scholarly journals DNA dynamics and computation based on toehold-free strand displacement

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hong Kang ◽  
Tong Lin ◽  
Xiaojin Xu ◽  
Qing-Shan Jia ◽  
Richard Lakerveld ◽  
...  
Keyword(s):  
Information Processing ◽  
Boolean Functions ◽  
The Other ◽  
Dna Nanostructures ◽  
Dna Dynamics ◽  
Strand Displacement ◽  
Equilibrium Control ◽  
Target Strand ◽  
Excess Amount ◽  
Kinetics Of

AbstractWe present a simple and effective scheme of a dynamic switch for DNA nanostructures. Under such a framework of toehold-free strand displacement, blocking strands at an excess amount are applied to displace the complementation of specific segments of paired duplexes. The functional mechanism of the scheme is illustrated by modelling the base pairing kinetics of competing strands on a target strand. Simulation reveals the unique properties of toehold-free strand displacement in equilibrium control, which can be leveraged for information processing. Based on the controllable dynamics in the binding of preformed DNA nanostructures, a multi-input-multi-output (MIMO) Boolean function is controlled by the presence of the blockers. In conclusion, we implement two MIMO Boolean functions (one with 4-bit input and 2-bit output, and the other with 16-bit input and 8-bit output) to showcase the controllable dynamics.

Kinetics of Strand Displacement and Hybridization on Wireframe DNA Nanostructures: Dissecting the Roles of Size, Morphology, and Rigidity

ACS Nano ◽  
2018 ◽  
Vol 12 (12) ◽  
pp. 12836-12846 ◽  
Author(s):  
Casey M. Platnich ◽  
Amani A. Hariri ◽  
Janane F. Rahbani ◽  
Jesse B. Gordon ◽  
Hanadi F. Sleiman ◽  
...  
Keyword(s):  
Dna Nanostructures ◽  
Strand Displacement ◽  
Kinetics Of

scholarly journals Handhold-mediated strand displacement: a nucleic acid-based mechanism for generating far-from-equilibrium assemblies through templated reactions

2020 ◽  
Author(s):  
Javier Cabello-Garcia ◽  
Wooli Bae ◽  
Guy-Bart V. Stan ◽  
Thomas E. Ouldridge
Keyword(s):  
Nucleic Acid ◽  
Biological Systems ◽  
Dna Nanotechnology ◽  
Central Mechanism ◽  
Dna Duplexes ◽  
Strand Displacement ◽  
Target Strand ◽  
Far From Equilibrium ◽  
Kinetics Of ◽  
Moderate Length

Toehold-mediated strand displacement (TMSD) is a nucleic acid-based reaction wherein an invader strand (I) replaces an incumbent strand (N) in a duplex with a target strand (T). TMSD is driven by toeholds, overhanging single-stranded domains in T recognised by I. Although TMSD is responsible for the outstanding potential of dynamic DNA nanotechnology1, 2, TMSD cannot implement templating, the central mechanism by which biological systems generate complex, far-from equilibrium assemblies like RNA or proteins3, 4. Therefore, we introduce handhold-mediated strand displacement (HMSD). Handholds are toehold analogues located in N and capable of implementing templating. We measure the kinetics of 98 different HMSD systems to demonstrate that handholds can accelerate the rate of invader-target (IT) binding by more than 4 orders of magnitude. Furthermore, handholds of moderate length accelerate reactions whilst allowing detachment of the product IT from N. We are thus able to experimentally demonstrate the use of HMSD-based templating to produce highly-specific far-from-equilibrium DNA duplexes.

Does Performing Other Audit Tasks Affect Going-Concern Judgments?

1999 ◽  
Vol 74 (4) ◽  
pp. 493-508 ◽  
Author(s):  
Stephen E. Rau ◽  
Donald V. Moser
Keyword(s):  
Information Processing ◽  
Review Process ◽  
Negative Information ◽  
The Other ◽  
Positive Information ◽  
Going Concern ◽  
Staff Members

This study examines whether personally performing other audit tasks can bias supervising seniors' going-concern judgments. During an audit, the senior performs some audit tasks him/herself and delegates other tasks to staff members. When personally performing an audit task, the senior would focus on the evidence related to that task. We predict that such evidence will have greater influence on the senior's subsequent going-concern judgment. The results of our experiment are consistent with our predictions. When provided with an identical set of information, seniors who performed another audit task for which the underlying facts of the case reflected positively (negatively) on the company's viability, subsequently made going-concern judgments that were relatively more positive (negative). Our results also demonstrate that the well-documented tendency of auditors to attend more to negative information does not always dominate auditors' information processing. Subjects who performed the task for which the underlying facts reflected positively on the company's viability directed their attention to such positive information and, consequently, both their memory and judgments were more positive than those of subjects in the other conditions. Recent findings indicating that biases in seniors' going-concern judgments may not be fully offset in the review process are discussed along with other potential implications of our results.

The Reactivity of Different Active Forms of Sodium Carbonate with Respect to Sulfur Dioxide

1992 ◽  
Vol 57 (11) ◽  
pp. 2302-2308
Author(s):  
Karel Mocek ◽  
Erich Lippert ◽  
Emerich Erdös
Keyword(s):  
Thermal Decomposition ◽  
Liquid Phase ◽  
Sulfur Dioxide ◽  
Specific Surface ◽  
Surface Area ◽  
Sodium Carbonate ◽  
Room Temperature ◽  
Active Form ◽  
The Other ◽  
Kinetics Of

The kinetics of the reaction of solid sodium carbonate with sulfur dioxide depends on the microstructure of the solid, which in turn is affected by the way and conditions of its preparation. The active form, analogous to that obtained by thermal decomposition of NaHCO3, emerges from the dehydration of Na2CO3 . 10 H2O in a vacuum or its weathering in air at room temperature. The two active forms are porous and have approximately the same specific surface area. Partial hydration of the active Na2CO3 in air at room temperature followed by thermal dehydration does not bring about a significant decrease in reactivity. On the other hand, if the preparation of anhydrous Na2CO3 involves, partly or completely, the liquid phase, the reactivity of the product is substantially lower.

scholarly journals Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids

2017 ◽  
Vol 121 (12) ◽  
pp. 2594-2602 ◽  
Author(s):  
Xiaoping Olson ◽  
Shohei Kotani ◽  
Bernard Yurke ◽  
Elton Graugnard ◽  
William L. Hughes
Keyword(s):  
Nucleic Acids ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Locked Nucleic Acids ◽  
Dna Strand ◽  
Kinetics Of

On the kinetics of Hadamard-type fractional differential systems

2020 ◽  
Vol 23 (2) ◽  
pp. 553-570 ◽  
Author(s):  
Li Ma
Keyword(s):  
Differential Operator ◽  
Numerical Simulations ◽  
Type Inequality ◽  
The Other ◽  
Differential Systems ◽  
Fractional Differential Systems ◽  
Fractional Differential Operator ◽  
Fractional Differential ◽  
Kinetics Of ◽  
Theoretical Results

AbstractThis paper is devoted to the investigation of the kinetics of Hadamard-type fractional differential systems (HTFDSs) in two aspects. On one hand, the nonexistence of non-trivial periodic solutions for general HTFDSs, which are considered in some functional spaces, is proved and the corresponding eigenfunction of Hadamard-type fractional differential operator is also discussed. On the other hand, by the generalized Gronwall-type inequality, we estimate the bound of the Lyapunov exponents for HTFDSs. In addition, numerical simulations are addressed to verify the obtained theoretical results.

scholarly journals Kinetics of Toehold-Mediated DNA Strand Displacement Depend on FeII4L4 Tetrahedron Concentration

Nano Letters ◽  
2021 ◽  
Vol 21 (3) ◽  
pp. 1368-1374
Author(s):  
Jinbo Zhu ◽  
Filip Bošković ◽  
Bao-Nguyen T. Nguyen ◽  
Jonathan R. Nitschke ◽  
Ulrich F. Keyser
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Kinetics Of

Development of DNA computing and information processing based on DNA-strand displacement

2015 ◽  
Vol 58 (10) ◽  
pp. 1515-1523 ◽  
Author(s):  
Yafei Dong ◽  
Chen Dong ◽  
Fei Wan ◽  
Jing Yang ◽  
Cheng Zhang
Keyword(s):  
Information Processing ◽  
Dna Computing ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand

On 1-stable perfectly balanced Boolean functions

2017 ◽  
Vol 27 (2) ◽  
Author(s):  
Stanislav V. Smyshlyaev
Keyword(s):  
Boolean Function ◽  
Boolean Functions ◽  
The Other ◽  
Correlation Immunity ◽  
Other Hand

AbstractThe paper is concerned with relations between the correlation-immunity (stability) and the perfectly balancedness of Boolean functions. It is shown that an arbitrary perfectly balanced Boolean function fails to satisfy a certain property that is weaker than the 1-stability. This result refutes some assertions by Markus Dichtl. On the other hand, we present new results on barriers of perfectly balanced Boolean functions which show that any perfectly balanced function such that the sum of the lengths of barriers is smaller than the length of variables, is 1-stable.

Evoked Potentials by Letters in Printed and Script Forms

1984 ◽  
Vol 59 (1) ◽  
pp. 227-232 ◽  
Author(s):  
Luciano Mecacci ◽  
Dario Salmaso
Keyword(s):  
Information Processing ◽  
Evoked Potentials ◽  
Visual Evoked Potentials ◽  
Adult Male ◽  
Visual Information ◽  
The Other ◽  
Behavioral Data ◽  
Evoked Responses ◽  
Amplitude Component ◽  
Male Subjects

Visual evoked potentials were recorded for 6 adult male subjects in response to single vowels and consonants in printed and script forms. Analysis showed the vowels in the printed form to have evoked responses with shorter latency (component P1 at about 133 msec.) and larger amplitude (component P1-N1) than the other letter-typeface combinations. No hemispheric asymmetries were found. The results partially agree with the behavioral data on the visual information-processing of letters.

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