Neda Nazemifard

DNA dynamics in nanoscale confinement under asymmetric pulsed field electrophoresis.

The difficulty of fabricating tight nanoscale confinements has limited the understanding of DNA dynamics inside structures with pores smaller than the persistence length ( 50 nm) of DNA molecules. Our group has developed colloidal selfassembly (CSA) of crystalline arrays of particles within microfluidic channels as a powerful tool for the easy fabrication of ordered nanoporous media. Angular separation of DNA has been achieved using asymmetric pulsed field electrophoresis within such crystalline arrays. Here, nanoparticle arrays with particles as small as 100 nm (corresponding to ca. 15 nm pore sizes) were successfully fabricated, and the mechanism of DNA transport in highly confined pores was studied. DNA separation was conducted using a microfluidic chip filled with an array of nanoparticles as a sieving matrix. A schematic of the PDMS microchip is shown in Figure 1a. Aqueous suspensions of monodisperse silica colloids (Bangs Laboratories, Fishers, IN) of 100, 330, and 700 nm diameter were used to form self-assembled nanoparticle arrays inside the microchips. SEM images of the self-assembled structure reveal a closely packed hexagonal array of nanoparticles, where the size of pores (the smallest opening between the particles, dp) were around 15 % of the particle size, i.e., dp = 15, 50, and 105 nm for 100, 330, and 700 nm particles, respectively. Angular separation of DNA molecules under a pulsed field was achieved by injecting DNA samples into the separation chamber, as illustrated in Figure 1b. The applied pulsed potentials generated asymmetric obtuse-angle pulsed fields across the separation chamber, where the angle between the pulsed fields is ca. 1358 and E1 = 1.4E2 in all experiments. Within the separation chamber, different sizes of DNA separate from each other and form individual streams, each stream deflecting an angle q from the injection angle, as shown in Figure 1c. It was observed that q was highly dependent on the frequency, electric field strength, and DNA size. We have developed a geometric model that links these operating parameters to molecular size and separation angle, q. A geometric model was first introduced by Austin et al. to quantify one-dimensional zone electrophoretic separation of DNA within a microfabricated array structure under a pulsed field. Their attempt to fit the model to their observations required a coiling factor, 9] accounting for incomplete stretching of DNA. Here, a similar geometric model was developed for continuous two-dimensional angular separation of DNA under a pulsed field. We have assumed fully stretched DNA, so no fitting coefficient is utilized. The model is based on the known separation mechanism of DNA molecules under asymmetric obtuse-angle pulse fields. According to this model, DNA reptates along the direction of the electric field as a flexible rod with a constant length (L). Once the direction of the electric field is changed, the molecule backtracks to a new direction as shown in Figure 2a–c. For small frequencies, when the molecule has enough time to reorient itself to the new direction and travel distances larger than its own length, a simple geometric equation can be derived. The model relates the net angular distance that the molecule travels at the end of one cycle (deflection angle, q) to the molecular size (L), electric fields (E1, E2), and frequency (f): Figure 1. a) Schematic and b,c) photomicrographs of the DNA separation microchip used in this work. DNA solution is injected continuously into the separation chamber. White arrows represent the directions of the applied electric fields (b). The separation chamber is filled with nanoparticle arrays. Different sizes of DNA molecules separate from each other and form individual streams, each deflecting an angle q from the injection angle (c).

Thermal graphene metamaterials and epsilon-near-zero high temperature plasmonics

The key feature of a thermophotovoltaic (TPV) emitter is the enhancement of thermal emission corresponding to energies just above the bandgap of the absorbing photovoltaic cell and simultaneous suppression of thermal emission below the bandgap. We show here that a single layer plasmonic coating can perform this task with high efficiency. Our key design principle involves tuning the epsilon-near-zero frequency (plasma frequency) of the metal acting as a thermal emitter to the electronic bandgap of the semiconducting cell. This approach utilizes the change in reflectivity of a metal near its plasma frequency (epsilon-near-zero frequency) to lead to spectrally selective thermal emission and can be adapted to large area coatings using high temperature plasmonic materials. We provide a detailed analysis of the spectral and angular performance of high temperature plasmonic coatings as TPV emitters. We show the potential of such high temperature plasmonic thermal emitter coatings (p-TECs) for narrowband near-field thermal emission. We also show the enhancement of near-surface energy density in graphene-multilayer thermal metamaterials due to a topological transition at an effective epsilon-near-zero frequency. This opens up spectrally selective thermal emission from graphene multilayers in the infrared frequency regime. Our design paves the way for the development of single layer p-TECs and graphene multilayers for spectrally selective radiative heat transfer applications.

Axial super-resolution evanescent wave tomography

Optical tomographic reconstruction of a three-dimensional (3D) nanoscale specimen is hindered by the axial diffraction limit, which is 2-3 times worse than the focal plane resolution. We propose and experimentally demonstrate an axial super-resolution evanescent wave tomography method that enables the use of regular evanescent wave microscopes like the total internal reflection fluorescence microscope beyond surface imaging and achieve a tomographic reconstruction with axial super-resolution. Our proposed method based on Fourier reconstruction achieves axial super-resolution by extracting information from multiple sets of 3D fluorescence images when the sample is illuminated by an evanescent wave. We propose a procedure to extract super-resolution features from the incremental penetration of an evanescent wave and support our theory by one-dimensional (along the optical axis) and 3D simulations. We validate our claims by experimentally demonstrating tomographic reconstruction of microtubules in HeLa cells with an axial resolution of ∼130  nm. Our method does not require any additional optical components or sample preparation. The proposed method can be combined with focal plane super-resolution techniques like stochastic optical reconstruction microscopy and can also be adapted for THz and microwave near-field tomography.

Nonmonotonous variation of DNA angular separation during asymmetric pulsed field electrophoresis

Asymmetric pulsed field electrophoresis within crystalline arrays is used to generate angular separation of DNA molecules. Four regimes of the frequency response are observed, a low frequency rise in angular separation, a plateau, a subsequent decline, and a second plateau at higher frequencies. It is shown that the frequency response for different sized DNA is governed by the relation between pulse time and the reorientation time of DNA molecules. The decline in angular separation at higher frequencies has not previously been analyzed. Real‐time videos of single DNA molecules migrating under high frequency‐pulsed electric field show the molecules no longer follow the head to tail switching, ratchet mechanism seen at lower frequencies. Once the pulse period is shorter than the reorientation time, the migration mechanism changes significantly. The molecule reptates along the average direction of the two electric fields, which reduces the angular separation. A freely jointed chain model of DNA is developed where the porous structure is represented with a hexagonal array of obstacles. The model qualitatively predicts the variation of DNA angular separation with respect to frequency.

Electric Field Gradients in Micro/Nanofluidic Devices

Electrokinetic is one of the most common tools used to control the transport phenomena in micro/nanofluidic devices. To design a successful process, it is important to have a precise knowledge of parameters affecting electrokinetic transport. One of these parameters is the applied electric field. When the local values of the electric field deviate significantly from the nominal values, the assumption of a homogeneous field is an oversimplification resulting in failed or low efficiency processes. In this manuscript, the sources of inducing field gradients and their implications were investigated. Of particular interests are micro-fabricated arrays used extensively in microfluidic devices either as sieving matrices or mixing enhancers. A comprehensive parametric study was conducted to understand how the posts arrangements (hexagonal and square), distance and size, and surface charge change the field gradients. Our results provide criteria at which the assumption of uniform field is valid, which can have important implications in designing microfluidic units where either a high field gradient is favored (mixing) or not (separation).Copyright

Characterization of electroosmotic flow through nanoporous self-assembled arrays.

Characterization of EOF mobility for Tris and TBE buffer solutions is performed in nanoporous arrays using the fluorescent marker method to examine the magnitude of EOFs through nanopores with mean diameters close to electric double layer thickness (Debye length). Structures made from solid silica nanospheres with effective pore sizes from 104 nm down to 8 nm are produced within the microchannel using an evaporation self‐assembly method. EOF results in nanoporous matrices show higher EOF mobilities for stronger electrolyte solutions, which are drastically different compared to microchannel EOF. The effects of scaling are also examined by comparing the EOF mobility for varying ratios of pore diameters to the Debye length, which shows a surprising consistency across all particle sizes examined. This work demonstrates various factors which must be considered when designing nanofluidic devices, and discusses the causes of these small scale effects.

The Effect of Geometry on Sample Leakage in Multi-Channel Microfluidic Devices

Electrokinetic sheath-flow is one of the techniques used to manipulate sample migration and prevent cross-contamination in multi-channel microfluidic devices. To achieve a successful design, it is important to predict the sample behaviour in advance. We use finite element method to investigate the effect of channel geometry on sample leakage in the presence of electrokinetic sheath-flow. A typical multi-channel device consisting of a main fractionation channel connected to a few collection channels is considered. It has been observed experimentally that the depth of different components of the microfluidic device can change the sample leakage. In-detail investigations are made here in order to find the fundamental cause of the observed behaviour. Simulation results confirmed that by increasing the depth ratio of the collection channels to the main channel the sample leakage would decrease. Simulations are also performed to find criteria for choosing an optimum depth ratio for the channels in terms of both high functionality and ease of fabrication for any specific application.Copyright

Role of patterned surface charge heterogeneity on particle deposition

A finite element analysis of the fluid flow and the colloidal particle transport equations near a micropatterned charged substrate under radial impinging jet flow conditions is presented to investigate the charge heterogeneity effects on particle deposition. The particle Sherwood number representing the dimensionless particle deposition flux is obtained as a function of the radial distance from the stagnation point. The charge heterogeneity is modeled as concentric bands bearing positive and negative charges on the substrate. When a negatively-charged particle approaches such a charge heterogeneous substrate, it experiences an alternating attractive and repulsive force due to the presence of different charges on the substrate. Consequently, as the particle moves radially outward from the stagnation point, it experiences a periodic array of favorable (attractive) and unfavorable (repulsive) regions on the substrate, giving rise to an oscillatory trajectory. The numerical results obtained from the finite element model are in excellent agreement with existing theoretical and experimental values of deposition rates on homogeneous collector surfaces. However, the results for particle deposition over a heterogeneous substrate depict a significant deviation from those predicted by the patchwise heterogeneity model due to the coupled influence of hydrodynamic interactions and the surface chemical heterogeneity of the collector. The particles that do not deposit over an unfavorable repulsive band are convected to the next favorable band by the tangential velocity. This increases the particle concentration at the leading edge of each favorable band resulting in an increase in particle deposition over the favorable bands and the overall deposition rate on to the collector. Application of this phenomenon will be discussed in context of developing micropatterned surfaces with engineered particle capture properties.