This disclosure provides methods and devices for the label-free detection of target molecules of interest. The principles of the disclosure are particularly applicable to the detection of biological molecules (e.g., DNA, RNA, and protein) using standard SiO.sub.2-based microarray technology.

Systems, computer program products, and methods for using a flow cell array are provided herein. A computer program product includes a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a device to cause the device to determine placement of multiple reaction site openings, wherein each reaction site opening is connected to a first sub-surface channel; connect the first sub-surface channel to two or more additional sub-surface channels by multiple vias; and provide a material for multiple reaction sites, wherein an overlap of the multiple reaction site openings and the material delineate the multiple reaction sites.

Apparatus, computer program products, and methods for using a flow cell array are provided herein. A computer program product includes a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a device to cause the device to determine placement of one or more reaction sites on a first component; provide a material for the reaction sites in one or more surface channels of the first component; connect the first component to a second component to form an array, wherein the surface channels of the first component connect the reaction sites with one or more vias, and wherein the second component comprises the vias connected to multiple sub-surface channels; and align the surface channels of the first component with the vias of the second component to form a connection between the first component and the second component.

Systems, computer program products, and methods for using a flow cell array are provided herein. A system includes at least one processor coupled to a memory and configured for delivering multiple items of chemical matter independently to multiple reaction sites of a flow cell array across multiple distinct instances of time; imaging multiple parallel chemical reactions at the multiple reaction sites of the flow cell array; and recording an emission from each of the multiple chemical reactions site.

Systems, computer program products, and methods for using a flow cell array are provided herein. A system includes at least one processor coupled to a memory and configured for determining placement of multiple reaction site openings, wherein each reaction site opening is connected to a first sub-surface channel; connecting the first sub-surface channel to two or more additional sub-surface channels by multiple vias; and providing a material for multiple reaction sites, wherein an overlap of the multiple reaction site openings and the material delineate the multiple reaction sites.

Screening assays and methods of performing such assays are provided. In certain examples, the assays and methods may be designed to determine whether or not two or more species can associate with each other. In some examples, the assays and methods may be used to determine if a known antigen binds to an unknown monoclonal antibody.

A method for making a microfluidic device having one or more different patterned polymeric hydrogel nanostructure is provided. The method includes: providing a first substrate having a first patterned array of polymeric hydrogel nanostructures on a first interior surface and a peripheral surface portion; providing a second substrate having a second interior surface and a side wall with an end surface; and bonding the end surface of the second substrate to the peripheral surface portion of the first substrate such that the first and second interior surfaces define a hermetic cavity within the bonded first and second substrate. The microfluidic device can be designed to include a variety of different patterned array of polymeric hydrogel nanostructures depending on the desired application and properties for the device.

Methods for regulating and continuously monitoring a chemical synthesis reaction using micro-objects and electro-magnetic radiation include introducing micro-objects to a reaction mixture, determining a plasmon resonance of the micro-object based on a characteristic of the micro-object, and applying electro-magnetic radiation that is wavelength-matched to the plasmon resonance of the micro-object.

Methods of liquid-phase synthesis of polymers using polymer substrates and systems for facilitating such methods allow gating of a synthetic reaction into a binary (reacted or unreacted) readout. Polymer substrates are used as carriers for molecular reagents and act as separation tags that allow them to be purified using nanoscale deterministic lateral displacement. Two polymer substrates are linked together by a bond-forming reaction to form a longer polymer that includes a synthetic product. The synthetic product can be purified away from unreacted polymers/reagents using strand-length dependent lateral displacement.

There is disclosed a process for in vitro synthesis and assembly of long, gene-length polynucleotides based upon assembly of multiple shorter oligonucleotides synthesized in situ on a microarray platform. Specifically, there is disclosed a process for in situ synthesis of oligonucleotide fragments on a solid phase microarray platform and subsequent, on device assembly of larger polynucleotides composed of a plurality of shorter oligonucleotide fragments.