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  1 / 696 MEDLINE  
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[PMID]:29348493
[Au] Autor:Song Y; Kim S; Heller MJ; Huang X
[Ad] Endereço:Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. yjunsong@gmail.com.
[Ti] Título:DNA multi-bit non-volatile memory and bit-shifting operations using addressable electrode arrays and electric field-induced hybridization.
[So] Source:Nat Commun;9(1):281, 2018 01 18.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:DNA has been employed to either store digital information or to perform parallel molecular computing. Relatively unexplored is the ability to combine DNA-based memory and logical operations in a single platform. Here, we show a DNA tri-level cell non-volatile memory system capable of parallel random-access writing of memory and bit shifting operations. A microchip with an array of individually addressable electrodes was employed to enable random access of the memory cells using electric fields. Three segments on a DNA template molecule were used to encode three data bits. Rapid writing of data bits was enabled by electric field-induced hybridization of fluorescently labeled complementary probes and the data bits were read by fluorescence imaging. We demonstrated the rapid parallel writing and reading of 8 (2 ) combinations of 3-bit memory data and bit shifting operations by electric field-induced strand displacement. Our system may find potential applications in DNA-based memory and computations.
[Mh] Termos MeSH primário: Computadores Moleculares
DNA/química
Armazenamento e Recuperação da Informação
[Mh] Termos MeSH secundário: Biomimética
DNA/genética
Desenho de Equipamento
Hibridização Genética
Análise de Sequência com Séries de Oligonucleotídeos
Processamento de Sinais Assistido por Computador
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180120
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02705-8


  2 / 696 MEDLINE  
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[PMID]:28467664
[Au] Autor:Gamella M; Privman M; Bakshi S; Melman A; Katz E
[Ad] Endereço:Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699-5810, USA.
[Ti] Título:DNA Release from Fe -Cross-Linked Alginate Films Triggered by Logically Processed Biomolecular Signals: Integration of Biomolecular Computing and Actuation.
[So] Source:Chemphyschem;18(13):1811-1821, 2017 Jul 05.
[Is] ISSN:1439-7641
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Signal-controlled release of DNA from Fe -cross-linked alginate hydrogel electrochemically deposited on an electrode surface was studied. The multiple input signals were logically processed with the help of the enzyme-biocatalyzed reactions. Boolean logic gates, OR, AND, INH, were realized with the biocatalytic reactions performed by the enzymes entrapped in the alginate film. Hydrogen peroxide produced by the enzymatic reactions resulted in the degradation of the alginate hydrogel and DNA release. The alginate degradation was facilitated by the formation of free radicals in the Fenton-type reaction catalyzed by iron cations cross-linking the alginate hydrogel. The studied approach is versatile and can be adapted to various chemical signals processed by various enzymes with differently implemented Boolean logic. This work illustrates a novel concept of functional integration of biomolecular computing and actuation.
[Mh] Termos MeSH primário: Alginatos/química
Computadores Moleculares
Reagentes para Ligações Cruzadas/química
DNA/metabolismo
Compostos Férricos/química
Lógica
[Mh] Termos MeSH secundário: Animais
Biocatálise
DNA/química
Esterases/química
Esterases/metabolismo
Glucose Oxidase/química
Glucose Oxidase/metabolismo
Ácido Glucurônico/química
Ácidos Hexurônicos/química
Peroxidase do Rábano Silvestre/química
Peroxidase do Rábano Silvestre/metabolismo
Lactato Desidrogenases/química
Lactato Desidrogenases/metabolismo
Oxigenases de Função Mista/química
Oxigenases de Função Mista/metabolismo
Nanopartículas/química
Nanopartículas/metabolismo
Dióxido de Silício/química
Dióxido de Silício/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Alginates); 0 (Cross-Linking Reagents); 0 (Ferric Compounds); 0 (Hexuronic Acids); 7631-86-9 (Silicon Dioxide); 8A5D83Q4RW (Glucuronic Acid); 8C3Z4148WZ (alginic acid); 9007-49-2 (DNA); EC 1.- (Mixed Function Oxygenases); EC 1.1.- (Lactate Dehydrogenases); EC 1.1.3.4 (Glucose Oxidase); EC 1.11.1.- (Horseradish Peroxidase); EC 1.13.12.4 (lactate 2-monooxygenase); EC 3.1.- (Esterases)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170504
[St] Status:MEDLINE
[do] DOI:10.1002/cphc.201700301


  3 / 696 MEDLINE  
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[PMID]:29317787
[Au] Autor:Toumey C
[Ad] Endereço:Center for Environmental Nanoscience & Risk at the University of South Carolina, Columbia, SC, USA. Toumey@mailbox.sc.edu.
[Ti] Título:Reality, fantasy and civility in molecular assemblers.
[So] Source:Nat Nanotechnol;13(1):2-3, 2018 01.
[Is] ISSN:1748-3395
[Cp] País de publicação:England
[La] Idioma:eng
[Mh] Termos MeSH primário: Nanotecnologia
[Mh] Termos MeSH secundário: Computadores Moleculares
Dissidências e Disputas
História do Século XXI
Seres Humanos
Modelos Teóricos
Nanotecnologia/história
Nanotecnologia/organização & administração
[Pt] Tipo de publicação:HISTORICAL ARTICLE; JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180208
[Lr] Data última revisão:
180208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180111
[St] Status:MEDLINE
[do] DOI:10.1038/s41565-017-0050-6


  4 / 696 MEDLINE  
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[PMID]:29317786
[Ti] Título:Bigger and cheaper.
[So] Source:Nat Nanotechnol;13(1):1, 2018 01.
[Is] ISSN:1748-3395
[Cp] País de publicação:England
[La] Idioma:eng
[Mh] Termos MeSH primário: Computadores Moleculares
DNA
Nanotecnologia
[Mh] Termos MeSH secundário: Seres Humanos
[Pt] Tipo de publicação:EDITORIAL
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180208
[Lr] Data última revisão:
180208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180111
[St] Status:MEDLINE
[do] DOI:10.1038/s41565-017-0054-2


  5 / 696 MEDLINE  
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[PMID]:27775906
[Au] Autor:Lu Y; Higgins MD; Noel A; Leeson MS; Chen Y
[Ti] Título:The Effect of Two Receivers on Broadcast Molecular Communication Systems.
[So] Source:IEEE Trans Nanobioscience;15(8):891-900, 2016 12.
[Is] ISSN:1558-2639
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Molecular communication is a paradigm that utilizes molecules to exchange information between nano-machines. When considering such systems where multiple receivers are present, prior work has assumed for simplicity that they do not interfere with each other. This paper aims to address this issue and shows to what extent an interfering receiver, [Formula: see text], will have an impact on the target receiver, [Formula: see text], with respect to Bit Error Rate (BER) and capacity. Furthermore, approximations of the Binomial distribution are applied to reduce the complexity of calculations. Results show the sensitivity in communication performance due to the relative location of the interfering receiver. Critically, placing [Formula: see text] between the transmitter [Formula: see text] and [Formula: see text] causes a significant increase in BER or decrease in capacity.
[Mh] Termos MeSH primário: Comunicação
Simulação por Computador
Computadores Moleculares
Modelos Teóricos
Nanotecnologia/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1708
[Cu] Atualização por classe:171222
[Lr] Data última revisão:
171222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161025
[St] Status:MEDLINE
[do] DOI:10.1109/TNB.2016.2620339


  6 / 696 MEDLINE  
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[PMID]:27775531
[Au] Autor:Manocha P; Chandwani G; Das S
[Ti] Título:Dielectrophoretic Relay Assisted Molecular Communication for In-Sequence Molecule Delivery.
[So] Source:IEEE Trans Nanobioscience;15(7):781-791, 2016 10.
[Is] ISSN:1558-2639
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:With current research focus to interconnect the molecular communication environment with external environment, it is imperative to design external devices working on molecular communication schemes to be interfaced with in-vivo molecular network. Recently, efforts have been made to integrate molecular communication with Lab-on-chip (LOC); one of the techniques used in LOC for manipulation and transportation of molecules is Dielctrophoresis (DEP). We propose the use of DEP in molecular communication to maintain in-sequence delivery of molecules. DEP planar electrodes are modeled as relays used in telecommunications. We describe the theoretical system model and analyze the effect of introducing DEP relays in diffusive channel in terms of probability of in-sequence delivery of molecules. Information rate of DEP-based channel is analytically obtained for in-sequence delivery. The numerical results obtained show that the information rate for in-sequence delivery of molecules through diffusive channel increases by 26% if DEP relays are used in the channel. Though the system is sensitive to noise variance, incorporation of DEP relay results in a substantial improvement in the capacity of the channel.
[Mh] Termos MeSH primário: Computadores Moleculares
Eletroforese/métodos
Dispositivos Lab-On-A-Chip
[Mh] Termos MeSH secundário: Eletrodos
Análise de Fourier
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171222
[Lr] Data última revisão:
171222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161025
[St] Status:MEDLINE
[do] DOI:10.1109/TNB.2016.2618904


  7 / 696 MEDLINE  
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[PMID]:27775529
[Au] Autor:Shitiri E; Cho HS
[Ti] Título:A Biochemical Oscillator Using Excitatory Molecules for Nanonetworks.
[So] Source:IEEE Trans Nanobioscience;15(7):765-774, 2016 10.
[Is] ISSN:1558-2639
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:For nanonetworks to be able to achieve large-scale functionality, such as to respond collectively to a trigger, synchrony between nanomachines is essential. However, to facilitate synchronization, some sort of physical clocking mechanism is required, such as the oscillators driven by auto-inhibitory molecules or by auto-inducing molecules. In this study, taking inspiration from the widely studied biological oscillatory phenomena called Calcium (Ca ) oscillations, we undertake a different approach to design an oscillator. Our model employs three different types of excitatory molecules that work in tandem to generate oscillatory phenomenon in the concentration levels of the molecule of interest. The main objective of the study is to model a high frequency biochemical oscillator, along with the investigations to identify and determine the parameters that affect the period of the oscillations. The investigations entail and highlight the design of the reserve unit, a reservoir of the molecule of interest, as a key factor in realizing a high frequency stable biochemical oscillator.
[Mh] Termos MeSH primário: Relógios Biológicos/fisiologia
Cálcio/metabolismo
Computadores Moleculares
Nanotecnologia/métodos
[Mh] Termos MeSH secundário: Sinalização do Cálcio
Modelos Biológicos
Nanoestruturas/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
SY7Q814VUP (Calcium)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171222
[Lr] Data última revisão:
171222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161025
[St] Status:MEDLINE
[do] DOI:10.1109/TNB.2016.2616539


  8 / 696 MEDLINE  
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[PMID]:28432850
[Au] Autor:Sakowski S; Krasinski T; Sarnik J; Blasiak J; Waldmajer J; Poplawski T
[Ad] Endereço:.
[Ti] Título:A detailed experimental study of a DNA computer with two endonucleases.
[So] Source:Z Naturforsch C;72(7-8):303-313, 2017 Jul 14.
[Is] ISSN:0939-5075
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro's group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effect of the number of states, the length of input data, and the nondeterminism on the computing process. We also tested different automata (with three, four, and six states) running on various accepted input words of different lengths such as ab, aab, aaab, ababa, and of an unaccepted word ba. Moreover, this article presents the reaction optimization and the methods of eliminating certain biochemical problems occurring in the implementation of a biomolecular DNA automaton based on two endonucleases.
[Mh] Termos MeSH primário: Automação/métodos
Computadores Moleculares
DNA/metabolismo
Endonucleases/metabolismo
[Mh] Termos MeSH secundário: Sequência de Bases
DNA/genética
DNA Ligases/metabolismo
Desoxirribonucleases de Sítio Específico do Tipo II/metabolismo
Modelos Teóricos
Oligonucleotídeos/genética
Oligonucleotídeos/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Oligonucleotides); 9007-49-2 (DNA); EC 3.1.- (Endonucleases); EC 3.1.21.- (endodexoyribonuclease BbvI); EC 3.1.21.4 (Deoxyribonucleases, Type II Site-Specific); EC 6.5.1.- (DNA Ligases)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170927
[Lr] Data última revisão:
170927
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170423
[St] Status:MEDLINE


  9 / 696 MEDLINE  
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[PMID]:28368824
[Au] Autor:Arifler D; Arifler D
[Ti] Título:Monte Carlo Analysis of Molecule Absorption Probabilities in Diffusion-Based Nanoscale Communication Systems with Multiple Receivers.
[So] Source:IEEE Trans Nanobioscience;16(3):157-165, 2017 Apr.
[Is] ISSN:1558-2639
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:For biomedical applications of nanonetworks, employing molecular communication for information transport is advantageous over nano-electromagnetic communication: molecular communication is potentially biocompatible and inherently energy-efficient. Recently, several studies have modeled receivers in diffusion-based molecular communication systems as "perfectly monitoring" or "perfectly absorbing" spheres based on idealized descriptions of chemoreception. In this paper, we focus on perfectly absorbing receivers and present methods to improve the accuracy of simulation procedures that are used to analyze these receivers. We employ schemes available from the chemical physics and biophysics literature and outline a Monte Carlo simulation algorithm that accounts for the possibility of molecule absorption during discrete time steps, leading to a more accurate analysis of absorption probabilities. Unlike most existing studies that consider a single receiver, this paper analyzes absorption probabilities for multiple receivers deterministically or randomly deployed in a region. For random deployments, the ultimate absorption probabilities as a function of transmitter-receiver distance are shown to fit well to power laws; the exponents derived become more negative as the number of receivers increases up to a limit beyond which no additional receivers can be "packed" in the deployment region. This paper is expected to impact the design of molecular nanonetworks with multiple absorbing receivers.
[Mh] Termos MeSH primário: Comunicação
Computadores Moleculares
Modelos Teóricos
Método de Monte Carlo
Nanotecnologia/métodos
[Mh] Termos MeSH secundário: Difusão
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171107
[Lr] Data última revisão:
171107
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170404
[St] Status:MEDLINE
[do] DOI:10.1109/TNB.2017.2687978


  10 / 696 MEDLINE  
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[PMID]:28346402
[Au] Autor:Weinberg BH; Pham NTH; Caraballo LD; Lozanoski T; Engel A; Bhatia S; Wong WW
[Ad] Endereço:Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, Massachusetts, USA.
[Ti] Título:Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells.
[So] Source:Nat Biotechnol;35(5):453-462, 2017 May.
[Is] ISSN:1546-1696
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Engineered genetic circuits for mammalian cells often require extensive fine-tuning to perform as intended. We present a robust, general, scalable system, called 'Boolean logic and arithmetic through DNA excision' (BLADE), to engineer genetic circuits with multiple inputs and outputs in mammalian cells with minimal optimization. The reliability of BLADE arises from its reliance on recombinases under the control of a single promoter, which integrates circuit signals on a single transcriptional layer. We used BLADE to build 113 circuits in human embryonic kidney and Jurkat T cells and devised a quantitative, vector-proximity metric to evaluate their performance. Of 113 circuits analyzed, 109 functioned (96.5%) as intended without optimization. The circuits, which are available through Addgene, include a 3-input, two-output full adder; a 6-input, one-output Boolean logic look-up table; circuits with small-molecule-inducible control; and circuits that incorporate CRISPR-Cas9 to regulate endogenous genes. BLADE enables execution of sophisticated cellular computation in mammalian cells, with applications in cell and tissue engineering.
[Mh] Termos MeSH primário: Técnicas de Reprogramação Celular/métodos
Redes Reguladoras de Genes/genética
Engenharia Genética/métodos
Modelos Genéticos
Proteoma/genética
Transdução de Sinais/genética
[Mh] Termos MeSH secundário: Simulação por Computador
Computadores Moleculares
Seres Humanos
Células Jurkat
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Proteome)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170927
[Lr] Data última revisão:
170927
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170328
[St] Status:MEDLINE
[do] DOI:10.1038/nbt.3805



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