Browsing by Author "Muniyat, Mir Ishruna"
Now showing 1 - 1 of 1
Results Per Page
Sort Options
- ItemOpen AccessWaterfall: An Online Sequential Monte Carlo Strategy for Conformational Sampling(2020-05-08) Muniyat, Mir Ishruna; MacCallum, Justin L.; Derksen, Darren J.; Noskov, Sergei Yu; Kusalik, Peter G.Conformational sampling of physical systems, such as biomolecules, remains challenging since their energy landscapes are rugged with energetic and entropic barriers. Metastable states on a landscape are often separated by substantial energetic barriers and numerous local minima where a system can easily get trapped. Entropic barriers, arising from many possible conformations of a system, make finding the important states a needle-in-a-haystack problem. Enhanced sampling algorithms can potentially overcome both barriers, making it possible to sample the important states efficiently. However, existing algorithms come with certain limitations. We developed ``Waterfall Sampling” to overcome some of the limitations of existing algorithms. The algorithm employs a Sequential Monte Carlo strategy where it promotes exploration of the high-probability regions on the conformational landscape. It is an online method, that is, we can keep adding states indefinitely to improve statistics. We successfully tested Waterfall on a data-guided integrative structural biology problem and compared its efficiency with the existing algorithms.