Patent ID: 7931867

Claim:
A system, comprising: a substrate, comprising: a first layer comprising a first surface having at least first and second material regions, the first and second material regions having one or more chemical or physical properties that differ when the first and second regions are exposed to a first chemical environment, wherein said first material region comprises a transparent material, and said second material comprises an opaque metal with any associated metal oxide; wherein the first layer comprises a layer of the first material and a layer of the second material, wherein the layer of second material is a discontinuous layer disposed over the layer of first material layer resulting in a first surface of the first layer having apertures with exposed regions of first material, the apertures having a cross-sectional dimension that is from about 10 nm to about 200 nm; a second layer, comprising a coating material that associates preferentially with the second material regions, disposed selectively over second material regions to provide a second surface to the substrate, whereby the coating material covers substantially all of the second material regions, whereby at least portions of the first material regions exposed by the aperture are not coated by the second layer, and wherein the second surface that is substantially uniform with respect to the one or more chemical or physical properties, when the second surface is exposed to the first chemical environment; and an optical detection system positioned to receive optical signals from a reaction fluid disposed upon the substrate.