Programmable Sequence Research Articles

Programmable Fluidic Production of Microparticles with Configurable Anisotropy

We report a technique for continuous production of microparticles of variable size with new forms of anisotropy including alternating bond angles, configurable patchiness, and uniform roughness. The sequence and shape of the anisotropic particles are configured by exploiting a combination of confinement effects and microfluidics to pack precursor colloids with different properties into a narrow, terminal channel. The width and length of the channel relative to the particle size fully specify the configuration of the anisotropic particle that will be produced. The precursor spheres packed in the production zone are then permanently bonded into particles by thermal fusing. The flow in the production zone is reversed to release the particles for collection and use. Particles produced have linear chain structure with precisely configured, repeatable bond angles. With software programmable microfluidics, sequence and shape anisotropy are combined to yield synthesized homogeneous (type "A"), surfactantlike (type "A-B") or triblock (type "A-B-A") internal sequences in a single device. By controlling the dimensions of the microfluidic production zone, triangular prisms and particles with controlled roughness and patchiness are produced. The fabrication method is performed with precursors spheres with diameter as small as 3.0 microm.

Genetic Engineering of Self-Assembled Protein Hydrogel Based on Elastin-like Sequences with Metal Binding Functionality

Recombinant DNA methods have been exploited to enable the creation of protein-based block copolymers with programmable sequences, desired properties, and predictable three-dimensional structures. These advantages over conventional polymer counterparts facilitate the utility of this new class of biomaterials in a wide range of applications. In this project, we exploited the environmental application of protein-based block copolymers based on elastin-like protein (ELP) sequences. Triblock copolymers containing charged and hydrophobic segments were synthesized. Chain lengths of each segment were manipulated in order to maintain a gelation point below room temperature. Polyhistidine sequences were successfully incorporated into the hydrophilic segment without disruption of the self-assembled hydrogel formation. The microscopic structure was further investigated using laser confocal microscopy. The metal binding capability and capacity of resulting hydrogel were studied to demonstrate the functionality of polyhistidine and its environmental application for heavy metal removal. Reversibility of metal binding was demonstrated, indicating the cost-effectiveness of this hydrogel. Significantly, we envision that this versatile strategy of incorporating functional groups within a 3-D protein network provides new possibilities in creation of biomaterials with great control over structure-property relationships.

Parametric imaging of contrast ultrasound for the evaluation of neovascularization in liver tumors

To assess the efficacy of parametric imaging for the diagnosis of neovascularization in liver tumors. The subjects were 17 rabbits (five with normal liver and 12 with VX2 tumor implanted in the liver). The contrast agents used were SonoVue (Bracco, Milan, Italy). A diagnostic ultrasound system was used with a programmable replenishment sequence. The images obtained between the initial frame after the high mechanical index (MI) scan, which diminishes microbubbles in the scan volume, and the current frame were coded in color according to the arrival and peak times. After the experiment, the tumors were excised and sectioned. Sections were prepared for light microscopy with hematoxylin-eosin (HE) staining and CD31 staining to evaluate vascular density. Arrival time imaging (ATI) delineated the fine blood vessels (100-200 mum in diameter) in all of the rabbits. Tortuous and meandering tumor vessels were visualized in the VX2 tumors. Differences of perfusion velocity between tumor tissue and tumor-free areas were shown in peak time imaging (PTI). Vascularity evaluated on the ATI and perfusion speed recognized on the ATI and PTI were related to the vascular density measured by pathological investigation. Parametric imaging is a promising new method for the visualization of perfusion and the estimation of tumor blood vessels.

Engineering hydrogen‐bonded duplexes

AbstractBased on several simple, readily available building blocks, oligoamide strands carrying various arrays of hydrogen‐bond donors and acceptors, i.e. hydrogen‐bonding sequences, have been designed and synthesized. Detailed characterization indicates that these oligoamide strands associate via their hydrogen‐bonding edges into doubled stranded pairs (duplexes), which are characterized by programmable sequence specificity and adjustable stability. Using these hydrogen‐bonded duplexes as association units, supramolecular structures, such as β‐sheets and non‐covalent block copolymers, are obtained by simply mixing the corresponding components. Recently, by incorporating reversible covalent interactions into these hydrogen‐bonded duplexes, sequence‐specific formation of covalently linked structures has been realized under thermodynamic conditions, which has opened an entirely new avenue to the development of previously unknown dynamic covalent structures such as various block copolymers. Copyright © 2007 Society of Chemical Industry

Ferrofluid lithography

A novel self-aligned ‘soft masking’ method that is compatible with traditionalphotolithographic processes is demonstrated. This method uses a suspension of ultrafineiron oxide grains (ferrofluid) to protect or de-protect selected areas of a magneticallypatterned substrate according to a programmable sequence. Automatic mask formation andregistration is controlled by ferromagnetic alignment marks patterned on a substrate.External magnetic field bias applied to the system causes ferrofluid to aggregate only overdesignated areas on the surface, thereby masking those areas from UV or chemicalexposure.

Programmable Self-Aligning Ferrofluid Masks for Lithographic Applications

A novel self-aligned soft method that is compatible with traditional photolithographic processes is demonstrated. This method uses a suspension of ultra-fine iron oxide grains (ferrofluid) to protect or de-protect selected areas of a magnetically patterned substrate according to a programmable sequence. Automatic mask formation and registration is controlled by ferromagnetic alignment marks patterned on a substrate. External magnetic fields applied to the system causes ferrofluid to aggregate only over designated areas on the surface, thereby masking those areas from UV and/or chemical exposure.

Design of a sequence-specific DNA bisintercalator.

Programmable bisintercalators: Symmetric synthetic DNA bisintercalators (see picture) based on the H-pin polyamide motif afford high affinity and programmable sequence specificity.

The myosin coiled-coil is a truly elastic protein structure.

Coiled-coils occur in a variety of proteins involved in mechanical and structural tasks in the cell. Their mechanical properties are important in various contexts ranging from hair elasticity to synaptic fusion. Beyond their importance in biology, coiled-coils have also attracted interest as programmable protein sequences for the design of novel hydrogels and materials. We have studied the elastic properties of the myosin coiled-coil at the single molecule level. The coiled-coil undergoes a massive structural transition at forces between 20 and 25 pN where the coil extends to about 2.5 times its original length. Unlike all other proteins investigated mechanically so far, this transition is reversible on a timescale of less than a second, making the coiled-coil a truly elastic protein.

Non-covalent synthesis in aqueous solution of discrete multi-porphyrin aggregates with programmable stoichiometry and sequence.

This unprecedented calixarene templated, noncovalent synthesis of multi-porphyrin complexes in aqueous solution makes it possible to plan the nature, stoichiometry, and sequence of porphyrins. The proposed method presents the same accuracy of the covalent approach and a 100% yield, but it is not as time-consuming as the latter method.

Step-by-step engineered multiparticle entanglement

After quantum particles have interacted, they generally remain in an entangled state and are correlated at a distance by quantum-mechanical links that can be used to transmit and process information in nonclassical ways. This implies programmable sequences of operations to generate and analyze the entanglement of complex systems. We have demonstrated such a procedure for two atoms and a single-photon cavity mode, engineering and analyzing a three-particle entangled state by a succession of controlled steps that address the particles individually. This entangling procedure can, in principle, operate on larger numbers of particles, opening new perspectives for fundamental tests of quantum theory.

Architecture for hardware implementation of programmableternary de Bruijn sequence generators

An architecture for direct hardware implementation of programmable ternary de Bruijn sequence generators is described. The approach employed is based on the use of two recently introduced ternary logic components: the J3K3 flip-flop sequencer and the hybrid implemented U-gate. Generation of de Bruijn sequences and the proposed implementation approach are described with the aid of an example.

Tritium Pellet Injector for TFTR

The tritium pellet injector (TPI) for the Tokamak Fusion Test Reactor (TFTR) will provide a tritium pellet fueling capability with pellet speeds in the 1- to 3-km/s range for the TFTR deuterium-tritium (D-T) phase. The existing TFTR deuterium pellet injector (DPI) has been modified at Oak Ridge National Laboratory (ORNL) to provide a four-shot, tritium-compatible, pipe-gun configuration with three upgraded single-stage pneumatic guns and a two-stage light gas gun driver. The TPI was designed to provide pellets ranging from 3.3 to 4.5 mm in diameter in arbitrarily programmable firing sequences at speeds up to approximately 1.5 km/s for the three single-stage drivers and 2.5 to 3 km/s for the two-stage driver. Injector operation is controlled by a programmable logic controller. The new pipe-gun injector assembly was installed in the modified DPI guard vacuum box, and modifications were made to the internals of the DPI vacuum injection line, including a new pellet diagnostics package. Assembly of these modified parts with existing DPI components was then completed, and the TPI was tested at ORNL with deuterium pellet. Results of the limited testing program at ORNL are described. The TPI is being installed on TFTR to support the D-D run period in 1992.more » In 1993, the tritium pellet injector will be retrofitted with a D-T fuel manifold and secondary tritium containment systems and integrated into TFTR tritium processing systems to provide full tritium pellet capability.« less

A Computer Controlled Device to Facilitate Studies of the Kinetics of Ligand-Binding: Binding of Diazepam to Bovine Brain Membranes

A device to facilitate kinetic receptor filtration assays is described. The receptor containing membranes and the labeled ligand are placed in two separate syringes and are rapidly mixed into a collecting syringe using a pneumatic ram. Shortly after the start of mixing, a pneumatically controlled valve switches the collecting syringe containing the receptor-ligand mixture to the filtration unit. Filtration is performed on glass/microfiber filters or equivalent by pushing the plunger of the collecting syringe by a stepper motor. A valve positioner controlling several valves allows the filtered membranes to be washed and dried by pressure in any user programmable sequence. Further filtration of the receptor-ligand mixture can be programmed at selected time points. The entire system is controlled by an IBM-PC. With this system, the association and dissociation of diazepam from crude bovine-brain membranes has been studied at 4 degrees C. The dissociation shows a biphasic pattern with half lifes of 1.3 and more than 23 minutes respectively. Association appears to be into a single compartment.

Development of centrally controlled synchrotron radiation lithography beamline system

The centrally controlled beamline system for synchrotron radiation lithography has been investigated using the SORTEC storage ring(l GeV). From a practical standpoint, the recently built beamlines aim at attaining a centrally controlled beamline system, which is also serially interfaced with the storage ring. In operating the beamlines, not only local control, but also a central control notion is adopted. The central beamline control system comprises a beamline main computer and a programmable sequence controller (PSC) link. The local beamline control system consists of a PSC, a control panel, and a personal computer. The beamline main computer collects each beamline status datum through the PSC link, receiving the storage ring data from the main computer of the 1 GeV synchrotron radiation (SR) source. A novel oscillating mirror mechanism is proposed, in which the mirror chamber, driven by a combination of a cam mechanism and pulse motor installed in air, is oscillated to scan the mirror, thus producing high reliability and compact design. In addition, a practical beamline structure is offered which fulfills system vacuum protection and protects operators from radiation exposure.

Programmable fiber optic signal processor

Signal storage in a single-mode optical fiber with programmable time delay is described. The reflectivity monitored delay line contains three Fabry-Perot interferometers arranged in serial fashion. By thermally tuning two of the interferometers for near-zero reflectance and the third for relatively high ( Omega 14%) reflectance, any of three possible time delays can be selected. Generation of programmable binary sequences is also demonstrated. >

Interlock systems using programmable sequence controllers and a monitoring system of the Photon Factory beamlines

Fully utilizing programmable sequence controllers, interlock systems for the Photon Factory beamlines were newly designed and constructed for providing the reliable and versatile control logic that is required for beamline characteristics. The systems, accommodated with radiation safety and vacuum interlock logic as well as protection logic for various components against heat and radiation damage, are in operation on eight beamlines. A centralized monitoring system, to which all interlock systems for the beamlines are connected through optical fiber links, was constructed for simultaneously monitoring the operation status of the interlock systems. Individual operations of each interlock system are also controlled by the monitoring system. Log data collected by the monitoring system are summarized and analyzed in order to provide the necessary information for smooth and safe operation as well as for further improvements of the beamlines. The interlock and the monitoring systems are described along with operational remarks.

Simplified eight-shot pneumatic pellet injector for plasma fueling applications on the Princeton Beta Experiment and on the Advanced Toroidal Facility

Plasma fueling via injection of solid hydrogenic pellets has expanded the operating range for tokamaks and stellarators to higher densities than attainable with gas puffing. Pellet injection has also resulted in improved plasma energy confinement in tokamak discharges for which the pellet or pellets penetrate deep into the plasma core. The eight-shot pneumatic pellet injector described herein has been developed for use on the Princeton Beta Experiment and on the Advanced Toroidal Facility for routine plasma fueling and for confinement optimization studies. The injector is based upon the so-called ‘‘pipe-gun’’ concept, which generates deuterium and hydrogen pellets by direct condensation in the gun barrel tubes, segments of which are cooled below the hydrogen triple-point temperature by contact with a liquid-helium-cooled block. Control of the pellet length is achieved both by regulating the deuterium fill pressure and by establishing temperature gradients along the barrel tubes. This injector features eight independent gun barrel assemblies mounted around the perimeter of a single cold block, each coupled to an ORNL-designed fast propellant valve. Thus, the injector is capable of injecting arbitrarily programmable sequences of up to eight pellets of sizes ranging from 1 to 3 mm at speeds up to 1500 m/s.

Laser velocimetry for benthic sediment transport

Two deep-sea laser Doppler velocimeter (LDV) systems are described. The first, a backscatter instrument, measures the two horizontal components of velocity at a programmable sequence of heights above the seafloor, from a few cm's to roughly 40 cm. The second instrument, a forward scatter system, measures the downstream and vertical velocities in an inverted bottom flume, SeaDuct, thereby also obtaining the Reynold's stress. Both instruments sample the velocity at 32 Hz although the actual velocity “realization” rate for the backscatter instrument depends strongly on the suspended mass concentration in the water column. In this paper we describe the LDV instrumentation and present example data. The observations with the backscatter system in natural flows were taken at the HEBBLE site in water depth of 4815 m and over a region of microtopography. These suggest departure of the velocity profile from the logarithmic wall layer which may be due to a lack of statistical stationarity, but a consistent change in direction of flow over the short range of heights suggests steering by bottom bedforms. The turbulent kinetic energy appears to vary weakly near bottom. Data from the SeaDuct system at a fixed height, taken at USGS site ‘Q’, indicate constancy of the drag coefficient and the ratio of stress to total turbulent intensity. The stress-suspended load relationship for the sediment at this site shows large erosion at low stress, with no evidence of a critical stress for initiation of motion.

Radiation safety interlock system for Photon Factory X-ray beam lines

Self-contained interlock systems for the X-ray beam lines of the Photon Factory were designed and fabricated in order to protect experimenters and the service staff from radiation hazards while at the same time providing experimenters with smooth and easy access to the synchrotron radiation sources. The interlock systems utilize programmable sequence controllers in order to meet the individual safety logic required for beam line characteristics. The environment as well as components related to the interlock systems, system features, safety logic and operating conditions are described along with the design principles. A few operational remarks concerning the interlock systems are also presented.

Fast, versatile, and inexpensive pulse sequence generator

A fast, versatile, and inexpensive programmable digital pulse sequence generator (PSG) suitable for use in broadline pulsed NMR has been developed. Its features include 20 ns resolution of pulse duration, operation without direct computer supervision, and enough flexibility to produce essentially any pulse sequence. The architecture and construction of the PSG are discussed, and an example of its programming is presented.