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

• biosp_berkeley.pdf · application/pdf · 4352 kbytes

• 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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