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Markov Chains of Infinite Order and Asymptotic Satisfaction of Balance: Application to the Adaptive Integration Method
David J. Earl, Michael W. Deem
Adaptive Monte Carlo methods can be viewed as implementations of Markov chains with infinite memory. We derive a general condition for the convergence of a Monte Carlo method whose…
Length, Protein-Protein Interactions, and Complexity
Taison Tan, Daan Frenkel, Vishal Gupta +1
The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large scale genome sequencing efforts has been unclear. We propose her…
Epitope analysis for influenza vaccine design
Enrique T. Munoz, Michael W. Deem
Until now, design of the annual influenza vaccine has relied on phylogenetic or whole-sequence comparisons of the viral coat proteins hemagglutinin and neuraminidase, with vaccine…
Evolvability is a Selectable Trait
David J. Earl, Michael W. Deem
Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein s…
Correlations in the T Cell Response to Altered Peptide Ligands
Jeong-Man Park, Michael W. Deem
The vertebrate immune system is a wonder of modern evolution. Occasionally, however, correlations within the immune system lead to inappropriate recruitment of preexisting T cells…
Modulation of Base Specific Mutation and Recombination Rates Enables Functional Adaptation within the Context of the Genetic Code
Taison Tan, Leonard D. Bogarad, Michael W. Deem
The persistence of life requires populations to adapt at a rate commensurate with the dynamics of their environment. Successful populations that inhabit highly variable environment…