Continuous Droplet-Actuating Platforms via an Electric Field Gradient: Electrowetting and Liquid Dielectrophoresis.

This work develops a technology for actuating droplets of any size without the requirement for high voltages or active control systems, which are typically found in competitive systems. The droplet actuation relies on two microelectrodes separated by a variable gap distance to generate an electrostatic gradient. The physical mechanism for the droplet motion is a combination of liquid dielectrophoresis and electrowetting. Investigating the system behavior as a function of the driving frequency identified the relative contribution of these two mechanisms and the optimum operating conditions. A fixed signal frequency of 0.5 kHz actuated various liquids and contaminants. Droplet actuation was demonstrated on several platforms, including linear, radial-symmetric, and bilateral-symmetric droplet motion. The electrode designs are scalable and can be fabricated on a flexible and optically transparent substrate: these key advancements will enable consumer applications that were previously inaccessible. A self-cleaning platform was also tested under laboratory conditions and on the road. This technology has significant potential in microfluidics and self-cleaning platforms, for example, in the automotive sector to clean body parts, camera covers, and sensors.

Optical properties and carrier dynamics in Co-doped ZnO nanorods.

The controlled modification of the electronic properties of ZnO nanorods via transition metal doping is reported. A series of ZnO nanorods were synthesized by chemical bath growth with varying Co content from 0 to 20 atomic% in the growth solution. Optoelectronic behavior was probed using cathodoluminescence, time-resolved luminescence, transient absorbance spectroscopy, and the incident photon-to-current conversion efficiency (IPCE). Analysis indicates the crucial role of surface defects in determining the electronic behavior. Significantly, Co-doping extends the light absorption of the nanorods into the visible region, increases the surface defects, and shortens the non-radiative lifetimes, while leaving the radiative lifetime constant. Furthermore, for 1 atomic% Co-doping the IPCE of the ZnO nanorods is enhanced. These results demonstrate that doping can controllably tune the functional electronic properties of ZnO nanorods for applications.

Cobalt-Doped ZnO Nanorods Coated with Nanoscale Metal-Organic Framework Shells for Water-Splitting Photoanodes.

Developing highly efficient and stable photoelectrochemical (PEC) water-splitting electrodes via inexpensive, liquid phase processing is one of the key challenges for the conversion of solar energy into hydrogen for sustainable energy production. ZnO represents one the most suitable semiconductor metal oxide alternatives because of its high electron mobility, abundance, and low cost, although its performance is limited by its lack of absorption in the visible spectrum and reduced charge separation and charge transfer efficiency. Here, we present a solution-processed water-splitting photoanode based on Co-doped ZnO nanorods (NRs) coated with a transparent functionalizing metal-organic framework (MOF). The light absorption of the ZnO NRs is engineered toward the visible region by Co-doping, while the MOF significantly improves the stability and charge separation and transfer properties of the NRs. This synergetic combination of doping and nanoscale surface functionalization boosts the current density and functional lifetime of the photoanodes while achieving an unprecedented incident photon to current efficiency (IPCE) of 75% at 350 nm, which is over 2 times that of pristine ZnO. A theoretical model and band structure for the core-shell nanostructure is provided, highlighting how this nanomaterial combination provides an attractive pathway for the design of robust and highly efficient semiconductor-based photoanodes that can be translated to other semiconducting oxide systems.

Computer Aided Patterning Design for Self-Assembled Microsphere Lithography (SA-MSL).

In this paper, we use a finite difference time domain solver to simulate the near field optical properties of self-assembled microsphere arrays when exposed to an incoherent light source. Such arrays are typically used for microsphere lithography where each sphere acts as a ball lens, focusing ultraviolet light into an underlying photoresist layer. It is well known that arrays of circular features can be patterned using this technique. However, here, our simulations show that additional nanometer scale features can be introduced to the pattern by optimising the sphere dimensions and exposure conditions. These features are shown to arise from the contact points between the microspheres which produce paths for light leakage. For hexagonally close packed arrays, the six points of contact lead to star shapes in the photoresist. These star shapes have subfeature sizes comparable to the current achievable resolution of low-cost fabrication techniques.

Controlling the growth of single crystal ZnO nanowires by tuning the atomic layer deposition parameters of the ZnO seed layer.

Semiconducting nanowires (NWs) offer exciting prospects for a wide range of technological applications. The translation of NW science into technology requires reliable high quality large volume production. This study provides an in-depth investigation of the parameters using an atomic layer deposition system to grow zinc oxide (ZnO) seed layers followed by the chemical bath deposition (CBD) of ZnO NWs to demonstrate the low-cost production of uniform single crystal wurtzite phase ZnO NWs that is scalable to large area substrates. The seed layer texture and the morphology of the NWs grown were systematically investigated using atomic force microscopy as a function of the seed layer deposition parameters. It is shown that the NWs growth orientation can be controlled by tuning the seed layer deposition parameters while maintaining the same CBD conditions. Likewise, the diameters and the surface densities of the NWs varied from 23 to 56 nm and 40 to 327 NWs µm-2, respectively. Significantly, the relationship between the seed layer structure and the NW density indicates a clear correlation between the density of seed layer surface features and the resulting surface NW density of NWs grown.

Scattering of spoof surface plasmon polaritons in defect-rich THz waveguides.

We report on the first observation of 'Spoof' Surface Plasmon Polariton (SPP) scattering from surface defects on metal-coated 3D printed, corrugated THz waveguiding surfaces. Surface defects, a result of the printing process, are shown to assist the direct coupling of the incident free-space radiation into a spoof SPP wave; removing the need to bridge the photon momentum gap using knife-edge or prism coupling. The free space characteristics, propagation losses and confinement of the spoof SPPs to the surface are measured, and the results are compared to finite-difference time domain simulations. Angular resolved THz spectroscopy measurements reveal the scattering patterns from surfaces and are compared with Mie theory, taking into account the shortened wavelength of the photons in their bound SPP state compared to their free space wavelength. These results confirm yet another similarity between the properties of THz spoof SPPs and their natural, non-spoof, counterparts at optical and infrared frequencies which also, unexpectedly, adds functionality to the structures.

Field imaging near to the surface of terahertz reflective optics using a vector network analyzer.

A vector network analyzer-based quasi-optical measurement system that is suitable for mapping electric field intensity and phase near to the surface of terahertz reflective optics is presented. The system uses a fixed five parabolic mirror and transmitter/receiver head arrangement that has the benefit of requiring only the sample to be swept during measurement. The system has been tested with a micromilled aluminum zone plate reflector used as an exemplar structure. The measured focal point of the zone plate reflector, at its designed frequency of 1 THz, is shown to correspond well to both finite difference time-domain simulations and analytical theory.

Model for large-area monolayer coverage of polystyrene nanospheres by spin coating.

Nanosphere lithography, an inexpensive and high throughput technique capable of producing nanostructure (below 100 nm feature size) arrays, relies on the formation of a monolayer of self-assembled nanospheres, followed by custom-etching to produce nanometre size features on large-area substrates. A theoretical model underpinning the self-ordering process by centrifugation is proposed to describe the interplay between the spin speed and solution concentration. The model describes the deposition of a dense and uniform monolayer by the implicit contribution of gravity, centrifugal force and surface tension, which can be accounted for using only the spin speed and the solid/liquid volume ratio. We demonstrate that the spin recipe for the monolayer formation can be represented as a pathway on a 2D phase plane. The model accounts for the ratio of polystyrene nanospheres (300 nm), water, methanol and surfactant in the solution, crucial for large area uniform and periodic monolayer deposition. The monolayer is exploited to create arrays of nanoscale features using 'short' or 'extended' reactive ion etching to produce 30-60 nm (diameter) nanodots or 100-200 nm (diameter) nanoholes over the entire substrate, respectively. The nanostructures were subsequently utilized to create master stamps for nanoimprint lithography.

MRFy: Remote Homology Detection for Beta-Structural Proteins Using Markov Random Fields and Stochastic Search.

We introduce MRFy, a tool for protein remote homology detection that captures beta-strand dependencies in the Markov random field. Over a set of 11 SCOP beta-structural superfamilies, MRFy shows a 14 percent improvement in mean Area Under the Curve for the motif recognition problem as compared to HMMER, 25 percent improvement as compared to RAPTOR, 14 percent improvement as compared to HHPred, and a 18 percent improvement as compared to CNFPred and RaptorX. MRFy was implemented in the Haskell functional programming language, and parallelizes well on multi-core systems. MRFy is available, as source code as well as an executable, from http://mrfy.cs.tufts.edu/.

Compressive genomics for protein databases.

MOTIVATION: The exponential growth of protein sequence databases has increasingly made the fundamental question of searching for homologs a computational bottleneck. The amount of unique data, however, is not growing nearly as fast; we can exploit this fact to greatly accelerate homology search. Acceleration of programs in the popular PSI/DELTA-BLAST family of tools will not only speed-up homology search directly but also the huge collection of other current programs that primarily interact with large protein databases via precisely these tools. RESULTS: We introduce a suite of homology search tools, powered by compressively accelerated protein BLAST (CaBLASTP), which are significantly faster than and comparably accurate with all known state-of-the-art tools, including HHblits, DELTA-BLAST and PSI-BLAST. Further, our tools are implemented in a manner that allows direct substitution into existing analysis pipelines. The key idea is that we introduce a local similarity-based compression scheme that allows us to operate directly on the compressed data. Importantly, CaBLASTP's runtime scales almost linearly in the amount of unique data, as opposed to current BLASTP variants, which scale linearly in the size of the full protein database being searched. Our compressive algorithms will speed-up many tasks, such as protein structure prediction and orthology mapping, which rely heavily on homology search. AVAILABILITY: CaBLASTP is available under the GNU Public License at http://cablastp.csail.mit.edu/ CONTACT: bab@mit.edu.

Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data.

BACKGROUND: New technology has resulted in high-throughput screens for pairwise genetic interactions in yeast and other model organisms. For each pair in a collection of non-essential genes, an epistasis score is obtained, representing how much sicker (or healthier) the double-knockout organism will be compared to what would be expected from the sickness of the component single knockouts. Recent algorithmic work has identified graph-theoretic patterns in this data that can indicate functional modules, and even sets of genes that may occur in compensatory pathways, such as a BPM-type schema first introduced by Kelley and Ideker. However, to date, any algorithms for finding such patterns in the data were implemented internally, with no software being made publically available. RESULTS: Genecentric is a new package that implements a parallelized version of the Leiserson et al. algorithm (J Comput Biol 18:1399-1409, 2011) for generating generalized BPMs from high-throughput genetic interaction data. Given a matrix of weighted epistasis values for a set of double knock-outs, Genecentric returns a list of generalized BPMs that may represent compensatory pathways. Genecentric also has an extension, GenecentricGO, to query FuncAssociate (Bioinformatics 25:3043-3044, 2009) to retrieve GO enrichment statistics on generated BPMs. Python is the only dependency, and our web site provides working examples and documentation. CONCLUSION: We find that Genecentric can be used to find coherent functional and perhaps compensatory gene sets from high throughput genetic interaction data. Genecentric is made freely available for download under the GPLv2 from http://bcb.cs.tufts.edu/genecentric.

Terahertz near-field imaging using subwavelength plasmonic apertures and a quantum cascade laser source.

The first demonstration, to our knowledge, of near-field imaging using subwavelength plasmonic apertures with a terahertz quantum cascade laser source is presented. "Bull's-eye" apertures, featuring subwavelength circular apertures flanked by periodic annular corrugations were created using a novel fabrication method. A fivefold increase in intensity was observed for plasmonic apertures over plain apertures of the same diameter. Detailed studies of the transmitted beam profiles were undertaken for apertures with both planarized and corrugated exit facets, with the former producing spatially uniform intensity profiles and subwavelength spatial resolution. Finally, a proof-of-concept imaging experiment is presented, where an inhomogeneous pharmaceutical drug coating is investigated.

A thermally actuated microgripper as an electrochemical sensor with the ability to manipulate single cells.

The design and fabrication of a thermally actuated polymeric microgripper incorporating a bare gold working electrode is described. Initial electrochemical tests confirm that the microgripper sensor works as an effective microelectrode, opening up exciting possibilities in single cell measurements.