Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models
نویسندگان
چکیده
منابع مشابه
Enhanced modeling via network theory: Adaptive sampling of Markov state models.
Computer simulations can complement experiments by providing insight into molecular kinetics with atomic resolution. Unfortunately, even the most powerful supercomputers can only simulate small systems for short timescales, leaving modeling of most biologically relevant systems and timescales intractable. In this work, however, we show that molecular simulations driven by adaptive sampling of n...
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Network Growth Models such as Preferential Attachment and Duplication/Divergence are popular generative models with which to study complex networks in biology, sociology, and computer science. However, analyzing them within the framework of model selection and statistical inference is often complicated and computationally difficult, particularly when comparing models that are not directly relat...
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Abstract. I describe a new Markov chain method for sampling from the distribution of the state sequences in a non-linear state space model, given the observation sequence. This method updates all states in the sequence simultaneously using an embedded Hidden Markov model (HMM). An update begins with the creation of a “pool” of K states at each time, by applying some Markov chain update to the c...
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CHENG-DER FUH and INCHI HU 1 Graduate Institute of Statistics, National Central University, Chongli, Taiwan, Republic of China and Institute of Statistical Science, Academia Sinica, Nakang, Taipei 115, Taiwan, Republic of China. E-mail: [email protected] 2 Department of Information and Systems Management, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Honh Ko...
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Renormalization Group (RG) theory provides the theoretical framework to define rigorous effective theories, i.e., systematic low-resolution approximations of arbitrary microscopic models. Markov state models are shown to be rigorous effective theories for Molecular Dynamics (MD). Based on this fact, we use real space RG to vary the resolution of the stochastic model and define an algorithm for ...
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ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2010
ISSN: 1549-9618,1549-9626
DOI: 10.1021/ct900620b