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Digital Signal Processing with Protein Molecules and DNA Strands
Keshab K. Parhi

Citation
Keshab K. Parhi. "Digital Signal Processing with Protein Molecules and DNA Strands". Talk or presentation, 10, November, 2010.

Abstract
Digital signal processing (DSP) refers to non-terminating computations where computations are carried out repetitively on incoming samples. Digital signal processing has been applied in audio, speech, video, image, and wired and wireless applications. This talk will focus on signal processing of proteins using bio-chemical reactions. Past work on signal processing of chemical reaction networks (CRNs) at Stanford, Berkeley and LBL has provided a foundation for this effort. Our work differs in two respects. First, our work is based on digital signal processing as opposed to analog. Second, this work is based on synthesis as opposed to analysis of CRNs. In this talk, we review simple chemical computations that are one-time computations that terminate. All DSP computations are iterative, and require realization of delay elements. The delay operation refers to transfer operation from one protein to another protein. The delay element can be part of a feed-forward path or a feedback loop. Implementing a delay operation through the chemical reactions is a non-trivial task, and is one of the major contributions of our work. We describe a 3-phase synchronization scheme, referred to as RGB scheme, as a robust method of synchronization in biochemical reactions. The RGB scheme is then used to synthesize biochemical reactions for simple FIR and IIR digital filters. Ordinary differential equations based solutions are presented for the synthezied biochemical reactions. A substrate is then considered for realizing these chemical reactions by DNA strands, based on work at Caltech. Simulation results of the chemical reactions using DNA strands are then presented to prove robustness and effectiveness of the proposed approach. An example is shown to illustrate that the RGB scheme can also be used as a clock in synchronous CRNs. Several limitations are then addressed, and ongoing efforts are described. Applications of the proposed methodology for biosensing, drug delivery, cross-talk cancellation and equalization of protein-protein reactions are then outlined.

Electronic downloads

Citation formats  
  • HTML
    Keshab K.  Parhi. <a
    href="http://chess.eecs.berkeley.edu/pubs/779.html"
    ><i>Digital Signal Processing with Protein
    Molecules and DNA Strands</i></a>, Talk or
    presentation,  10, November, 2010.
  • Plain text
    Keshab K.  Parhi. "Digital Signal Processing with
    Protein Molecules and DNA Strands". Talk or
    presentation,  10, November, 2010.
  • BibTeX
    @presentation{Parhi10_DigitalSignalProcessingWithProteinMoleculesDNAStrands,
        author = {Keshab K.  Parhi},
        title = {Digital Signal Processing with Protein Molecules
                  and DNA Strands},
        day = {10},
        month = {November},
        year = {2010},
        abstract = {Digital signal processing (DSP) refers to
                  non-terminating computations where computations
                  are carried out repetitively on incoming samples.
                  Digital signal processing has been applied in
                  audio, speech, video, image, and wired and
                  wireless applications. This talk will focus on
                  signal processing of proteins using bio-chemical
                  reactions. Past work on signal processing of
                  chemical reaction networks (CRNs) at Stanford,
                  Berkeley and LBL has provided a foundation for
                  this effort. Our work differs in two respects.
                  First, our work is based on digital signal
                  processing as opposed to analog. Second, this work
                  is based on synthesis as opposed to analysis of
                  CRNs. In this talk, we review simple chemical
                  computations that are one-time computations that
                  terminate. All DSP computations are iterative, and
                  require realization of delay elements. The delay
                  operation refers to transfer operation from one
                  protein to another protein. The delay element can
                  be part of a feed-forward path or a feedback loop.
                  Implementing a delay operation through the
                  chemical reactions is a non-trivial task, and is
                  one of the major contributions of our work. We
                  describe a 3-phase synchronization scheme,
                  referred to as RGB scheme, as a robust method of
                  synchronization in biochemical reactions. The RGB
                  scheme is then used to synthesize biochemical
                  reactions for simple FIR and IIR digital filters.
                  Ordinary differential equations based solutions
                  are presented for the synthezied biochemical
                  reactions. A substrate is then considered for
                  realizing these chemical reactions by DNA strands,
                  based on work at Caltech. Simulation results of
                  the chemical reactions using DNA strands are then
                  presented to prove robustness and effectiveness of
                  the proposed approach. An example is shown to
                  illustrate that the RGB scheme can also be used as
                  a clock in synchronous CRNs. Several limitations
                  are then addressed, and ongoing efforts are
                  described. Applications of the proposed
                  methodology for biosensing, drug delivery,
                  cross-talk cancellation and equalization of
                  protein-protein reactions are then outlined.},
        URL = {http://chess.eecs.berkeley.edu/pubs/779.html}
    }
    

Posted by Jan Reineke on 15 Nov 2010.
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