Smoothing of depinning transitions for directed polymers with quenched disorder

Quantitative Disorder Effects in Low-Dimensional Spin Systems

The Imry-Ma phenomenon, predicted in 1975 by Imry and Ma and rigorously established in 1989 by Aizenman and Wehr, states that first-order phase transitions of low-dimensional spin systems are 'rounded' by the addition of a quenched random field coupled to the quantity undergoing the transition. The phenomenon applies to a wide class of spin systems in dimensions d ≤ 2 and to spin systems possessing a continuous symmetry in dimensions d ≤ 4 . This work provides quantitative estimates for the Imry-Ma phenomenon: in a cubic domain of side length L, we study the effect of the boundary conditions on the spatial and thermal average of the quantity coupled to the random field. We show that the boundary effect diminishes at least as fast as an inverse power of log log L in general two-dimensional spin systems. For systems possessing a continuous symmetry, we show that the boundary effect diminishes at least as fast as an inverse power of L in two and three dimensions and at least as fast as an inverse power of log log L in four dimensions. Finally, we establish a partial uniqueness results for translation-covariant Gibbs states, and prove that, for almost every realization of the random field, all such states must agree on the thermally-averaged value of the quantity coupled to the random field. Specific models of interest for the obtained results include the random-field q-state Potts model, the Edwards-Anderson spin glass model, and the random-field spin O(n) models.

Kardar-Parisi-Zhang equation in a half space with flat initial condition and the unbinding of a directed polymer from an attractive wall

We present an exact solution for the height distribution of the KPZ equation at any time t in a half space with flat initial condition. This is equivalent to obtaining the free-energy distribution of a polymer of length t pinned at a wall at a single point. In the large t limit a binding transition takes place upon increasing the attractiveness of the wall. Around the critical point we find the same statistics as in the Baik-Ben-Arous-Péché transition for outlier eigenvalues in random matrix theory. In the bound phase, we obtain the exact measure for the endpoint and the midpoint of the polymer at large time. We also unveil curious identities in distribution between partition functions in half-space and certain partition functions in full space for Brownian-type initial condition.

Theory of force-extension curves for modular proteins and DNA hairpins

We study a model describing the force-extension curves of modular proteins, nucleic acids, and other biomolecules made out of several single units or modules. At a mesoscopic level of description, the configuration of the system is given by the elongations of each of the units. The system free energy includes a double-well potential for each unit and an elastic nearest-neighbor interaction between them. Minimizing the free energy yields the system equilibrium properties whereas its dynamics is given by (overdamped) Langevin equations for the elongations, in which friction and noise amplitude are related by the fluctuation-dissipation theorem. Our results, both for the equilibrium and the dynamical situations, include analytical and numerical descriptions of the system force-extension curves under force or length control and agree very well with actual experiments in biomolecules. Our conclusions also apply to other physical systems comprising a number of metastable units, such as storage systems or semiconductor superlattices.

DNA unzipping phase diagram calculated via replica theory

We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). Toward this end, we study a statistical-mechanics model for the fluctuating structure of a long molecule of dsDNA, and compute the equilibrium phase diagram for the experiment in which the molecule is unzipped under applied force. We consider a perfect-matching dsDNA model, in which the loops are volume-excluding chains with arbitrary loop exponent c . We include stacking interactions, hydrogen bonds, and main-chain entropy. We include sequence heterogeneity at the level of random sequences; in particular, there is no correlation in the base-pairing (bp) energy from one sequence position to the next. We present heuristic arguments to demonstrate that the low-temperature macrostate does not exhibit degenerate ergodicity breaking. We use this claim to understand the results of our replica-theoretic calculation of the equilibrium properties of the system. As a function of temperature, we obtain the minimal force at which the molecule separates completely. This critical-force curve is a line in the temperature-force phase diagram that marks the regions where the molecule exists primarily as a double helix versus the region where the molecule exists as two separate strands. We compare our random-sequence model to magnetic tweezer experiments performed on the 48 502 bp genome of bacteriophage lambda . We find good agreement with the experimental data, which is restricted to temperatures between 24 and 50 degrees C . At higher temperatures, the critical-force curve of our random-sequence model is very different for that of the homogeneous-sequence version of our model. For both sequence models, the critical force falls to zero at the melting temperature T_{c} like |T-T_{c}|;{alpha} . For the homogeneous-sequence model, alpha=1/2 almost exactly, while for the random-sequence model, alpha approximately 0.9 . Importantly, the shape of the critical-force curve is connected, via our theory, to the manner in which the helix fraction falls to zero at T_{c} . The helix fraction is the property that is used to classify the melting transition as a type of phase transition. In our calculation, the shape of the critical-force curve holds strong evidence that the zero-force melting transition of long natural dsDNA should be classified as a higher-order (continuous) phase transition. Specifically, the order is 3rd or greater.

Loop dynamics in DNA denaturation

The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The long-time decay of the autocorrelation function is expressed in terms of the loop exponent c both for homopolymers and heteropolymers. This suggests an experimental method for measuring the exponent c using florescence correlation spectroscopy.