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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,…
Polymer Reptation in Disordered Media
D. Cule, T. Hwa
The effect of ambient disorders and sequence heterogeneities on the reptation of a long polymer is studied with the aid of a disordered tube model. The dynamics of a random heterop…
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…