Пененко А.В., Троеглазова Т.С., Зубаирова У.С., Байшибаев Д.Ж., Николаев С.В.
Применение технологии CUDA для моделирования процессов реакции-диффузии на двумерном клеточном ансамбле
Математическая биология и биоинформатика. 2014;9(2):491-503.
doi: 10.17537/2014.9.491.
Список литературы
- Thompson AW. On Growth and Form: The Complete Revised Edition. New York: Dover; 1992. doi: 10.1017/CBO9781107325852
- Morphogenesis: Origins of Patterns and Shapes. Eds. Bourgine P., Lesne A. Springer; 2011. doi: 10.1007/978-3-642-13174-5
- Lutolf MP, Hubbell JA. Synthetic biomaterials as instructive extracellular microenvironments for morphogenesis in tissue engineering. Nature Biotechnology. 2005;23:47-55. doi: 10.1038/nbt1055
- Sangan RS, Sangwan-Norrel BS, Harada H. In vitro techniques and plant morphogenesis: fundamental aspects and practical applications. Plant Biotechnology. 1997;14(2):93-100. doi: 10.5511/plantbiotechnology.14.93
- Reddi AH. Morphogenesis and tissue engineering of bone and cartilage: Inductive signals, stem cells, and biomimetic biomaterials. Tissue Engineering. 2000;6(4):351-359. doi: 10.1089/107632700418074
- Reddi AH. Role of morphogenetic proteins in skeletal tissue engineering and regeneration. Nature Biotechnology. 1998;16:247-252. doi: 10.1038/nbt0398-247
- Turing AM. The chemical basis of morphogenesis. Philosophical Transactions of the Royal Society of London. Series B. 1952;237(641):37-72. doi: 10.1098/rstb.1952.0012
- Schwank G, Basler K. Regulation of organ growth by morphogen gradients. Cold Spring Harbor Perspectives in Biology. 2010;2(1):a001669. doi: 10.1101/cshperspect.a001669
- Meinhardt H. Models for the generation and interpretation of gradients. Cold Spring Harbor Perspectives in Biology. 2009;1(4):a001362. doi: 10.1101/cshperspect.a001362
- Voss-Bohme A. Multi-Scale modeling in morphogenesis: A critical analysis of the cellular potts model. PLoS ONE. 2012;7(9):e42852. doi: 10.1371/journal.pone.0042852
- Coskuna H, Lib Y, Mackeyd MA. Ameboid cell motility: A model and inverse problem, with an application to live cell imaging data. Journal of Theoretical Biology. 2007;244(2):169-179. doi: 10.1016/j.jtbi.2006.07.025
- Kabanikhin SI. Obratnye i nekorrektnye zadachi. Uchebnik dlia studentov vysshikh uchebnykh zavedenii (Inverse and Ill-Posed Problems. Student Handbook). Novosibirsk: Siberian Scientific Publishers; 2009. 458 p. (in Russ.).
- Zubairova US, Golushko SK, Penenko AV, Nikolaev SV. An L-System for modeling of unidimensionally growing flat plant tissues. Vavilovskii zhurnal genetiki i selektsii (Russian Journal of Genetics: Applied Research). 2014;18(4/2):945-952 (in Russ.).
- Wolpert L. Positional information and the spatial pattern of cellular differentiation. J. Theor. Biol. 1969;25(1):1-47. doi: 10.1016/S0022-5193(69)80016-0
- Sanders Dzh, Kendrot E. Tekhnologiia CUDA v primerakh: vvedenie v programmirovanie graficheskikh protsessorov. Moscow; 2011. 232 p. Translation of: Sanders J, Kandrot E. CUDA by Example: An Introduction to General-Purpose GPU Programming. Addison-Wesley; 2010.
- Boreskov A, Kharlamov A, Markovskii ND, Mikushin D, Mortikov E, Myl'tsev A, Sakharnykh N, Frolov V. Parallel'nye vychisleniia na GPU. Arkhitektura i programmnaia model' CUDA (Parallel computing on GPU. Architecture and CUDA programming model): a textbook. Moscow; 2012. 336 p. (in Russ.).
- Swat M., Thomas G.L., Belmonte J.M., Shirinifard A., Hmeljak D., Glazier J.A. Multi-Scale Modeling of Tissues Using CompuCell3D. Computational Methods in Cell Biology. 2012;110:325-366. doi: 10.1016/B978-0-12-388403-9.00013-8
- Nikolaev SV, Zubairova US, Fadeev SI, Mjolsness ED, Kolchanov NA. Study of a one-dimensional model, accounting for cell division, of regulation of the renewing zone size in a biological tissue. Journal of Applied and Industrial Mathematics. 2011;5(4):601-611. doi: 10.1134/S1990478911040156
- Nikolaev SV, Zubairova US, Penenko AV, Mjolsness ED, Shapiro BE, Kolchanov NA. Model of structuring the stem cell niche in shoot apical meristem of Arabidopsis thaliana. Doklady Biological Sciences. 2013;452(1):316-319. doi: 10.1134/S0012496613050104
- Samarskii AA, Vabishchevich PN. Vychislitel'naia teploperedacha (Computational Heat Transfer). Moscow; 2003 (in Russ.).
- Sanderson AR, Meyer MD, Kirby RM, Johnson CR. A framework for exploring numerical solutions of advection-reaction-diffusion equations using a GPU-based approach. Computing and Visualization in Science. 2009;12(4):155-170. doi: 10.1007/s00791-008-0086-0
- Hochbruck M, Ostermann A. Exponential integrators. Acta Numerica. 2010;19:209-286. doi: 10.1017/S0962492910000048
- Einkemmer L, Ostermann A. Exponential Integrators on Graphic Processing Units ArXiv. 2013. Article ID 1309.4616.
- Penenko VV, Tsvetova EA, Penenko AV. Variational approach and Euler’s integrating factors for environmental studies. CAMWA. 2014;67(12):2240-2256. doi: 10.1016/j.camwa.2014.04.004
- Hesstvedt E, Hov O, Isaacsen I. Quasi-steady-state-approximation in air pollution modelling: comparison of two numerical schemes for oxidant prediction. Int. J. Chem. Kinet. 1978;10:971-994. doi: 10.1002/kin.550100907
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