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Generalized Markov Models of Infectious Disease Spread: A Novel Framework for Developing Dynamic Health Policies.

ABSTRACT: We propose a class of mathematical models for the transmission of infectious diseases in large populations. This class of models, which generalizes the existing discrete-time Markov chain models of infectious diseases, is compatible with efficient dynamic optimization techniques to assist real-time selection and modification of public health interventions in response to evolving epidemiological situations and changing availability of information and medical resources. While retaining the strength of existing classes of mathematical models in their ability to represent the within-host natural history of disease and between-host transmission dynamics, the proposed models possess two advantages over previous models: (1) these models can be used to generate optimal dynamic health policies for controlling spreads of infectious diseases, and (2) these models are able to approximate the spread of the disease in relatively large populations with a limited state space size and computation time.

SUBMITTER: Yaesoubi R

PROVIDER: S-EPMC3182455 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature

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Generalized Markov Models of Infectious Disease Spread: A Novel Framework for Developing Dynamic Health Policies.

Yaesoubi Reza R Cohen Ted T

European journal of operational research 20111201 3

We propose a class of mathematical models for the transmission of infectious diseases in large populations. This class of models, which generalizes the existing discrete-time Markov chain models of infectious diseases, is compatible with efficient dynamic optimization techniques to assist real-time selection and modification of public health interventions in response to evolving epidemiological situations and changing availability of information and medical resources. While retaining the strengt ...[more]

PMID: 21966083

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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.

Dataset Information

Generalized Markov Models of Infectious Disease Spread: A Novel Framework for Developing Dynamic Health Policies.

Publications

Generalized Markov Models of Infectious Disease Spread: A Novel Framework for Developing Dynamic Health Policies.

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