Comment on "Why is the DNA denaturation transition first order?"

In this comment we argue that while the conclusions in the original paper (Y. Kafri, D. Mukamel and L. Peliti, Phys. Rev. Lett. 85, 4988 (2000)) are correct for asymptotically long DNA chains, they do not apply to the chains used in typical experiments. In the added last paragraph, we point out that for real DNA the average distance between denatured loops is not of the order of the persistence length of a single-stranded chain but much larger. This corroborates our reasoning that the double helix between loops is quite rigid, and thereby our conclusion.Comment: 1 page, REVTeX. Last paragraph adde

Phase Rotation, Cooling And Acceleration Of Muon Beams: A Comparison Of Different Approaches

Experimental and theoretical activities are underway at CERN with the aim of examining the feasibility of a very-high-flux neutrino source. In the present scheme, a high-power proton beam (some 4 MW) bombards a target where pions are produced. The pions are collected and decay to muons under controlled optical condition. The muons are cooled and accelerated to a final energy of 50 GeV before being injected into a decay ring where they decay under well-defined conditions of energy and emittance. We present the most challenging parts of the whole scenario, the muon capture, the ionisation-cooling and the first stage of the muon acceleration. Different schemes, their performance and the technical challenges are compared.Comment: LINAC 2000 CONFERENCE, paper ID No. THC1

Probing molecular free energy landscapes by periodic loading

Single molecule pulling experiments provide information about interactions in biomolecules that cannot be obtained by any other method. However, the reconstruction of the molecule's free energy profile from the experimental data is still a challenge, in particular for the unstable barrier regions. We propose a new method for obtaining the full profile by introducing a periodic ramp and using Jarzynski's identity for obtaining equilibrium quantities from non-equilibrium data. Our simulated experiments show that this method delivers significant more accurate data than previous methods, under the constraint of equal experimental effort.Comment: 4 pages, 3 figure

Dynamical Properties of Two Coupled Hubbard Chains at Half-filling

Using grand canonical Quantum Monte Carlo (QMC) simulations combined with Maximum Entropy analytic continuation, as well as analytical methods, we examine the one- and two-particle dynamical properties of the Hubbard model on two coupled chains at half-filling. The one-particle spectral weight function, $A({\bf k},\omega)$, undergoes a qualitative change with interchain hopping $t_\perp$ associated with a transition from a four-band insulator to a two-band insulator. A simple analytical model based on the propagation of exact rung singlet states gives a good description of the features at large $t_\perp$. For smaller $t_\perp$, $A({\bf k}, \omega)$ is similar to that of the one-dimensional model, with a coherent band of width the effective antiferromagnetic exchange $J$ reasonably well-described by renormalized spin-wave theory. The coherent band rides on a broad background of width several times the parallel hopping integral $t$, an incoherent structure similar to that found in calculations on both the one- and two-dimensional models. We also present QMC results for the two-particle spin and charge excitation spectra, and relate their behavior to the rung singlet picture for large $t_\perp$ and to the results of spin-wave theory for small $t_\perp$.Comment: 9 pages + 10 postscript figures, submitted to Phys.Rev.B, revised version with isotropic t_perp=t data include

Renormalized SO(5) symmetry in ladders with next-nearest-neighbor hopping

We study the occurrence of SO(5) symmetry in the low-energy sector of two-chain Hubbard-like systems by analyzing the flow of the running couplings ($g$-ology) under renormalization group in the weak-interaction limit. It is shown that SO(5) is asymptotically restored for low energies for rather general parameters of the bare Hamiltonian. This holds also with inclusion of a next-nearest-neighbor hopping which explicitly breaks particle-hole symmetry provided one accounts for a different single-particle weight for the quasiparticles of the two bands of the system. The physical significance of this renormalized SO(5) symmetry is discussed.Comment: Final version: to appear in Phys. Rev. Lett., sched. Mar. 9

Correlation functions near Modulated and Rough Surfaces

In a system with long-ranged correlations, the behavior of correlation functions is sensitive to the presence of a boundary. We show that surface deformations strongly modify this behavior as compared to a flat surface. The modified near surface correlations can be measured by scattering probes. To determine these correlations, we develop a perturbative calculation in the deformations in height from a flat surface. Detailed results are given for a regularly patterned surface, as well as for a self-affinely rough surface with roughness exponent $\zeta$. By combining this perturbative calculation in height deformations with the field-theoretic renormalization group approach, we also estimate the values of critical exponents governing the behavior of the decay of correlation functions near a self-affinely rough surface. We find that for the interacting theory, a large enough $\zeta$ can lead to novel surface critical behavior. We also provide scaling relations between roughness induced critical exponents for thermodynamic surface quantities.Comment: 31 pages, 2 figure

Bubble dynamics in DNA

The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland-Scheraga model. Characteristic bubble closing and opening times can be determined from the corresponding first passage time problem, and are sensitive to the specific parameters entering the model. A multistate unzipping model with constant rates recently applied to DNA breathing dynamics [G. Altan-Bonnet et al, Phys. Rev. Lett. 90, 138101 (2003)] emerges as a limiting case.Comment: 9 pages, 2 figure