Control of Noise in Chemical and Biochemical Information Processing

Privman, Vladimir

doi:10.1002/ijch.201000066

Cited by 39 publications

(104 citation statements)

References 223 publications

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“…This is typical for biocatalytic reactions. 14,32,42 Thus, in addition to its built-in inaccuracy, the non-filtered AND gate will also significantly amplifies input noise as it is passed to the output (numerical estimates not detailed here suggest the value of , ≃ 4.5, indicating input-to-output noise amplification by a factor of approximately 450%).…”

Section: Resultsmentioning

confidence: 97%

“…26,28 However, the problem of the output signal discrimination can be resolved more efficiently by adding "chemical-filter" reaction steps which modify convex response functions characteristic of most (bio)catalytic processes, to sigmoidal. 32 These novel (bio)chemical "filter" systems have recently been designed [33][34][35][36] and optimized as standalone elements for inclusion in biochemical logic networks. Specifically, we have demonstrated that integration of a filter system with digital biosensing approach can significantly improve performance, enabling differentiation between output-0 and 1 values corresponding to normal physiological and pathophysiological concentrations of biomarkers 36 for liver, as well as abdominal trauma and soft-tissue injuries.…”

Section: Molecularmentioning

confidence: 99%

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Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid “Filter” Response

et al. 2012

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We report the first realization of a biomolecular AND gate function with double-sigmoid response (sigmoid in both inputs). Two enzyme biomarker inputs activate the gate output signal which can then be used as indicating liver injury, but only when both of these inputs have elevated pathophysiological concentrations, effectively corresponding to logic-1 of the binary gate functioning. At lower, normal physiological concentrations, defined as logic-0 inputs, the liver-injury output levels are not obtained. High-quality gate functioning in handling of various sources of noise, on time scales of relevance to potential applications is enabled by utilizing "filtering" effected by a simple added biocatalytic process. The resulting gate response is sigmoid in both inputs when proper system parameters are chosen, and the gate properties are theoretically analyzed within a model devised to evaluate its noise-handling properties.

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Section: Resultsmentioning

confidence: 97%

Section: Molecularmentioning

confidence: 99%

Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid “Filter” Response

et al. 2012

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“…Perfect separation of the 0 and 1 output signals was found to persist at significantly longer times as well, up to 3 h. The robustness of this analytical system has allowed its practical use in human serum solutions [46]. The ''filter'' approach is actually much broader than it is exemplified above and will be beneficial for many biocatalytic cascades processing digitized input signals [49].…”

Section: Application Of Filter Systems For Improving Digitalization Omentioning

confidence: 92%

“…However, while improving the binary-signal separation, such filtering can decrease the overall signal strength, which could be an added source of relative noise [49]. Thus, this approach is useful for larger times when the decrease in the absorbance reaches its saturation, which is of relevance in actuation applications [45].…”

Section: Application Of Filter Systems For Improving Digitalization Omentioning

confidence: 99%

Enzyme Logic Digital Biosensors for Biomedical Applications

Katz

Wang

2012

Biomolecular Information Processing

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Despite the great success and rapid development of chemical [1][2][3][4][5][6][7] and biochemical [8][9][10][11][12][13] computing systems, most of them represent only the proof of the concept demonstrating the possibility of performing computing/logic operations with the use of molecular systems. They are not ready yet for any practical application. Indeed, these unconventional chemical computing systems are hardly organized in small circuitries, and are capable of solving only basic arithmetic/logic operations on the timescale of minutes or even hours. On the other hand, application of molecular logic systems for analytical purposes could yield a novel class of sensors that are able to accept many input signals and produce binary outputs in the form of ''YES''/''NO,'' which are particularly important for biomedical applications. This approach has been already successfully applied to analyze protein libraries associated with multiple sclerosis [14]. Logically processed feedback between drug delivery application and physiological conditions can significantly improve drug targeting and efficiency [15]. The well-developed field of DNA biocomputing [16] spins out from solving combinatorial problems [17] to analyzing biomedical multiparameter physiological conditions [18]. Programmable and autonomous DNA computing systems operating in vitro have demonstrated logic multiparameter analysis of disease-related biomolecular markers, and can be applied in future for in situ medical diagnosis and cure [18,19]. For example, biosensor systems for detecting genetic modifications in avian influenza [20] were developed on the basis of the DNA computing principles, in which various oligonucleotide signals were logically processed by a DNA logic network. Coupling enzyme logic systems with controlled self-assembly of nanoparticles allowed logic AND/OR responses to cancer markers matrix-metalloproteinases: MMP2 and MMP7) [21].The logically controlled aggregation of the superparamagnetic Fe 3 O 4 nanoparticles was detected by magnetic resonance imaging (MRI), thus promising easy adaptation of the method to future in vivo medical applications. The results of the logically processed biomolecular signals can be stored in enzyme-controlled set-reset flip-flop memory units [22]. The terminal memory units can be Biomolecular Information Processing: From Logic Systems to Smart Sensors and Actuators, First Edition. Edited by Evgeny Katz.

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“…Experimental realizations of the sigmoidal behavior ( Figure 12.4) have been an ongoing effort [190,191], based on the ideas [1,10,187,189] that an additional reactant, F, which depletes the product, but can only consume (react fast with) a small quantity of it, will suppress the response at small inputs without voiding the saturation property at large inputs, thus yielding a sigmoidal response. In connection with the system of the type defined in Eq.…”

Section: Noise Handling At the Gate Level And Beyondmentioning

confidence: 99%

Control of Noise in Chemical and Biochemical Information Processing

Cited by 39 publications

References 223 publications

Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid “Filter” Response

Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid “Filter” Response

Enzyme Logic Digital Biosensors for Biomedical Applications

Approaches to Control of Noise in Chemical and Biochemical Information and Signal Processing

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