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Physical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction
Ulrich Gerland, J. David Moroz, Terence Hwa
We study theoretical ``design principles'' for transcription factor-DNA interaction in bacteria, focusing particularly on the statistical interaction of the transcription factors (…
On the Selection and Evolution of Regulatory DNA Motifs
Ulrich Gerland, Terence Hwa
The mutation and selection of regulatory DNA sequences is presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and ind…
DNA Sequence Evolution with Neighbor-Dependent Mutation
Peter F. Arndt, Christopher B. Burge, Terence Hwa
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this cl…
Statistical mechanics of secondary structures formed by random RNA sequences
R. Bundschuh, T. Hwa
The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models…
Glass transition in secondary structures formed by random RNA sequences
R. Bundschuh, T. Hwa
Formation of RNA secondary structures is an example of the sequence-structure problem omnipresent in biopolymers. A theoretical question of recent interest is whether a random RNA…
Force-induced denaturation of RNA
Ulrich Gerland, Ralf Bundschuh, Terence Hwa
We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates…