#[1]Monte Carlo eXtreme: GPU-based Monte Carlo Simulations Papers 1.1. [2]MCX 1.2. [3]MCX-CL 1.3. [4]MMC 1.4. [5]General MC algorithm 1.5. [6]Applications If you use MCX/MMC/MCX-CL in your research, we appreciate if you can cite our relevant papers in your publications. 1.1. MCX * [Fang2009] Qianqian Fang and David Boas, "Monte Carlo Simulation of Photon Migration in 3D Turbid Media Accelerated by Graphics Processing Units," Opt. Express, vol. 17, issue 22, pp. 20178-20190 (2009). * Summary: original MCX paper * Download: [7]http://www.osapublishing.org/oe/abstract.cfm?uri=oe-17-22-20178 1.2. MCX-CL * [Yu2018] Leiming Yu, Fanny Nina-Paravecino, David Kaeli, Qianqian Fang, "Scalable and massively parallel Monte Carlo photon transport simulations for heterogeneous computing platforms," J. Biomed. Opt. 23(1), 010504 (2018). * Summary: original MCX-CL (OpenCL) paper * Download: [8]https://doi.org/10.1117/1.JBO.23.1.010504 1.3. MMC * [Fang2019] Qianqian Fang* and Shijie Yan, “Graphics processing unit-accelerated mesh-based Monte Carlo photon transport simulations,” J. of Biomedical Optics, 24(11), 115002 (2019). * Summary: GPU-accelerated (OpenCL) MMC algorithm and software - MMCL * Download: [9]http://dx.doi.org/10.1117/1.JBO.24.11.115002 * [Yan2019] Shijie Yan, Anh Phong Tran, Qianqian Fang*, “A dual-grid mesh-based Monte Carlo algorithm for efficient photon transport simulations in complex 3-D media,” J. of Biomedical Optics, 24(2), 020503 (2019). * Summary: Dual-grid MMC for faster and more accurate mesh-based simulations * Download: [10]http://dx.doi.org/10.1117/1.JBO.24.2.020503 * [Yao2016] Ruoyang Yao, Xavier Intes, Qianqian Fang*, "Generalized mesh-based Monte Carlo for wide-field illumination and detection via mesh retessellation," Biomed. Optics Express, 7(1), 171-184, (2016) * Summary: Widefield MMC * Download: [11]https://www.osapublishing.org/boe/abstract.cfm?uri=boe-7-1-171 * [Jin2012] Chen J, Fang Q, Intes X, “Mesh-based Monte Carlo method in time-domain widefield fluorescence molecular tomography,” J. of Biomedical Optics, 17(10), 106009 (2012). * Summary: Axis-aligned wide-field MMC algorithm for fluorescence molecular tomography * Download: [12]https://doi.org/10.1117/1.JBO.17.10.106009 * [Fang2012] Qianqian Fang and David R. Kaeli, "Accelerating mesh-based Monte Carlo method on modern CPU architectures ," Biomed. Opt. Express 3(12), 3223-3230 (2012) * Summary: SIMD MMC * Download: [13]https://www.osapublishing.org/boe/abstract.cfm?uri=boe-3-12-322 3 * [Fang2011] Qianqian Fang, “Comment on ‘A study on tetrahedron-based inhomogeneous Monte-Carlo optical simulation’,” Biomed. Opt. Express, vol. 2, issue 5, pp. 1258-1264, 2011. * Summary: MMC ray-tracing comparisons * Download: [14]https://www.osapublishing.org/boe/abstract.cfm?uri=boe-2-5-1258 * [Fang2010] Qianqian Fang, "Mesh-based Monte Carlo method using fast ray-tracing in Plücker coordinates," Biomed. Opt. Express 1(1), 165-175 (2010) * Summary: original MMC paper * Download: [15]https://www.osapublishing.org/boe/abstract.cfm?uri=boe-1-1-165 1.4. General MC algorithm * [Yan2020] Shijie Yan, Ruoyang Yao, Xavier Intes, and Qianqian Fang, "Accelerating Monte Carlo modeling of structured-light-based diffuse optical imaging via 'photon sharing'," Opt. Lett. 45, 2842-2845 (2020) * Summary: Photon sharing for simultaneous simulations of multiple patterns * Download: [16]https://www.biorxiv.org/content/10.1101/2020.02.16.951590v2 * [Yao2018] Ruoyang Yao, Xavier Intes, Qianqian Fang*, "A direct approach to compute Jacobians for diffuse optical tomography using perturbation Monte Carlo-based photon 'replay'," Biomed. Optics Express 9(10), 4588-4603, (2018) * Summary: Building Jacobians with replay in MCX/MMC * Download: [17]https://www.osapublishing.org/boe/abstract.cfm?uri=boe-9-10-458 8 * [Yuan2018] Yaoshen Yuan, Leiming Yu, Zafer Doğan, Qianqian Fang, "Graphics processing units-accelerated adaptive nonlocal means filter for denoising three-dimensional Monte Carlo photon transport simulations," J. of Biomedical Optics, 23(12), 121618 (2018). * Summary: Denoising MC simulation using a noise-adaptive filter * Download: [18]https://www.spiedigitallibrary.org/journalArticle/Download?full DOI=10.1117%2F1.JBO.23.12.121618 1.5. Applications * [Yuan2020] Yaoshen Yuan, Paolo Cassano, Matthew Pias, Qianqian Fang*, (2020) "Transcranial photobiomodulation with near-infrared light from childhood to elderliness: simulation of dosimetry,", Neurophotonics, 7(1), 015009, URL: [19]https://doi.org/10.1117/1.NPh.7.1.015009 * Summary: PBM dosage over lifespan * Download: [20]https://doi.org/10.1117/1.NPh.7.1.015009 * [Brain2Mesh2020] Anh Phong Tran† , Shijie Yan† , Qianqian Fang*, (2020) "Improving model-based fNIRS analysis using mesh-based anatomical and light-transport models," Neurophotonics, 7(1), 015008, URL: [21]https://doi.org/10.1117/1.NPh.7.1.015008 * Summary: Brain2Mesh - a one-liner for brain mesh generator ([22]http://mcx.space/brain2mesh) * Download: [23]https://doi.org/10.1117/1.NPh.7.1.015008 * [Cassano2019] Tran AP+, Cassano P+, Katnani H, Bleier BS, Hamblin MR, Yuan Y, Fang Q*, (2019) “Selective photobiomodulation for emotion regulation: model-based dosimetry study,” Neurophotonics 6(1) 015004, PMCID: PMC6366475 * Summary: Use MCX to systematically study transcranial or intranasal photobiomodulation (t-PBM/i-PBM) light dosage * Download: [24]https://doi.org/10.1117/1.NPh.6.1.015004 * [Draghici2018] Draghici AE, Potart D, Hollmann JL, Pera V, Fang Q, DiMarzio CA, Andrew Taylor J, Niedre MJ, Shefelbine SJ, (2018) “Near infrared spectroscopy for measuring changes in bone hemoglobin content after exercise in individuals with spinal cord injury,” J Orthop Res. 36(1), 183-191, PMCID: PMC5711624 * Summary: Use MCX to study NIR imaging of human bones in spinal cord injury * Download: [25]https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711624/ * [Verleker2016] Verleker AP, Shaffer M, Fang Q, Choi, MR, Clare S. Stantz KM, (2016) “Optical dosimetry probes to validate Monte Carlo and Empirical-method based NIR dose planning in the brain”, Appl. Optics, 55(34) 9875-9888, PMCID: PMC5483856 * Summary: Optical dosimetry study using MCX for photodynamic therapy (PDT) in the brain * Download: [26]https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483856/ References 1. http://mcx.space/wiki/index.cgi?action=rss 2. http://mcx.space/wiki/index.cgi?Citation#MCX 3. http://mcx.space/wiki/index.cgi?Citation#MCX_CL 4. http://mcx.space/wiki/index.cgi?Citation#MMC 5. http://mcx.space/wiki/index.cgi?Citation#General_MC_algorithm 6. http://mcx.space/wiki/index.cgi?Citation#Applications 7. http://www.osapublishing.org/oe/abstract.cfm?uri=oe-17-22-20178 8. https://doi.org/10.1117/1.JBO.23.1.010504 9. http://dx.doi.org/10.1117/1.JBO.24.11.115002 10. http://dx.doi.org/10.1117/1.JBO.24.2.020503 11. https://www.osapublishing.org/boe/abstract.cfm?uri=boe-7-1-171 12. https://doi.org/10.1117/1.JBO.17.10.106009 13. https://www.osapublishing.org/boe/abstract.cfm?uri=boe-3-12-3223 14. https://www.osapublishing.org/boe/abstract.cfm?uri=boe-2-5-1258 15. https://www.osapublishing.org/boe/abstract.cfm?uri=boe-1-1-165 16. https://www.biorxiv.org/content/10.1101/2020.02.16.951590v2 17. https://www.osapublishing.org/boe/abstract.cfm?uri=boe-9-10-4588 18. https://www.spiedigitallibrary.org/journalArticle/Download?fullDOI=10.1117/1.JBO.23.12.121618 19. https://doi.org/10.1117/1.NPh.7.1.015009 20. https://doi.org/10.1117/1.NPh.7.1.015009 21. https://doi.org/10.1117/1.NPh.7.1.015008 22. http://mcx.space/brain2mesh 23. https://doi.org/10.1117/1.NPh.7.1.015008 24. https://doi.org/10.1117/1.NPh.6.1.015004 25. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711624/ 26. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483856/