A Formal Combinational Logic Synthesis With Chemical Reaction Networks

Ge, Lulu; Zhong, Zhiwei; Wen, Donglin; You, Xiaohu; Zhang, Chuan

doi:10.1109/tmbmc.2016.2640287

Cited by 21 publications

(17 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Computational power of chemical reaction networks. Previous research demonstrated techniques of achieving complex behaviors in mass-action chemistry, such as computing algebraic functions and polynomials [4,19,18], logarithms [7], implementing logic gates and finite state machines [12,16,10], and neural networks [11,18]. Moreover, the Turing completeness of chemistry has been proven, using the strategy of implementing polynomial ODEs (which have been previously shown to be Turing universal) in mass-action chemical kinetics [9].…”

Section: Related Workmentioning

confidence: 99%

CRN++: Molecular programming language

2020

View full text Add to dashboard Cite

Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine.A key technical challenge lies in embedding computation in molecular contexts where electronic micro-controllers cannot be inserted. This necessitates effective representation of computation using molecular components. While previous work established the Turing-completeness of chemical reactions, defining representations that are faithful, efficient, and practical remains challenging. This paper introduces CRN ++ , a new language for programming deterministic (mass-action) chemical kinetics to perform computation. We present its syntax and semantics, and build a compiler translating CRN ++ programs into chemical reactions, thereby laying the foundation of a comprehensive framework for molecular programming. Our language addresses the key challenge of embedding familiar imperative constructs into a set of chemical reactions happening simultaneously and manipulating real-valued concentrations. Although some deviation from ideal output value cannot be avoided, we develop methods to minimize the error, and implement error analysis tools. We demonstrate the feasibility of using CRN ++ on a suite of well-known algorithms for discrete and real-valued computation. CRN ++ can be easily extended to support new commands or chemical reaction implementations, and thus provides a foundation for developing more robust and practical molecular programs.

show abstract

Section: Related Workmentioning

confidence: 99%

CRN++: Molecular programming language

2020

View full text Add to dashboard Cite

show abstract

“…The corresponding simulation result is shown in Figure 16. Figure 15 An approach for a 3-input gate in [35]. In addition, [83] proposes a design approach for the operation of all the Boolean logic gates, including AND, NAND, OR, NOR, XOR and XNOR operations.…”

Section: Digital Logicmentioning

confidence: 99%

DNA computing for combinational logic

Zhang

Zhuang

et al. 2018

Sci. China Inf. Sci.

Self Cite

View full text Add to dashboard Cite

With the progressive scale-down of semiconductor's feature size, people are looking forward to More Moore and More than Moore. In order to offer a possible alternative implementation process, people are trying to figure out a feasible transfer from silicon to molecular computing. Such transfer lies on bio-based modules programming with computer-like logic, aiming at realizing the Turing machine. To accomplish this, the DNA-based combinational logic is inevitably the first step we have taken care of. This timely overview paper introduces combinational logic synthesized in DNA computing from both analog and digital perspectives separately. State-of-the-art research progress is summarized for interested readers to quick understand DNA computing, initiate discussion on existing techniques and inspire innovation solutions. We hope this paper can pave the way for the future DNA computing synthesis.

show abstract

“…The deduced system behavior is obtained by the CRN model via ordinary differential equations (ODEs) [10]. Such a CRN model can be applied to real molecular system analysis [11], and also can simplify the process of designing engineered systems [12,13]. Guaranteed by [11], the designed formal CRN can be mapped to real DNA strand displacement reactions using unimolecular and bimolecular reactions.…”

Section: Introductionmentioning

confidence: 99%

“…Using other rate constants is likely to lead to different conclusions. After constructing each single MUX with CRN using the oneto-one mapping method proposed in [13], the entire PUF is synthesized by cascading all the multiplexers according to the designed PUF configuration. Four MUX PUFs, 8, 16, 32, 64stage molecular PUFs, are simulated using molecular reactions, and their uniqueness and reliability properties are investigated.…”

Section: Introductionmentioning

confidence: 99%

Molecular MUX-Based Physical Unclonable Functions

Ge,

Parhi

2020

Preprint

Self Cite

View full text Add to dashboard Cite

Physical unclonable functions (PUFs) are small circuits that are widely used as hardware security primitives for authentication. These circuits can generate unique signatures because of the inherent randomness in manufacturing and process variations. This paper introduces molecular PUFs based on multiplexer (MUX) PUFs using dual-rail representation. It may be noted that molecular PUFs have not been presented before. Each molecular multiplexer is synthesized using 16 molecular reactions. The intrinsic variations of the rate constants of the molecular reactions are assumed to provide inherent randomness necessary for uniqueness of PUFs. Based on Gaussian distribution of the rate constants of the reactions, this paper simulates intra-chip and inter-chip variations of linear molecular MUX PUFs containing 8, 16, 32 and 64 stages. These variations are, respectively, used to compute reliability and uniqueness. It is shown that, for the rate constants used in this paper, although 8-state molecular MUX PUFs are not useful as PUFs, PUFs containing 16 or higher stages are useful as molecular PUFs. Like electronic PUFs, increasing the number of stages increases uniqueness and reliability of the PUFs.

show abstract

A Formal Combinational Logic Synthesis With Chemical Reaction Networks

Cited by 21 publications

References 35 publications

CRN++: Molecular programming language

CRN++: Molecular programming language

DNA computing for combinational logic

Molecular MUX-Based Physical Unclonable Functions

Contact Info

Product

Resources

About