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Multicanonical molecular dynamics by variable-temperature thermostats and variable-pressure barostats
Cheng Zhang, Michael W. Deem
Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to…
Finite population size effects in quasispecies models with single-peak fitness landscape
David B. Saakian, Michael W. Deem, Chin Kun Hu
We consider finite population size effects for Crow-Kimura and Eigen quasispecies models with single peak fitness landscape. We formulate accurately the iteration procedure for the…
Quasispecies Theory for Evolution of Modularity
Jeong-Man Park, Liang Ren Niestemski, Michael W. Deem
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 s…
Low-dimensional clustering detects incipient dominant influenza strain clusters
Jiankui He, Michael W. Deem
Influenza has been circulating in the human population and has caused three pandemics in the last century (1918 H1N1, 1957 H2N2, 1968 H3N2). The 2009 A(H1N1) was classified by the…
A Novel Sequence-Based Antigenic Distance Measure for H1N1, with Application to Vaccine Effectiveness and the Selection of Vaccine Strains
Keyao Pan, Krystina C. Subieta, Michael W. Deem
H1N1 influenza causes substantial seasonal illness and was the subtype of the 2009 influenza pandemic. Precise measures of antigenic distance between the vaccine and circulating vi…
Predicting Fixation Tendencies of the H3N2 Influenza Virus by Free Energy Calculation
Keyao Pan, Michael W. Deem
Influenza virus evolves to escape from immune system antibodies that bind to it. We used free energy calculations with Einstein crystals as reference states to calculate the differ…