Exemplary embodiments of the present disclosure can include, for example, an atomic force microscopy (AFM) system, including a cantilever(s), an optical pickup unit(s) (OPU(s)) including a laser positioned over the cantilever(s), and a power source providing noise with a noise level that is below 300 Picometers. The noise level of the power source can be below 200 Picometers. A digitizing arrangement can be included which can be associated with the OPU. The digitizing arrangement(s) can have a bandwidth of about 2 MHZ. The OPU(s) can have a detection bandwidth of at least 80 MHZ. The exemplary apparatus can be combined with a chemical protocol and statistical signal processing and image analysis procedures to map DNA at high speed and accuracy.

A debris collection and metrology system for collecting and analyzing debris from a tip used in nanomachining processes, the system including an irradiation source, an irradiation detector, an actuator, and a controller. The irradiation source is operable to direct incident irradiation onto the tip, and the irradiation detector is operable to receive a sample irradiation from the tip, the sample irradiation being generated as a result of the direct incident irradiation being applied onto the tip. The controller is operatively coupled to an actuator system and the irradiation detector, and the controller is operable to receive a first signal based on a first response of the irradiation detector to the sample irradiation, and the controller is operable to effect relative motion between the tip and at least one of the irradiation source and the irradiation detector based on the first signal.

A debris collection and metrology system for collecting and analyzing debris from a tip used in nanomachining processes, the system including an irradiation source, an irradiation detector, an actuator, and a controller. The irradiation source is operable to direct incident irradiation onto the tip, and the irradiation detector is operable to receive a sample irradiation from the tip, the sample irradiation being generated as a result of the direct incident irradiation being applied onto the tip. The controller is operatively coupled to an actuator system and the irradiation detector, and the controller is operable to receive a first signal based on a first response of the irradiation detector to the sample irradiation, and the controller is operable to effect relative motion between the tip and at least one of the irradiation source and the irradiation detector based on the first signal.

Methods and apparatuses are disclosed for detecting a presence of a mismatched pair in an oligonucleotide duplex that is attached to a solid substrate using an atomic force microscope. In particular, methods and apparatuses of the invention allow qualitative and quantitative analysis of the presence of a mismatched pair in a sample of oligonucleotide duplex using an atomic force microscope comprising an AFM cantilever that includes a DNA mismatch repair protein. Methods and apparatuses of the invention allow detection of gene mutation without a need for amplification, labeling, or modification of the sample. Such apparatuses and methods can be used in a wide variety of clinical diagnostic applications including detection and/or analysis of biomarkers related to, but not limited to, cancer, trauma, sepsis, aseptic inflammation, myocardial infarction, stroke, transplantation, diabetes, sickle cell disease, as well as other clinical conditions.

A system and method is provided for of characterizing nanostructured surfaces. A nanostructure sample is placed in an SEM chamber and imaged. The system and method locates one of the nanostructures using images from the SEM imaging, excises a top portion of the nanostructure, places said top portion on a substrate such that the nanostructures are perpendicular to the substrate and a base of the top portion contacts the substrate, performs high energy ion beam assisted deposition of metal at the base to attach the top portion to the substrate, SEM imaging the top portions in the SEM chamber, determining coordinates of the top portions relative to the substrate from the SEM imaging of the top portions, placing the substrate in an AFM chamber, and performing AFM imaging of the top portions using the coordinates previously determined.

A system and method is provided for of characterizing nanostructured surfaces. A nanostructure sample is placed in an SEM chamber and imaged. The system and method locates one of the nanostructures using images from the SEM imaging, excises a top portion of the nanostructure, places said top portion on a substrate such that the nanostructures are perpendicular to the substrate and a base of the top portion contacts the substrate, performs high energy ion beam assisted deposition of metal at the base to attach the top portion to the substrate, SEM imaging the top portions in the SEM chamber, determining coordinates of the top portions relative to the substrate from the SEM imaging of the top portions, placing the substrate in an AFM chamber, and performing AFM imaging of the top portions using the coordinates previously determined.

A large radius probe for a surface analysis instrument such as an atomic force microscope (AFM). The probe is microfabricated to have a tip with a hemispherical distal end or apex. The radius of the apex is the range of about a micron making the probes particularly useful for nanoindentation analyses. The processes of the preferred embodiments allow such large radius probes to be batch fabricated to facilitate cost and robustness.

A debris collection and metrology system for collecting and analyzing debris from a tip used in nanomachining processes, the system including an irradiation source, an irradiation detector, an actuator, and a controller. The irradiation source is operable to direct incident irradiation onto the tip, and the irradiation detector is operable to receive a sample irradiation from the tip, the sample irradiation being generated as a result of the direct incident irradiation being applied onto the tip. The controller is operatively coupled to an actuator system and the irradiation detector, and the controller is operable to receive a first signal based on a first response of the irradiation detector to the sample irradiation, and the controller is operable to effect relative motion between the tip and at least one of the irradiation source and the irradiation detector based on the first signal.

A debris collection and metrology system for collecting and analyzing debris from a tip used in nanomachining processes, the system including an irradiation source, an irradiation detector, an actuator, and a controller. The irradiation source is operable to direct incident irradiation onto the tip, and the irradiation detector is operable to receive a sample irradiation from the tip, the sample irradiation being generated as a result of the direct incident irradiation being applied onto the tip. The controller is operatively coupled to an actuator system and the irradiation detector, and the controller is operable to receive a first signal based on a first response of the irradiation detector to the sample irradiation, and the controller is operable to effect relative motion between the tip and at least one of the irradiation source and the irradiation detector based on the first signal.

A method of forming a micropattern, a substrate surface inspection apparatus, a cantilever set for an atomic force microscope, and a method of analyzing a surface of a semiconductor substrate, and a probe tip the method including forming pinning patterns on a semiconductor substrate; forming a neutral pattern layer in spaces between the pinning patterns; and inspecting a surface of a guide layer that includes the pinning patterns and the neutral pattern layer by using an atomic force microscope (AFM).