Synthesizing LDPC Belief Propagation Decoding with Molecular Reactions

2019 IEEE International Workshop on Signal Processing Systems (SiPS)

et al. 2019

Self Cite

By constructing chemical reaction networks (CRNs), this paper proposes a method of synthesizing polar decoder using belief propagation (BP) algorithm and successive cancellation (SC) algorithm, respectively. Theoretical analysis and simulation results have validated the feasibility of the method. Reactions in the proposed design could be experimentally implemented with DNA strand displacement reactions, making the proposed polar decoders promising for wide application in nanoscale devices.

“…For the probability-based multiplication, e.g., P z = P x ×P y , reactions in Eq. (17) proposed by [3] are adopted.…”

Section: A Probability-based Mathematical Operationsmentioning

confidence: 99%

“…Compared with [3], which uses six reactions to achieve the same function P z = P x /(P x + P y ), we only use two reactions here without altering the function. The ODE-based proof of Eq.…”

Section: A Probability-based Mathematical Operationsmentioning

confidence: 99%

Section: Remarksmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Molecular Polar Belief Propagation Decoder and Successive Cancellation Decoder

Zhong¹,

Ge²,

2019 IEEE International Workshop on Signal Processing Systems (SiPS)

et al. 2019

Self Cite

“…Moreover, CRNs could be employed to not only analyse the existing chemical systems but also construct new chemical systems in a convenient way, without considering the physical substrate. Using CRNs, researchers have designed novel molecular devices that achieve functions originally in electronic field, e.g., combinational logic, sequential logic, discrete-time signal processing computations, and arithmetic elements [33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51]. CRNs are always modeled in terms of mass-action kinetics [52,53], which are demonstrated by ordinary differential equations (ODEs) [54][55][56][57][58].…”

Section: Chemical Reaction Networkmentioning

confidence: 99%

DNA computing for combinational logic

Zhuang

et al. 2018

Sci. China Inf. Sci.

Self 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.

A Uniform Molecular Low-Density Parity Check Decoder

et al. 2018

ACS Synth. Biol.

Self Cite

Error correction codes, such as low-density parity check (LDPC) codes, are required to be larger scale to meet the increasing demands for reliable and massive data transmission. However, the construction of such a large-scale decoder will result in high complexity and hinder its silicon implementation. Thanks to the advantages of natural computing in high parallelism and low power, we propose a method to synthesize a uniform molecular LDPC decoder by implementing the beliefpropagation algorithm with chemical reaction networks (CRNs). This method enables us to flexibly design the LDPC decoder with arbitrary code length, code rate, and node degrees. Compared with existing methods, our proposal reduces the number of reactions to update the variable nodes by 42.86% and the check nodes by 47.37%. Numerical results are presented to show the feasibility and validity of our proposal.