Using Stochastic Models Calibrated from Nanosecond Non-Equilibrium Simulations to Approximate Mesoscale Information

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dc.contributor.authorCalderon, Christopher P.en_US
dc.contributor.authorJanosi, Loranten_US
dc.contributor.authorKosztin, Ioanen_US
dc.date.accessioned2018-06-19T17:13:02Zen_US
dc.date.available2018-06-19T17:13:02Zen_US
dc.date.issued2008-10en_US
dc.date.noteOctober 2008en_US
dc.description.abstractWe demonstrate how the surrogate process approximation (SPA) method can be used to compute both the potential of mean force (PMF) along a reaction coordinate and the associated diffusion coefficient using a relatively small (10-20) set of bidirectional non-equilibrium trajectories coming from a complex system. Our method provides confidence bands which take the variability of the initial condition, continuous nature of the work paths, and thermal fluctuations into account. Maximum likelihood type methods are used to estimate a stochastic differential equation (SDE) approximating the dynamics and assist in these computations. For each observed time series, we estimate a new SDE resulting in a collection of SPA models. The physical significance of the collection of SPA models is discussed and methods for exploiting information in this population of models are suggested. Molecular dynamics(MD) simulations of potassium ion dynamics inside a gramicidin A channel are used to demonstrate the methodology, although SPA type modeling has also proven useful in analyzing single-molecule experimental time series [J. Phys. Chem. B,ﾠ113, 118 (2009)].en_US
dc.format.extent20 ppen_US
dc.identifier.citationCalderon, Christopher P., Janosi, Lorant and Kosztin, Ioan. "Using Stochastic Models Calibrated from Nanosecond Non-Equilibrium Simulations to Approximate Mesoscale Information." (2008) <a href="https://hdl.handle.net/1911/102102">https://hdl.handle.net/1911/102102</a>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/102102en_US
dc.language.isoengen_US
dc.titleUsing Stochastic Models Calibrated from Nanosecond Non-Equilibrium Simulations to Approximate Mesoscale Informationen_US
dc.typeTechnical reporten_US
dc.type.dcmiTexten_US
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