Browsing by Author "Niestemski, Liang Ren"

Now showing 1 - 3 of 3
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    Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system
    (IOP Publishing, 2013) Han, Pu; Niestemski, Liang Ren; Barrick, Jeffrey E.; Deem, Michael W.; Bioengineering; Physics and Astronomy
    Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called "spacers" into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population.
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    Prediction of heart rate response to conclusion of the spontaneous breathing trial by fluctuation dissipation theory
    (IOP Publishing, 2013) Chen, Man; Niestemski, Liang Ren; Prevost, Robert; McRae, Michael; Cholleti, Sharath; Najarro, Gabriel; Buchman, Timothy G.; Deem, Michael W.; Bioengineering; Physics and Astronomy
    The non-equilibrium fluctuation dissipation theorem is applied to predict how critically ill patients respond to treatment, based upon data currently collected by standard hospital monitoring devices. This framework is demonstrated on a common procedure in critical care: the spontaneous breathing trial. It is shown that the responses of groups of similar patients to the spontaneous breathing trial can be predicted by the non-equilibrium fluctuation dissipation approach. This mathematical framework, when fully formed and applied to other clinical interventions, may serve as part of the basis for personalized critical care.
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    Quasispecies theory for evolution of modularity
    (American Physical Society, 2015) Park, Jeong-Man; Niestemski, Liang Ren; Deem, Michael W.; Bioengineering; Physics and Astronomy
    Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a quasispecies theory for the dynamics of modularity in populations of these systems. We show how the steady-state fitness in a randomly changing environment can be computed. We derive a fluctuation dissipation relation for the rate of change of modularity and use it to derive a relationship between rate of environmental changes and rate of growth of modularity. We also find a principle of least action for the evolved modularity at steady state. Finally, we compare our predictions to simulations of protein evolution and find them to be consistent.