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Translocation of structured polynucleotides through nanopores
Ulrich Gerland, Ralf Bundschuh, Terence Hwa
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired r…
Analytical study of the effect of recombination on evolution via DNA shuffling
Weiqun Peng, Herbert Levine, Terence Hwa +1
We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selecti…
Localization of Denaturation Bubbles in Random DNA Sequences
Terence Hwa, Enzo Marinari, Kim Sneppen +1
We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are…
The style of genetic computing
Nicolas E. Buchler, Ulrich Gerland, Terence Hwa
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a the…
Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation
Peter F. Arndt, Dmitri A. Petrov, Terence Hwa
Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into…