Bibliography of: Models Molecular

  1. Goss, P.J. and Peccoud, J.. "Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets." Proc Natl Acad Sci U S A. 95 (12). 1998. pp. 6750-5.
    [ .pdf ] [ PubMed ]

    An integrated understanding of molecular and developmental biology must consider the large number of molecular species involved and the low concentrations of many species in vivo. Quantitative stochastic models of molecular interaction networks can be expressed as stochastic Petri nets (SPNs), a mathematical formalism developed in computer science. Existing software can be used to define molecular interaction networks as SPNs and solve such models for the probability distributions of molecular species. This approach allows biologists to focus on the content of models and their interpretation, rather than their implementation. The standardized format of SPNs also facilitates the replication, extension, and transfer of models between researchers. A simple chemical system is presented to demonstrate the link between stochastic models of molecular interactions and SPNs. The approach is illustrated with examples of models of genetic and biochemical phenomena where the ULTRASAN package is used to present results from numerical analysis and the outcome of simulations.

    Keywords: *Computer Simulation ; Human ; *Models Molecular ; *Molecular Biology ; *Stochastic Processes


  2. Zauner, K.P. and Conrad, M.. "Enzymatic computing." Biotechnol Prog. 17 (3). 2001. pp. 553-9.
    [ .pdf ] [ PubMed ]

    The conformational dynamics of enzymes is a computational resource that fuses milieu signals in a nonlinear fashion. Response surface methodology can be used to elicit computational functionality from enzyme dynamics. We constructed a tabletop prototype to implement enzymatic signal processing in a device context and employed it in conjunction with malate dehydrogenase to perform the linearly inseparable exclusive-or operation. This shows that proteins can execute signal processing operations that are more complex than those performed by individual threshold elements. We view the experiments reported, though restricted to the two-variable case, as a stepping stone to computational networks that utilize the precise reproducibility of proteins, and the concomitant reproducibility of their nonlinear dynamics, to implement complex pattern transformations.

    Keywords: Calcium_chemistry ; Calcium_metabolism ; Enzymes_*chemistry ; Enzymes_*metabolism ; Image Processing ; Computer-Assisted ; Magnesium_chemistry ; Magnesium_metabolism ; Malate Dehydrogenase_chemistry ; Malate Dehydrogenase_metabolism ; Models Chemical ; *Models Molecular ; Osmolar Concentration ; Protein Conformation