Software Technology for System and Method for Programmable Illumination Pattern Generation

Invented by Michael Seul, Chiu Wo Chau, Bioarray Solutions Ltd

The Bioarray Solutions Ltd invention works as follows

Background for System and Method for Programmable Illumination Pattern Generation

I?Ions Electric Fields and Fluid Flow: Field Induced Formation of Planar Bead Arrays

Electrokinesis” refers to the phenomenon of electromagnetic fields causing a mobile ions around charged objects in an electrolyte. A diffuse ion cloud is formed when an object with a given surface charge is immersed into a solution containingions to screen it. The arrangement of two layers of immobile charges and a screening cloud of mobile counter-ions in the solution is called a “double layer”. The fluid is not electroneutral in this area of finite thickness. The region is not electroneutral because of the electric fields that act on it. These ions will cause the fluid to entrain in the diffuse layer. The fluid’s spatial distribution will determine the flow fields. The simplest form of electrokinetic phenomena is electroosmosis. This happens when an electric field is applied parallelly to the surface of a sample vessel or electrode with fixed surface charges. For example, a silicon oxide electrode (in neutral pH range). The electric field accelerates counter-ions in an electrode double layer, causing them to drag along solvent molecules and resulting in bulk fluid flow. This effect may be significant in narrow capillaries, and can be used to your advantage when designing fluid pumping systems.

Electrophoresis” is a similar phenomenon. It refers to field-induced transports of charged particles in an electrolyte. An electric field accelerates the mobile ions within the particle’s double layer, just like electroosmosis. Contrary to the previous case, if the particle is mobile, it will compensate the field-induced motion (and the resulting Ionic Current) by moving in an opposite direction. The role of electrophoresis is important in industrial coating processes. It is also of interest, along with electroosis, in connection with the development capillary electrophoresis to be a majorstay in modern bioanalytical seperation technology.

In restricted geometries such as the one of a shallow experiment chamber, such as a?sandwich’, it is possible to observe the effects of electroosmotic flow in confined spaces. Two planar electrodes. The surface charge distribution and topography on the bounding electrode surfaces are crucial in determining the nature of electroosmotic flow. This is a “sandwich”. An electrochemical cell can be made by two electrodes separated by a small gap. The oxide-capped silicon wafer will form the bottom electrode, while the optically transparent, conducting ITO will form the other electrode. “The silicon (Si) wafer is a thin slice from a single crystal silicon. It has been doped to achieve electrical conductivity at suitable levels and then insulated from electrolyte solution with a thin layer silicon oxide (SiOx).

A (DC or AC electric field applied to the electrode surface can induce the reversible aggregation beads into planar aggregates. The phenomenon was previously observed in a cell made from two conductive ITO electrodes. (Richetti Prost, Barois, J. Physique Lettr. 45, L-1137 to L-1143 (1984), which the contents are incorporated in this document by reference). However, it was previously demonstrated that electrokinetic flow is responsible for the attractive interaction between beads (Yeh Seul and Shraiman?Assembly Of Ordered Colloidal Aggregates By Electric Field Induced Fluid Flu?, Nature 386 57?59 (1997)), whose contents are also incorporated in this document by reference). This flow is due to the effect of non-uniformities in spatial distribution of current near the electrode. These non-uniformities can be explained by the presence of colloidal beads near the electrode. Each bead blocks the movement of ions within the electrolyte. It has been shown that a single bead can generate a toroidal fluid flow centered at the bead when it is placed close to the electrode’s surface. Multiple methods can be used to create fluid flow lateral toward low impedance regions by intentionally creating spatial non-uniformities. These methods will be described in the following sections.

Particles embedded within the electrokinetic flow can be advected without regard to their particular chemical or biological nature while simultaneously altering flow field. The electric field-induced assembly planar aggregates or arrays can be applied to a variety of colloidal particles, including: beaded polymer resins (beads) ), lipids vesicles and whole chromosomes. Cells and biomolecules such as DNA and proteins, as well metal or semiconductor clusters and colloids.

The flow-mediated attraction between beads can travel a great distance. This is important for the applications that will be described. Planar aggregates form when an electric field is applied externally and then disassemble once the field is removed. The array assembly process is determined by the strength of the applied field. This determines the arrangement of the beads within the array. As a function, the applied voltage increases and beads form planar aggregates. These are composed of particles that are mobile and loosely packed. Then, they adopt a tighter packing and then exhibit a spatial arrangement resembling a raft or bubbles. Reversible transitions are possible between states of increasing internal ordeal, and complete disassembly is possible when applied voltage is removed. Another arrangement is that beads at low initial concentration form small clusters, which then assume positions within an orderly?superstructure?.

II?”Patterning Silicon Oxide Electrode Surfaces

Electrode patterning in accordance with a predetermined design facilitates the quasi-permanent modification of the electrical impedance of the EIS (Electrolyte-Insulator-Semiconductor) structure of interest here. Electrode-patterning modifies the EIS impedance spatially to determine the ionic current near the electrode. Beads can either seek out or avoid high ionic current regions depending on the frequency of the electric field. Spatial patterning allows for explicit external control over the shape and placement of beads arrays.

There are many methods for patterning, but two techniques offer the most advantages. The first is UV-mediated regrowth of a thin layer of oxide on a properly prepared silicon substrate. This method avoids photolithographic resist patterning or etching. The UV illumination mediates the transformation of exposed silicon to oxide in the presence of oxygen. The thickness of the oxide layer is dependent on its exposure time. This can be spatially modulated through the use of patterned masks in the UV illumination path. This thickness modulation, which is typically around 10 Angstroms in size, results in spatial modulations in the Si/SiOx interface’s impedance. It leaves a flat, chemically homogeneous surface that is exposed to the electrolyte solution. Photochemical oxidation (UV-mediated photochemical oxygenation) of a suitable chemical substance may produce spatial modulations in electrode surface charge distribution. This is done by first depositing a monolayer film onto the SiOx surface. This allows fine control of local features and electrokinetic flow.

A variation on this photochemical modulation involves the creation of lateral variations in the EIS impedance, and thus in the current generated by the applied electric field. This can be achieved by controlling UV exposure to cause a slow lateral variation of the oxide thickness and/or the surface charge density. Controlling lateral gradients is key to inducing lateral bead transportation. It also facilitates fundamental operations such as the capture and channeling beads to a predetermined destination using conduits made of impedance elements embedded in Si/SiOx interface. Photochemical patterning of functionalized chemicals overlayers can also be applied to other types electrode surfaces, including ITO.

III?Light-controlled Modulation of the Interfacial Impedance

The basis for controlling the electrokinetic forces that mediate the aggregation of beads is the spatial and temporal modulation in the EIS-impedance according to a pattern or external illumination. Remote control of the formation, placement, and rearrangement bead arrays is possible via light-modulated electrokinetic assembly. This allows for a wide variety of interactive manipulations of colloidal beads as well as biomolecules.

It will help to review the photoelectric properties of semiconductors in order to understand the basic principle of this method. This includes the EIS structure, the Insulating SiOx and Semiconductor structures (I), E (Electrolyte solution) and S (Semiconductor). The photoelectric characteristics of this structure are closely related to those of a standard Metal-Insulator-Semiconductor (MIS) or Metal-Oxide-Semiconductor (MOS) devices which are described in S. M. Sze, ?The Physics of Semiconductors?, 2nd Edition, Chapt. 7 (Wiley Interscience 1981), whose contents are incorporated by reference.

The interface between semiconductor and insulating oxide layers deserves special attention. Understanding the MOS structure’s electrical response to light is crucial. This concept refers to a small, but finite space charge region that forms at the Si/SiOx Interface in the presence of an applied bias potential. An effective bias in the form a junction potential is present for the EIS structure under all conditions. Space charge regions form due to distortions of the semiconductor’s conduction and valence bands (?bandbending?). The interface is in its vicinity. This is due to the fact that the interface has a bias potential. However, the insulating oxide prevents charge transfer. In electrochemical terms, this means that the EIS structure eliminates Faradaic effect. Instead, opposite sign charges accumulate on either side the insulating oxide layer to generate a finite degree of polarization.

In the presence a reverse bias, the conduction and valence band edges of an N-doped semiconductor bend upwards near the Si/SiOx Interface and electrons flow out from the interfacial area in response to the corresponding voltage gradient. A majority carrier depletion layer forms near the Si/SiOx Interface. This region is able to produce electron-hole pairs through light absorption. If they don’t recombine instantaneously, electron-hole pairs can be split by the local acting electric field and a corresponding current flows. This latter effect allows for control over the electrokinetic assembly beads in an electrolyte solution.

Two aspects of an equivalent circuit that represents the EIS structure can be used to better understand the frequency dependence of light-induced modulation. The first is a close analogy between the detailed electrical characteristics at the electrolyteoxide interface and the depletion layer at interface between semiconductor and insulator. The depletion layer has similar electrical characteristics to the double layer. It also exhibits a voltage-dependent capacitance. The depletion layer’s impedance can be reduced by illumination, as we have already discussed. The second reason is that the oxide layer’s capacitive electrical response means that it will only pass current above a threshold (?threshold?) frequency. If the applied voltage frequency exceeds the threshold, illumination may lower the effective impedance for the entire EIS structure.

Effective reduction of EIS impedance is also dependent on light intensity, which affects the rate at which electron-hole pairs are generated. The majority of photogenerated electrons are free to flow out of the depletion area and contribute to the photocurrent, even if there is no significant recombination. The rest of the hole charge builds up near the Si/SiOx Interface and blocks the electric field from the depletion area. The rate of recombination decreases and electron-hole separation efficiency (and hence the photocurrent) decreases. Given the values of frequency, amplitude, and voltage applied, it is expected that the current will increase in intensity as the illumination intensifies. Then, it will decrease. The impedance decreases initially to a minimum (at maximum current), and then it decreases.

This intensity dependence can be used to inducing the lateral displacement beads between partially covered and fully masked regions. The fully exposed areas will correspond to regions of interface with the lowest impedance and therefore the highest current. Beads will be drawn into these areas as the illumination intensities increase. The effective EIS impedance of fully exposed regions will decrease as the photocurrent increases. This can lead to an inversion of current’s lateral gradient. The fully exposed areas will be used to draw beads. You can also use time-varying variations in the illumination pattern to influence bead movement.

IV?Integration in Biochemical Analysis in a Miniaturized and Planar Format

Planar array assays are a good option for biomolecular screening and medical diagnostics. They have the advantage of high parallelity and automation, which allows them to achieve high throughput in multi-step, complex analytical protocols. Miniaturization will reduce pertinent mixing times due to the small spatial scale. It will also result in reduced sample and reagent volumes, as well a reduction in power requirements. Integration of biochemical analytical methods into a miniaturized system surfaced on a planar substrate (chip?) would be significant. This would result in significant improvements in performance and cost reductions in diagnostic and analytical procedures.