Biochip, Microfluidic and
Organ-on-Chip Fabrication
At Nanosystems JP Inc., we offer full-service biochip and microfluidic chip fabrication on glass, silicon, and polymer substrates. 500 × 600 mm large-format glass processing for low cost-per-chip on biosensor arrays. NIL, replicated from e-beam-written masters, for sub-50 nm nanopores and LSPR structures; feature size confirmed per program. PDMS soft lithography for organ-on-chip. DRIE for Bio-MEMS. All bonding methods.
glass, silicon, polymer
LSPR structures
for chip sealing
Glass, silicon, and polymer each with distinct advantages
The substrate defines fabrication route, optical properties, chemical resistance, thermal stability, cost, and biocompatibility. We fabricate on all three, and build hybrid chips combining two.
Glass
Glass is the workhorse substrate for high-performance microfluidic chips: optically transparent for fluorescence imaging and absorbance measurement, resistant to most acids, bases, and solvents that dissolve PDMS (HF-based chemistries excepted), and compatible with high-temperature sterilization. Our 500 × 600 mm large-format glass processing enables more chips per run than any wafer-format foundry, dramatically reducing cost-per-chip for array biosensors and diagnostic plates.
Standard glass materials: borosilicate (Eagle XG, Pyrex), quartz (UV-transparent for 200 nm excitation), fused silica (lowest autofluorescence), and soda lime (lowest cost for disposable chips). Channels and features defined by HF wet etching (isotropic, rounded profile), laser ablation, or ICP-RIE (anisotropic, vertical walls). Thin film electrode deposition of Au, Pt, ITO, TiN available on the same substrate before bonding.
Silicon
Silicon offers capabilities unavailable in glass or polymer: DRIE creates high-aspect-ratio channels, pillars, and filter structures with near-vertical sidewalls at up to 50:1 aspect ratio, enabling size-based cell sorting, deterministic lateral displacement arrays, and nanofluidic confinement that polymer chips cannot achieve. Silicon also enables on-chip CMOS readout integration via TSV, connecting microfluidic sensors to signal conditioning circuits on the same die.
Standard semiconductor lithography (KrF stepper, mask aligner) provides sub-1 µm feature resolution. Thin film piezoelectric (PZT, AlN) and electrode materials are deposited on the same silicon substrate, enabling acoustic actuation, DEP trapping, and electrochemical detection. Glass-on-silicon hybrid chips (glass cover bonded anodically to Si channel layer) provide optical access through the glass while retaining silicon's structural precision.
Polymer
Polymer chips dominate biomedical research and point-of-care diagnostics, not because they are technically superior, but because they are cheap, fast to prototype, and disposable. PDMS (polydimethylsiloxane) is the gold standard for research: bonded to glass or another PDMS layer by O₂ plasma activation, it forms the channels of organ-on-chip devices, droplet generators, and pneumatic valve arrays (Quake valves) within days of design iteration.
For production volumes, injection-molded PC, COP, and PMMA chips reproduce the reviewed channel design at lower cost than PDMS casting (draft, wall thickness and shrinkage are adjusted in the DFM review). COP (cyclo-olefin polymer) has negligible autofluorescence, critical for fluorescence-based assays where PDMS background interferes with detection. Thermal NIL on PMMA replicates nanostructures (gratings, nanopores, LSPR features) directly into polymer substrates for combined micro-nano chips.
Every technique needed for
micro-to-nano scale biochips
Biochip fabrication combines lithography, etching, thin film deposition, replication, and bonding, often on the same chip. All techniques are available, coordinated in a single project.
Photolithography
E-beam (20 nm), KrF stepper (~150 nm class, up to 12 inch), mask aligner (4 µm, up to 500 × 600 mm), and polymer film lithography (PET/PEN, 400 × 500 mm). Front-to-back alignment for double-sided microfluidic structures. SU-8 thick photoresist (up to 500 µm) for tall MEMS channel walls and master molds for PDMS soft lithography. Large-format mask aligner processes glass biochip arrays at 500 × 600 mm in a single step.
Wet & Dry Etching
HF etching of borosilicate and quartz glass for isotropic rounded microchannels, the standard for glass electrophoresis and DNA separation chips. KOH and TMAH anisotropic etching of silicon for V-groove and pyramidal structures. DRIE for high-aspect-ratio Si channels, through-holes, and micropillar filter arrays up to 50:1. ICP-RIE for glass and quartz with near-vertical sidewalls. KOH or TMAH etching gives smooth {111} facets for single-molecule nanofluidics; channel roughness is confirmed per program.
Nanoimprinting (NIL)
UV and thermal nanoimprint lithography for sub-50 nm nanostructures integrated into biochip substrates. DNA sequencing nanopore arrays: NIL defines the nanopore geometry in resist, dry etch transfers to SiN membrane. LSPR biosensor chips: NIL patterns gold nanopillar or nanohole arrays for label-free plasmon-resonance sensing. Thermal NIL on PMMA for polymer biochips with nanofluidic confinement channels. Master mold fabrication (Si e-beam, Ni electroformed).
Thin-Film Electrodes
Biocompatible electrode metals deposited by PVD sputtering and e-beam evaporation: gold (Au) for thiol-chemistry biofunctionalization, platinum (Pt) for electrochemical detection and electroporation, ITO (indium tin oxide) for transparent electrodes compatible with optical detection through the electrode, and TiN for capacitive sensing. Lift-off patterning defines electrode arrays with sub-5 µm features. Multi-electrode arrays (MEA) for neural recording chips fabricated on glass or Si substrates.
PDMS Soft Lithography
The standard rapid-prototyping route for research-grade microfluidic chips. SU-8 photolithography on a silicon wafer defines the channel master mold, channel heights from 5 µm to 500 µm. Liquid PDMS is poured over the master, degassed, cured at 70 °C, and peeled off, producing a negative replica of the channels in transparent, flexible PDMS. Multiple PDMS layers are bonded by O₂ plasma activation to create three-dimensional channel networks, pneumatic valves (Quake valve architecture), and organ-on-chip structures. Design-to-first-chip turnaround: 3 to 5 days once the SU-8 master is available, scope agreed per project.
Injection Molding & Thermal NIL
For production volumes (thousands to millions of chips), injection molding of PC, COP, and PMMA produces biochip substrates at cents-per-chip, far below the cost of individually cast PDMS or etched glass chips. We fabricate the injection mold tooling (Si or Ni master). Thermal NIL on PMMA replicates nanoscale features (100 nm to 5 µm gratings, nanopore templates, nanowell arrays) directly during molding, combining micro and nano features in a single fabrication step.
Sub-50 nm structures for DNA,
single molecules, and plasmonics
Biochip applications increasingly require nanoscale features invisible to standard UV lithography. Our NIL and e-beam capabilities bring sub-50 nm resolution to biochip fabrication at production-relevant scales.
Six bonding methods, matched
to your substrate combination
Bonding seals the microfluidic channels and is the step that most often determines chip yield. The wrong bonding method causes channel collapse, delamination, or optical scattering. We offer every relevant bonding method, matched to the substrate combination and application requirement.
Glass, silicon, and polymer key parameters side by side
| Parameter | Glass | Silicon | Polymer (PDMS/PC/COP) |
|---|---|---|---|
| Max Substrate Size | 500 × 600 mm panel | Up to 12 inch (300 mm) | PDMS: cast; Mold: up to 12 inch |
| Channel Patterning | HF wet etch, ICP-RIE, laser | DRIE (50:1), KOH, TMAH | Soft litho (PDMS), injection mold, NIL |
| Min Feature Size | ~2 µm (ICP-RIE) | ~0.5 µm (DRIE) | ~5 µm (mold); <100 nm (NIL) |
| Optical Transparency | Excellent (UV to NIR) | Opaque (IR only) | PDMS: excellent; COP: very good |
| Chemical Resistance | Excellent, inert to most solvents | Excellent (oxide passivated) | PDMS: swells in organics; COP: good |
| Biocompatibility | Excellent, medical-device (biocompatibility evaluated per program) | Good (oxide surface) | PDMS: excellent; polyimide: medical-grade PI available (biocompatibility evaluated per program) |
| Thermal Stability | Borosilicate to ~500 °C; fused silica well above 1000 °C | Up to 1000 °C | PDMS: typically to ~150 to 200 °C; PI: grade-dependent (cure and service temperatures qualified per stack and duration) |
| Electrode Integration | Au, Pt, ITO, direct deposition | Au, Pt, TiN, standard CMOS | Limited, low-temp metals only |
| CMOS Integration | Via TSV in hybrid chip | Native, same wafer | No |
| Bonding Methods | Anodic, fusion, adhesive | Anodic (to glass), fusion | O₂ plasma (PDMS), thermal (PC/COP) |
| Cost (per chip) | Medium, low at 500 × 600 mm scale | Medium-high | Lowest (PDMS research; mold: very low) |
| Prototype Turnaround | 1-3 weeks | 2-4 weeks | PDMS: 3-5 days after master; mold: 4-8 weeks |
Life sciences, diagnostics,
and biomedical devices
DNA Sequencing Flow Cells
Glass flow cells with NIL-defined nanopore arrays and precision microchannels for nanopore sequencing and optical sequencing platforms. Fusion or anodic bonding provides the hermetic seal and UV transparency required. Large-format glass processing enables 96-well or 384-well array formats at competitive cost.
Point-of-Care Diagnostics
COP injection-molded chips for lateral flow assay, RT-PCR, immunoassay, and CRISPR-based diagnostics. COP's low autofluorescence enables fluorescence readout. PDMS prototype geometry can inform the COP production design; wall thickness, draft, demolding, bonding, shrinkage and surface chemistry are reviewed before transfer. Thousands to millions of chips per batch at production cost.
Organ-on-a-Chip / OOC
Multilayer PDMS chips with Quake pneumatic valves, peristaltic pumps, and mechanical stretch membranes for microphysiological systems, lung, gut, blood-brain barrier, and kidney-on-chip. PDMS-to-PDMS plasma bonding creates three-dimensional vascular and tissue channel networks. COP versions available for mass production.
LSPR Label-Free Biosensors
Gold nanostructure arrays (nanopillars, nanoholes, nanoslits) on glass substrates by NIL and lift-off. Surface functionalized with antibodies, aptamers, or nucleic acid probes. Localized surface plasmon resonance detects binding of target molecules, protein, nucleic acid, or small molecule, without fluorescent labels. For clinical diagnostics and drug discovery.
Cell Sorting & DEP Trapping
Silicon DRIE micropillar arrays for deterministic lateral displacement (DLD) size-based cell sorting. ITO or Pt electrode arrays on glass for dielectrophoretic (DEP) trapping and manipulation. Tumor cell isolation from blood, circulating tumor DNA (ctDNA) concentration, and rare cell analysis for liquid biopsy applications.
Neural Recording Chips (MEA)
Multi-electrode arrays (MEA) for neural signal recording and stimulation, Pt or TiN electrodes on glass or Si substrate, passivated with SU-8 or polyimide, with DRIE through-holes for neuron interface. Biocompatible polyimide RDL for flexible implantable probe variants. For brain-computer interface research and epilepsy monitoring.
Single-Molecule Analysis
E-beam patterned nanofluidic channels (<100 nm depth) for DNA stretching and single-molecule fluorescence mapping. Zero-mode waveguides (ZMW) patterned by e-beam or NIL in gold film for single-molecule sequencing by synthesis. Nanowell arrays (femtoliter volume) for digital ELISA and single-enzyme assays.
Drug Delivery & Microencapsulation
PDMS and glass droplet microfluidic chips for monodisperse emulsion generation, microencapsulation, and drug-loaded microsphere production. T-junction and flow-focusing geometries produce droplets from 5 µm to 500 µm with CV <2%. Glass chips preferred for surfactant-tolerant surfaces and elevated temperature operation.
Cell Culture & Perfusion
Large-format glass multi-well plates and flow-through cell culture chambers, processed on 500 × 600 mm glass panels for cost-effective production of multi-channel cell culture arrays. Integrated Au or ITO electrodes for transepithelial electrical resistance (TEER) measurement. SU-8 cell culture scaffold structures for 3D spheroid culture.
What makes our biochip capability
different
500 × 600 mm glass, lowest chip cost
Processing biochip substrates at 500 × 600 mm panel scale produces far more chips per run than 4- or 6-inch wafer formats. For array biosensors and diagnostic plates with hundreds of chips per substrate, this single capability can reduce chip cost by 5-10× compared to wafer-scale foundries.
Nano to micro, one coordinated process flow
Sub-50 nm NIL nanopores integrated into microfluidic chips, scheduled within the same project as the microfluidic layers. E-beam direct write for custom nanoscale geometries. Nanofluidic + microfluidic hybrid chip design is handled by one engineering team with a single project timeline.
All three substrate families
Glass for optical biochips, silicon for Bio-MEMS and CMOS integration, PDMS for soft lithography prototypes, COP/PC/PMMA for injection-molded production. The material choice is driven by your device requirement, not by what the foundry happens to process.
PDMS to production, reviewed transfer
Prototype in PDMS (3 to 5 day turnaround subject to master availability and scope), then transition to injection-molded COP or PC; wall thickness, draft, demolding, bonding, shrinkage and surface chemistry are reviewed before transfer. Mold tooling is included in the program, and the channel design is carried from soft lithography to molded production with the adjustments identified in that review.
All bonding methods
O₂ plasma for PDMS-glass and PDMS-PDMS, anodic for glass-Si hermetic, fusion for glass-glass UV-transparent, thermal for PC/COP, all six bonding methods available. Chip sealing is included in the same project as the upstream device fabrication. Bond quality verified by optical inspection and leak testing before delivery.
NDA available on request
Biochip designs, channel layouts, electrode geometries, surface chemistry protocols, and assay designs, represent years of development. An NDA can be arranged before any design files or technical details are shared, just mention it in your first message. Initial inquiries and quotes can proceed without one. Pure-play foundry: we do not develop competing biochip products.
Start your project.
Initial response typically within one business day.
Share your process requirements, substrate, and production volume. A Nanosystems JP Inc. engineer will give an initial response typically within one business day. Full quote typically within 7-10 business days, subject to project complexity and NDA requirements.