Smart molecules at work—mimicking advanced logic operations

Andréasson, Joakim; Pischel, Uwe

doi:10.1039/b820280j

Cited by 426 publications

(304 citation statements)

References 39 publications

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“…Biochemical processes, 1-8 and more generally, chemical kinetics, [9][10][11][12][13][14][15] Presently, biochemical information processing systems are not intended as a replacement of Si devices, but rather aim at offering additional functionalities in situations where direct wiring to computers and power sources is not practical such as in many biomedical applications. [23][24][25] However, even for near-term applications, scalable and versatile networking paradigms are crucial.…”

Section: Introductionmentioning

confidence: 99%

Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic

et al. 2010

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The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by H 2 O 2 , was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved capabilities for design of scalable biomolecular information processing systems.Web-link to future updates of this article: www.clarkson.edu/Privman/231.pdf 600-2 - IntroductionBiochemical processes, 1-8 and more generally, chemical kinetics, [9][10][11][12][13][14][15] Presently, biochemical information processing systems are not intended as a replacement of Si devices, but rather aim at offering additional functionalities in situations where direct wiring to computers and power sources is not practical such as in many biomedical applications. [23][24][25] However, even for near-term applications, scalable and versatile networking paradigms are crucial. Recent studies suggest 8,58,59 that the level of noise in biochemical systems is quite high as compared to electronics. This includes noise both the input/output signals and in the "gate machinery" chemical (e.g., enzyme) concentrations. Avoiding noise amplification by appropriate network design is therefore quite important even for small networks, similar to recent findings 60 for networking of neurons. Present estimates 8,61 suggest that, not only analog but also digital error correction will be required for networks involving more than order 10 processing steps.-3 -Considerations of scalability and control of noise have set the stage for new challenges.Large-scale interconnectivity and fault-tolerance cannot be achieved without the development of a "toolbox" of new network elements including filters, signal splitters, signal balancers, resetting functions, etc. These analog network elements for biochemical computing might not follow too closely the device components of Si electronics. In fact, concepts borrowed from natural systems, specifically, memory involving processes 62 have recently received attention in unconventional information processing studies. However, as a rule none of the standard elements for networking for (ultimately, digital) information processing has been experimentally realized to date in a setting demonstrating interconnectivity ...

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Section: Introductionmentioning

confidence: 99%

Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic

et al. 2010

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“…Thus, a DNA-based molecular 2-to-4 DC system was successfully constructed as proof-of-principle. As shown in its logic circuit (Figure 4i), a 2-to-4 DC integrates one NOR gate, two complementary INHIBIT gates and one AND gate, 36 which all share the same inputs and initial MB platform. The developed DC presents two distinct advantages.…”

Section: Advanced Logic Circuits For Nonarithmetic Information Procesmentioning

confidence: 99%

DNA-based advanced logic circuits for nonarithmetic information processing

Liu

Dong

et al. 2015

NPG Asia Mater

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DNA has been used as a building block to construct a series of complex logic circuits to perform nonarithmetic functions, including a multiplexer, demultiplexer, encoder and decoder. This is the first time that DNA has been used to cover this broad range of logic circuits, demonstrating the versatility and power of DNA computation to process information on the molecular level. The above logic circuits all share the same DNA platform, indicating the great prospects for DNA computation. The enzyme-free system developed here provides a novel prototype for the design of DNA-based, high-level molecular logic circuits. Considering its biocompatibility, DNA computation could find potential applications in biological and biomedical fields in the not-too-distant future.

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“…[1][2][3] The challenge of achieving the design of molecules that are capable of a predetermined logic operation has received important backup from smart applications of molecular logic gates in sensing, drug delivery, theranostics, and materials chemistry. [4][5][6][7][8][9][10] Among the different logic operations, those that imply a memory function belong to the most demanding ones in terms of their chemical design.…”

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confidence: 99%

A supramolecular keypad lock

et al. 2015

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The reversible photoswitching between an anthracene derivative and its [4+4] dimer, using the template effect of the CB8 macrocycle, was demonstrated. This example of supramolecular chemistry in water was harnessed to demonstrate the operation of a keypad lock device that is driven by means of light and chemicals as inputs.The use of molecular species for achieving information processing of chemical, photonic or electrochemical signals according to the principles of binary coding (0 and 1) and Boolean language continues to receive wide attention. [1][2][3] The challenge of achieving the design of molecules that are capable of a predetermined logic operation has received important backup from smart applications of molecular logic gates in sensing, drug delivery, theranostics, and materials chemistry. [4][5][6][7][8][9][10] Among the different logic operations, those that imply a memory function belong to the most demanding ones in terms of their chemical design. 11 This type of logic, known as sequential logic, results in differentiated outputs depending on the input history of the device. Current research activities along these lines have their focus on the implementation of flip-flops and molecular keypad locks. Photochromic switches have been often exploited for these purposes. [12][13][14][15] However, chemically-addressable systems and redox-switchable molecular devices were also used for the demonstration of molecular keypad locks [16][17][18][19] and flip-flops. 20,21 Surprisingly, the exploitation of supramolecular host-guest phenomena for the demonstration of keypad lock functions has no precedence in the literature. In recent reports host-guest complexes with cucurbit [7]uril (CB7) and cucurbit [8]uril (CB8) were used to demonstrate the reconfigurable and resettable operation of logic gates in aqueous solution. 22,23 Cucurbiturils have drawn much attention for their very high binding constants of cationic guests (up to 10 17 M À1 ) 24 and their supramolecular application potential with a strong focus on biological and pharmacological contexts, and analytical problems is beginning to reveal. [25][26][27][28][29][30][31][32][33][34][35] In the present work we take advantage of the specific complexation properties of the CB8 macrocycle. Unlike the smaller homologues CB6 and CB7, that commonly offer space for only one guest molecule, the larger CB8 often accommodates two guests and the resulting complexes may feature new emission properties (e.g., excimer fluorescence) or lead to fluorescence self-quenching. [35][36][37][38] Additionally, the resulting pre-organization of the two guests may facilitate intracomplex photoreactions that would not happen at the dilute concentrations of the free dye molecules. [38][39][40] In a wider context, host-templated photodimerizations have been used in the design of photoswitchable supramolecular polymers. [40][41][42] Herein we designed the anthracene derivative 1 (see the ESI † for details of the synthesis and Scheme 1 for the structure) which contains a positively ...

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Smart molecules at work—mimicking advanced logic operations

Cited by 426 publications

References 39 publications

Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic

Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic

DNA-based advanced logic circuits for nonarithmetic information processing

A supramolecular keypad lock

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