Numerical Determination of the Translocation Rate of Particles Through a Pore

Geier, Stephanie; Hernández-Ortíz, Juan P.; Pablo, Juan J. de

doi:10.1002/cite.201000218

Cited by 2 publications

(1 citation statement)

References 9 publications

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“…Brownian dynamics (BD) simulations were performed to simulate the DNA dumbbell conformation within the nanoslits. Long-range hydrodynamic interactions were included through a Green’s function formalism and calculated with the O ( N ) General Geometry Ewald-like Method (GGEM). − There is a combination of confinement effects for the dumbbell conformation. A molecule in a slit experiences a de Gennes’ regime (confinement size ∼ R g ) in the microchannel, and within the nanoslit width, an Odjik regime (confinement size ∼ l p ) ,, in the nanoslit height.…”

Section: Dna Model and Simulation Approachmentioning

confidence: 99%

Presentation of Large DNA Molecules for Analysis as Nanoconfined Dumbbells

Kounovsky-Shafer

Hernández-Ortíz

et al. 2013

Macromolecules

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The analysis of very large DNA molecules intrinsically supports long-range, phased sequence information, but requires new approaches for their effective presentation as part of any genome analysis platform. Using a multi-pronged approach that marshaled molecular confinement, ionic environment, and DNA elastic properties–but tressed by molecular simulations–we have developed an efficient and scalable approach for presentation of large DNA molecules within nanoscale slits. Our approach relies on the formation of DNA dumbbells, where large segments of the molecules remain outside the nanoslits used to confine them. The low ionic environment, synergizing other features of our approach, enables DNA molecules to adopt a fully stretched conformation, comparable to the contour length, thereby facilitating analysis by optical microscopy. Accordingly, a molecular model is proposed to describe the conformation and dynamics of the DNA molecules within the nanoslits; a Langevin description of the polymer dynamics is adopted in which hydrodynamic effects are included through a Green’s function formalism. Our simulations reveal that a delicate balance between electrostatic and hydrodynamic interactions is responsible for the observed molecular conformations. We demonstrate and further confirm that the “Odijk regime” does indeed start when the confinement dimensions size are of the same order of magnitude as the persistence length of the molecule. We also summarize current theories concerning dumbbell dynamics.

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Section: Dna Model and Simulation Approachmentioning

confidence: 99%

Presentation of Large DNA Molecules for Analysis as Nanoconfined Dumbbells

Kounovsky-Shafer

Hernández-Ortíz

et al. 2013

Macromolecules

View full text Add to dashboard Cite

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Parallel O(N) Stokes’ solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries

Zhao

Jiang

et al. 2017

The Journal of Chemical Physics

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An efficient parallel Stokes’ solver has been developed for complete description of hydrodynamic interactions between Brownian particles in bulk and confined geometries. A Langevin description of the particle dynamics is adopted, where the long-range interactions are included using a Green’s function formalism. A scalable parallel computational approach is presented, where the general geometry Stokeslet is calculated following a matrix-free algorithm using the general geometry Ewald-like method. Our approach employs a highly efficient iterative finite-element Stokes’ solver for the accurate treatment of long-range hydrodynamic interactions in arbitrary confined geometries. A combination of mid-point time integration of the Brownian stochastic differential equation, the parallel Stokes’ solver, and a Chebyshev polynomial approximation for the fluctuation-dissipation theorem leads to an O(N) parallel algorithm. We illustrate the new algorithm in the context of the dynamics of confined polymer solutions under equilibrium and non-equilibrium conditions. The method is then extended to treat suspended finite size particles of arbitrary shape in any geometry using an immersed boundary approach.

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Numerical Determination of the Translocation Rate of Particles Through a Pore

Cited by 2 publications

References 9 publications

Presentation of Large DNA Molecules for Analysis as Nanoconfined Dumbbells

Presentation of Large DNA Molecules for Analysis as Nanoconfined Dumbbells

Parallel O(N) Stokes’ solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries

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