We use a lattice Boltzmann based Brownian dynamics simulation to investigate the dependence of DNA thermophoresis on its interaction with dissolved salts. We find the thermal diffusion coefficient D{T} depends on the molecule size, in contrast with previous simulations without electrostatics. The measured S{T} also depends on the Debye length. This suggests thermophoresis of DNA is influenced by the electrostatic interactions between the polymer beads and the salt ions. However, when electrostatic forces are weak, DNA thermophoresis is not found, suggesting that other repulsive forces such as the excluded volume force prevent thermal migration.

We study a layer of grains atop a plate which oscillates sinusoidally in the direction of gravity, using three-dimensional, time-dependent numerical solutions of continuum equations to Navier-Stokes order as well as hard-sphere molecular dynamics simulations. For high accelerational amplitudes of the plate, the layer exhibits a steady-state "density inversion" in which a high-density portion of the layer is supported by a lower-density portion. At low accelerational amplitudes, the layer exhibits oscillatory time dependence that is strongly correlated to the motion of the plate. We show that continuum simulations yield results consistent with molecular dynamics results in both regimes. 05.65.+b,47.57.Gc Although experimental [1,2] and computational [3][4][5][6][7] evidence demonstrate the potential for hydrodynamic models to describe important aspects of granular flow, a general set of governing equations for granular media is not yet recognized [8,9]. Several proposed rapid granular flow models use binary, inelastic hard-sphere collision operators in kinetic theory to derive equations of motion for the continuum fields: number density n, velocity u, and granular temperature T [10-12]. As Eshuis, et al [9] stated in 2010, "The holy grail question in research on granular dynamics is [13,14], To what extent can granular flow be described by a continuum approach?" Density inversion, in which a low-density region near the bottom of a granular layer supports a higher-density region above it, has proven to be significant for the study of granular hydrodynamics. This phenomenon has been identified in vertically shaken layers [7,9,[15][16][17] as well as in layers flowing parallel to a surface, such as in gravity-driven flow down an incline [18,19].In their seminal investigation [7], Lan and Rosato studied density inversion in vertically vibrated granular media. A layer of grains with depth H and uniform diameter σ atop a plate that oscillates sinusoidally with frequency f and amplitude A will leave the plate at some time in the oscillation cycle if the maximum acceleration of the plate a max = A (2πf ) 2 exceeds the acceleration of gravity g. The oscillating plate can be characterized by the dimensionless parameters Γ = a max /g and f * = f H/g. Lan and Rosato studied density inversion in such a system by conducting soft-sphere discrete element method (DEM) simulations and comparing these results to kinetic theory predictions of Richman and Martin [20].These continuum predictions did not account for the time dependence of the layer or the plate, but rather treated the oscillating plate as a source of thermal energy and assumed one-dimensional (1-D) steady-state density and temperature distributions as functions of height in the cell. To characterize the rate of kinetic energy input through shaking, they used the dimensionless RMS speed of the bottom plate V b = (2πf A) / √ 2σg as their control parameter. It has since become common to instead use the dimensionless shaking strength [15]In Fig. 5 of their manuscript, L...

We use a lattice-Boltzmann based Brownian dynamics simulation to investigate the separation of different lengths of DNA through the combination of a trapping force and the microflow created by counter-rotating vortices. We can separate most long DNA molecules from shorter chains that have lengths differing by as little as 30%. The sensitivity of this technique is determined by the flow rate, size of the trapping region, and the trapping strength. We expect that this technique can be used in microfluidic devices to separate long DNA fragments that result from techniques such as restriction enzyme digests of genomic DNA. V C 2015 AIP Publishing LLC.[http://dx.doi.org/10.1063/1.4926667] The development of novel methods for manipulating biopolymers such as DNA is required for the continued advancement of microfluidic devices. Techniques such as restriction enzyme digests for genomic sequencing rely on the detection of DNA that differ in length by sometimes thousands of base pairs. 1 Methods that separate DNA strands with resolutions on the order of kilobase pairs are required to analyze the products of this technique. To gain an insight into possible techniques to separate polymers, it can be helpful to review the methods to separate particles in microfluidic devices. Experimental work has shown how hydrodynamic mechanisms can lead to separation of particles based on size and deformability. 2 Eddies, microvortices, and hydrodynamic tweezers have been used to trap and sort particles. The mechanism of the trapping and sorting arises from the differences between interactions of the particles with the fluid. [2][3][4][5][6][7][8] In particular, counter-rotating vortices have been used to sort particles and manipulate biopolymers. They have been used to deposit DNA precisely across electrodes 9 and trap DNA. 10,11 Vortex flow may therefore be a good basis for a technique for sorting DNA by length.Streaming flow has been used in experiments to separate colloids of different size. Previous work on DNA has shown that counter-rotating vortices can be used to trap DNA dynamically. Long strands of DNA have been observed to stretch between the centers of two counter-rotating vortices. The polymer stays trapped in this state for significant amounts of time. 12 In a different experiment, the vortices were used to thermally cycle the polymer and allow replication via the polymerase chain reaction (PCR). The DNA is also trapped against one wall by a thermophoretic force in these experiments. 10 The strength of the trap is controlled by the gradient in temperature created by a focused infrared laser beam.Trapping DNA at one wall by counter-rotating vortices has also been explored in simulation and found to depend on the Peclet number, Pe ¼ u max L/D m , where u max is the maximum speed of the vortex, L is the box size, and D m is the diffusion coefficient of one bead in the

No abstract

No abstract