Interplanetary Communications

Pierce, John R.; Cutler, C. C.

doi:10.1016/b978-1-4831-9959-7.50006-2

Cited by 17 publications

(18 citation statements)

References 5 publications

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“…The key pieces of information theory needed to do this were published by Claude Shannon in 1948 ( 12 ) and 1949 ( 27 ). Then, in 1959 Pierce and Cutler used information theory to define an efficiency measure for satellite communications ( 28 , 29 ), where P /N is the `signal-to-noise ratio', the power P dissipated at the receiver in joules per second, versus the thermal noise power N interfering with the signal there. This formula was derived from Claude Shannon's famous channel capacity equation, in which the bandwidth W defines the range of frequencies used in the communications as, for example, by a radio station ( 12 , 13 , 27 ).…”

Section: Introductionmentioning

confidence: 99%

70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence

Schneider¹

2010

Nucleic Acids Research

101

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The relationship between information and energy is key to understanding biological systems. We can display the information in DNA sequences specifically bound by proteins by using sequence logos, and we can measure the corresponding binding energy. These can be compared by noting that one of the forms of the second law of thermodynamics defines the minimum energy dissipation required to gain one bit of information. Under the isothermal conditions that molecular machines function this is joules per bit ( is Boltzmann's constant and T is the absolute temperature). Then an efficiency of binding can be computed by dividing the information in a logo by the free energy of binding after it has been converted to bits. The isothermal efficiencies of not only genetic control systems, but also visual pigments are near 70%. From information and coding theory, the theoretical efficiency limit for bistate molecular machines is ln 2 = 0.6931. Evolutionary convergence to maximum efficiency is limited by the constraint that molecular states must be distinct from each other. The result indicates that natural molecular machines operate close to their information processing maximum (the channel capacity), and implies that nanotechnology can attain this goal.

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Section: Introductionmentioning

confidence: 99%

70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence

Schneider¹

2010

Nucleic Acids Research

101

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“…where 0 < ǫ t ≤ 1 [12]. This expression was first used to describe the efficiency of satellite communications in terms of the 'signal-to-noise' ratio, P/N [30].…”

Section: A Lower Bound On the Dimensionality Of Molecular Machinesmentioning

confidence: 99%

“…Examining Fig 3B, we notice several important features. For lattice packings, since log δ ≤ 0, there is no more than one center per unit sphere packing volume for D ∈ [0, 30]. There is exactly one in D = 0 and D = 24: these are the densest sparse packings.…”

Section: Coding Space As a Fitness Landscapementioning

confidence: 99%

Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences

Schneider¹,

Jejjala²

2019

PLoS ONE

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Restriction enzymes recognize and bind to specific sequences on invading bacteriophage DNA. Like a key in a lock, these proteins require many contacts to specify the correct DNA sequence. Using information theory we develop an equation that defines the number of independent contacts, which is the dimensionality of the binding. We show that EcoRI, which binds to the sequence GAATTC, functions in 24 dimensions. Information theory represents messages as spheres in high dimensional spaces. Better sphere packing leads to better communications systems. The densest known packing of hyperspheres occurs on the Leech lattice in 24 dimensions. We suggest that the single protein EcoRI molecule employs a Leech lattice in its operation. Optimizing density of sphere packing explains why 6 base restriction enzymes are so common.

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“…where the bandwidth W defines the range of frequencies used in communication and P/N is the 'signal to noise' ratio. In 1959, in the context of satellite communication, efficiency ǫ has been defined from the information theoretical point of view (Pierce and Cutler 1959;Raisbeck 1963)…”

Section: Information Theoretical Analysis Of Devr Regulonmentioning

confidence: 99%

Analysis of DevR regulated genes in Mycobacterium tuberculosis

et al. 2014

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The DevRS two component system of Mycobacterium tuberculosis is responsible for its dormancy in host and becomes operative under hypoxic condition. It is experimentally known that phosphorylated DevR controls the expression of several downstream genes in a complex manner. In the present work we propose a theoretical model to show role of binding sites in DevR mediated gene expression. Individual and collective role of binding sites in regulating DevR mediated gene expression has been shown via modeling. Objective of the present work is twofold. First, to describe qualitatively the temporal dynamics of wild type genes and their known mutants. Based on these results we propose that DevR controlled gene expression follows a specific pattern which is efficient in describing other DevR mediated gene expression. Second, to analyze behavior of the system from information theoretical point of view. Using the tools of information theory we have calculated molecular efficiency of the system and have shown that it is close to the maximum limit of isothermal efficiency.

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Interplanetary Communications

Cited by 17 publications

References 5 publications

70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence

70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence

Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences

Analysis of DevR regulated genes in Mycobacterium tuberculosis

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