scholarly journals Engineering the Stability of Nanozyme-Catalyzed Product for Colorimetric Logic Gate Operations

Molecules ◽  
2021 ◽  
Vol 26 (21) ◽  
pp. 6494
Author(s):  
Lianlian Fu ◽  
Deshuai Yu ◽  
Dijuan Zou ◽  
Hao Qian ◽  
Youhui Lin
Keyword(s):  
Glucose Oxidase ◽  
Xanthine Oxidase ◽  
Color Change ◽  
Logic Gate ◽  
Logic Gates ◽  
Boolean Logic ◽  
Blue Color ◽  
Push Forward ◽  
Logic Operations ◽  
The Stability

Recently, the design and development of nanozyme-based logic gates have received much attention. In this work, by engineering the stability of the nanozyme-catalyzed product, we demonstrated that the chromogenic system of 3, 3′, 5, 5′-tetramethylbenzidine (TMB) can act as a visual output signal for constructing various Boolean logic operations. Specifically, cerium oxide or ferroferric oxide-based nanozymes can catalyze the oxidation of colorless TMB to a blue color product (oxTMB). The blue-colored solution of oxTMB could become colorless by some reductants, including the reduced transition state of glucose oxidase and xanthine oxidase. As a result, by combining biocatalytic reactions, the color change of oxTMB could be controlled logically. In our logic systems, glucose oxidase, β-galactosidase, and xanthine oxidase acted as inputs, and the state of oxTMB solution was used as an output. The logic operation produced a colored solution as the readout signal, which was easily distinguished with the naked eye. More importantly, the study of such a decolorization process allows the transformation of previously designed AND and OR logic gates into NAND and NOR gates. We propose that this work may push forward the design of novel nanozyme-based biological gates and help us further understand complex physiological pathways in living systems.

scholarly journals Nano-bio-computing lipid nanotablet

2019 ◽  
Vol 5 (2) ◽  
pp. eaau2124 ◽  
Author(s):  
Jinyoung Seo ◽  
Sungi Kim ◽  
Ha H. Park ◽  
Da Yeon Choi ◽  
Jwa-Min Nam
Keyword(s):  
Lipid Bilayer ◽  
Logic Gate ◽  
Logic Gates ◽  
Boolean Logic ◽  
Circuit Board ◽  
Particle Assembly ◽  
Supported Lipid Bilayer ◽  
Particle Level ◽  
Logic Operations ◽  
And Control

Using nanoparticles as substrates for computation enables algorithmic and autonomous controls of their unique and beneficial properties. However, scalable architecture for nanoparticle-based computing systems is lacking. Here, we report a platform for constructing nanoparticle logic gates and circuits at the single-particle level on a supported lipid bilayer. Our “lipid nanotablet” platform, inspired by cellular membranes that are exploited to compartmentalize and control signaling networks, uses a lipid bilayer as a chemical circuit board and nanoparticles as computational units. On a lipid nanotablet, a single-nanoparticle logic gate senses molecules in solution as inputs and triggers particle assembly or disassembly as an output. We demonstrate a set of Boolean logic operations, fan-in/fan-out of logic gates, and a combinational logic circuit such as a multiplexer. We envisage that our approach to modularly implement nanoparticle circuits on a lipid bilayer will create new paradigms and opportunities in molecular computing, nanoparticle circuits, and systems nanoscience.

scholarly journals Digital logic gates in soft, conductive mechanical metamaterials

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Charles El Helou ◽  
Philip R. Buskohl ◽  
Christopher E. Tabor ◽  
Ryan L. Harne
Keyword(s):  
Integrated Circuits ◽  
Electronic Materials ◽  
Polymer Networks ◽  
Conductive Polymer ◽  
Network Connectivity ◽  
Logic Gates ◽  
Boolean Logic ◽  
Digital Logic ◽  
Mechanical Metamaterials ◽  
Logic Operations

AbstractIntegrated circuits utilize networked logic gates to compute Boolean logic operations that are the foundation of modern computation and electronics. With the emergence of flexible electronic materials and devices, an opportunity exists to formulate digital logic from compliant, conductive materials. Here, we introduce a general method of leveraging cellular, mechanical metamaterials composed of conductive polymers to realize all digital logic gates and gate assemblies. We establish a method for applying conductive polymer networks to metamaterial constituents and correlate mechanical buckling modes with network connectivity. With this foundation, each of the conventional logic gates is realized in an equivalent mechanical metamaterial, leading to soft, conductive matter that thinks about applied mechanical stress. These findings may advance the growing fields of soft robotics and smart mechanical matter, and may be leveraged across length scales and physics.

scholarly journals High Speed All-Optical Logic Gate Using QD-SOA and its Application

2017 ◽  
Author(s):  
Shuai Zhao ◽  
Hongyu Hu
Keyword(s):  
High Speed ◽  
Logic Gate ◽  
Logic Gates ◽  
Boolean Logic ◽  
Hole Burning ◽  
Spectral Hole Burning ◽  
Optical Logic ◽  
Carrier Heating ◽  
Optical Logic Gates ◽  
All Optical

The scheme to realize high speed (~250Gb/s) all-optical Boolean logic gates using semiconductor optica amplifiers with quantum-dot (QD-SOA) is introduced and analyzed in this review. Numerical simulation method was presented by solving the rate equation and taking into account nonlinear dynamics including carrier heating and spectral hole-burning. Binary phase shift keyed (BPSK) signal and on-off keyed signal are used to generate high speed all-optical logic gates. The applications based on all-optical logic gates such as, all-optical latches, pseudo random bit sequence (PRBS) generation and all-optical encryption, are also discussed in this review. Results show that the scheme based on QD-SOA is a promising method for the realization of high speed all-optical communication system in the future.

scholarly journals A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Trevor Y. H. Ho ◽  
Alexander Shao ◽  
Zeyu Lu ◽  
Harri Savilahti ◽  
Filippo Menolascina ◽  
...  
Keyword(s):  
Logic Gate ◽  
Logic Gates ◽  
Identification Problem ◽  
Boolean Logic ◽  
Structure Alignment ◽  
Homologous Proteins ◽  
Highly Active ◽  
Split Protein ◽  
Rational Inference ◽  
Site Identification

AbstractSplit inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augment a mini-Mu transposon-based screening approach and devise the intein-assisted bisection mapping (IBM) method. IBM robustly reveals clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further show that the use of inteins expands functional sequence space for splitting a protein. We also demonstrate the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins, and that basal activities of highly active proteins can be mitigated by splitting them. Our work offers a generalizable and systematic route towards creating split protein-intein fusions for synthetic biology.

scholarly journals Contextual dependencies expand the re-usability of genetic inverters

2020 ◽  
Author(s):  
Huseyin Tas ◽  
Lewis Grozinger ◽  
Ruud Stoof ◽  
Victor de Lorenzo ◽  
Angel Goñi-Moreno
Keyword(s):  
Synthetic Biology ◽  
Computational Analysis ◽  
Logic Gate ◽  
Logic Gates ◽  
Boolean Logic ◽  
Regulatory Proteins ◽  
Genetic Circuits ◽  
Genetic Construct ◽  
Genetic Components ◽  
Logic Functions

The design and implementation of Boolean logic functions in living cells has become a very active field within synthetic biology. By controlling networks of regulatory proteins, novel genetic circuits are engineered to generate predefined output responses. Although many current implementations focus solely on the genetic components of the circuit, the host context in which the circuit performs is crucial for its outcome. Here, we characterise 20 genetic NOT logic gates (inverters) in up to 7 bacterial-based contexts each, to finally generate 135 different functions. The contexts we focus on are particular combinations of four plasmid backbones and three hosts, two Escherichia coli and one Pseudomonas putida strains. Each NOT logic gate shows seven different logic behaviours, depending on the context. That is, gates can be reconfigured to fit response requirements by changing only contextual parameters. Computational analysis shows that this range of behaviours improves the compatibility between gates, because there are considerably more possibilities for combination than when considering a unique function per genetic construct. Finally, we address the issue of interoperability and portability by measuring, scoring, and comparing gate performance across contexts. Rather than being a limitation, we argue that the effect of the genetic background on synthetic constructs expand the scope of the functions that can be engineered in complex cellular environments, and advocate for considering context as a fundamental design parameter for synthetic biology.

Reconfigurable Logic Gates Based on Programable Multistable Mechanisms

2020 ◽  
Vol 12 (2) ◽  
Author(s):  
Mohamed Zanaty ◽  
Hubert Schneegans ◽  
Ilan Vardi ◽  
Simon Henein
Keyword(s):  
Logic Gate ◽  
Beam Theory ◽  
Logic Gates ◽  
Building Blocks ◽  
Reconfigurable Logic ◽  
Logical Function ◽  
Element Analysis ◽  
Binary Logic ◽  
Geometric Data ◽  
The Stability

Abstract Binary logic gates are building blocks of computing machines, in particular, electronic computers. One variant is the programable logic gate, also known as the reconfigurable logic gate, in which the logical function implemented can be modified. In this paper, we construct a mechanism to implement a reconfigurable logic gate. This mechanism is based on the concept of programable multistable mechanisms which we introduced in previous work. The application of a programable multistable mechanism is superior to the different bistable mechanisms previously used to implement logic gates since a single mechanism can be used to implement several logic functions. Our reconfigurable logic gates use a novel geometric construction where the geometric data depend on the stability behavior of the mechanism. There are 16 binary logic gates and our construction can theoretically produce nine of these and our physical model produces six logical gates. Input and output of the mechanism are displacement and the mechanisms can be combined serially, i.e., output of a mechanism is an input for another. We show that we can implement nor and nand gates, so combinations of our mechanism can express any logical function. The mechanism is therefore theoretically universal, i.e., implement any computation. We give an analytic model of the mechanism based on Euler–Bernoulli beam theory to find the geometric data, then validate it using finite element analysis and experimental demonstration.

scholarly journals ANALYSIS OF AN EXPERIMENTAL QUANTUM LOGIC GATE BY COMPLEMENTARY CLASSICAL OPERATIONS

2006 ◽  
Vol 21 (24) ◽  
pp. 1837-1850 ◽  
Author(s):  
HOLGER F. HOFMANN ◽  
RYO OKAMOTO ◽  
SHIGEKI TAKEUCHI
Keyword(s):  
Quantum Logic ◽  
Logic Gate ◽  
Bell State ◽  
Logic Gates ◽  
Basis Sets ◽  
Entanglement Generation ◽  
Quantum Logic Gates ◽  
State Discrimination ◽  
Logic Operations

Quantum logic gates can perform calculations much more efficiently than their classical counterparts. However, the level of control needed to obtain a reliable quantum operation is correspondingly higher. In order to evaluate the performance of experimental quantum gates, it is therefore necessary to identify the essential features that indicate quantum coherent operation. In this paper, we show that an efficient characterization of an experimental device can be obtained by investigating the classical logic operations on a pair of complementary basis sets. It is then possible to obtain reliable predictions about the quantum coherent operations of the gate such as entanglement generation and Bell state discrimination even without performing these operations directly.

scholarly journals Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Madeline E Sherlock ◽  
Narasimhan Sudarsan ◽  
Shira Stav ◽  
Ronald R Breaker
Keyword(s):  
De Novo ◽  
Rna World ◽  
Logic Gate ◽  
Logic Gates ◽  
Boolean Logic ◽  
Control Synthesis ◽  
Messenger Rnas ◽  
Phosphoribosyl Pyrophosphate ◽  
Rna Molecules ◽  
Regulatory Systems

Gene control systems sometimes interpret multiple signals to set the expression levels of the genes they regulate. In rare instances, ligand-binding riboswitch aptamers form tandem arrangements to approximate the function of specific two-input Boolean logic gates. Here, we report the discovery of riboswitch aptamers for phosphoribosyl pyrophosphate (PRPP) that naturally exist either in singlet arrangements, or occur in tandem with guanine aptamers. Tandem guanine-PRPP aptamers can bind the target ligands, either independently or in combination, to approximate the function expected for an IMPLY Boolean logic gate to regulate transcription of messenger RNAs for de novo purine biosynthesis in bacteria. The existence of sophisticated all-RNA regulatory systems that sense two ancient ribonucleotide derivatives to control synthesis of RNA molecules supports the hypothesis that RNA World organisms could have managed a complex metabolic state without the assistance of protein regulatory factors.

scholarly journals ORGANIC MEMRISTOR DEVICES FOR LOGIC ELEMENTS WITH MEMORY

2012 ◽  
Vol 22 (11) ◽  
pp. 1250283 ◽  
Author(s):  
VICTOR EROKHIN ◽  
GERARD DAVID HOWARD ◽  
ANDREW ADAMATZKY
Keyword(s):  
Low Power ◽  
Logic Gate ◽  
Logic Gates ◽  
Full Adder ◽  
Experimental Results ◽  
Boolean Logic ◽  
Next Generation ◽  
Nanoscale Fabrication ◽  
Thresholding Function ◽  
With Memory

Memristors are promising next-generation memory candidates that are nonvolatile, possess low power requirements and are capable of nanoscale fabrication. In this article, we physically realize and describe the use of organic memristors in designing stateful boolean logic gates for the AND OR and NOT operations. The output of these gates is analog and dependent on the length of time that suitable charge is applied to the inputs, displaying a learning property. Results may be also interpreted in a traditional binary manner through the use of a suitable thresholding function at the output. The memristive property of the gate allows for the production of analog outputs that vary based on the charge-dependent nonvolatile state of the memristor. We provide experimental results of physical fabrication of three types of logic gate. A simulation of a one-bit full adder comprised of memristive logic gates is also included, displaying varying response to two distinct input patterns.

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