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<citation key="bernstein_simulating_2005">
<article_title>Simulating mesoscopic reaction-diffusion
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<author>Bernstein</author>
<journal_title>Physical review. E, Statistical, nonlinear,
and soft matter physics</journal_title>
<volume>71</volume>
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<cYear>2005</cYear>
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041103.
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<journal_title>Journal of Chemical Physics</journal_title>
<volume>115</volume>
<doi>10.1063/1.1378322</doi>
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Journal of Chemical Physics, 115, 1716–1733.
https://doi.org/10.1063/1.1378322</unstructured_citation>
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<journal_title>PLoS computational biology</journal_title>
<issue>2</issue>
<volume>15</volume>
<doi>10.1371/journal.pcbi.1006830</doi>
<cYear>2019</cYear>
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15(2), e1006830.
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<issue>12</issue>
<volume>21</volume>
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<issn>1367-4803</issn>
<cYear>2005</cYear>
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(2005). Stochastic reaction-diffusion simulation with MesoRD.
Bioinformatics, 21(12), 2923–2924.
https://doi.org/10.1093/bioinformatics/bti431</unstructured_citation>
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<issue>2</issue>
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230–236. https://doi.org/10.1049/sb:20045021</unstructured_citation>
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J.-J., Sekar, J. A. P., Gupta, S., Korsunsky, I., Arora, A., Barua, D.,
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rule-based modeling. Bioinformatics, 32(21), 3366–3368.
https://doi.org/10.1093/bioinformatics/btw469</unstructured_citation>
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<doi>10.1007/BF02181277</doi>
<cYear>1997</cYear>
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https://doi.org/10.1007/BF02181277</unstructured_citation>
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