orientational process induced by electric field has mathematical difficulties. Simulation studies early made are applied for arbitrary electric field strength but they have a disadvantage; they require computer simulations that are too extensive.…”

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“…In the past, applications of theoretical methods in combination with numerical techniques allowed us to remove the low electric field condition for the theoretical study of electric dichroism of DNA fragments in the steady-state. 14 In the present work, we propose to extend that calculation to study the transient electric dichroism of DNA fragments. We use a rigid bent rod molecule (BRM) model to describe the particles in solution.…”

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Electric linear dichroism transients of bent DNA fragments

Umazano

Bertolotto

2013

The Journal of Chemical Physics

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We study the effect of translational-rotational hydrodynamic coupling on the transient electric linear dichroism of DNA fragments in aqueous solution. As opposed to previous theoretical works, where analytic solutions valid in the limit of low electric field were reported, we present here a numerical approach which allows to obtain numerical results valid independently from the applied electric field strength. Numerical procedures here used are an extension to the transient-state of those developed in a previous work for the study of the problem in the steady-state. The molecular orientational processes induced by an electric field is characterized with statistical arguments solving the FokkerPlanck equation by means of the finite difference method to know the orientational distribution function of molecules.

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Flexible bent rod model with a saturating induced dipole moment to study the electric linear dichroism of DNA fragments

Bertolotto

Umazano

2016

AIP Advances

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In the present work we make a theoretical study of the steady state electric linear dichroism of DNA fragments in aqueous solution. The here developed theoretical approach considers a flexible bent rod model with a saturating induced dipole moment. The electric polarizability tensor of bent DNA fragments is calculated considering a phenomenological model which theoretical and experimental backgroung is presented here. The model has into account the electric polarizability longitudinal and transversal to the macroion. Molecular flexibility is described using an elastic potential. We consider DNA fragments originally bent with bending fluctuations around an average bending angle. The induced dipole moment is supposed constant once the electric field strength grows up at critical value. To calculate the reduced electric linear dichroism we determine the optical factor considering the basis of the bent DNA perpendicular to the molecular axis. The orientational distribution function has into account the anisotropic electric properties and the molecule flexibility. We applied the present theoretical background to fit electric dichroism experimental data of DNA fragments reported in the bibliography in a wide range of molecular weight and electric field. From these fits, values of DNA physical properties are estimated. We compare and discuss the results here obtained with the theoretical and experimental data presented by other authors. The original contributions of this work are: the inclusion of the transversal electric polarizability saturating with the electric field, the description of the electric properties with an electric polarizability tensor dependant on the bending angle and the use of an arc model originally bent.

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Influence of hydrodynamic coupling on the electric linear dichroism of DNA fragments

Cited by 3 publications

References 19 publications

Brownian Motion of Boomerang Colloidal Particles

Brownian Motion of Boomerang Colloidal Particles

Electric linear dichroism transients of bent DNA fragments

Flexible bent rod model with a saturating induced dipole moment to study the electric linear dichroism of DNA fragments

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