{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T23:16:41Z","timestamp":1776122201500,"version":"3.50.1"},"reference-count":39,"publisher":"Association for Computing Machinery (ACM)","issue":"4","license":[{"start":{"date-parts":[[2024,6,21]],"date-time":"2024-06-21T00:00:00Z","timestamp":1718928000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"funder":[{"name":"National Natural Science Fund of China for Excellent Young Scientists Fund Program (Overseas), the National Natural Science Foundation of China","award":["62372109"],"award-info":[{"award-number":["62372109"]}]},{"name":"Fujian Natural Science Funds","award":["2023J06017"],"award-info":[{"award-number":["2023J06017"]}]}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":["ACM Trans. Des. Autom. Electron. Syst."],"published-print":{"date-parts":[[2024,7,31]]},"abstract":"<jats:p>Continuous-flow microfluidic biochips are gaining increasing attention with promising applications for automatically executing various laboratory procedures in biology and biochemistry. Biochips with distributed channel-storage architectures enable each channel to switch between the roles of transportation and storage. Consequently, fluid transportation, caching, and fetch can occur concurrently through different flow paths. When two dissimilar types of fluidic flows occur through the same channels in a time-interleaved manner, it may cause contamination to the latter as some residues of the former flow may be stuck at the channel wall during transportation. To remove the residues, wash operations are introduced as an essential step to avoid incorrect assay outcomes. However, existing work has been considered that the washing capacity of a buffer fluid is unlimited. In the actual scenario, a fixed-volume buffer fluid irrefutably possesses a limited washing capacity, which can be successively consumed while washing away residues from the channels. Hence, capacity-aware wash scheme is a basic requirement to fulfil the dynamic fluid scheduling and channel storage. In this paper, we formulate a practical wash optimization problem for microfluidic biochips, which considers the requirements of dynamic fluid scheduling, channel storage, as well as washing capacity constraints of buffer fluids simultaneously, and present an efficient design flow to solve this problem systematically. Given the high-level synthesis result of a biochemical application and the corresponding component placement solution, our goal is to complete a contamination-aware flow-path planning with short flow-channel length. Meanwhile, the biochemical application can be executed efficiently and correctly with an optimized capacity-aware wash scheme. Experimental results show that compared to a state-of-the-art washing method, the proposed method achieves an average reduction of 26.1%, 43.1%, and 34.1% across all the benchmarks with respect to the total channel length, total wash time, and execution time of bioassays, respectively.<\/jats:p>","DOI":"10.1145\/3659952","type":"journal-article","created":{"date-parts":[[2024,4,17]],"date-time":"2024-04-17T12:14:34Z","timestamp":1713356074000},"page":"1-28","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Capacity-Aware Wash Optimization with Dynamic Fluid Scheduling and Channel Storage for Continuous-Flow Microfluidic Biochips"],"prefix":"10.1145","volume":"29","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3626-8183","authenticated-orcid":false,"given":"Zhisheng","family":"Chen","sequence":"first","affiliation":[{"name":"Xiamen University, Xiamen, China and Northwestern Polytechnical University, Xi'an, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8861-1619","authenticated-orcid":false,"given":"Xu","family":"Hu","sequence":"additional","affiliation":[{"name":"Fuzhou University, Fuzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6368-2414","authenticated-orcid":false,"given":"Wenzhong","family":"Guo","sequence":"additional","affiliation":[{"name":"Fuzhou University, Fuzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3099-4371","authenticated-orcid":false,"given":"Genggeng","family":"Liu","sequence":"additional","affiliation":[{"name":"Fuzhou University, Fuzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0563-1145","authenticated-orcid":false,"given":"Jiaxuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Northwestern Polytechnical University, Xi'an, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7348-5625","authenticated-orcid":false,"given":"Tsungyi","family":"Ho","sequence":"additional","affiliation":[{"name":"The Chinese University of Hong Kong, Hong Kong, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5396-110X","authenticated-orcid":false,"given":"Xing","family":"Huang","sequence":"additional","affiliation":[{"name":"Northwestern Polytechnical University, Xi'an, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2024,6,21]]},"reference":[{"key":"e_1_3_1_2_2","doi-asserted-by":"publisher","DOI":"10.1103\/RevModPhys.77.977"},{"key":"e_1_3_1_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mne.2019.01.003"},{"key":"e_1_3_1_4_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.239.4839.487"},{"key":"e_1_3_1_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/nm.2408"},{"key":"e_1_3_1_6_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja037166v"},{"key":"e_1_3_1_7_2","doi-asserted-by":"crossref","unstructured":"Xing Huang Tsung-Yi Ho Wenzhong Guo Bing Li Krishnendu Chakrabarty and Ulf Schlichtmann. 2021. Computer-aided design techniques for flow-based microfluidic lab-on-a-chip systems. ACM Computing Surveys 54 5 (2021) 1\u201329.","DOI":"10.1145\/3450504"},{"key":"e_1_3_1_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vlsi.2021.09.002"},{"key":"e_1_3_1_9_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biophys.36.040306.132646"},{"key":"e_1_3_1_10_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-90-481-9029-4_17"},{"key":"e_1_3_1_11_2","first-page":"49:1\u201349:6","volume-title":"Proceedings of the 54th Annual Design Automation Conference","author":"Liu Chunfeng","year":"2017","unstructured":"Chunfeng Liu, Bing Li, Hailong Yao, Paul Pop, Tsung-Yi Ho, and Ulf Schlichtmann. 2017. Transport or store?: Synthesizing flow-based microfluidic biochips using distributed channel storage. In Proceedings of the 54th Annual Design Automation Conference. 49:1\u201349:6."},{"key":"e_1_3_1_12_2","first-page":"1525","volume-title":"Proceedings of the Design, Automation and Test in Europe Conference","author":"Chen Zhisheng","year":"2019","unstructured":"Zhisheng Chen, Xing Huang, Wenzhong Guo, Bing Li, Tsung-Yi Ho, and Ulf Schlichtmann. 2019. Physical synthesis of flow-based microfluidic biochips considering distributed channel storage. In Proceedings of the Design, Automation and Test in Europe Conference. IEEE, 1525\u20131530."},{"key":"e_1_3_1_13_2","doi-asserted-by":"publisher","DOI":"10.1109\/TC.2021.3054689"},{"key":"e_1_3_1_14_2","doi-asserted-by":"publisher","DOI":"10.1109\/TCAD.2020.2994267"},{"key":"e_1_3_1_15_2","first-page":"244","volume-title":"Proceedings of the 19th Asia and South Pacific Design Automation Conference","author":"Hu Kai","year":"2014","unstructured":"Kai Hu, Tsung-Yi Ho, and Krishnendu Chakrabarty. 2014. Wash optimization for cross-contamination removal in flow-based microfluidic biochips. In Proceedings of the 19th Asia and South Pacific Design Automation Conference. IEEE, 244\u2013249."},{"key":"e_1_3_1_16_2","doi-asserted-by":"publisher","DOI":"10.1109\/TCAD.2015.2488485"},{"issue":"1","key":"e_1_3_1_17_2","first-page":"29","article-title":"Design and optimization of a cyberphysical digital-microfluidic biochip for the polymerase chain reaction","volume":"34","author":"Luo Yan","year":"2014","unstructured":"Yan Luo, Bhargab B. Bhattacharya, Tsung-Yi Ho, and Krishnendu Chakrabarty. 2014. Design and optimization of a cyberphysical digital-microfluidic biochip for the polymerase chain reaction. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 34, 1 (2014), 29\u201342.","journal-title":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems"},{"key":"e_1_3_1_18_2","first-page":"1531","volume-title":"Proceedings of the Design, Automation and Test in Europe Conference","author":"Lin Yu-Huei","year":"2019","unstructured":"Yu-Huei Lin, Tsung-Yi Ho, Bing Li, and Ulf Schlichtmann. 2019. Block-flushing: A block-based washing algorithm for programmable microfluidic devices. In Proceedings of the Design, Automation and Test in Europe Conference. IEEE, 1531\u20131536."},{"key":"e_1_3_1_19_2","doi-asserted-by":"publisher","DOI":"10.1109\/TCAD.2017.2729463"},{"key":"e_1_3_1_20_2","doi-asserted-by":"publisher","DOI":"10.1145\/1973009.1973091"},{"key":"e_1_3_1_21_2","doi-asserted-by":"publisher","DOI":"10.1145\/2593069.2593189"},{"key":"e_1_3_1_22_2","volume-title":"Proceeding of 19th Workshop on Synthesis And System Integration of Mixed Information technologies","author":"Wang Qin","year":"2015","unstructured":"Qin Wang, Yiren Shen, Hailong Yao, Tsung-Yi Ho, and Yici Cai. 2015. Contamination-aware routing flow for both functional and washing droplets in digital microfluidic biochips. In Proceeding of 19th Workshop on Synthesis And System Integration of Mixed Information technologies."},{"issue":"8","key":"e_1_3_1_23_2","first-page":"1283","article-title":"Integrated functional and washing routing optimization for cross-contamination removal in digital microfluidic biochips","volume":"35","author":"Yao Hailong","year":"2015","unstructured":"Hailong Yao, Qin Wang, Yiren Shen, Tsung-Yi Ho, and Yici Cai. 2015. Integrated functional and washing routing optimization for cross-contamination removal in digital microfluidic biochips. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 35, 8 (2015), 1283\u20131296.","journal-title":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems"},{"key":"e_1_3_1_24_2","doi-asserted-by":"publisher","DOI":"10.1049\/iet-cdt.2018.5037"},{"key":"e_1_3_1_25_2","first-page":"413","volume-title":"Proceeding of 32nd International Conference on VLSI Design and 18th International Conference on Embedded Systems","author":"Datta Piyali","year":"2019","unstructured":"Piyali Datta, Arpan Chakraborty, and Rajat Kumar Pal. 2019. A capacity-aware wash optimization for contamination removal in programmable microfluidic biochip devices. In Proceeding of 32nd International Conference on VLSI Design and 18th International Conference on Embedded Systems. IEEE, 413\u2013418."},{"key":"e_1_3_1_26_2","doi-asserted-by":"publisher","DOI":"10.1080\/03772063.2020.1811784"},{"key":"e_1_3_1_27_2","doi-asserted-by":"publisher","DOI":"10.1109\/TCAD.2019.2912936"},{"key":"e_1_3_1_28_2","first-page":"1","volume-title":"Proceedings of the International Conference on Computer-Aided Design","author":"Huang Xing","year":"2020","unstructured":"Xing Huang, Youlin Pan, Grace Li Zhang, Bing Li, Wenzhong Guo, Tsung-Yi Ho, and Ulf Schlichtmann. 2020. PathDriver: A path-driven architectural synthesis flow for continuous-flow microfluidic biochips. In Proceedings of the International Conference on Computer-Aided Design. IEEE, 1\u20138."},{"issue":"7","key":"e_1_3_1_29_2","doi-asserted-by":"crossref","first-page":"2185","DOI":"10.1109\/TCAD.2021.3103832","article-title":"PathDriver+: Enhanced path-driven architecture design for flow-based microfluidic biochips","volume":"41","author":"Huang Xing","year":"2021","unstructured":"Xing Huang, Youlin Pan, Grace Li Zhang, Bing Li, Wenzhong Guo, Tsung-Yi Ho, and Ulf Schlichtmann. 2021. PathDriver+: Enhanced path-driven architecture design for flow-based microfluidic biochips. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 41, 7 (2021), 2185\u20132198.","journal-title":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems"},{"key":"e_1_3_1_30_2","first-page":"1","volume-title":"Proceedings of the International Conference on Computer Aided Design","author":"Huang Xing","year":"2021","unstructured":"Xing Huang, Youlin Pan, Zhen Chen, Wenzhong Guo, Robert Wille, Tsung-Yi Ho, and Ulf Schlichtmann. 2021. BigIntegr: One-pass architectural synthesis for continuous-flow microfluidic lab-on-a-chip systems. In Proceedings of the International Conference on Computer Aided Design. IEEE, 1\u20138."},{"issue":"1","key":"e_1_3_1_31_2","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1109\/TCAD.2022.3166105","article-title":"Design automation for continuous-flow lab-on-a-chip systems: A one-pass paradigm","volume":"42","author":"Huang Xing","year":"2022","unstructured":"Xing Huang, Youlin Pan, Zhen Chen, Wenzhong Guo, Lu Wang, Qingshan Li, Robert Wille, Tsung-Yi Ho, and Ulf Schlichtmann. 2022. Design automation for continuous-flow lab-on-a-chip systems: A one-pass paradigm. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 42, 1 (2022), 327\u2013331.","journal-title":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems"},{"key":"e_1_3_1_32_2","doi-asserted-by":"publisher","DOI":"10.1109\/TCAD.2014.2336215"},{"key":"e_1_3_1_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/B978-012370522-8.50024-8"},{"key":"e_1_3_1_34_2","doi-asserted-by":"publisher","DOI":"10.1109\/TCAD.2017.2748003"},{"key":"e_1_3_1_35_2","first-page":"145: 1\u20136","volume-title":"Proceedings of the 56th Annual Design Automation Conference","author":"Huang Xing","year":"2019","unstructured":"Xing Huang, Tsung-Yi Ho, Wenzhong Guo, Bing Li, and Ulf Schlichtmann. 2019. MiniControl: Synthesis of continuous-flow microfluidics with strictly constrained control ports. In Proceedings of the 56th Annual Design Automation Conference. 145: 1\u20136."},{"key":"e_1_3_1_36_2","doi-asserted-by":"publisher","DOI":"10.1109\/TCAD.2022.3157691"},{"key":"e_1_3_1_37_2","doi-asserted-by":"publisher","DOI":"10.1145\/3544585.3544600"},{"key":"e_1_3_1_38_2","doi-asserted-by":"publisher","DOI":"10.1039\/c0lc00537a"},{"key":"e_1_3_1_39_2","doi-asserted-by":"publisher","DOI":"10.5555\/3224467.3224791"},{"key":"e_1_3_1_40_2","first-page":"587","volume-title":"Proceedings of the Asia and South Pacific Design Automation Conference","author":"Wang Qin","year":"2016","unstructured":"Qin Wang, Yizhong Ru, Hailong Yao, Tsung-Yi Ho, and Yici Cai. 2016. Sequence-pair-based placement and routing for flow-based microfluidic biochips. In Proceedings of the Asia and South Pacific Design Automation Conference. 587\u2013592."}],"container-title":["ACM Transactions on Design Automation of Electronic Systems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3659952","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3659952","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T00:58:30Z","timestamp":1750294710000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3659952"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,21]]},"references-count":39,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2024,7,31]]}},"alternative-id":["10.1145\/3659952"],"URL":"https:\/\/doi.org\/10.1145\/3659952","relation":{},"ISSN":["1084-4309","1557-7309"],"issn-type":[{"value":"1084-4309","type":"print"},{"value":"1557-7309","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,21]]},"assertion":[{"value":"2023-11-20","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-04-13","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-06-21","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}