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Jutta Rogal et al.
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L. M. Ghiringhelli et al.
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Aryeh Warmflash et al.
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Live Rekvig et al.
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Chantal Valeriani et al.
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Eduardo Sanz et al.
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Order-parameter-based Monte Carlo simulation of crystallization
M Chopra et al.
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W Ren et al.
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D Moroni et al.
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RB Best et al.
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A Ma et al.
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E Weinan et al.
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AK Faradjian et al.
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String method for the study of rare events
E Weinan et al.
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GE Crooks et al.
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