Abstract: A method for operating a data processing system to find peaks in a mass spectrum that includes an ordered set of measurements of the abundances of species as a function of the mass/charge ratio of the species is disclosed. The method includes selecting a candidate blob that has a plurality of blob peaks from the mass spectrum. The data processing system selects a candidate blob peak for characterization. The candidate blob peak is approximated by a first species peak using a species peak model having a plurality of parameters by fitting the species peak model to a portion of the blob that has values that are substantially free of contributions from other species peaks that overlap with the first species peak and that are not represented by the species peak model. The first species peak is then subtracted from the candidate blob.

Abstract: A method for operating a data processing system to find peaks in a mass spectrum that includes an ordered set of measurements of the abundances of species as a function of the mass/charge ratio of the species is disclosed. The method includes selecting a candidate blob that has a plurality of blob peaks from the mass spectrum. The data processing system selects a candidate blob peak for characterization. The candidate blob peak is approximated by a first species peak using a species peak model having a plurality of parameters by fitting the species peak model to a portion of the blob that has values that are substantially free of contributions from other species peaks that overlap with the first species peak and that are not represented by the species peak model. The first species peak is then subtracted from the candidate blob.

Abstract: An atomic force microscope (AFM) comprises a physical system and a controller comprising a plurality of digital filters and configured to control the physical system. The AFM is tuned by performing automatic loop shaping on a loop response defined by a frequency response of the physical system and a frequency response of the controller, and adjusting a gain of the controller according to a peak in a magnitude of the loop response.

Abstract: A filter and method for filtering a signal are disclosed. The filter is equivalent to a plurality of bi-quad filters connected in series, and is implemented on a digital processor that receives a sequence of signal values at a sampling rate characterized by a sampling interval and generates a filtered signal value upon receiving each received signal value. The filter has a latency that is less than the sampling interval. The filtered values can be generated by adding a term to a received signal value and multiplying the sum by a gain constant that depends on the filter constants. The added term does not depend on the current received signal value. The filter can be implemented in fixed-point integer arithmetic.

Abstract: A method for operating a data processing system to simulate a physical system is disclosed. The physical system receives a time-varying input and generates a time-varying output. A model of the physical system is provided. The model depends on values of the time-varying input and an internal state in the physical system, the internal state is not directly measurable. The model includes a bi-quad component that models a resonance or anti-resonance of the physical system. For each of a plurality of time points, a current input value for the time-varying input is received. An internal state vector having a value of the internal state at a current time point as one component thereof is computed and computing an estimate of a system output at that time point, the system output being directly measurable. In one aspect of the invention, the internal state vector depends on a previous value of the internal state vector and the current input value.

Abstract: A filter and method for filtering a signal are disclosed. The filter is equivalent to a plurality of bi-quad filters connected in series, and is implemented on a digital processor that receives a sequence of signal values at a sampling rate characterized by a sampling interval and generates a filtered signal value upon receiving each received signal value. The filter has a latency that is less than the sampling interval. The filtered values can be generated by adding a term to a received signal value and multiplying the sum by a gain constant that depends on the filter constants. The added term does not depend on the current received signal value. The filter can be implemented in fixed-point integer arithmetic.

Abstract: An atomic force microscope (AFM) comprises a physical system and a controller comprising a plurality of digital filters and configured to control the physical system. The AFM is tuned by performing automatic loop shaping on a loop response defined by a frequency response of the physical system and a frequency response of the controller, and adjusting a gain of the controller according to a peak in a magnitude of the loop response.

Abstract: An atomic force microscope (AFM) apparatus for determining a topography of a sample surface is disclosed. The AFM apparatus comprises: a controller having a controller frequency response and being configured to provide a controller output signal. The controller comprises an integrator that provides an integrator output signal, and a filter block. The AFM apparatus also comprises a physical system having a physical system response and being configured to receive the controller output signal and to provide a probe height in response to the controller output signal. The physical system comprises an actuator configured to maintain a deflection of a probe tip relative to the sample surface. The deflection being is indicated by a deflection signal, and the filter block of the controller provides an inverse of the physical system response, such that the probe height is substantially equal to the integrator output signal.

Abstract: Linear PID controllers have a transfer function that resembles the frequency response of a notch filter. The PID parameters, KP, KI, and KD (proportional, integral, and derivative gains, respectively) can be extracted from the parameters of a linear notch filter. The linearized modes of scanning probe microscope (SPM) actuators have frequency responses that resemble those of simple second order resonance. Reasonable feedback control can be achieved by an inverse dynamics model of the resonance. A properly parameterized notch filter can cancel the dynamics of a resonance to give good closed-loop response.

Abstract: A signal demodulator and the method of using the same in a scanning probe microscope or the like to provide a feedback path with reduced latency are disclosed. The demodulator includes an input port, a first mixer and a first integrator. The input port receives an input signal having a frequency component at a signal frequency. The input signal is characterized by a signal amplitude at that frequency. The first mixer mixes the input signal with a first local oscillator signal at the signal frequency to generate a first mixed signal. The first integrator integrates the first mixed signal for an integer number of periods of the signal frequency to provide a first output signal.

Abstract: An optical disk structure and optical disk recorder which enables data to be re-written onto the recording layer of the optical disk. A clock reference structure is permanently formed along servo tracks of the optical disk. An optical transducer is coupled to the clock reference structure and generates a clock reference signal simultaneously with writing new data onto the recording layer of the optical disk. The data is written as data marks along the servo tracks. Each of the data marks includes edges. The edges of the data marks are recorded in synchronization with a write clock. The write clock is phase-locked with the clock reference signal. Therefore, the edges of the data marks are aligned with the clock reference structure with sub-bit accuracy. Standard DVD-ROM disk readers are not able to detect the high spatial frequency of the clock reference structure.

Abstract: A signal demodulator and the method of using the same in a scanning probe microscope or the like to provide a feedback path with reduced latency are disclosed. The demodulator includes an input port, a first mixer and a first integrator. The input port receives an input signal having a frequency component at a signal frequency. The input signal is characterized by a signal amplitude at that frequency. The first mixer mixes the input signal with a first local oscillator signal at the signal frequency to generate a first mixed signal. The first integrator integrates the first mixed signal for an integer number of periods of the signal frequency to provide a first output signal.

Abstract: An optical disk structure and optical disk recorder which enables data to be re-written onto the recording layer of the optical disk. A clock reference structure is permanently formed along servo tracks of the optical disk. An optical transducer is coupled to the clock reference structure and generates a clock reference signal simultaneously with writing new data onto the recording layer of the optical disk. The data is written as data marks along the servo tracks. Each of the data marks includes edges. The edges of the data marks are recorded in synchronization with a write clock. The write clock is phase-locked with the clock reference signal. Therefore, the edges of the data marks are aligned with the clock reference structure with sub-bit accuracy. Standard DVD-ROM disk readers are not able to detect the high spatial frequency of the clock reference structure.

Abstract: In accordance with the invention, an inverse filter is used to improve scanned images from a scanning probe microscope by removing the effect of the scanning system dynamics from the image data. This may be done in-line or as a post-processing operation.

Abstract: In accordance with the invention, an estimator is used in the controller portion of a scanning probe microscope to provide precise position estimates of the probe tip which is controlled in the vertical direction by a microelectromechanical system (MEMS) actuator. The precise position estimates typically enhance the ability of the scanning probe microscope to follow the surface and typically provide improved measurements of the surface topography.

Abstract: Linear PID controllers have a transfer function that resembles the frequency response of a notch filter. The PID parameters, KP, KI, and KD (proportional, integral, and derivative gains, respectively) can be extracted from the parameters of a linear notch filter. The linearized modes of scanning probe microscope (SPM) actuators have frequency responses that resemble those of simple second order resonance. Reasonable feedback control can be achieved by an inverse dynamics model of the resonance. A properly parameterized notch filter can cancel the dynamics of a resonance to give good closed-loop response.

Abstract: In accordance with the invention, rapid surface seeks to the measurement surface by a scanning probe microscope are enabled by using an actuator coupled to a position sensor.

Abstract: An optical disk structure and optical disk recorder which enables data to be rewritten onto the recording layer of the optical disk. A clock reference structure is permanently formed along servo tracks of the optical disk. An optical transducer is coupled to the clock reference structure and generates a clock reference signal simultaneously with writing new data onto the recording layer of the optical disk. The data is written as data marks along the servo tracks. Each of the data marks includes edges. The edges of the data marks are recorded in synchronization with a write clock. The write clock is phase-locked with the clock reference signal. Therefore, the edges of the data marks are aligned with the clock reference structure with sub-bit accuracy. Standard DVD-ROM disk readers are not able to detect the high spatial frequency of the clock reference structure.

Abstract: An optical disk structure and optical disk recorder which enables data to be re-written onto the recording layer of the optical disk. A clock reference structure is permanently formed along servo tracks of the optical disk. An optical transducer is coupled to the clock reference structure and generates a clock reference signal simultaneously with writing new data onto the recording layer of the optical disk. The data is written as data marks along the servo tracks. Each of the data marks includes edges. The edges of the data marks are recorded in synchronization with a write clock. The write clock is phase-locked with the clock reference signal. Therefore, the edges of the data marks are aligned with the clock reference structure with sub-bit accuracy. Standard DVD-ROM disk readers are not able to detect the high spatial frequency of the clock reference structure.

Abstract: An optical disk structure and optical disk recorder which enables data to be rewritten onto the recording layer of the optical disk. A clock reference structure is permanently formed along servo tracks of the optical disk. An optical transducer is coupled to the clock reference structure and generates a clock reference signal simultaneously with writing new data onto the recording layer of the optical disk. The data is written as data marks along the servo tracks. Each of the data marks includes edges. The edges of the data marks are recorded in synchronization with a write clock. The write clock is phase-locked with the clock reference signal. Therefore, the edges of the data marks are aligned with the clock reference structure with sub-bit accuracy. Standard DVD-ROM disk readers are not able to detect the high spatial frequency of the clock reference structure.