Enzymatic pattern processing

Zauner, Klaus-Peter; Conrad, Michael

doi:10.1007/s001140050740

Cited by 14 publications

(8 citation statements)

References 9 publications

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“…Ions not involved as reactants have in numerous cases been found to enhance enzymatic activity [300,301] and an activating effect has been found [302] for Mg 2+ (and exists according to our observations [297] also of Ca 2+ ) affecting MDH. On the other hand, high ionic strength unspecifically suppresses MDH activity [303].…”

Section: Conformation-based Computationsupporting

confidence: 77%

“…Therefore the catalytic activity of such enzymes provides a sensitive indicator of conformation change. Experimental studies with the enzyme malate dehydrogenase (MDH) showed that divalent ions can be used to modulate its activity [297]. If inputs are coded with ionic signals and the concentration of the product formed by the reaction catalyzed by MDH is regarded as the output signal a variety of logic gates (AND, OR, XOR, NAND, NOR) with a response time of less than 10 s have been implemented using Mg 2+ and Ca 2+ as input signals [298].…”

Section: Conformation-based Computationmentioning

confidence: 99%

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Molecular Information Technology

Zauner

2005

Critical Reviews in Solid State and Materials Sciences

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ABSTRACT:Molecular materials are endowed with unique properties of unrivaled potential for high density integration of computing systems. Present applications of molecules range from organic semiconductor materials for low-cost circuits to genetically modified proteins for commercial imaging equipment. To fully realize the potential of molecules in computation, information processing concepts that relinquish narrow prescriptive control over elementary structures and functions are needed, and self-organizing architectures have to be developed. Investigations into qualitatively new concepts of information processing are underway in the areas of reaction-diffusion computing, self-assembly computing, and conformation-based computing. Molecular computing is best considered not as competitor for conventional computing, but as an opportunity for new applications. Microrobotics and bioimmersive computing are among the domains likely to benefit from advances in molecular computing. Progress will depend on both novel computing concepts and innovations in materials. This article reviews current directions in the use of bulk and single molecules for information processing. KEY WORDS:polymer electronics, molecular switches, self-assembly computing, conformation-based computation, self-organizing materials, bioimmersive computing

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Section: Conformation-based Computationsupporting

confidence: 77%

Section: Conformation-based Computationmentioning

confidence: 99%

Molecular Information Technology

Zauner

2005

Critical Reviews in Solid State and Materials Sciences

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“…Non-linear and non-monotonic responses in biological systems offer the possibility of implementing functions such as the XOR. Ross and co-workers demonstrated a simple enzymatic reaction scheme capable of implementing a biochemical XOR function (Hjelmfelt, Weinberger et al 1991;Arkin and Ross 1994) and Zauner and Conrad experimentally demonstrated an implementation of the XOR function by exploiting the nonmonotonic response of the mitochondrial malate dehydrogenase (mMDH) reaction rate to ion concentrations (Mg 2+ , Ca 2+ ) (Zauner and Conrad 2000).…”

Section: Structure Of the Modelmentioning

confidence: 99%

The potential for signal integration and processing in interacting MAP kinase cascades

Schwacke

Voit

2007

Journal of Theoretical Biology

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The cellular response to environmental stimuli requires biochemical information processing through which sensory inputs and cellular status are integrated and translated into appropriate responses by way of interacting networks of enzymes. One such network, the mitogen-activated protein (MAP) kinase cascade is a highly conserved signal transduction module that propagates signals from cell surface receptors to various cytosolic and nuclear targets by way of a phosphorylation cascade. We have investigated the potential for signal processing within a network of interacting feed-forward kinase cascades typified by the MAP kinase cascade. A genetic algorithm was used to search for sets of kinetic parameters demonstrating representative key input-output patterns of interest. We discuss two of the networks identified in our study, one implementing the exclusive-or function (XOR) and another implementing what we refer to as an in-band detector (IBD) or two-sided threshold. These examples confirm the potential for logic and amplitude-dependent signal processing in interacting MAP kinase cascades demonstrating limited cross-talk. Specifically, the XOR function allows the network to respond to either one, but not both signals simultaneously, while the IBD permits the network to respond exclusively to signals within a given range of strength, and to suppress signals below as well as above this range. The solution to the XOR problem is interesting in that it requires only two interacting pathways, crosstalk at only one layer, and no feedback or explicit inhibition. These types of responses are not only biologically relevant but constitute signal processing modules that can be combined to create other logical functions and that, in contrast to amplification, cannot be achieved with a single cascade or with two non-interacting cascades. Our computational results revealed surprising similarities between experimental data describing the JNK/MKK4/MKK7 pathway and the solution for the IBD that evolved from the genetic algorithm. The evolved IBD not only exhibited the required non-monotonic signal strength-response, but also demonstrated transient and sustained responses that properly reflected the input signal strength, dependence on both of the MAPKKs for signaling, phosphorylation site preferences by each of the MAPKKs, and both activation and inhibition resulting from the overexpression of one of the MAPKKs.

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“…Shamayaev and G.Y. Peshkov, unpublished results), pattern recognition (Zauner and Conrad 2000) and universal logical computation Adamatzky 2001).…”

Section: Introductionmentioning

confidence: 99%

Collision-free path planning in the Belousov-Zhabotinsky medium assisted by a cellular automaton

Adamatzky

Costello

2002

Naturwissenschaften

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We offer a new approach to computing a shortest collision-free path in a space containing obstacles, using an experimental chemical processor, based on the Belousov-Zhabotinsky (BZ) reaction. The chemical processor was then coupled via optical links with a two-dimensional cellular automaton (CA) processor. In the BZ chemical processor obstacles are represented by sites of local stimulation generated by an array of silver wires. Circular excitation waves are generated which travel through the medium and approximate a scalar distance-to-obstacle field. The field is taken as the initial configuration of the CA processor, which calculates a tree of 'many-sources-one-destination' shortest paths using wave spreading in a discrete excitable medium. We describe a hybrid (experimental chemical and software based) parallel processor (with parallel inputs and outputs) which uses the principles of wave-based computing in both the physical and computational levels of its architecture.

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Enzymatic pattern processing

Abstract: A table-top prototype has been constructed

Cited by 14 publications

References 9 publications

Molecular Information Technology

Molecular Information Technology

The potential for signal integration and processing in interacting MAP kinase cascades

Collision-free path planning in the Belousov-Zhabotinsky medium assisted by a cellular automaton

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