Giant Acceleration of DNA Diffusion in an Array of Entropic Barriers

Kim, Daniel; Bowman, Clark; Bonis-O’Donnell, Jackson Travis Del; Matzavinos, Anastasios; Stein, Derek

doi:10.1103/physrevlett.118.048002

Cited by 36 publications

(25 citation statements)

References 34 publications

(35 reference statements)

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“…to separate DNA. Numerous theoretical studies have examined the subtle physical mechanisms at play when long DNA fragments (as well as short rod‐like molecules ) move between deep wells and narrow channels .…”

Section: Introductionmentioning

confidence: 99%

Electrophoretic ratcheting of spherical particles in well/channel microfluidic devices: Making particles move against the net field

2020

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We examine the electrophoresis of spherical particles in microfluidic devices made of alternating wells and narrow channels, including a system previously used to separate DNA molecules. Our computer simulations predict that such systems can be used to separate spherical particles of different sizes that share the same free-solution mobility. Interestingly, the electrophoretic velocity shows an inversion as the field intensity is increased: while small particles have higher velocities at low field, the situation is reversed at high fields with the larger particles then moving faster. The resulting nonlinearity suggests that asymmetric pulsed electric fields could be used to build separation ratchets: particles then have a net size-dependent velocity in the presence of a zero-mean external field. Exploiting the inversion mentioned above, we show how to design pulsed field sequences that make particles move against the mean field (an example of negative mobility). Finally, we demonstrate that it is possible to use pulsed fields to make particles of different sizes move in opposite directions, even though their charge have the same sign. Keywords:colloidal particles / computational modeling / electrophoresis / Langevin dynamics simulations / ratchet effect

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Section: Introductionmentioning

confidence: 99%

Electrophoretic ratcheting of spherical particles in well/channel microfluidic devices: Making particles move against the net field

2020

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“…Previous experimental studies on particle motion in periodic potentials in the fluid phase have examined diffusive and * madhavi.krishnan@uzh.ch field-driven transport of single colloidal particles and DNA, in spatially modulated gravitational and optical fields, and configurational entropy landscapes [9][10][11][12][13]. Typically these investigations use field-driven transport to separate a mixture of molecular species, exploiting the nonlinear response in object mobility to a spatially varying potential [14,15].…”

Section: Introductionmentioning

confidence: 99%

Lattice diffusion of a single molecule in solution

Ruggeri

Krishnan

2017

Phys. Rev. E

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The ability to trap a single molecule in an electrostatic potential well in solution has opened up new possibilities for the use of molecular electrical charge to study macromolecular conformation and dynamics at the level of the single entity. Here we study the diffusion of a single macromolecule in a two-dimensional lattice of electrostatic traps in solution. We report the ability to measure both the size and effective electrical charge of a macromolecule by observing single-molecule transport trajectories, typically a few seconds in length, using fluorescence microscopy. While, as shown previously, the time spent by the molecule in a trap is a strong function of its effective charge, we demonstrate here that the average travel time between traps in the landscape yields its hydrodynamic radius. Tailoring the pitch of the lattice thus yields two different experimentally measurable time scales that together uniquely determine both the size and charge of the molecule. Since no information is required on the location of the molecule between consecutive departure and arrival events at lattice sites, the technique is ideally suited to measurements on weakly emitting entities such as single molecules.

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“…In addition, the angular speed corresponding to the maximum effective diffusion coefficient D ef f is not the same as the angular speed at which average velocity V x is maximum. Note that in the previous works [29][30][31][32][33] the giant acceleration of diffusion usually appears in a tilted periodic potential, however, in the present system the appearance of the giant acceleration of diffusion cannot require a constant force.…”

Section: A Longitudinal Direction Rectification and Diffusionmentioning

confidence: 90%

Transport and diffusion properties of Brownian particles powered by a rotating wheel

2017

Phys. Rev. E

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Diffusion and rectification of Brownian particles powered by a rotating wheel are numerically investigated in a two-dimensional channel. The nonequilibrium driving comes from the rotating wheel, which can break thermodynamical equilibrium and induce the directed transport in an asymmetric potential. It is found that the direction of the transport along the potential is determined by the asymmetry of the potential and the position of the wheel. The average velocity is a peaked function of the angular speed (or the diffusion coefficient) and the position of the peak shifts to large angular speed(or diffusion coefficient) when the diffusion coefficient (or the angular speed) increases. There exists an optimal angular speed (or diffusion coefficient) at which the effective diffusion coefficient takes its maximal value. Remarkably, the giant acceleration of diffusion is observed by suitably adjusting the system parameters. The parameters corresponding to the maximum effective diffusion coefficient are not the same as the parameters at which average velocity is maximum.

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Giant Acceleration of DNA Diffusion in an Array of Entropic Barriers

Cited by 36 publications

References 34 publications

Electrophoretic ratcheting of spherical particles in well/channel microfluidic devices: Making particles move against the net field

Electrophoretic ratcheting of spherical particles in well/channel microfluidic devices: Making particles move against the net field

Lattice diffusion of a single molecule in solution

Transport and diffusion properties of Brownian particles powered by a rotating wheel

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