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Markov versus quantum dynamic models of belief change during evidence monitoring.

ABSTRACT: Two different dynamic models for belief change during evidence monitoring were evaluated: Markov and quantum. They were empirically tested with an experiment in which participants monitored evidence for an initial period of time, made a probability rating, then monitored more evidence, before making a second rating. The models were qualitatively tested by manipulating the time intervals in a manner that provided a test for interference effects of the first rating on the second. The Markov model predicted no interference, whereas the quantum model predicted interference. More importantly, a quantitative comparison of the two models was also carried out using a generalization criterion method: the parameters were fit to data from one set of time intervals, and then these same parameters were used to predict data from another set of time intervals. The results indicated that some features of both Markov and quantum models are needed to accurately account for the results.

SUBMITTER: Busemeyer JR

PROVIDER: S-EPMC6889126 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Markov versus quantum dynamic models of belief change during evidence monitoring.

Busemeyer Jerome R JR Kvam Peter D PD Pleskac Timothy J TJ

Scientific reports 20191202 1

Two different dynamic models for belief change during evidence monitoring were evaluated: Markov and quantum. They were empirically tested with an experiment in which participants monitored evidence for an initial period of time, made a probability rating, then monitored more evidence, before making a second rating. The models were qualitatively tested by manipulating the time intervals in a manner that provided a test for interference effects of the first rating on the second. The Markov model ...[more]

PMID: 31792262

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Project description:CONSPECTUS: Protein function is inextricably linked to protein dynamics. As we move from a static structural picture to a dynamic ensemble view of protein structure and function, novel computational paradigms are required for observing and understanding conformational dynamics of proteins and its functional implications. In principle, molecular dynamics simulations can provide the time evolution of atomistic models of proteins, but the long time scales associated with functional dynamics make it difficult to observe rare dynamical transitions. The issue of extracting essential functional components of protein dynamics from noisy simulation data presents another set of challenges in obtaining an unbiased understanding of protein motions. Therefore, a methodology that provides a statistical framework for efficient sampling and a human-readable view of the key aspects of functional dynamics from data analysis is required. The Markov state model (MSM), which has recently become popular worldwide for studying protein dynamics, is an example of such a framework. In this Account, we review the use of Markov state models for efficient sampling of the hierarchy of time scales associated with protein dynamics, automatic identification of key conformational states, and the degrees of freedom associated with slow dynamical processes. Applications of MSMs for studying long time scale phenomena such as activation mechanisms of cellular signaling proteins has yielded novel insights into protein function. In particular, from MSMs built using large-scale simulations of GPCRs and kinases, we have shown that complex conformational changes in proteins can be described in terms of structural changes in key structural motifs or "molecular switches" within the protein, the transitions between functionally active and inactive states of proteins proceed via multiple pathways, and ligand or substrate binding modulates the flux through these pathways. Finally, MSMs also provide a theoretical toolbox for studying the effect of nonequilibrium perturbations on conformational dynamics. Considering that protein dynamics in vivo occur under nonequilibrium conditions, MSMs coupled with nonequilibrium statistical mechanics provide a way to connect cellular components to their functional environments. Nonequilibrium perturbations of protein folding MSMs reveal the presence of dynamically frozen glass-like states in their conformational landscape. These frozen states are also observed to be rich in β-sheets, which indicates their possible role in the nucleation of β-sheet rich aggregates such as those observed in amyloid-fibril formation. Finally, we describe how MSMs have been used to understand the dynamical behavior of intrinsically disordered proteins such as amyloid-β, human islet amyloid polypeptide, and p53. While certainly not a panacea for studying functional dynamics, MSMs provide a rigorous theoretical foundation for understanding complex entropically dominated processes and a convenient lens for viewing protein motions.

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Markov versus quantum dynamic models of belief change during evidence monitoring.

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Markov versus quantum dynamic models of belief change during evidence monitoring.

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