SHF: Small: A reconfigurable architecture for digital circuit computation by fast, robust, and leakless DNA strand displacement cascades
SHF: Small: A reconfigurable architecture for digital circuit computation by fast, robust, and leakless DNA strand displacement cascades
批准号:
1718938
负责人:
Erik Winfree
金额:
$46.5万
依托单位国家:
美国
项目类别:
Standard Grant
财政年份:
2017
资助国家:
美国
项目状态:
已结题
起止时间:
2017-07-01 至 2020-12-31
中文摘要
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英文摘要
The promise of molecular programming lies in its ability to not only process information autonomously, but to do so in a biochemical context in order to sense and actuate matter. For its simplicity and its programmability, one attractive option for chemical information processing is built upon the DNA strand displacement (DSD) primitive, where a soup of rationally designed nucleotide sequences interact, react, and recombine over time in order to carry out sophisticated computation. The focus of this proposal is the creation of a reconfigurable DSD architecture akin to a molecular breadboard. Its purpose is to "scale-up" what is possible with this technology and to "scale-out" its adoption to new contexts and new areas of study. A small number of fast, robust and well-understood molecular components will be developed that compose seamlessly. The necessary tools to facilitate rapid circuit design and characterization will also be developed. The reconfigurable architecture will be designed to meet the challenges required in real-world applications ranging from point-of-care diagnostics to sensing and actuation within molecular systems. Due to its ease of use, we envision that this molecular breadboard will be an ideal vehicle to teach molecular programming and to facilitate wider adoption of DSD systems.Building on a new leak reduction paradigm for DNA strand displacement systems, a new design for robust molecular computing gates will be developed, experimentally tested, and refined. By perfecting a set of molecular components suitable for use in modular and reconfigurable circuits, this will result in a fixed set of dozens of high quality gates that can be arbitrarily wired-up in order to create bespoke molecular circuits. A compiler will be developed that takes as input a circuit or logic function and provides as output the optimized set of biochemical "wires" necessary to activate the desired logic behavior. If successful, it will be possible to create and execute fast, leakless and robust molecular circuits, for circuits 2×-10× larger than have been previously demonstrated and with completion times 10×-100× faster. This increase in complexity creates an even greater need for design verification that will be addressed by the development of more efficient kinetic simulation software. The breadboard promises to be robust enough for immediate use in applications, such as diagnostics and molecular imaging, and in new contexts such as paper-based devices.
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Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates
推断具有局部上下文相关阿伦尼乌斯速率的 DNA 结构动力学基本步骤模型的参数
DOI:
10.1007/978-3-319-66799-7_12
发表时间:
2017
期刊:
Lecture notes in computer science
影响因子:
--
作者:
[Zolaktaf, Sedigheh, Dannenberg, Frits, Rudelis, Xander, Condon, Anne, Schaeffer, Joseph M, Thachuk, Chris, Winfree, Erik]
通讯作者:
Winfree, Erik
DOI:
10.1098/rsif.2018.0107
发表时间:
2018-12-01
期刊:
JOURNAL OF THE ROYAL SOCIETY INTERFACE
影响因子:
3.9
作者:
[Berleant, Joseph, Berlind, Christopher, Winfree, Erik]
通讯作者:
Winfree, Erik
Verifying chemical reaction network implementations: A pathway decomposition approach
验证化学反应网络的实现:路径分解方法
DOI:
10.1016/j.tcs.2017.10.011
发表时间:
2017
期刊:
Theoretical Computer Science
影响因子:
1.1
作者:
[Shin, Seung Woo, Thachuk, Chris, Winfree, Erik]
通讯作者:
Winfree, Erik
Towards space- and energy-efficient computations
迈向空间和能源高效的计算
DOI:
--
发表时间:
2019
期刊:
The Energetics of Computing in Life and Machines
影响因子:
--
作者:
[Condon, Anne, Thachuk, Chris]
通讯作者:
Thachuk, Chris
DOI:
10.1016/j.tcs.2018.10.027
发表时间:
2019-09-20
期刊:
THEORETICAL COMPUTER SCIENCE
影响因子:
1.1
作者:
[Breik, Keenan, Thachuk, Chris, Soloveichik, David]
通讯作者:
Soloveichik, David
共 8 条
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批准号:1844818
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资助金额:$1.5万
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Speaker support for workshop on advances in molecular programming and computing
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HCC: Large: Collaborative Research: DNA Machine Builder: Creative molecular-machine design through mass-scale crowdsourcing
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SHF:Medium:Collaborative Research:Scaling Up Programmable and Algorithmic DNA Self-Assembly
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Student travel support for DNA17
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Future directions for molecular programming: DNA17 special session
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资助金额:$1.5万
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Collaborative Research: The Molecular Programming Project
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Collaborative Research: EMT/MISC: Behavior Based Molecular Robotics
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财政年份:2008
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负责人:Erik Winfree
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EMT: Toward Large Scale Integrated Nucleic Acid Circuits
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Nano: Collaborative Research: EMT: Toward Universal Bottom-Up Nanofabrication with DNA
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NANO: Collaborative Research: EMT: Algorithmic error-correction in biologically inspired self-assembly and computation
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资助金额:$20.0万
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依托单位:
NANO: Controlling Errors in Algorithmic Self-Assembly: Characterization, Modeling, and Implementation
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项目类别:Continuing Grant
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资助金额:$30.0万
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财政年份:2004
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依托单位:
ITR/SY(CISE): Biomolecular Computing by DNA/Enzyme Systems
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批准号:0113443
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项目类别:Standard Grant
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资助金额:$44.96万
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负责人:Erik Winfree
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PECASE: Foundations of Autonomous Biomolecular Computation
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项目类别:Continuing Grant
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资助金额:$50.0万
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财政年份:2001
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负责人:Erik Winfree
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依托单位:
国内基金
海外基金
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