290 7.6  High-Throughput Techniques

Following the treatment with an appropriate photoresist developer leaves a surface pattern

consisting of some regions of exposed substrate, where, in some of the regions, the photo­

resist still remains. The exposed regions are accessible to further chemical etching treatment,

but regions masked by the remaining photoresist are not. Chemical etching treatment thus

results in etched pattern onto the substrate itself. Also, at this stage, deposition or growth

onto the patterned substrate can be performed, of one or more thin layers or additional

material, for example, to generate electrically conducting, or insulating, regions of the

patterned surface.

This can be achieved using a range of techniques including thermal oxidation and chem­

ical vapor deposition, physical vapor deposition methods such as sputtering and evaporative

deposition, and epitaxy methods (which deposit crystalline layers onto the substrate sur­

face) (Figure 7.4b). Evaporative deposition is commonly used for controlled coating of a sub­

strate in one or more thin metallic layers. This is typically achieved by placing the substrate

in a high vacuum chamber (a common vacuum chamber used is a Knudsen cell) and then

by winding solid metallic wire (e.g., gold, nickel, chromium are the common metals used)

around a tungsten filament. The tungsten filament is then electrically heated to vaporize

the metal wire, which solidifies on contact with the substrate surface. The method is essen­

tially the same as that used for positive shadowing in electron microscopy (see Chapter 5).

Following any additional deposition, any remaining photoresist can be removed using spe­

cific organic solvent treatment to leave a complex patterned surface consisting of etches and

deposition areas.

Sputtering is an alternative to vapor deposition for coating a substrate in a thin layer of

metal. Sputter deposition involves ejecting material from a metal target that is a source onto

the surface of the substrate to be coated. Typically, this involves gas plasma of an inert gas

such as argon. Positive argon ions, Ar+​, are confined and accelerated onto the target using

magnetic fields in a magnetron device to bombard the metal sample to generate ejected metal

atoms of several tens of keV of energy. These can then impact and bind to the substrate sur­

face as well as cause some resputtering of metal atoms previously bound to the surface.

Sputter deposition is largely complementary to evaporative deposition. One important

advantage of sputtering is that it can be applied to metals with very high vaporization

temperatures that may not be easy to achieve with typical evaporative deposition devices.

Also, the greater speed of ejected metal atoms compared to the more passive diffusive speed

from evaporative deposition results in greater adhesion to substrate surfaces in general. The

principal disadvantage of sputtering over evaporative deposition is that sputtering does not

generate a distinct metallic shadow around topographic features in the same way that evap­

orative deposition does because of the extra energy of the ejected metal atoms, resulting in

a diffusive motion around the edges of these surface features; this can make the process of

lift-​off more difficult.

Microfabrication methods have been used in conjunction with biological conjugation

tools (see the previous section of this chapter) to biochemically functionalize surfaces, for

example, to generate platforms for adhesion of single DNA molecules to form DNA curtains

(see Chapter 6). Also, by combining controlled metallic deposition on a microfabricated sur­

face with specific biochemical functionalization, it is possible to generate smart bioelectronics

circuitry. Smart surface structures can also utilize molecular self-​assembly techniques, such

as DNA origami (discussed in Chapter 9).

Important recent advances have been made in the area of nanophotonics using

microfabrication and nanofabrication technologies. Many silicon-​based substrates, such as

silicon dioxide “glass,” have low optical absorption and a reasonably high refractive index of

~1.5 in the visible light spectrum range, implying that they are optically transparent and can

also act as photonic waveguides for visible light. A key benefit here in terms of biophysical

applications is that laser excitation light for fluorescence microscopy can be guided through

a silicon-​based microfabricated device across significant distances; for example, if coupled to

an optic fiber delivery system to extend to waveguide distance, this is potentially only limited

by the optical fiber repeater distance of several tens of kilometers.

This potentially circumvents the need to have objective lens standard optical microscopy-​

based delivery and capture methods for light and so facilitates miniaturization of devices that