A Poisson Process Generator Based on Multiple Thermal Noise Amplifiers for Parallel Stochastic Simulation of Biochemical Reactions
In this paper, we propose a novel Poisson process generator that uses multiple thermal noise amplifiers (TNAs) as a source of randomness and controls its event rate via a frequency-locked loop (FLL). The increase in the number of TNAs extends the effective bandwidth of amplified thermal noise and he...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-03-01
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| Series: | Electronics |
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| Online Access: | https://www.mdpi.com/2079-9292/11/7/1039 |
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| author | Yeji Jo Kyusik Mun Yeonjoo Jeong Joon Young Kwak Jongkil Park Suyoun Lee Inho Kim Jong-Keuk Park Gyu-Weon Hwang Jaewook Kim |
| author_facet | Yeji Jo Kyusik Mun Yeonjoo Jeong Joon Young Kwak Jongkil Park Suyoun Lee Inho Kim Jong-Keuk Park Gyu-Weon Hwang Jaewook Kim |
| author_sort | Yeji Jo |
| collection | DOAJ |
| description | In this paper, we propose a novel Poisson process generator that uses multiple thermal noise amplifiers (TNAs) as a source of randomness and controls its event rate via a frequency-locked loop (FLL). The increase in the number of TNAs extends the effective bandwidth of amplified thermal noise and hence enhances the maximum event rate the proposed architecture can generate. Verilog-A simulation of the proposed Poisson process generator shows that its maximum event rate can be increased by a factor of 26.5 when the number of TNAs increases from 1 to 10. In order to realize parallel stochastic simulations of the biochemical reaction network, we present a fundamental reaction building block with continuous-time multiplication and addition using an AND gate and a 1-bit current-steering digital-to-analog converter, respectively. Stochastic biochemical reactions consisting of the fundamental reaction building blocks are simulated in Verilog-A, demonstrating that the simulation results are consistent with those of conventional Gillespie algorithm. An increase in the number of TNAs to accelerate the Poisson events and the use of digital AND gates for robust reaction rate calculations allow for faster and more accurate stochastic simulations of biochemical reactions than previous parallel stochastic simulators. |
| first_indexed | 2024-03-09T11:58:33Z |
| format | Article |
| id | doaj.art-74c48375e9d84e50848b6c8967e8219a |
| institution | Directory Open Access Journal |
| issn | 2079-9292 |
| language | English |
| last_indexed | 2024-03-09T11:58:33Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Electronics |
| spelling | doaj.art-74c48375e9d84e50848b6c8967e8219a2023-11-30T23:06:32ZengMDPI AGElectronics2079-92922022-03-01117103910.3390/electronics11071039A Poisson Process Generator Based on Multiple Thermal Noise Amplifiers for Parallel Stochastic Simulation of Biochemical ReactionsYeji Jo0Kyusik Mun1Yeonjoo Jeong2Joon Young Kwak3Jongkil Park4Suyoun Lee5Inho Kim6Jong-Keuk Park7Gyu-Weon Hwang8Jaewook Kim9Center for Neuromorphic Engineering, Korea Institutes of Science and Technology, Seoul 02792, KoreaCenter for Neuromorphic Engineering, Korea Institutes of Science and Technology, Seoul 02792, KoreaCenter for Neuromorphic Engineering, Korea Institutes of Science and Technology, Seoul 02792, KoreaCenter for Neuromorphic Engineering, Korea Institutes of Science and Technology, Seoul 02792, KoreaCenter for Neuromorphic Engineering, Korea Institutes of Science and Technology, Seoul 02792, KoreaCenter for Neuromorphic Engineering, Korea Institutes of Science and Technology, Seoul 02792, KoreaCenter for Neuromorphic Engineering, Korea Institutes of Science and Technology, Seoul 02792, KoreaCenter for Neuromorphic Engineering, Korea Institutes of Science and Technology, Seoul 02792, KoreaCenter for Neuromorphic Engineering, Korea Institutes of Science and Technology, Seoul 02792, KoreaCenter for Neuromorphic Engineering, Korea Institutes of Science and Technology, Seoul 02792, KoreaIn this paper, we propose a novel Poisson process generator that uses multiple thermal noise amplifiers (TNAs) as a source of randomness and controls its event rate via a frequency-locked loop (FLL). The increase in the number of TNAs extends the effective bandwidth of amplified thermal noise and hence enhances the maximum event rate the proposed architecture can generate. Verilog-A simulation of the proposed Poisson process generator shows that its maximum event rate can be increased by a factor of 26.5 when the number of TNAs increases from 1 to 10. In order to realize parallel stochastic simulations of the biochemical reaction network, we present a fundamental reaction building block with continuous-time multiplication and addition using an AND gate and a 1-bit current-steering digital-to-analog converter, respectively. Stochastic biochemical reactions consisting of the fundamental reaction building blocks are simulated in Verilog-A, demonstrating that the simulation results are consistent with those of conventional Gillespie algorithm. An increase in the number of TNAs to accelerate the Poisson events and the use of digital AND gates for robust reaction rate calculations allow for faster and more accurate stochastic simulations of biochemical reactions than previous parallel stochastic simulators.https://www.mdpi.com/2079-9292/11/7/1039Poisson process generatorthermal noise amplifierAND gatestochastic simulationbiochemical reactions |
| spellingShingle | Yeji Jo Kyusik Mun Yeonjoo Jeong Joon Young Kwak Jongkil Park Suyoun Lee Inho Kim Jong-Keuk Park Gyu-Weon Hwang Jaewook Kim A Poisson Process Generator Based on Multiple Thermal Noise Amplifiers for Parallel Stochastic Simulation of Biochemical Reactions Electronics Poisson process generator thermal noise amplifier AND gate stochastic simulation biochemical reactions |
| title | A Poisson Process Generator Based on Multiple Thermal Noise Amplifiers for Parallel Stochastic Simulation of Biochemical Reactions |
| title_full | A Poisson Process Generator Based on Multiple Thermal Noise Amplifiers for Parallel Stochastic Simulation of Biochemical Reactions |
| title_fullStr | A Poisson Process Generator Based on Multiple Thermal Noise Amplifiers for Parallel Stochastic Simulation of Biochemical Reactions |
| title_full_unstemmed | A Poisson Process Generator Based on Multiple Thermal Noise Amplifiers for Parallel Stochastic Simulation of Biochemical Reactions |
| title_short | A Poisson Process Generator Based on Multiple Thermal Noise Amplifiers for Parallel Stochastic Simulation of Biochemical Reactions |
| title_sort | poisson process generator based on multiple thermal noise amplifiers for parallel stochastic simulation of biochemical reactions |
| topic | Poisson process generator thermal noise amplifier AND gate stochastic simulation biochemical reactions |
| url | https://www.mdpi.com/2079-9292/11/7/1039 |
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