The fluid mechanics of genome mapping

Dorfman, Kevin D.

doi:10.1002/aic.14002

Cited by 27 publications

(18 citation statements)

References 70 publications

(138 reference statements)

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“…Nanotechnologies enable the monitoring of steric, electric, and hydrodynamic interactions in confined flows, and open up new horizons in the engineering of new molecular biology assays 1 , the enhancement of osmotic energy conversion 2 , or the development of new fluid functions, including among others fluidic diodes 3 . Accurate flow characterization is most commonly carried out using image-based particle velocimetry 4 .…”

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confidence: 99%

Metrology of confined flows using wide field nanoparticle velocimetry

Ranchon

Picot

Bancaud

2015

Sci Rep

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The manipulation of fluids in micro/nanofabricated systems opens new avenues to engineer the transport of matter at the molecular level. Yet the number of methods for the in situ characterization of fluid flows in shallow channels is limited. Here we establish a simple method called nanoparticle velocimetry distribution analysis (NVDA) that relies on wide field microscopy to measure the flow rate and channel height based on the fitting of particle velocity distributions along and across the flow direction. NVDA is validated by simulations, showing errors in velocity and height determination of less than 1% and 8% respectively, as well as with experiments, in which we monitor the behavior of 200 nm nanoparticles conveyed in channels of ~1.8 μm in height. We then show the relevance of this assay for the characterization of flows in bulging channels, and prove its suitability to characterize the concentration of particles across the channel height in the context of visco-elastic focusing. Our method for rapid and quantitative flow characterization has therefore a broad spectrum of applications in micro/nanofluidics, and a strong potential for the optimization of Lab-on-Chips modules in which engineering of confined transport is necessary.

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confidence: 99%

Metrology of confined flows using wide field nanoparticle velocimetry

Ranchon

Picot

Bancaud

2015

Sci Rep

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“…With 10% of the single channel occupied by molecules, the net throughput of well‐stretched DNA is ∼10 Mbp/s, (0.6 Gbp/min) or roughly 2 bacterial genomes/s. DNA mapping and the role of fluid dynamics in DNA linearization has very recently been reviewed by Dorfman …”

Section: Linearizing Dna By Flowmentioning

confidence: 99%

Long‐range mapping of DNA

Crothers

2013

Biopolymers

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“…1,2 A thorough understanding of the fundamental physics of such systems is vital for various applications that require stretching of DNA in channels, including DNA sorting, 3 DNA denaturation mapping, 4,5 and genome mapping. [6][7][8][9] A number of other studies have examined the confinement effects on DNA in embedded nanotopography devices composed of a nanoslit with nanogrooves or nanopits etched into one surface deeper than the surrounding slit. While the pits and grooves generally promote entropic trapping of the DNA, some portion of the contour of the molecule can occupy the narrow region of the slit outside these structures.…”

Section: Introductionmentioning

confidence: 99%

Equilibrium organization, conformation, and dynamics of two polymers under box-like confinement

Polson,

Rehel

2021

Preprint

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Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as flexible hard-sphere chains, and the box has a square cross-section of side length L and a height that is small enough to compress the polymers in that dimension. For sufficiently large L, the system behaviour approaches that of an isolated polymer in a slit. However, the combined effects of crowding and confinement on the polymer organization, conformation and equilibrium dynamics become significant when L/R * g,xy 5, where R * g,xy is the transverse radius of gyration for a slit geometry. In this regime, the centre-of-mass probability distribution in the transverse plane exhibits a depletion zone near the centre of the cavity (except at very small L) and a 4-fold symmetry with quasi-discrete positions. Reduction in polymer size with decreasing L arises principally from confinement rather than inter-polymer crowding. By contrast, polymer diffusion and internal motion are strongly affected by inter-polymer crowding. The two polymers tend to occupy opposite positions relative to the box centre, about which they diffuse relatively freely. Qualitatively, this static and dynamical behaviour differs significantly from that previously observed for confinement of two polymers to a narrow channel. The simulation results for a suitably chosen box width are qualitatively consistent with results from a recent experimental study of two λ-DNA chains confined to a nanofluidic cavity.

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The fluid mechanics of genome mapping

Cited by 27 publications

References 70 publications

Metrology of confined flows using wide field nanoparticle velocimetry

Metrology of confined flows using wide field nanoparticle velocimetry

Long‐range mapping of DNA

Equilibrium organization, conformation, and dynamics of two polymers under box-like confinement

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