
Contents
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I/O functions emerge from the kinetics of chemical binding I/O functions emerge from the kinetics of chemical binding
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I/O functions from a single binding site I/O functions from a single binding site
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Steeper I/O functions from cooperative binding Steeper I/O functions from cooperative binding
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Chemical circuitry supports analogue processing Chemical circuitry supports analogue processing
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Chemical circuits cover the time domain Chemical circuits cover the time domain
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What makes a protein circuit efficient? What makes a protein circuit efficient?
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Managing noise in a protein circuit Managing noise in a protein circuit
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Noise reducer of last resort Noise reducer of last resort
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Maximizing efficiency in a parallel array Maximizing efficiency in a parallel array
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Summary: Pros and cons of computing with chemical circuits Summary: Pros and cons of computing with chemical circuits
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Information processing by electrical circuits Information processing by electrical circuits
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How electrical circuits meet the need for speed over distance How electrical circuits meet the need for speed over distance
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How circuits built from ion channels operate electrically How circuits built from ion channels operate electrically
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I/O function of the basic circuit I/O function of the basic circuit
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An electrical circuit’s hyperbolic I/O supports six operators An electrical circuit’s hyperbolic I/O supports six operators
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How electrical circuits support analogue processing How electrical circuits support analogue processing
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How voltage-gated channels meet a need for speed over distance How voltage-gated channels meet a need for speed over distance
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How a voltage-gated calcium channel links electrical to chemical How a voltage-gated calcium channel links electrical to chemical
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Constraints on information processing by circuits of ion channels Constraints on information processing by circuits of ion channels
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Biophysical constraints Biophysical constraints
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What limits the number of channels in a circuit? What limits the number of channels in a circuit?
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Providing speed and accuracy with low energy density circuits Providing speed and accuracy with low energy density circuits
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6 Information Processing in Protein Circuits
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Published:June 2015
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Abstract
A protein circuit processes information like an electronic circuit -- by passing a signal through successive components that transform it according to their particular input-output (I/O) functions. The chemical binding and catalysis allow a range of molecular devices: amplifiers, oscillators, switches, level detectors, and so on. These compute directly, and thus efficiently, but suffer from noise. Signal-to-noise is improved by connecting proteins in complexes, by confining circuits in small compartments, and by passing signals through parallel arrays of identical molecules. An array matches the number of its molecules to the statistics of the input and thus avoid excess capacity. Although chemical computing is versatile and uses least possible space and energy, it relies on diffusion, which beyond a few micrometers, is slow. Fast signaling over distance requires electrical circuits served by protein ion channels. An electrical signal, compared to a G protein’s chemical signal, uses 100-fold more energy. Consequently information rates via electrical signals are limited by high energy costs and the low density of energy supply.
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