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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…
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…
Dynamics of Competitive Evolution on a Smooth Landscape
Weiqun Peng, Ulrich Gerland, Terence Hwa +1
We study competitive DNA sequence evolution directed by {\it in vitro} protein binding. The steady-state dynamics of this process is well described by a shape-preserving pulse whic…
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…
RNA secondary structure formation: a solvable model of heteropolymer folding
R. Bundschuh, T. Hwa
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particu…
Optimal Detection of Sequence Similarity by Local Alignment
Terence Hwa, Michael Lassig
The statistical properties of local alignment algorithms with gaps are analyzed theoretically for uncorrelated and correlated DNA sequences. In the vicinity of the log-linear phase…
Static and Dynamic Properties of Inhomogeneous Elastic Media on Disordered Substrate
D. Cule, T. Hwa
The pinning of an inhomogeneous elastic medium by a disordered substrate is studied analytically and numerically. The static and dynamic properties of a -dimensional system are…
Polymer Adsorption on Disordered Substrate
T. Hwa, D. Cule
We analyze the recently proposed "pattern-matching" phase of a Gaussian random heteropolymer adsorbed on a disordered substrate [S. Srebnik, A.K. Chakraborty and E.I. Shakhnovich,…
On Nonlinear Diffusion with Multiplicative Noise
M. A. Muñoz, T. Hwa
Nonlinear diffusion is studied in the presence of multiplicative noise. The nonlinearity can be viewed as a ``wall'' limiting the motion of the diffusing field. A dynamic phase tra…